Gavin Ha
| Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022) |
| git_url: https://git.bioconductor.org/packages/TitanCNA |
| git_branch: RELEASE_3_15 |
| git_last_commit: 6cb0738 |
| git_last_commit_date: 2022-04-26 11:19:29 -0400 (Tue, 26 Apr 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:22:25 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the TitanCNA package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TitanCNA.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 2015/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TitanCNA 1.34.0 (landing page) Gavin Ha
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: TitanCNA |
| Version: 1.34.0 |
| Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TitanCNA.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings TitanCNA_1.34.0.tar.gz |
| StartedAt: 2022-10-19 04:50:00 -0400 (Wed, 19 Oct 2022) |
| EndedAt: 2022-10-19 04:56:36 -0400 (Wed, 19 Oct 2022) |
| EllapsedTime: 395.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: TitanCNA.Rcheck |
| Warnings: 2 |
##############################################################################
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###
### Running command:
###
### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TitanCNA.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings TitanCNA_1.34.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/TitanCNA.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.34.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package '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 'F:/biocbuild/bbs-3.15-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'
loadBXcountsFromBEDDir: no visible global function definition for
'RangedData'
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 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 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 '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 '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
'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 '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 : <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 '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'
wigToRangedData: no visible global function definition for 'RangedData'
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 RangedData 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 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",
"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 for x64 is not available
File 'F:/biocbuild/bbs-3.15-bioc/R/library/TitanCNA/libs/x64/TitanCNA.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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
TitanCNA-package 35.01 0.50 38.66
runEMclonalCN 25.28 0.23 25.52
getPositionOverlap 8.77 0.21 8.98
filterData 8.58 0.22 8.81
TitanCNA-plotting 7.79 0.06 7.85
correctReadDepth 7.45 0.30 7.97
computeSDbwIndex 6.84 0.09 6.93
* 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
'F:/biocbuild/bbs-3.15-bioc/meat/TitanCNA.Rcheck/00check.log'
for details.
TitanCNA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL TitanCNA ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library' * installing *source* package 'TitanCNA' ... ** using staged installation ** libs gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fwd_backC_clonalCN.c -o fwd_backC_clonalCN.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getPositionOverlapC.c -o getPositionOverlapC.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c register.c -o register.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c viterbiC_clonalCN.c -o viterbiC_clonalCN.o gcc -shared -s -static-libgcc -o TitanCNA.dll tmp.def fwd_backC_clonalCN.o getPositionOverlapC.o register.o viterbiC_clonalCN.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-TitanCNA/00new/TitanCNA/libs/x64 ** 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' ** 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 | 0.91 | 0.01 | 0.92 | |
| TitanCNA-package | 35.01 | 0.50 | 38.66 | |
| TitanCNA-plotting | 7.79 | 0.06 | 7.85 | |
| computeSDbwIndex | 6.84 | 0.09 | 6.93 | |
| correctCN | 0.81 | 0.02 | 0.85 | |
| correctReadDepth | 7.45 | 0.30 | 7.97 | |
| filterData | 8.58 | 0.22 | 8.81 | |
| getPositionOverlap | 8.77 | 0.21 | 8.98 | |
| haplotype | 0 | 0 | 0 | |
| loadAlleleCounts | 0.67 | 0.10 | 0.77 | |
| loadDefaultParameters | 0 | 0 | 0 | |
| runEMclonalCN | 25.28 | 0.23 | 25.52 | |
| viterbiClonalCN | 0.48 | 0.02 | 0.50 | |
| wigImport | 0.27 | 0.04 | 0.31 | |