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This page was generated on 2023-10-20 09:38:14 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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

Package 2104/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TitanCNA 1.38.0  (landing page)
Gavin Ha
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/TitanCNA
git_branch: RELEASE_3_17
git_last_commit: 0c39794
git_last_commit_date: 2023-04-25 10:31:43 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for TitanCNA on kjohnson2


To the developers/maintainers of the TitanCNA 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: TitanCNA
Version: 1.38.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TitanCNA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TitanCNA_1.38.0.tar.gz
StartedAt: 2023-10-19 07:07:27 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 07:19:13 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 705.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: TitanCNA.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TitanCNA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TitanCNA_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/TitanCNA.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 ‘TitanCNA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TitanCNA’ version ‘1.38.0’
* 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::desc’ by ‘dplyr::desc’ 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 ‘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 ‘data.table::between’ by ‘dplyr::between’ when loading ‘TitanCNA’
  Warning: replacing previous import ‘BiocGenerics::combine’ by ‘dplyr::combine’ when loading ‘TitanCNA’
  Warning: replacing previous import ‘IRanges::collapse’ by ‘dplyr::collapse’ when loading ‘TitanCNA’
  Warning: replacing previous import ‘GenomicRanges::setdiff’ by ‘dplyr::setdiff’ when loading ‘TitanCNA’
  Warning: replacing previous import ‘dplyr::select’ by ‘VariantAnnotation::select’ when loading ‘TitanCNA’
See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/TitanCNA.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
  installed size is  7.2Mb
  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 startup messages can be suppressed ... 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 is not available
* 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   28.599  0.511  52.079
runEMclonalCN      20.204  0.268  35.048
getPositionOverlap  8.490  0.124  15.017
filterData          7.541  0.135  13.431
TitanCNA-plotting   6.408  0.162  11.700
correctReadDepth    6.169  0.111  11.099
computeSDbwIndex    4.727  0.057   8.587
* 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-3.17-bioc-mac-arm64/meat/TitanCNA.Rcheck/00check.log’
for details.



Installation output

TitanCNA.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘TitanCNA’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -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 -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c getPositionOverlapC.c -o getPositionOverlapC.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c register.c -o register.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c viterbiC_clonalCN.c -o viterbiC_clonalCN.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/4.3-arm64/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 ‘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 ‘IRanges::slice’ by ‘dplyr::slice’ 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::union’ by ‘dplyr::union’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::between’ by ‘dplyr::between’ when loading ‘TitanCNA’
Warning: replacing previous import ‘BiocGenerics::combine’ by ‘dplyr::combine’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::collapse’ by ‘dplyr::collapse’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomicRanges::setdiff’ by ‘dplyr::setdiff’ 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 ‘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 ‘IRanges::slice’ by ‘dplyr::slice’ 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::union’ by ‘dplyr::union’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::between’ by ‘dplyr::between’ when loading ‘TitanCNA’
Warning: replacing previous import ‘BiocGenerics::combine’ by ‘dplyr::combine’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::collapse’ by ‘dplyr::collapse’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomicRanges::setdiff’ by ‘dplyr::setdiff’ 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 ‘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 ‘IRanges::slice’ by ‘dplyr::slice’ 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::union’ by ‘dplyr::union’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::between’ by ‘dplyr::between’ when loading ‘TitanCNA’
Warning: replacing previous import ‘BiocGenerics::combine’ by ‘dplyr::combine’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::collapse’ by ‘dplyr::collapse’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomicRanges::setdiff’ by ‘dplyr::setdiff’ 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)

Tests output


Example timings

TitanCNA.Rcheck/TitanCNA-Ex.timings

nameusersystemelapsed
TitanCNA-output0.7880.0311.418
TitanCNA-package28.599 0.51152.079
TitanCNA-plotting 6.408 0.16211.700
computeSDbwIndex4.7270.0578.587
correctCN0.5950.0141.069
correctReadDepth 6.169 0.11111.099
filterData 7.541 0.13513.431
getPositionOverlap 8.490 0.12415.017
haplotype000
loadAlleleCounts0.7500.0681.338
loadDefaultParameters0.0010.0000.003
runEMclonalCN20.204 0.26835.048
viterbiClonalCN0.3390.0060.620
wigImport0.2440.0060.437