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CHECK report for TitanCNA on tokay1

This page was generated on 2018-04-12 13:24:10 -0400 (Thu, 12 Apr 2018).

Package 1402/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TitanCNA 1.16.0
Gavin Ha , Sohrab P Shah
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)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: TitanCNA
Version: 1.16.0
Command: rm -rf TitanCNA.buildbin-libdir TitanCNA.Rcheck && mkdir TitanCNA.buildbin-libdir TitanCNA.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TitanCNA.buildbin-libdir TitanCNA_1.16.0.tar.gz >TitanCNA.Rcheck\00install.out 2>&1 && cp TitanCNA.Rcheck\00install.out TitanCNA-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=TitanCNA.buildbin-libdir --install="check:TitanCNA-install.out" --force-multiarch --no-vignettes --timings TitanCNA_1.16.0.tar.gz
StartedAt: 2018-04-12 03:36:15 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 03:45:57 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 581.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: TitanCNA.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf TitanCNA.buildbin-libdir TitanCNA.Rcheck && mkdir TitanCNA.buildbin-libdir TitanCNA.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TitanCNA.buildbin-libdir TitanCNA_1.16.0.tar.gz >TitanCNA.Rcheck\00install.out 2>&1 && cp TitanCNA.Rcheck\00install.out TitanCNA-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=TitanCNA.buildbin-libdir --install="check:TitanCNA-install.out" --force-multiarch --no-vignettes --timings TitanCNA_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/TitanCNA.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'TitanCNA' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSYH6Sc/R.INSTALL35bc5cd36fd/TitanCNA/man/correctReadDepth.Rd:17: missing file link 'wigToRangedData'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSYH6Sc/R.INSTALL35bc5cd36fd/TitanCNA/man/correctReadDepth.Rd:58: missing file link 'wigToRangedData'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSYH6Sc/R.INSTALL35bc5cd36fd/TitanCNA/man/extractAlleleReadCounts.Rd:31: missing file link 'PileupParam'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSYH6Sc/R.INSTALL35bc5cd36fd/TitanCNA/man/extractAlleleReadCounts.Rd:59: missing file link 'PileupParam'
  Warning: replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'TitanCNA'
  Warning: replacing previous import 'data.table::between' by 'dplyr::between' when loading 'TitanCNA'
  Warning: replacing previous import 'GenomicRanges::setdiff' by 'dplyr::setdiff' when loading 'TitanCNA'
  Warning: replacing previous import 'IRanges::collapse' by 'dplyr::collapse' when loading 'TitanCNA'
  Warning: replacing previous import 'IRanges::desc' by 'dplyr::desc' when loading 'TitanCNA'
  Warning: replacing previous import 'GenomicRanges::union' by 'dplyr::union' when loading 'TitanCNA'
  Warning: replacing previous import 'data.table::first' by 'dplyr::first' when loading 'TitanCNA'
  Warning: replacing previous import 'GenomeInfoDb::intersect' by 'dplyr::intersect' when loading 'TitanCNA'
  Warning: replacing previous import 'IRanges::slice' by 'dplyr::slice' when loading 'TitanCNA'
  Warning: replacing previous import 'data.table::last' by 'dplyr::last' when loading 'TitanCNA'
  Warning: replacing previous import 'dplyr::select' by 'VariantAnnotation::select' when loading 'TitanCNA'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/TitanCNA.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  7.4Mb
  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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/TitanCNA.buildbin-libdir/TitanCNA/libs/i386/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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
TitanCNA-package   44.50   1.00   47.36
runEMclonalCN      30.73   0.31   31.07
filterData         11.78   0.27   12.04
correctReadDepth   11.63   0.17   11.80
getPositionOverlap 10.33   0.20   10.53
TitanCNA-plotting   9.36   0.10   10.02
computeSDbwIndex    7.15   0.06    7.22
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
TitanCNA-package   40.83   0.31   41.34
runEMclonalCN      26.08   0.09   26.60
getPositionOverlap 12.83   0.11   12.93
filterData         12.71   0.12   12.86
correctReadDepth   11.15   0.10   11.24
TitanCNA-plotting   7.36   0.05    7.41
computeSDbwIndex    6.43   0.00    6.43
* 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, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/TitanCNA.Rcheck/00check.log'
for details.

Installation output

TitanCNA.Rcheck/00install.out


install for i386

* installing *source* package 'TitanCNA' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c fwd_backC_clonalCN.c -o fwd_backC_clonalCN.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c getPositionOverlapC.c -o getPositionOverlapC.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c register.c -o register.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c viterbiC_clonalCN.c -o viterbiC_clonalCN.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o TitanCNA.dll tmp.def fwd_backC_clonalCN.o getPositionOverlapC.o register.o viterbiC_clonalCN.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/TitanCNA.buildbin-libdir/TitanCNA/libs/i386
** 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::between' by 'dplyr::between' when loading 'TitanCNA'
Warning: replacing previous import 'GenomicRanges::setdiff' by 'dplyr::setdiff' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::collapse' by 'dplyr::collapse' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::desc' by 'dplyr::desc' when loading 'TitanCNA'
Warning: replacing previous import 'GenomicRanges::union' by 'dplyr::union' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::first' by 'dplyr::first' when loading 'TitanCNA'
Warning: replacing previous import 'GenomeInfoDb::intersect' by 'dplyr::intersect' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::slice' by 'dplyr::slice' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::last' by 'dplyr::last' when loading 'TitanCNA'
Warning: replacing previous import 'dplyr::select' by 'VariantAnnotation::select' when loading 'TitanCNA'
** help
*** installing help indices
  converting help for package 'TitanCNA'
    finding HTML links ... done
    TitanCNA-dataset                        html  
    TitanCNA-output                         html  
    TitanCNA-package                        html  
    TitanCNA-plotting                       html  
    computeSDbwIndex                        html  
    correctReadDepth                        html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSYH6Sc/R.INSTALL35bc5cd36fd/TitanCNA/man/correctReadDepth.Rd:17: missing file link 'wigToRangedData'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSYH6Sc/R.INSTALL35bc5cd36fd/TitanCNA/man/correctReadDepth.Rd:58: missing file link 'wigToRangedData'
    extractAlleleReadCounts                 html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSYH6Sc/R.INSTALL35bc5cd36fd/TitanCNA/man/extractAlleleReadCounts.Rd:31: missing file link 'PileupParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSYH6Sc/R.INSTALL35bc5cd36fd/TitanCNA/man/extractAlleleReadCounts.Rd:59: missing file link 'PileupParam'
    filterData                              html  
    getPositionOverlap                      html  
    haplotype                               html  
    loadAlleleCounts                        html  
    loadDefaultParameters                   html  
    runEMclonalCN                           html  
    finding level-2 HTML links ... done

    viterbiClonalCN                         html  
    wigToRangedData                         html  
** 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::between' by 'dplyr::between' when loading 'TitanCNA'
Warning: replacing previous import 'GenomicRanges::setdiff' by 'dplyr::setdiff' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::collapse' by 'dplyr::collapse' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::desc' by 'dplyr::desc' when loading 'TitanCNA'
Warning: replacing previous import 'GenomicRanges::union' by 'dplyr::union' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::first' by 'dplyr::first' when loading 'TitanCNA'
Warning: replacing previous import 'GenomeInfoDb::intersect' by 'dplyr::intersect' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::slice' by 'dplyr::slice' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::last' by 'dplyr::last' when loading 'TitanCNA'
Warning: replacing previous import 'dplyr::select' by 'VariantAnnotation::select' when loading 'TitanCNA'
In R CMD INSTALL

install for x64

* installing *source* package 'TitanCNA' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c fwd_backC_clonalCN.c -o fwd_backC_clonalCN.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c getPositionOverlapC.c -o getPositionOverlapC.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c register.c -o register.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c viterbiC_clonalCN.c -o viterbiC_clonalCN.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o TitanCNA.dll tmp.def fwd_backC_clonalCN.o getPositionOverlapC.o register.o viterbiC_clonalCN.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/TitanCNA.buildbin-libdir/TitanCNA/libs/x64
** 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'
* MD5 sums
packaged installation of 'TitanCNA' as TitanCNA_1.16.0.zip
* DONE (TitanCNA)
In R CMD INSTALL
In R CMD INSTALL

Tests output

Example timings

TitanCNA.Rcheck/examples_i386/TitanCNA-Ex.timings

nameusersystemelapsed
TitanCNA-output3.200.043.25
TitanCNA-package44.50 1.0047.36
TitanCNA-plotting 9.36 0.1010.02
computeSDbwIndex7.150.067.22
correctReadDepth11.63 0.1711.80
extractAlleleReadCounts000
filterData11.78 0.2712.04
getPositionOverlap10.33 0.2010.53
haplotype000
loadAlleleCounts0.450.060.52
loadDefaultParameters0.080.020.09
runEMclonalCN30.73 0.3131.07
viterbiClonalCN1.140.031.17
wigToRangedData0.490.000.48

TitanCNA.Rcheck/examples_x64/TitanCNA-Ex.timings

nameusersystemelapsed
TitanCNA-output3.010.043.11
TitanCNA-package40.83 0.3141.34
TitanCNA-plotting7.360.057.41
computeSDbwIndex6.430.006.43
correctReadDepth11.15 0.1011.24
extractAlleleReadCounts000
filterData12.71 0.1212.86
getPositionOverlap12.83 0.1112.93
haplotype000
loadAlleleCounts0.630.020.65
loadDefaultParameters0.110.030.14
runEMclonalCN26.08 0.0926.60
viterbiClonalCN0.670.000.67
wigToRangedData0.560.000.56