Multiple platform build/check report for BioC 3.8 - CHECK report for TitanCNA on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:TitanCNA.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings TitanCNA_1.20.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/TitanCNA.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 ‘1.20.1’
* 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 ‘data.table::between’ by ‘dplyr::between’ when loading ‘TitanCNA’
  Warning: replacing previous import ‘dplyr::select’ by ‘VariantAnnotation::select’ when loading ‘TitanCNA’
See ‘/home/biocbuild/bbs-3.8-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 ‘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 ... WARNING
Unknown package ‘list’ in Rd xrefs
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
TitanCNA-package   76.728  0.156  38.484
TitanCNA-plotting  42.760  0.100  13.351
TitanCNA-output    32.972  0.116   6.939
runEMclonalCN      21.812  0.104  21.344
filterData          8.660  0.012   8.087
getPositionOverlap  8.464  0.012   8.470
correctReadDepth    7.672  0.040   7.719
computeSDbwIndex    6.236  0.012   6.076
* 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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/TitanCNA.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL TitanCNA
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘TitanCNA’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c fwd_backC_clonalCN.c -o fwd_backC_clonalCN.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c getPositionOverlapC.c -o getPositionOverlapC.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c register.c -o register.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c viterbiC_clonalCN.c -o viterbiC_clonalCN.o
gcc -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o TitanCNA.so fwd_backC_clonalCN.o getPositionOverlapC.o register.o viterbiC_clonalCN.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/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 ‘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
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 ‘data.table::between’ by ‘dplyr::between’ when loading ‘TitanCNA’
Warning: replacing previous import ‘dplyr::select’ by ‘VariantAnnotation::select’ when loading ‘TitanCNA’
* DONE (TitanCNA)

CHECK report for TitanCNA on malbec1

Summary

Command output

Installation output

Tests output

Example timings

name	user	system	elapsed
TitanCNA-output	32.972	0.116	6.939
TitanCNA-package	76.728	0.156	38.484
TitanCNA-plotting	42.760	0.100	13.351
computeSDbwIndex	6.236	0.012	6.076
correctReadDepth	7.672	0.040	7.719
extractAlleleReadCounts	0	0	0
filterData	8.660	0.012	8.087
getPositionOverlap	8.464	0.012	8.470
haplotype	0.004	0.000	0.000
loadAlleleCounts	1.112	0.016	1.131
loadDefaultParameters	0.000	0.000	0.001
runEMclonalCN	21.812	0.104	21.344
viterbiClonalCN	0.492	0.000	0.491
wigToRangedData	0.200	0.000	0.202