TitanCNA 1.15.0
Gavin Ha , Sohrab P Shah
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TitanCNA | | Last Changed Rev: 131890 / Revision: 131943 | | Last Changed Date: 2017-08-10 14:55:44 -0400 (Thu, 10 Aug 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ ERROR ] | | |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | ERROR | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | ERROR | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings TitanCNA_1.15.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/TitanCNA.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.15.0’
* 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::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’
See ‘/home/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
* 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’
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 LogRatio MajorCN 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 ... WARNING
Codoc mismatches from documentation object 'output-methods':
outputTitanResults
Code: function(data, convergeParams, optimalPath, filename = NULL,
is.haplotypeData = FALSE, posteriorProbs = FALSE,
subcloneProfiles = TRUE, correctResults = TRUE,
proportionThreshold = 0.05, proportionThresholdClonal
= 0.05, recomputeLogLik = TRUE, rerunViterbi = FALSE,
verbose = TRUE)
Docs: function(data, convergeParams, optimalPath, filename = NULL,
is.haplotypeData = FALSE, posteriorProbs = FALSE,
subcloneProfiles = TRUE, correctResults = TRUE,
proportionThreshold = 0.05, proportionThresholdClonal
= 0.05, verbose = TRUE)
Argument names in code not in docs:
recomputeLogLik rerunViterbi
Mismatches in argument names:
Position: 11 Code: recomputeLogLik Docs: verbose
Codoc mismatches from documentation object 'removeEmptyClusters':
removeEmptyClusters
Code: function(data, convergeParams, results, proportionThreshold =
0.001, proportionThresholdClonal = 0.05,
recomputeLogLik = TRUE, verbose = TRUE)
Docs: function(convergeParams, results, proportionThreshold = 0.001,
proportionThresholdClonal = 0.05)
Argument names in code not in docs:
data recomputeLogLik verbose
Mismatches in argument names (first 3):
Position: 1 Code: data Docs: convergeParams
Position: 2 Code: convergeParams Docs: results
Position: 3 Code: results Docs: proportionThreshold
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘TitanCNA-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: removeEmptyClusters
> ### Title: Post-process TitanCNA results by removing clusters with
> ### proportion of data points altered lower than a threshold. The number
> ### of clonal clusters, cellular prevalence, and normal contamination
> ### will be adjusted to reflect the remaining clonal clusters.
> ### Aliases: removeEmptyClusters
> ### Keywords: manip
>
> ### ** Examples
>
> data(EMresults)
>
> #### COMPUTE OPTIMAL STATE PATH USING VITERBI ####
> optimalPath <- viterbiClonalCN(data, convergeParams)
>
> #### FORMAT RESULTS ####
> results <- outputTitanResults(data, convergeParams, optimalPath,
+ filename = NULL, posteriorProbs = FALSE,
+ subcloneProfiles = TRUE)
outputTitanResults: Correcting results...
outputTitanResults: Recomputing log-likelihood.
titan: Running HMM...
fwdBack: Iteration 1 chr: 1
Using Coordinate Descent iteration 11 with Fval=-22824 and n=0.2643 (fixed), s=[0.00,0.55], phi=1.571
fwdBack: loglik=-34034.1335
fwdBack: priorN=0.0000
fwdBack: priorS=0.0000
fwdBack: priorVar=-793.5800
fwdBack: priorVarR=0.0000
fwdBack: priorPhi=0.0000
fwdBack: priorPiG=30.5572
fwdBack: priorPiZ=0.9808
fwdBack: EM iteration 1 complete loglik=-34796.1754
fwdBack: Elapsed time for iteration 1: 0.0425m
fwdBack: Total elapsed time: 0.0623m
>
> #### REMOVE EMPTY CLONAL CLUSTERS ####
> corrResults <- removeEmptyClusters(convergeParams, results, proportionThreshold = 0.001,
+ proportionThresholdClonal = 0.3)
Error in removeEmptyClusters(convergeParams, results, proportionThreshold = 0.001, :
could not find function "removeEmptyClusters"
Execution halted
* 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 ERROR, 2 WARNINGs, 3 NOTEs
See
‘/home/biocbuild/bbs-3.6-bioc/meat/TitanCNA.Rcheck/00check.log’
for details.