Back to Multiple platform build/check report for BioC 3.8 |
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This page was generated on 2019-04-16 11:50:31 -0400 (Tue, 16 Apr 2019).
Package 1566/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
TitanCNA 1.20.1 Gavin Ha
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |||||||
merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
Package: TitanCNA |
Version: 1.20.1 |
Command: /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 |
StartedAt: 2019-04-16 03:25:48 -0400 (Tue, 16 Apr 2019) |
EndedAt: 2019-04-16 03:37:55 -0400 (Tue, 16 Apr 2019) |
EllapsedTime: 726.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: TitanCNA.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /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 ### ############################################################################## ############################################################################## * 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.
TitanCNA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL TitanCNA ### ############################################################################## ############################################################################## * 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)
TitanCNA.Rcheck/TitanCNA-Ex.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 | |