############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:VariantTools.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings VariantTools_1.42.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/VariantTools.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 * running under: Ubuntu 22.04.3 LTS * using session charset: UTF-8 * checking for file ‘VariantTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘VariantTools’ version ‘1.42.0’ * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘VariantTools’ can be installed ... OK * checking installed package size ... NOTE installed size is 6.5Mb sub-directories of 1Mb or more: doc 5.4Mb * 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: Initial release (start date: 12 September, 2012) * 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 ... WARNING Missing or unexported object: ‘GenomicRanges::genome’ Unexported objects imported by ':::' calls: ‘BiocGenerics:::testPackage’ ‘IRanges:::unlist_as_integer’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE LowerFrequencyInOtherFilter : : no visible binding for global variable ‘control.alt.depth’ LowerFrequencyInOtherFilter : : no visible binding for global variable ‘control.total.depth’ ReadPositionTTestFilter : : no visible binding for global variable ‘read.pos.mean’ ReadPositionTTestFilter : : no visible binding for global variable ‘read.pos.mean.ref’ ReadPositionTTestFilter : : no visible binding for global variable ‘read.pos.var’ ReadPositionTTestFilter : : no visible binding for global variable ‘read.pos.var.ref’ ReadPositionTTestFilter : : no visible global function definition for ‘rawDepth’ StrandFETFilter : : no visible binding for global variable ‘count.plus.ref’ StrandFETFilter : : no visible binding for global variable ‘count.minus.ref’ StrandFETFilter : : no visible binding for global variable ‘count.plus’ StrandFETFilter : : no visible binding for global variable ‘count.minus’ calculateConcordanceMatrix: no visible binding for global variable ‘x’ caseControlFET: no visible binding for global variable ‘control.alt.depth’ caseControlFET: no visible binding for global variable ‘control.total.depth’ variantGR2Vcf: no visible global function definition for ‘variantGRangesIsDeprecated’ variantGR2Vcf: no visible global function definition for ‘makeVRangesFromVariantGRanges’ callVariants,GenomicRanges: no visible global function definition for ‘variantGRangesIsDeprecated’ callVariants,GenomicRanges: no visible global function definition for ‘variantGRangesToVRanges’ Undefined global functions or variables: control.alt.depth control.total.depth count.minus count.minus.ref count.plus count.plus.ref makeVRangesFromVariantGRanges rawDepth read.pos.mean read.pos.mean.ref read.pos.var read.pos.var.ref variantGRangesIsDeprecated variantGRangesToVRanges x * checking Rd files ... WARNING ./man/tallyVariants.Rd: non-ASCII input and no declared encoding problem found in ‘tallyVariants.Rd’ * checking Rd metadata ... OK * checking Rd cross-references ... OK * 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 installed files from ‘inst/doc’ ... NOTE The following directories should probably not be installed: ‘fig’ Consider the use of a .Rinstignore file: see ‘Writing R Extensions’, or move the vignette sources from ‘inst/doc’ to ‘vignettes’. * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘VariantTools-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: callSampleSpecificVariants > ### Title: Call Sample-Specific Variants > ### Aliases: callSampleSpecificVariants > ### callSampleSpecificVariants,BamFile,BamFile-method > ### callSampleSpecificVariants,character,character-method > ### callSampleSpecificVariants,GenomicRanges,GenomicRanges-method > ### callSampleSpecificVariants,VRanges,VRanges-method > ### SampleSpecificVariantFilters > > ### ** Examples > > bams <- LungCancerLines::LungCancerBamFiles() > if (requireNamespace("gmapR", quietly=TRUE)) { + tally.param <- TallyVariantsParam(gmapR::TP53Genome(), + high_base_quality = 23L, + which = gmapR::TP53Which()) + callSampleSpecificVariants(bams$H1993, bams$H2073, tally.param) + } else { + data(vignette) + calling.filters <- VariantCallingFilters(read.count = 3L) + called.variants <- callVariants(tallies_H1993, calling.filters) + callSampleSpecificVariants(called.variants, tallies_H2073, + coverage_H2073) + } Error in packageVersion("TxDb.Hsapiens.UCSC.hg19.knownGene") : there is no package called ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ Calls: TallyVariantsParam ... GeneGenome -> geneGenomeName -> paste0 -> packageVersion Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘VariantTools_unit_tests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘VariantTools.Rnw’... failed WARNING Errors in running code in vignettes: when running code in ‘VariantTools.Rnw’ ... > bam <- bams$H1993 > if (requireNamespace("gmapR", quietly = TRUE)) { + p53 <- gmapR:::exonsOnTP53Genome("TP53") + tally.param <- TallyVariantsParam(gmapR::TP53G .... [TRUNCATED] When sourcing ‘VariantTools.R’: Error: there is no package called ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ Execution halted * checking re-building of vignette outputs ... NOTE Error(s) in re-building vignettes: --- re-building ‘VariantTools.Rnw’ using Sweave Loading required package: S4Vectors Loading required package: stats4 Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: ‘S4Vectors’ The following object is masked from ‘package:utils’: findMatches The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: IRanges Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: VariantAnnotation Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: ‘MatrixGenerics’ The following objects are masked from ‘package:matrixStats’: colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: SummarizedExperiment Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: ‘Biobase’ The following object is masked from ‘package:MatrixGenerics’: rowMedians The following objects are masked from ‘package:matrixStats’: anyMissing, rowMedians Loading required package: Rsamtools Loading required package: Biostrings Loading required package: XVector Attaching package: ‘Biostrings’ The following object is masked from ‘package:base’: strsplit Attaching package: ‘VariantAnnotation’ The following object is masked from ‘package:base’: tabulate Error: processing vignette 'VariantTools.Rnw' failed with diagnostics: chunk 2 (label = callVariants) Error in loadNamespace(x) : there is no package called ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ --- failed re-building ‘VariantTools.Rnw’ SUMMARY: processing the following file failed: ‘VariantTools.Rnw’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 3 WARNINGs, 6 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/VariantTools.Rcheck/00check.log’ for details.