############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:HelloRanges.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings HelloRanges_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/HelloRanges.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 ‘HelloRanges/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘HelloRanges’ version ‘1.26.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomicRanges', 'Biostrings', 'BSgenome', 'GenomicFeatures', 'VariantAnnotation', 'Rsamtools', 'GenomicAlignments', 'rtracklayer', 'GenomeInfoDb', 'SummarizedExperiment', 'BiocIO' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘HelloRanges’ can be installed ... OK * checking installed package size ... OK * 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 ... NOTE Packages in Depends field not imported from: ‘BSgenome’ ‘GenomicAlignments’ ‘GenomicFeatures’ ‘VariantAnnotation’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. Unexported objects imported by ':::' calls: ‘BiocGenerics:::testPackage’ ‘IRanges:::subgrouping’ ‘S4Vectors:::make_zero_col_DataFrame’ 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 ... OK * checking Rd files ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘HelloRanges_unit_tests.R’ ERROR Running the tests in ‘tests/HelloRanges_unit_tests.R’ failed. Last 13 lines of output: Loading required package: GenomicAlignments Loading required package: BiocIO Attaching package: 'BiocIO' The following object is masked from 'package:rtracklayer': FileForFormat [1] TRUE > HelloRanges:::.test() Error in library("RUnit", quietly = TRUE) : there is no package called 'RUnit' Calls: -> -> library Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘tutorial.Rnw’... failed WARNING Errors in running code in vignettes: when running code in ‘tutorial.Rnw’ ... [386122] chr9:123627986-123627987:- chr9:123626395-123626396:- [386123] chr9:123628304-123628305:- chr9:123628109-123628110:- [386124] chr9:123629146-123629147:- chr9:123628375-123628376:- [386125] chr9:123631084-123631085:- chr9:123629244-123629245:- > library(TxDb.Hsapiens.UCSC.hg19.knownGene) When sourcing ‘tutorial.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 ‘tutorial.Rnw’ using Sweave 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 Loading required package: S4Vectors Loading required package: stats4 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: Biostrings Loading required package: XVector Attaching package: ‘Biostrings’ The following object is masked from ‘package:base’: strsplit Loading required package: BSgenome Loading required package: rtracklayer Loading required package: GenomicFeatures Loading required package: AnnotationDbi 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")'. Loading required package: VariantAnnotation Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: ‘matrixStats’ The following objects are masked from ‘package:Biobase’: anyMissing, rowMedians 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 The following object is masked from ‘package:Biobase’: rowMedians Loading required package: SummarizedExperiment Loading required package: Rsamtools Attaching package: ‘VariantAnnotation’ The following object is masked from ‘package:base’: tabulate Loading required package: GenomicAlignments Loading required package: BiocIO Attaching package: ‘BiocIO’ The following object is masked from ‘package:rtracklayer’: FileForFormat Assuming BED format for piped input Error: processing vignette 'tutorial.Rnw' failed with diagnostics: chunk 56 (label = answer-6) Error in library(TxDb.Hsapiens.UCSC.hg19.knownGene) : there is no package called ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ --- failed re-building ‘tutorial.Rnw’ SUMMARY: processing the following file failed: ‘tutorial.Rnw’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/HelloRanges.Rcheck/00check.log’ for details.