############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:GenVisR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GenVisR_1.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GenVisR.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GenVisR/DESCRIPTION’ ... OK * this is package ‘GenVisR’ version ‘1.39.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 21 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ... NOTE Found the following non-portable file paths: GenVisR/tests/testthat/_snaps/Waterfall-class/final-waterfall-and-left-sub-plot-alter-sectionwidth.svg GenVisR/tests/testthat/_snaps/Waterfall-class/final-waterfall-and-top-and-left-and-bottom-sub-plot.svg GenVisR/tests/testthat/_snaps/Waterfall-class/final-waterfall-and-top-sub-plot-alter-sectionheights.svg Tarballs are only required to store paths of up to 100 bytes and cannot store those of more than 256 bytes, with restrictions including to 100 bytes for the final component. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for sufficient/correct file permissions ... OK * checking whether package ‘GenVisR’ can be installed ... WARNING Found the following significant warnings: Warning: program compiled against libxml 212 using older 211 See ‘/home/biocbuild/bbs-3.21-bioc/meat/GenVisR.Rcheck/00install.out’ for details. * 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 code 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 ... NOTE Warning: program compiled against libxml 212 using older 211 A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * 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 Warning: program compiled against libxml 212 using older 211 Namespace in Imports field not imported from: ‘reshape2’ All declared Imports should be used. * checking S3 generic/method consistency ... WARNING Warning: program compiled against libxml 212 using older 211 See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... WARNING Warning: program compiled against libxml 212 using older 211 The argument of a replacement function which corresponds to the right hand side must be named ‘value’. * checking foreign function calls ... NOTE Warning: program compiled against libxml 212 using older 211 See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE Warning: program compiled against libxml 212 using older 211 buildWaterfallPlot,WaterfallData: no visible global function definition for ‘tail’ setTierTwo,data.table: no visible global function definition for ‘tail’ setTierTwo,data.table : a: no visible binding for global variable ‘tmp’ toLolliplot,GMS: no visible binding for global variable ‘missingINdex’ Undefined global functions or variables: missingINdex tail tmp Consider adding importFrom("utils", "tail") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) lohSpec.Rd:46: Lost braces; missing escapes or markup? 46 | consisting of elements from the set {"M", "F"}. Used to suppress the plotting | ^ * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Warning: program compiled against libxml 212 using older 211 All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 * checking Rd \usage sections ... NOTE Warning: program compiled against libxml 212 using older 211 The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘GenVisR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: Lolliplot-class > ### Title: Class Lolliplot > ### Aliases: Lolliplot-class Lolliplot > > ### ** Examples > > # Load a pre-existing data set > dataset <- PIK3CA > > # mode 1, amino acid changes are not present > > library(TxDb.Hsapiens.UCSC.hg38.knownGene) Loading required package: GenomicFeatures Loading required package: BiocGenerics Loading required package: generics Attaching package: ‘generics’ The following objects are masked from ‘package:base’: as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, 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: GenomeInfoDb Loading required package: GenomicRanges 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")'. > library(BSgenome.Hsapiens.UCSC.hg38) Loading required package: BSgenome Loading required package: Biostrings Loading required package: XVector Attaching package: ‘Biostrings’ The following object is masked from ‘package:base’: strsplit Loading required package: BiocIO Loading required package: rtracklayer Attaching package: ‘rtracklayer’ The following object is masked from ‘package:BiocIO’: FileForFormat > txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene > BSgenome <- BSgenome.Hsapiens.UCSC.hg38 > > keep <- c("Chromosome", "Start_Position", "End_Position", "Reference_Allele", + "Tumor_Seq_Allele2", "Tumor_Sample_Barcode", "Gene", "Variant_Classification") > dataset.mode1 <- dataset[,keep] > colnames(dataset.mode1) <- c("chromosome", "start", "stop", "reference", "variant", + "sample", "gene", "consequence") > > > # mode 2, amino acid changes are present > > keep <- c("Chromosome", "Start_Position", "End_Position", "Reference_Allele", + "Tumor_Seq_Allele2", "Tumor_Sample_Barcode", "Gene", "Variant_Classification", + "Transcript_ID", "HGVSp") > dataset.mode2 <- dataset[,keep] > colnames(dataset.mode2) <- c("chromosome", "start", "stop", "reference", "variant", + "sample", "gene", "consequence", "transcript", "proteinCoord") > > # run Lolliplot > > object <- Lolliplot(dataset.mode1, transcript="ENST00000263967", + species="hsapiens", txdb=txdb, BSgenome=BSgenome) This function is part of the new S4 feature and is under active development, did you mean to use lolliplot() with a lowercase l? Error in curl::curl_parse_url(url, baseurl = base_url, decode = FALSE) : Failed to parse URL: Bad scheme Calls: Lolliplot ... .useMart -> .cleanHostURL -> -> Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: • Waterfall-class/gene-plot-proportion-simple.svg • Waterfall-class/main-waterfall-add-layers.svg • Waterfall-class/main-waterfall-plot-base.svg • Waterfall-class/main-waterfall-plot-drop-true.svg • Waterfall-class/main-waterfall-plot-grid-true.svg • Waterfall-class/main-waterfall-plot-label.svg • Waterfall-class/main-waterfall-plot-samplenames-false.svg • Waterfall-class/main-waterfall-plot-xtitle-false.svg • Waterfall-class/mutation-plot-add-layers.svg • Waterfall-class/mutation-plot-burden-complex.svg • Waterfall-class/mutation-plot-burden-simple.svg • Waterfall-class/mutation-plot-frequency-complex.svg • Waterfall-class/mutation-plot-frequency-simple.svg Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 5 WARNINGs, 7 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/GenVisR.Rcheck/00check.log’ for details.