Movatterモバイル変換

################################################################################################################################################################## Running command:######   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Gviz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Gviz_1.54.0.tar.gz###############################################################################################################################################################* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/Gviz.Rcheck’* using R version 4.5.2 (2025-10-31)* using platform: x86_64-apple-darwin20* R was compiled by    Apple clang version 14.0.0 (clang-1400.0.29.202)    GNU Fortran (GCC) 14.2.0* running under: macOS Monterey 12.7.6* using session charset: UTF-8* using option ‘--no-vignettes’* checking for file ‘Gviz/DESCRIPTION’ ... OK* this is package ‘Gviz’ version ‘1.54.0’* package encoding: UTF-8* 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 ‘Gviz’ can be installed ... OK* checking installed package size ... INFO  installed size is  5.5Mb  sub-directories of 1Mb or more:    R         2.0Mb    extdata   2.5Mb* 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 ... OK* checking whether the namespace can be unloaded cleanly ... OK* checking whether startup messages can be suppressed ... 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 ... OK* checking Rd files ... OK* checking Rd metadata ... OK* checking Rd cross-references ... NOTEFound the following Rd file(s) with Rd \link{} targets missing packageanchors:  AlignmentsTrack-class.Rd: IRanges-class, GRanges-class, panel.grid  AnnotationTrack-class.Rd: IRanges-class, GRanges-class, panel.grid  BiomartGeneRegionTrack-class.Rd: Mart-class, getBM, GRanges-class,    IRanges-class, panel.grid  CustomTrack-class.Rd: GRanges-class, IRanges-class, panel.grid  DataTrack-class.Rd: IRanges-class, panel.loess, panel.bwplot,    horizonplot, GRanges-class, panel.grid  GdObject-class.Rd: GRanges-class, IRanges-class, panel.grid  GeneRegionTrack-class.Rd: IRanges-class, GRanges-class, panel.grid  GenomeAxisTrack-class.Rd: GRanges-class, IRanges-class, panel.grid  HighlightTrack-class.Rd: IRanges-class, GRanges-class, panel.grid  IdeogramTrack-class.Rd: GRanges-class, IRanges-class, panel.grid  NumericTrack-class.Rd: GRanges-class, IRanges-class, panel.grid  OverlayTrack-class.Rd: GRanges-class, IRanges-class, panel.grid  RangeTrack-class.Rd: GRanges-class, IRanges-class, panel.grid  ReferenceTrack-class.Rd: GRanges-class, IRanges-class, panel.grid  SequenceTrack-class.Rd: DNAStringSet-class, DNAString-class,    BSgenome-class, GRanges-class, IRanges-class, panel.grid  StackedTrack-class.Rd: GRanges-class, IRanges-class, panel.grid  settings.Rd: panel.grid, panel.xyplot, panel.bwplot, horizonplot,    panel.loessPlease provide package anchors for all Rd \link{} targets not in thepackage itself and the base packages.* 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 files in ‘vignettes’ ... OK* checking examples ... OKExamples with CPU (user + system) or elapsed time > 5s                               user system elapsedAlignmentsTrack-class        19.634  1.028  23.129GeneRegionTrack-class        15.245  0.163  15.746AnnotationTrack-class        14.062  0.236  14.587plotTracks                   10.675  0.095  11.464BiomartGeneRegionTrack-class  8.801  0.072   9.031GenomeAxisTrack-class         8.558  0.044   8.807SequenceTrack-class           7.605  0.506   8.309* checking for unstated dependencies in ‘tests’ ... OK* checking tests ...  Running ‘testthat.R’ OK* 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* DONEStatus: 1 NOTESee  ‘/Users/biocbuild/bbs-3.22-bioc/meat/Gviz.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Gviz###############################################################################################################################################################* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’* installing *source* package ‘Gviz’ ...** this is package ‘Gviz’ version ‘1.54.0’** using staged installation** R** data** inst** byte-compile and prepare package for lazy loading** help*** installing help indices** building package indices** installing vignettes** testing if installed package can be loaded from temporary location** testing if installed package can be loaded from final location** testing if installed package keeps a record of temporary installation path* DONE (Gviz)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"Copyright (C) 2025 The R Foundation for Statistical ComputingPlatform: x86_64-apple-darwin20R is free software and comes with ABSOLUTELY NO WARRANTY.You are welcome to redistribute it under certain conditions.Type 'license()' or 'licence()' for distribution details.R is a collaborative project with many contributors.Type 'contributors()' for more information and'citation()' on how to cite R or R packages in publications.Type 'demo()' for some demos, 'help()' for on-line help, or'help.start()' for an HTML browser interface to help.Type 'q()' to quit R.> library(testthat)> library(Gviz)Loading required package: S4VectorsLoading required package: stats4Loading required package: BiocGenericsLoading required package: genericsAttaching package: 'generics'The following objects are masked from 'package:base':    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,    setequal, unionAttaching package: 'BiocGenerics'The following objects are masked from 'package:stats':    IQR, mad, sd, var, xtabsThe 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.minAttaching package: 'S4Vectors'The following object is masked from 'package:utils':    findMatchesThe following objects are masked from 'package:base':    I, expand.grid, unnameLoading required package: IRangesLoading required package: GenomicRangesLoading required package: SeqinfoLoading required package: grid> > test_check("Gviz")Loading required package: BSgenomeLoading required package: BiostringsLoading required package: XVectorAttaching package: 'Biostrings'The following object is masked from 'package:grid':    patternThe following object is masked from 'package:base':    strsplitLoading required package: BiocIOLoading required package: rtracklayer[ FAIL 0 | WARN 1 | SKIP 1 | PASS 293 ]══ Skipped tests (1) ═══════════════════════════════════════════════════════════• Biomart not available (1): 'test_AllClasses.R:174:5'[ FAIL 0 | WARN 1 | SKIP 1 | PASS 293 ]> > proc.time()   user  system elapsed 101.643   7.207 151.908