############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings karyoploteR_1.31.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/karyoploteR.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘karyoploteR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘karyoploteR’ version ‘1.31.0’ * 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 ‘karyoploteR’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘regioneR’ ‘GenomicRanges’ A package should be listed in only one of these fields. * 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: NEW FEATURES Cannot process chunk/lines: SIGNIFICANT USER-VISIBLE CHANGES Cannot process chunk/lines: NEW FEATURES Cannot process chunk/lines: SIGNIFICANT USER-VISIBLE CHANGES * 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 ... NOTE checkRd: (-1) kpPlotBAMCoverage.Rd:48: Lost braces 48 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}. | ^ checkRd: (-1) kpPlotBAMDensity.Rd:48: Lost braces 48 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}. | ^ checkRd: (-1) kpPlotCoverage.Rd:46: Lost braces 46 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}. | ^ checkRd: (-1) kpPlotDensity.Rd:42: Lost braces 42 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}. | ^ checkRd: (-1) kpPlotManhattan.Rd:80: Lost braces 80 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}. | ^ checkRd: (-1) kpPlotMarkers.Rd:81: Lost braces 81 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}. | ^ checkRd: (-1) kpPlotRainfall.Rd:47: Lost braces 47 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}. | ^ checkRd: (-1) kpPoints.Rd:54: Lost braces 54 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}. | ^ checkRd: (-1) kpRect.Rd:55: Lost braces 55 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}. | ^ checkRd: (-1) plotKaryotype.Rd:61: Lost braces 61 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}. | ^ * 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 R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed kpPlotDensity 75.112 5.327 93.998 kpPlotGenes 49.883 1.069 62.004 mergeTranscripts 40.228 0.406 50.329 kpPlotHorizon 35.316 0.225 42.807 kpPlotRegions 28.341 0.200 34.020 kpPlotTranscripts 16.355 0.129 19.699 kpPlotBAMCoverage 13.794 0.544 16.643 kpPlotManhattan 9.789 0.320 12.056 makeGenesDataFromTxDb 6.829 0.101 8.585 kpAbline 5.130 1.362 7.735 addGeneNames 5.698 0.212 7.172 kpPlotMarkers 4.197 0.047 5.121 plotKaryotype 2.645 0.071 5.978 * 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 * DONE Status: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/karyoploteR.Rcheck/00check.log’ for details.