############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings karyoploteR_1.33.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/karyoploteR.Rcheck’ * using R Under development (unstable) (2024-11-14 r87333) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘karyoploteR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘karyoploteR’ version ‘1.33.0’ * 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 loading without being on the library search path ... 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: getCytobands.Rd: GenomicRanges, memoise, forget kpPlotBAMCoverage.Rd: bamsignals kpPlotBAMDensity.Rd: Rsamtools kpPlotBigWig.Rd: BigWigFile Please provide package anchors for all Rd \link{} targets not in the package 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 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 24.008 6.765 34.732 kpPlotGenes 12.861 0.099 12.969 mergeTranscripts 11.656 0.126 11.809 kpPlotHorizon 8.920 0.005 8.927 kpPlotRegions 7.660 0.001 7.666 kpPlotBAMCoverage 5.516 0.356 5.874 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/karyoploteR.Rcheck/00check.log’ for details.