############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:karyoploteR.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings karyoploteR_1.33.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/karyoploteR.Rcheck' * using R Under development (unstable) (2024-10-26 r87273 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'karyoploteR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'karyoploteR' version '1.33.0' * 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 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 ... 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 205.33 6.00 221.08 kpPlotGenes 26.81 0.67 27.71 mergeTranscripts 20.69 0.39 21.10 kpPlotHorizon 18.18 0.17 18.34 kpPlotRegions 14.62 0.08 14.72 kpPlotBAMCoverage 9.59 0.36 9.96 kpPlotTranscripts 9.17 0.05 9.22 kpPlotManhattan 5.83 0.22 6.04 * 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: 4 NOTEs See 'E:/biocbuild/bbs-3.21-bioc/meat/karyoploteR.Rcheck/00check.log' for details.