############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:scRNAseq.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings scRNAseq_2.21.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/scRNAseq.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * 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 ‘scRNAseq/DESCRIPTION’ ... OK * this is package ‘scRNAseq’ version ‘2.21.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘scRNAseq’ can be installed ... OK * 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 ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: AztekinTailData.Rd: reducedDims, SingleCellExperiment-class BachMammaryData.Rd: rowRanges, SingleCellExperiment-class BacherTCellData.Rd: colData, rowRanges, SingleCellExperiment-class BaronPancreasData.Rd: rowRanges, SingleCellExperiment-class BhaduriOrganoidData.Rd: rowRanges, SingleCellExperiment-class BuettnerESCData.Rd: altExps, rowRanges, SingleCellExperiment-class BunisHSPCData.Rd: colData, SingleCellExperiment-class CampbellBrainData.Rd: rowRanges, SingleCellExperiment-class ChenBrainData.Rd: rowRanges, SingleCellExperiment-class DarmanisBrainData.Rd: rowRanges, SingleCellExperiment-class ERCCSpikeInConcentrations.Rd: DataFrame-class ErnstSpermatogenesisData.Rd: rowRanges, SingleCellExperiment-class FletcherOlfactoryData.Rd: colData, rowRanges, SingleCellExperiment-class GiladiHSCData.Rd: colData, rowRanges, SingleCellExperiment-class GrunHSCData.Rd: rowRanges, SingleCellExperiment-class GrunPancreasData.Rd: altExps, rowRanges, SingleCellExperiment-class HeOrganAtlasData.Rd: rowRanges, SingleCellExperiment-class HermannSpermatogenesisData.Rd: SingleCellExperiment-class HuCortexData.Rd: rowRanges, SingleCellExperiment-class JessaBrainData.Rd: colData, rowRanges, SingleCellExperiment-class KolodziejczykESCData.Rd: altExps, rowRanges, SingleCellExperiment-class KotliarovPBMCData.Rd: rowRanges, SingleCellExperiment-class LaMannoBrainData.Rd: rowRanges, SingleCellExperiment-class LawlorPancreasData.Rd: SingleCellExperiment-class LedergorMyelomaData.Rd: rowRanges, SingleCellExperiment-class LengESCData.Rd: rowRanges, SingleCellExperiment-class LunSpikeInData.Rd: altExp, altExps, rowRanges, SingleCellExperiment-class MacoskoRetinaData.Rd: rowRanges, SingleCellExperiment-class MairPBMCData.Rd: rowRanges, SingleCellExperiment-class MarquesBrainData.Rd: rowRanges, SingleCellExperiment-class MessmerESCData.Rd: altExps, rowRanges, SingleCellExperiment-class MuraroPancreasData.Rd: altExps, rowRanges, SingleCellExperiment-class NestorowaHSCData.Rd: colData, reducedDims, altExps, rowRanges, SingleCellExperiment-class NowakowskiCortexData.Rd: rowRanges, SingleCellExperiment-class, reducedDims PaulHSCData.Rd: rowRanges, SingleCellExperiment-class PollenGliaData.Rd: rowRanges, SingleCellExperiment-class ReprocessedData.Rd: altExps, metadata, rowRanges, SingleCellExperiment-class RichardTCellData.Rd: altExps, rowRanges, SingleCellExperiment-class RomanovBrainData.Rd: altExps, rowRanges, SingleCellExperiment-class SegerstolpePancreasData.Rd: altExps, rowData, rowRanges, SingleCellExperiment-class ShekharRetinaData.Rd: rowRanges, SingleCellExperiment-class StoeckiusHashingData.Rd: rowRanges, SingleCellExperiment-class TasicBrainData.Rd: altExps, rowRanges, SingleCellExperiment-class UsoskinBrainData.Rd: rowRanges, SingleCellExperiment-class WuKidneyData.Rd: rowRanges, SingleCellExperiment-class XinPancreasData.Rd: rowRanges, SingleCellExperiment-class ZeiselBrainData.Rd: altExps, rowRanges, SingleCellExperiment-class ZeiselNervousData.Rd: rowRanges, SingleCellExperiment-class ZhaoImmuneLiverData.Rd: rowRanges, colData, SingleCellExperiment-class ZhongPrefrontalData.Rd: rowRanges, SingleCellExperiment-class ZilionisLungData.Rd: rowRanges, colData, reducedDim, SingleCellExperiment-class countErccMolecules.Rd: DataFrame-class fetchDataset.Rd: ReloadedArray-class, dgCMatrix-class, readObject, SummarizedExperiment-class, uploadDirectory listDatasets.Rd: DataFrame-class polishDataset.Rd: SummarizedExperiment-class, SingleCellExperiment-class, altExp saveDataset.Rd: SummarizedExperiment-class, fetchMetadataSchema, uploadDirectory searchDatasets.Rd: gypsum.search.clause, fetchMetadataDatabase, DataFrame-class, translateTextQuery surveyDatasets.Rd: fetchMetadataDatabase, DataFrame-class 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed BhaduriOrganoidData 22.843 8.279 31.393 BacherTCellData 16.074 5.565 22.697 ZeiselNervousData 14.879 6.246 22.693 HeOrganAtlasData 12.230 6.627 19.366 ErnstSpermatogenesisData 9.789 4.272 15.265 JessaBrainData 8.651 4.038 13.785 StoeckiusHashingData 8.445 1.488 10.720 BachMammaryData 6.814 1.484 9.277 GiladiHSCData 4.692 2.324 7.600 LunSpikeInData 5.821 1.128 7.446 AztekinTailData 6.209 0.674 7.103 ZhaoImmuneLiverData 4.663 2.146 7.637 ZilionisLungData 4.094 1.220 5.911 NestorowaHSCData 4.125 0.903 5.443 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.21-data-experiment/meat/scRNAseq.Rcheck/00check.log’ for details.