############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:curatedPCaData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings curatedPCaData_1.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-data-experiment/meat/curatedPCaData.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘curatedPCaData/DESCRIPTION’ ... OK * this is package ‘curatedPCaData’ version ‘1.5.0’ * 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 ‘curatedPCaData’ 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: getPCa.Rd: MultiAssayExperiment-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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... 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 getPCaSummaryStudies 207.346 15.222 241.315 getPCaSummarySamples 27.235 2.834 32.733 getPCaSummarySurv 26.949 0.783 30.173 getPCaSummaryTable 25.998 0.769 29.049 curatedPCaDatasets_abida 16.876 1.278 19.430 curatedPCaDatasets_taylor 16.012 1.267 18.345 curatedPCaDatasets_barbieri 14.067 2.478 18.673 curatedPCaDatasets_ren 14.406 1.680 16.970 getPCa 14.293 1.460 17.104 curatedPCaDatasets_tcga 14.063 0.730 16.011 curatedPCaDatasets_weiner 12.125 1.550 14.749 curatedPCaDatasets_sun 12.170 1.271 14.259 curatedPCaDatasets_kunderfranco 11.403 1.287 13.620 curatedPCaDatasets_igc 11.204 1.213 13.319 curatedPCaDatasets_friedrich 10.979 1.321 13.145 curatedPCaDatasets_icgcca 10.977 1.245 13.380 curatedPCaDatasets_kim 10.898 0.915 12.823 curatedPCaDatasets_wallace 10.717 1.039 12.711 curatedPCaDatasets_wang 10.755 1.001 12.580 curatedPCaDatasets_chandran 10.237 0.846 11.882 curatedPCaDatasets_true 9.635 1.073 11.624 curatedPCaDatasets_barwick 8.093 0.641 9.423 curatedPCaDatasets_baca 4.527 0.382 5.402 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘native_tests.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: 1 NOTE See ‘/home/biocbuild/bbs-3.22-data-experiment/meat/curatedPCaData.Rcheck/00check.log’ for details.