############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:HSMMSingleCell.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings HSMMSingleCell_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-data-experiment/meat/HSMMSingleCell.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘HSMMSingleCell/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘HSMMSingleCell’ version ‘1.18.0’ * 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 ‘HSMMSingleCell’ can be installed ... OK * checking installed package size ... NOTE installed size is 16.1Mb sub-directories of 1Mb or more: data 16.0Mb * checking package 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 R 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 ... OK * checking for missing documentation entries ... WARNING Undocumented data sets: ‘HSMM_expr_matrix’ ‘HSMM_sample_sheet’ ‘HSMM_gene_annotation’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 ... WARNING Note: significantly better compression could be obtained by using R CMD build --resave-data old_size new_size compress HSMM_expr_matrix.rda 15.6Mb 9.0Mb xz HSMM_gene_annotation.rda 451Kb 287Kb xz * checking files in ‘vignettes’ ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': ‘HSMMSingleCell-vignette-concordance.tex’, ‘HSMMSingleCell-vignette.Rnw’, ‘HSMMSingleCell-vignette.bbl’, ‘HSMMSingleCell-vignette.log’, ‘HSMMSingleCell-vignette.pdf’, ‘HSMMSingleCell-vignette.synctex.gz’, ‘HSMMSingleCell-vignette.tex’, ‘HSMMSingleCell-vignette.toc’, ‘monocle_alg.bib’, ‘whbiocvignette.sty’ Files named as vignettes but with no recognized vignette engine: ‘vignettes/HSMMSingleCell-vignette.Rnw’ (Is a VignetteBuilder field missing?) The following files look like leftovers/mistakes: ‘HSMMSingleCell-vignette.bbl’, ‘HSMMSingleCell-vignette.log’, ‘HSMMSingleCell-vignette.toc’ Please remove them from your package. * checking examples ... NONE * checking PDF version of manual ... OK * DONE Status: 3 WARNINGs, 1 NOTE See ‘/home/biocbuild/bbs-3.16-data-experiment/meat/HSMMSingleCell.Rcheck/00check.log’ for details.