############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:curatedTBData.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings curatedTBData_2.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-data-experiment/meat/curatedTBData.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 ‘curatedTBData/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘curatedTBData’ version ‘2.2.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘curatedTBData’ 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 ... NOTE checkRd: (-1) DataSummary.Rd:28: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:29: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:31: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:32: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:33: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:34: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:35: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:36: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:37: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:38: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:39: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:40: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:41: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:42: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:43: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:44: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:45: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:46: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:47: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:48: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:49: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:50: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:51: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:52: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:53: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:54: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:55: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:56: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:57: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:58: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:59: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:60: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:61: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:62: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:63: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:64: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:65: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:71: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:72: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:73: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:74: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:75: Lost braces in \itemize; meant \describe ? checkRd: (-1) DataSummary.Rd:76: Lost braces in \itemize; meant \describe ? checkRd: (-1) SignatureInfoTraining.Rd:16: Lost braces in \itemize; meant \describe ? checkRd: (-1) SignatureInfoTraining.Rd:17: Lost braces in \itemize; meant \describe ? checkRd: (-1) SignatureInfoTraining.Rd:18: Lost braces in \itemize; meant \describe ? checkRd: (-1) SignatureInfoTraining.Rd:19: Lost braces in \itemize; meant \describe ? checkRd: (-1) SignatureInfoTraining.Rd:20: Lost braces in \itemize; meant \describe ? checkRd: (-1) SignatureInfoTraining.Rd:21: Lost braces in \itemize; meant \describe ? checkRd: (-1) SignatureInfoTraining.Rd:22: Lost braces in \itemize; meant \describe ? checkRd: (-1) SignatureInfoTraining.Rd:23: Lost braces in \itemize; meant \describe ? checkRd: (-1) SignatureInfoTraining.Rd:24: Lost braces in \itemize; meant \describe ? checkRd: (-1) SignatureInfoTraining.Rd:25: Lost braces in \itemize; meant \describe ? checkRd: (-1) SignatureInfoTraining.Rd:26: Lost braces in \itemize; meant \describe ? checkRd: (-1) SignatureInfoTraining.Rd:27: Lost braces in \itemize; meant \describe ? checkRd: (-1) SignatureInfoTraining.Rd:28: Lost braces in \itemize; meant \describe ? checkRd: (-1) SignatureInfoTraining.Rd:29: Lost braces in \itemize; meant \describe ? checkRd: (-1) SignatureInfoTraining.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) SignatureInfoTraining.Rd:31: Lost braces in \itemize; meant \describe ? checkRd: (-1) SignatureInfoTraining.Rd:32: Lost braces in \itemize; meant \describe ? checkRd: (-1) SignatureInfoTraining.Rd:33: Lost braces in \itemize; meant \describe ? checkRd: (-1) SignatureInfoTraining.Rd:34: Lost braces in \itemize; meant \describe ? checkRd: (-1) SignatureInfoTraining.Rd:35: Lost braces in \itemize; meant \describe ? checkRd: (-1) SignatureInfoTraining.Rd:36: Lost braces in \itemize; meant \describe ? checkRd: (-1) SignatureInfoTraining.Rd:37: Lost braces in \itemize; meant \describe ? checkRd: (-1) SignatureInfoTraining.Rd:38: Lost braces in \itemize; meant \describe ? checkRd: (-1) SignatureInfoTraining.Rd:39: Lost braces in \itemize; meant \describe ? checkRd: (-1) SignatureInfoTraining.Rd:40: Lost braces in \itemize; meant \describe ? checkRd: (-1) SignatureInfoTraining.Rd:41: Lost braces in \itemize; meant \describe ? checkRd: (-1) SignatureInfoTraining.Rd:42: Lost braces in \itemize; meant \describe ? checkRd: (-1) SignatureInfoTraining.Rd:43: Lost braces in \itemize; meant \describe ? checkRd: (-1) SignatureInfoTraining.Rd:44: Lost braces in \itemize; meant \describe ? checkRd: (-1) SignatureInfoTraining.Rd:45: Lost braces in \itemize; meant \describe ? checkRd: (-1) SignatureInfoTraining.Rd:46: Lost braces in \itemize; meant \describe ? checkRd: (-1) SignatureInfoTraining.Rd:47: Lost braces in \itemize; meant \describe ? * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented data sets: ‘Clinical_Information’ 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 ... WARNING Data codoc mismatches from Rd file 'DataSummary.Rd': Variables in data frame 'DataSummary' Code: Age Control Country/Region DiagnosisMethod GEOAccession GeneralType HIVStatus LTBI Notes OD PTB Platform Tissue Total Docs: Age Control DiagnosisMethod GeneralType GeographicalRegion HIVStatus LTBI Notes OD PTB Platform Study Tissue Total * 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 ... NOTE Note: found 3 marked UTF-8 strings * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed combine_objects 16.365 0.587 17.632 curatedTBData 9.736 0.346 10.849 * 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 WARNINGs, 2 NOTEs See ‘/home/biocbuild/bbs-3.20-data-experiment/meat/curatedTBData.Rcheck/00check.log’ for details.