############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:EpiTxDb.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings EpiTxDb_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/EpiTxDb.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 ‘EpiTxDb/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘EpiTxDb’ version ‘1.18.0’ * 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 ‘EpiTxDb’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘GenomicFeatures::makeTxDbPackage’ by ‘txdbmaker::makeTxDbPackage’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::supportedUCSCFeatureDbTables’ by ‘txdbmaker::supportedUCSCFeatureDbTables’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromGFF’ by ‘txdbmaker::makeTxDbFromGFF’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbPackageFromBiomart’ by ‘txdbmaker::makeTxDbPackageFromBiomart’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::supportedMiRBaseBuildValues’ by ‘txdbmaker::supportedMiRBaseBuildValues’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::supportedUCSCFeatureDbTracks’ by ‘txdbmaker::supportedUCSCFeatureDbTracks’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::browseUCSCtrack’ by ‘txdbmaker::browseUCSCtrack’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::getChromInfoFromBiomart’ by ‘txdbmaker::getChromInfoFromBiomart’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromGRanges’ by ‘txdbmaker::makeTxDbFromGRanges’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::supportedUCSCtables’ by ‘txdbmaker::supportedUCSCtables’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromBiomart’ by ‘txdbmaker::makeTxDbFromBiomart’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::UCSCFeatureDbTableSchema’ by ‘txdbmaker::UCSCFeatureDbTableSchema’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromEnsembl’ by ‘txdbmaker::makeTxDbFromEnsembl’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeTxDb’ by ‘txdbmaker::makeTxDb’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeFDbPackageFromUCSC’ by ‘txdbmaker::makeFDbPackageFromUCSC’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromUCSC’ by ‘txdbmaker::makeTxDbFromUCSC’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbPackageFromUCSC’ by ‘txdbmaker::makeTxDbPackageFromUCSC’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makePackageName’ by ‘txdbmaker::makePackageName’ when loading ‘EpiTxDb’ Warning: replacing previous import ‘GenomicFeatures::makeFeatureDbFromUCSC’ by ‘txdbmaker::makeFeatureDbFromUCSC’ when loading ‘EpiTxDb’ See ‘/home/biocbuild/bbs-3.20-bioc/meat/EpiTxDb.Rcheck/00install.out’ for details. * 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 ... NOTE Unexported objects imported by ':::' calls: ‘AnnotationDbi:::.getMetaValue’ ‘AnnotationDbi:::.valid.metadata.table’ ‘AnnotationDbi:::.valid.table.colnames’ ‘AnnotationDbi:::dbEasyQuery’ ‘AnnotationDbi:::dbQuery’ ‘AnnotationDbi:::smartKeys’ ‘BiocGenerics:::replaceSlots’ See the note in ?`:::` about the use of this operator. * 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) makeEpiTxDb.Rd:20: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeEpiTxDb.Rd:21-23: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeEpiTxDb.Rd:24-25: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeEpiTxDb.Rd:26-27: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeEpiTxDb.Rd:28-29: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeEpiTxDb.Rd:30-31: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeEpiTxDb.Rd:32: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeEpiTxDb.Rd:33-34: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeEpiTxDb.Rd:43-44: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeEpiTxDb.Rd:45-46: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeEpiTxDb.Rd:47-49: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeEpiTxDb.Rd:50-51: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeEpiTxDb.Rd:52-53: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeEpiTxDb.Rd:54-55: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeEpiTxDb.Rd:62-63: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeEpiTxDb.Rd:64-66: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeEpiTxDb.Rd:67-69: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeEpiTxDb.Rd:70-71: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeEpiTxDb.Rd:72-73: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeEpiTxDb.Rd:74-75: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeEpiTxDb.Rd:82-83: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeEpiTxDb.Rd:84-85: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeEpiTxDb.Rd:86-88: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeEpiTxDb.Rd:94: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeEpiTxDb.Rd:95: Lost braces in \itemize; meant \describe ? * checking Rd metadata ... OK * checking Rd cross-references ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... OK * 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: 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/EpiTxDb.Rcheck/00check.log’ for details.