############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GenomicFeatures.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings GenomicFeatures_1.51.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GenomicFeatures.Rcheck’ * using R Under development (unstable) (2023-02-14 r83833) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 * running under: Ubuntu 20.04.6 LTS * using session charset: UTF-8 * checking for file ‘GenomicFeatures/DESCRIPTION’ ... OK * this is package ‘GenomicFeatures’ version ‘1.51.4’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomeInfoDb', 'GenomicRanges', 'AnnotationDbi' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘GenomicFeatures’ 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 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 ... NOTE ':::' call which should be '::': ‘rtracklayer:::tableNames’ See the note in ?`:::` about the use of this operator. Unexported objects imported by ':::' calls: ‘AnnotationDbi:::.getMetaValue’ ‘AnnotationDbi:::.valid.colnames’ ‘AnnotationDbi:::.valid.metadata.table’ ‘AnnotationDbi:::.valid.table.colnames’ ‘AnnotationDbi:::dbEasyQuery’ ‘AnnotationDbi:::dbQuery’ ‘AnnotationDbi:::smartKeys’ ‘BiocGenerics:::testPackage’ ‘GenomeInfoDb:::check_tax_id’ ‘GenomeInfoDb:::getSeqlevelsReplacementMode’ ‘GenomeInfoDb:::lookup_organism_by_tax_id’ ‘GenomeInfoDb:::lookup_tax_id_by_organism’ ‘GenomeInfoDb:::make_circ_flags_from_circ_seqs’ ‘GenomeInfoDb:::normarg_new2old’ ‘GenomicRanges:::unsafe.transcriptLocs2refLocs’ ‘GenomicRanges:::unsafe.transcriptWidths’ ‘IRanges:::regroupBySupergroup’ ‘S4Vectors:::V_recycle’ ‘S4Vectors:::anyMissingOrOutside’ ‘S4Vectors:::decodeRle’ ‘S4Vectors:::extract_data_frame_rows’ ‘S4Vectors:::quick_togroup’ ‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’ ‘rtracklayer:::resourceDescription’ 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 ... WARNING checkRd: (5) FeatureDb-class.Rd:31-34: \item in \describe must have non-empty label checkRd: (5) TxDb-class.Rd:30-33: \item in \describe must have non-empty label checkRd: (5) TxDb-class.Rd:34-39: \item in \describe must have non-empty label checkRd: (5) TxDb-class.Rd:40-43: \item in \describe must have non-empty label checkRd: (5) TxDb-class.Rd:44-52: \item in \describe must have non-empty label checkRd: (5) TxDb-class.Rd:53-59: \item in \describe must have non-empty label checkRd: (5) TxDb-class.Rd:60-65: \item in \describe must have non-empty label checkRd: (5) TxDb-class.Rd:66-71: \item in \describe must have non-empty label checkRd: (5) TxDb-class.Rd:72-80: \item in \describe must have non-empty label checkRd: (5) select-methods.Rd:21-25: \item in \describe must have non-empty label checkRd: (5) select-methods.Rd:26-50: \item in \describe must have non-empty label checkRd: (5) select-methods.Rd:51-55: \item in \describe must have non-empty label checkRd: (5) select-methods.Rd:56-62: \item in \describe must have non-empty label * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed makeFeatureDbFromUCSC 74.640 3.103 184.654 coverageByTranscript 68.774 2.148 70.924 coordinate-mapping-methods 53.461 3.140 57.283 makeTxDbFromBiomart 50.380 1.626 112.957 exonicParts 35.663 0.296 35.960 extractTranscriptSeqs 12.572 0.136 12.709 makeTxDbFromUCSC 9.114 0.077 30.980 makeTxDbFromGFF 7.832 0.041 7.872 transcriptLocs2refLocs 5.604 0.143 5.753 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘run_unitTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘GenomicFeatures.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/GenomicFeatures.Rcheck/00check.log’ for details.