############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomicFeatures.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomicFeatures_1.54.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/GenomicFeatures.Rcheck’ * using R version 4.3.2 Patched (2023-11-01 r85457) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GenomicFeatures/DESCRIPTION’ ... OK * this is package ‘GenomicFeatures’ version ‘1.54.3’ * 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 ... NOTE installed size is 5.5Mb sub-directories of 1Mb or more: R 2.0Mb extdata 3.0Mb * 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 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 ... OK * 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 ... ERROR Running examples in ‘GenomicFeatures-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: makeTxDbFromUCSC > ### Title: Make a TxDb object from annotations available at the UCSC Genome > ### Browser > ### Aliases: supportedUCSCtables browseUCSCtrack makeTxDbFromUCSC > > ### ** Examples > > ## --------------------------------------------------------------------- > ## A. BASIC USAGE > ## --------------------------------------------------------------------- > > ## Use ucscGenomes() from the rtracklayer package to display the list of > ## genomes available at UCSC: > library(rtracklayer) > ucscGenomes()[ , "db"] [1] "ailMel1" "allMis1" "anoCar1" "anoCar2" "anoGam1" [6] "anoGam3" "apiMel1" "apiMel2" "aplCal1" "aptMan1" [11] "aquChr2" "balAcu1" "bisBis1" "bosTau2" "bosTau3" [16] "bosTau4" "bosTau6" "bosTau7" "bosTau8" "bosTau9" [21] "braFlo1" "caeJap1" "caePb1" "caePb2" "caeRem2" [26] "caeRem3" "calJac1" "calJac3" "calJac4" "calMil1" [31] "canFam1" "canFam2" "canFam3" "canFam4" "canFam5" [36] "canFam6" "cavPor3" "cb1" "cb3" "ce10" [41] "ce11" "ce2" "ce4" "ce6" "cerSim1" [46] "chlSab2" "choHof1" "chrPic1" "ci1" "ci2" [51] "ci3" "criGri1" "criGriChoV1" "criGriChoV2" "danRer10" [56] "danRer11" "danRer3" "danRer4" "danRer5" "danRer6" [61] "danRer7" "dasNov3" "dipOrd1" "dm1" "dm2" [66] "dm3" "dm6" "dp2" "dp3" "droAna1" [71] "droAna2" "droEre1" "droGri1" "droMoj1" "droMoj2" [76] "droPer1" "droSec1" "droSim1" "droVir1" "droVir2" [81] "droYak1" "droYak2" "eboVir3" "echTel1" "echTel2" [86] "enhLutNer1" "equCab1" "equCab2" "equCab3" "eriEur1" [91] "eriEur2" "felCat3" "felCat4" "felCat5" "felCat8" [96] "felCat9" "fr1" "fr2" "fr3" "gadMor1" [101] "galGal2" "galGal3" "galGal4" "galGal5" "galGal6" [106] "galVar1" "gasAcu1" "geoFor1" "gorGor3" "gorGor4" [111] "gorGor5" "gorGor6" "hetGla1" "hetGla2" "hg16" [116] "hg17" "hg18" "hg19" "hg38" "hs1" [121] "latCha1" "loxAfr3" "macEug2" "macFas5" "manPen1" [126] "melGal1" "melGal5" "melUnd1" "micMur1" "micMur2" [131] "mm10" "mm39" "mm7" "mm8" "mm9" [136] "monDom1" "monDom4" "monDom5" "mpxvRivers" "musFur1" [141] "nanPar1" "nasLar1" "neoSch1" "nomLeu1" "nomLeu2" [146] "nomLeu3" "ochPri2" "ochPri3" "oreNil2" "ornAna1" [151] "ornAna2" "oryCun2" "oryLat2" "otoGar3" "oviAri1" [156] "oviAri3" "oviAri4" "panPan1" "panPan2" "panPan3" [161] "panTro1" "panTro2" "panTro3" "panTro4" "panTro5" [166] "panTro6" "papAnu2" "papAnu4" "papHam1" "petMar1" [171] "petMar2" "petMar3" "ponAbe2" "ponAbe3" "priPac1" [176] "proCap1" "pteVam1" "rheMac10" "rheMac2" "rheMac3" [181] "rheMac8" "rhiRox1" "rn3" "rn4" "rn5" [186] "rn6" "rn7" "sacCer1" "sacCer2" "sacCer3" [191] "saiBol1" "sarHar1" "sorAra1" "sorAra2" "speTri2" [196] "strPur1" "strPur2" "susScr11" "susScr2" "susScr3" [201] "taeGut1" "taeGut2" "tarSyr1" "tarSyr2" "tetNig1" [206] "tetNig2" "thaSir1" "triMan1" "tupBel1" "turTru2" [211] "vicPac1" "vicPac2" "wuhCor1" "xenLae2" "xenTro1" [216] "xenTro10" "xenTro2" "xenTro3" "xenTro7" "xenTro9" > > ## Display the list of tables known to work with makeTxDbFromUCSC(): > supportedUCSCtables("hg38") Error in names(trackIds) <- sub("^ ", "", nms) : attempt to set an attribute on NULL Calls: supportedUCSCtables ... trackNames -> .local -> ucscTracks -> ucscTracks -> .local Execution halted * 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 3 NOTEs See ‘/Users/biocbuild/bbs-3.18-bioc/meat/GenomicFeatures.Rcheck/00check.log’ for details.