############################################################################## ############################################################################## ### ### Running command: ### ### /home/hpages/bbs-3.18-bioc/R/bin/R CMD check --install=check:GenomicFeatures.install-out.txt --library=/home/hpages/bbs-3.18-bioc-testing/Rlibs --timings GenomicFeatures_1.53.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/hpages/bbs-3.18-bioc-testing/meat/GenomicFeatures.Rcheck’ * using R version 4.3.0 Patched (2023-05-23 r84466) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 12.2.0-17ubuntu1) 12.2.0 GNU Fortran (Ubuntu 12.2.0-17ubuntu1) 12.2.0 * running under: Ubuntu 23.04 * using session charset: UTF-8 * checking for file ‘GenomicFeatures/DESCRIPTION’ ... OK * this is package ‘GenomicFeatures’ version ‘1.53.0’ * 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 ... 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") tablename track subtrack 1 knownGene GENCODE V43 2 ncbiRefSeq NCBI RefSeq RefSeq All 3 ncbiRefSeqCurated NCBI RefSeq RefSeq Curated 4 ncbiRefSeqPredicted NCBI RefSeq RefSeq Predicted 5 ncbiRefSeqOther NCBI RefSeq RefSeq Other 6 refGene NCBI RefSeq UCSC RefSeq 7 ncbiRefSeqSelect NCBI RefSeq RefSeq Select+MANE 8 ncbiRefSeqHgmd NCBI RefSeq RefSeq HGMD 9 xenoRefGene Other RefSeq 10 wgEncodeGencodeBasicV34 All GENCODE V34 Basic 11 wgEncodeGencodeCompV34 All GENCODE V34 Comprehensive 12 wgEncodeGencodePseudoGeneV34 All GENCODE V34 Pseudogenes 13 wgEncodeGencode2wayConsPseudoV34 All GENCODE V34 2-way Pseudogenes 14 wgEncodeGencodePolyaV34 All GENCODE V34 PolyA 15 wgEncodeGencodeBasicV33 All GENCODE V33 Basic 16 wgEncodeGencodeCompV33 All GENCODE V33 Comprehensive 17 wgEncodeGencodePseudoGeneV33 All GENCODE V33 Pseudogenes 18 wgEncodeGencode2wayConsPseudoV33 All GENCODE V33 2-way Pseudogenes 19 wgEncodeGencodePolyaV33 All GENCODE V33 PolyA 20 wgEncodeGencodeBasicV31 All GENCODE V31 Basic 21 wgEncodeGencodeCompV31 All GENCODE V31 Comprehensive 22 wgEncodeGencodePseudoGeneV31 All GENCODE V31 Pseudogenes 23 wgEncodeGencode2wayConsPseudoV31 All GENCODE V31 2-way Pseudogenes 24 wgEncodeGencodePolyaV31 All GENCODE V31 PolyA 25 wgEncodeGencodeBasicV29 All GENCODE V29 Basic 26 wgEncodeGencodeCompV29 All GENCODE V29 Comprehensive 27 wgEncodeGencodePseudoGeneV29 All GENCODE V29 Pseudogenes 28 wgEncodeGencode2wayConsPseudoV29 All GENCODE V29 2-way Pseudogenes 29 wgEncodeGencodePolyaV29 All GENCODE V29 PolyA 30 wgEncodeGencodeBasicV28 All GENCODE V28 Basic 31 wgEncodeGencodeCompV28 All GENCODE V28 Comprehensive 32 wgEncodeGencodePseudoGeneV28 All GENCODE V28 Pseudogenes 33 wgEncodeGencode2wayConsPseudoV28 All GENCODE V28 2-way Pseudogenes 34 wgEncodeGencodePolyaV28 All GENCODE V28 PolyA 35 wgEncodeGencodeBasicV27 All GENCODE V27 Basic 36 wgEncodeGencodeCompV27 All GENCODE V27 Comprehensive 37 wgEncodeGencodePseudoGeneV27 All GENCODE V27 Pseudogenes 38 wgEncodeGencode2wayConsPseudoV27 All GENCODE V27 2-way Pseudogenes 39 wgEncodeGencodePolyaV27 All GENCODE V27 PolyA 40 wgEncodeGencodeBasicV26 All GENCODE V26 Basic 41 wgEncodeGencodeCompV26 All GENCODE V26 Comprehensive 42 wgEncodeGencodePseudoGeneV26 All GENCODE V26 Pseudogenes 43 wgEncodeGencode2wayConsPseudoV26 All GENCODE V26 2-way Pseudogenes 44 wgEncodeGencodePolyaV26 All GENCODE V26 PolyA 45 wgEncodeGencodeBasicV25 All GENCODE V25 Basic 46 wgEncodeGencodeCompV25 All GENCODE V25 Comprehensive 47 wgEncodeGencodePseudoGeneV25 All GENCODE V25 Pseudogenes 48 wgEncodeGencode2wayConsPseudoV25 All GENCODE V25 2-way Pseudogenes 49 wgEncodeGencodePolyaV25 All GENCODE V25 PolyA 50 wgEncodeGencodeBasicV24 All GENCODE V24 Basic 51 wgEncodeGencodeCompV24 All GENCODE V24 Comprehensive 52 wgEncodeGencodePseudoGeneV24 All GENCODE V24 Pseudogenes 53 wgEncodeGencode2wayConsPseudoV24 All GENCODE V24 2-way Pseudogenes 54 wgEncodeGencodePolyaV24 All GENCODE V24 PolyA 55 wgEncodeGencodeBasicV23 All GENCODE V23 Basic 56 wgEncodeGencodeCompV23 All GENCODE V23 Comprehensive 57 wgEncodeGencodePseudoGeneV23 All GENCODE V23 Pseudogenes 58 wgEncodeGencode2wayConsPseudoV23 All GENCODE V23 2-way Pseudogenes 59 wgEncodeGencodePolyaV23 All GENCODE V23 PolyA 60 wgEncodeGencodeBasicV22 All GENCODE V22 Basic 61 wgEncodeGencodeCompV22 All GENCODE V22 Comprehensive 62 wgEncodeGencodePseudoGeneV22 All GENCODE V22 Pseudogenes 63 wgEncodeGencode2wayConsPseudoV22 All GENCODE V22 2-way Pseudogenes 64 wgEncodeGencodePolyaV22 All GENCODE V22 PolyA 65 wgEncodeGencodeBasicV20 GENCODE V20 (Ensembl 76) Basic 66 wgEncodeGencodeCompV20 GENCODE V20 (Ensembl 76) Comprehensive 67 wgEncodeGencodePseudoGeneV20 GENCODE V20 (Ensembl 76) Pseudogenes 68 wgEncodeGencode2wayConsPseudoV20 GENCODE V20 (Ensembl 76) 2-way Pseudogenes 69 wgEncodeGencodePolyaV20 GENCODE V20 (Ensembl 76) PolyA 70 augustusGene AUGUSTUS 71 ccdsGene CCDS 72 geneid Geneid Genes 73 genscan Genscan Genes 74 knownGeneOld12 Old UCSC Genes 75 sgpGene SGP Genes 76 sibGene SIB Genes > supportedUCSCtables("hg19") tablename track subtrack 1 knownGene UCSC Genes 2 ncbiRefSeq NCBI RefSeq RefSeq All 3 ncbiRefSeqCurated NCBI RefSeq RefSeq Curated 4 ncbiRefSeqPredicted NCBI RefSeq RefSeq Predicted 5 ncbiRefSeqOther NCBI RefSeq RefSeq Other 6 refGene NCBI RefSeq UCSC RefSeq 7 ncbiRefSeqSelect NCBI RefSeq RefSeq Select 8 ncbiRefSeqHgmd NCBI RefSeq RefSeq HGMD 9 xenoRefGene Other RefSeq 10 acembly AceView Genes 11 augustusGene AUGUSTUS 12 ccdsGene CCDS 13 ensGene Ensembl Genes 14 exoniphy Exoniphy 15 wgEncodeGencodeBasicV34lift37 GENCODE V34lift37 Basic 16 wgEncodeGencodeCompV34lift37 GENCODE V34lift37 Comprehensive 17 wgEncodeGencodePseudoGeneV34lift37 GENCODE V34lift37 Pseudogenes 18 wgEncodeGencodeBasicV33lift37 GENCODE V33lift37 Basic 19 wgEncodeGencodeCompV33lift37 GENCODE V33lift37 Comprehensive 20 wgEncodeGencodePseudoGeneV33lift37 GENCODE V33lift37 Pseudogenes 21 wgEncodeGencodeBasicV31lift37 GENCODE V31lift37 Basic 22 wgEncodeGencodeCompV31lift37 GENCODE V31lift37 Comprehensive 23 wgEncodeGencodePseudoGeneV31lift37 GENCODE V31lift37 Pseudogenes 24 wgEncodeGencodeBasicV28lift37 GENCODE V28lift37 Basic 25 wgEncodeGencodeCompV28lift37 GENCODE V28lift37 Comprehensive 26 wgEncodeGencodePseudoGeneV28lift37 GENCODE V28lift37 Pseudogenes 27 wgEncodeGencodeBasicV27lift37 GENCODE Gene V27lift37 Basic 28 wgEncodeGencodeCompV27lift37 GENCODE Gene V27lift37 Comprehensive 29 wgEncodeGencodePseudoGeneV27lift37 GENCODE Gene V27lift37 Pseudogenes 30 wgEncodeGencodeBasicV24lift37 GENCODE Gene V24lift37 Basic 31 wgEncodeGencodeCompV24lift37 GENCODE Gene V24lift37 Comprehensive 32 wgEncodeGencodePseudoGeneV24lift37 GENCODE Gene V24lift37 Pseudogenes 33 wgEncodeGencodeBasicV19 GENCODE Genes V19 Basic 34 wgEncodeGencodeCompV19 GENCODE Genes V19 Comprehensive 35 wgEncodeGencodePseudoGeneV19 GENCODE Genes V19 Pseudogenes 36 wgEncodeGencode2wayConsPseudoV19 GENCODE Genes V19 2-way Pseudogenes 37 wgEncodeGencodePolyaV19 GENCODE Genes V19 PolyA 38 wgEncodeGencodeBasicV17 GENCODE Genes V17 Basic 39 wgEncodeGencodeCompV17 GENCODE Genes V17 Comprehensive 40 wgEncodeGencodePseudoGeneV17 GENCODE Genes V17 Pseudogenes 41 wgEncodeGencode2wayConsPseudoV17 GENCODE Genes V17 2-way Pseudogenes 42 wgEncodeGencodePolyaV17 GENCODE Genes V17 PolyA 43 wgEncodeGencodeBasicV14 GENCODE Genes V14 Basic 44 wgEncodeGencodeCompV14 GENCODE Genes V14 Comprehensive 45 wgEncodeGencodePseudoGeneV14 GENCODE Genes V14 Pseudogenes 46 wgEncodeGencode2wayConsPseudoV14 GENCODE Genes V14 2-way Pseudogenes 47 wgEncodeGencodePolyaV14 GENCODE Genes V14 PolyA 48 wgEncodeGencodeBasicV7 GENCODE Genes V7 Basic 49 wgEncodeGencodeCompV7 GENCODE Genes V7 Comprehensive 50 wgEncodeGencodePseudoGeneV7 GENCODE Genes V7 Pseudogenes 51 wgEncodeGencode2wayConsPseudoV7 GENCODE Genes V7 2-way Pseudogenes 52 wgEncodeGencodePolyaV7 GENCODE Genes V7 PolyA 53 geneid Geneid Genes 54 genscan Genscan Genes 55 nscanGene N-SCAN 56 knownGeneOld6 Old UCSC Genes 57 sgpGene SGP Genes 58 sibGene SIB Genes 59 vegaGene Vega Genes Vega Protein Genes 60 vegaPseudoGene Vega Genes Vega Pseudogenes 61 pseudoYale60 Yale Pseudo60 > > ## Open the UCSC track page for a given organism/table: > browseUCSCtrack("hg38", tablename="knownGene") > browseUCSCtrack("hg19", tablename="knownGene") > > browseUCSCtrack("hg38", tablename="ncbiRefSeqSelect") > browseUCSCtrack("hg19", tablename="ncbiRefSeqSelect") > > browseUCSCtrack("hg19", tablename="pseudoYale60") > > browseUCSCtrack("sacCer3", tablename="ensGene") > > ## Retrieve a full transcript dataset for Yeast from UCSC: > txdb1 <- makeTxDbFromUCSC("sacCer3", tablename="ensGene") Download the ensGene table ... Error: Failed to connect: Lost connection to MySQL server at 'waiting for initial communication packet', system error: 110 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 ... ‘GenomicFeatures.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 WARNING, 2 NOTEs See ‘/home/hpages/bbs-3.18-bioc-testing/meat/GenomicFeatures.Rcheck/00check.log’ for details.