############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:txdbmaker.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings txdbmaker_1.0.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/txdbmaker.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘txdbmaker/DESCRIPTION’ ... OK * this is package ‘txdbmaker’ version ‘1.0.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... 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 ‘txdbmaker’ 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 ... NOTE Unexported objects imported by ':::' calls: ‘AnnotationDbi:::dbEasyQuery’ ‘BiocGenerics:::testPackage’ ‘GenomeInfoDb:::check_tax_id’ ‘GenomeInfoDb:::lookup_organism_by_tax_id’ ‘GenomeInfoDb:::lookup_tax_id_by_organism’ ‘GenomeInfoDb:::make_circ_flags_from_circ_seqs’ ‘S4Vectors:::anyMissingOrOutside’ ‘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 ‘txdbmaker-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: makeTxDbFromBiomart > ### Title: Make a TxDb object from annotations available on a BioMart > ### database > ### Aliases: makeTxDbFromBiomart getChromInfoFromBiomart > > ### ** Examples > > ## --------------------------------------------------------------------- > ## A. BASIC USAGE > ## --------------------------------------------------------------------- > > ## We can use listDatasets() from the biomaRt package to list the > ## datasets available in the "ENSEMBL_MART_ENSEMBL" BioMart database: > library(biomaRt) > listMarts(host="https://www.ensembl.org") biomart version 1 ENSEMBL_MART_ENSEMBL Ensembl Genes 112 2 ENSEMBL_MART_MOUSE Mouse strains 112 3 ENSEMBL_MART_SNP Ensembl Variation 112 4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 112 > mart <- useEnsembl(biomart="ENSEMBL_MART_ENSEMBL", host="https://www.ensembl.org") > datasets <- listDatasets(mart) > head(datasets) dataset description 1 abrachyrhynchus_gene_ensembl Pink-footed goose genes (ASM259213v1) 2 acalliptera_gene_ensembl Eastern happy genes (fAstCal1.3) 3 acarolinensis_gene_ensembl Green anole genes (AnoCar2.0v2) 4 acchrysaetos_gene_ensembl Golden eagle genes (bAquChr1.2) 5 acitrinellus_gene_ensembl Midas cichlid genes (Midas_v5) 6 amelanoleuca_gene_ensembl Giant panda genes (ASM200744v2) version 1 ASM259213v1 2 fAstCal1.3 3 AnoCar2.0v2 4 bAquChr1.2 5 Midas_v5 6 ASM200744v2 > subset(datasets, grepl("elegans", dataset, ignore.case=TRUE)) dataset description 27 celegans_gene_ensembl Caenorhabditis elegans (Nematode, N2) genes (WBcel235) version 27 WBcel235 > > ## Retrieve the full transcript dataset for Worm: > txdb1 <- makeTxDbFromBiomart(dataset="celegans_gene_ensembl") Download and preprocess the 'transcripts' data frame ... OK Download and preprocess the 'chrominfo' data frame ... FAILED! (=> skipped) Download and preprocess the 'splicings' data frame ... OK Download and preprocess the 'genes' data frame ... OK Prepare the 'metadata' data frame ... Error in .prepareBiomartMetadata(mart, is_full_dataset, host, taxonomyId, : the BioMart database "ENSEMBL_MART_ENSEMBL" has no (or more than one) "celegans_gene_ensembl" datasets Calls: makeTxDbFromBiomart -> .prepareBiomartMetadata 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 ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/home/biocbuild/bbs-3.19-bioc/meat/txdbmaker.Rcheck/00check.log’ for details.