############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:customProDB.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings customProDB_1.43.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/customProDB.Rcheck’ * using R Under development (unstable) (2024-03-18 r86148) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) 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 ‘customProDB/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘customProDB’ version ‘1.43.1’ * 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 ‘customProDB’ 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 dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’ 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 ... NOTE Bed2Range: no visible binding for global variable ‘V5’ OutputNovelJun: no visible binding for global variable ‘jun_type’ OutputVarproseq: no visible binding for global variable ‘genename’ OutputVarproseq: no visible binding for global variable ‘txname’ OutputVarproseq: no visible binding for global variable ‘proname’ OutputVarproseq: no visible binding for global variable ‘aaref’ OutputVarproseq: no visible binding for global variable ‘aapos’ OutputVarproseq: no visible binding for global variable ‘aavar’ OutputVarproseq: no visible binding for global variable ‘rsid’ OutputVarproseq_single: no visible binding for global variable ‘genename’ OutputVarproseq_single: no visible binding for global variable ‘txname’ OutputVarproseq_single: no visible binding for global variable ‘proname’ OutputVarproseq_single: no visible binding for global variable ‘aaref’ OutputVarproseq_single: no visible binding for global variable ‘aapos’ OutputVarproseq_single: no visible binding for global variable ‘aavar’ OutputVarproseq_single: no visible binding for global variable ‘rsid’ Outputaberrant: no visible binding for global variable ‘pro_name’ Positionincoding: no visible binding for global variable ‘cds_start’ Positionincoding: no visible binding for global variable ‘cds_end’ PrepareAnnotationEnsembl: no visible binding for global variable ‘ensembl_gene_id’ PrepareAnnotationEnsembl: no visible binding for global variable ‘pro_name’ PrepareAnnotationEnsembl: no visible binding for global variable ‘chrom’ PrepareAnnotationEnsembl: no visible binding for global variable ‘name’ PrepareAnnotationEnsembl: no visible binding for global variable ‘alleleCount’ PrepareAnnotationEnsembl: no visible binding for global variable ‘alleles’ PrepareAnnotationRefseq: no visible binding for global variable ‘name’ PrepareAnnotationRefseq: no visible binding for global variable ‘mrnaAcc’ PrepareAnnotationRefseq: no visible binding for global variable ‘protAcc’ PrepareAnnotationRefseq: no visible binding for global variable ‘transcript’ PrepareAnnotationRefseq: no visible binding for global variable ‘chrom’ PrepareAnnotationRefseq: no visible binding for global variable ‘alleleCount’ PrepareAnnotationRefseq: no visible binding for global variable ‘alleles’ PrepareAnnotationRefseq: no visible binding for global variable ‘COSMIC’ Varlocation: no visible binding for global variable ‘pro_name’ Undefined global functions or variables: COSMIC V5 aapos aaref aavar alleleCount alleles cds_end cds_start chrom ensembl_gene_id genename jun_type mrnaAcc name pro_name proname protAcc rsid transcript txname * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘customProDB-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: PrepareAnnotationEnsembl > ### Title: prepare annotation from ENSEMBL > ### Aliases: PrepareAnnotationEnsembl > > ### ** Examples > > > ensembl <- useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl", + host="may2015.archive.ensembl.org", path="/biomart/martservice", + archive=FALSE) Warning: Ensembl will soon enforce the use of https. Ensure the 'host' argument includes "https://" > > annotation_path <- tempdir() > transcript_ids <- c("ENST00000234420", "ENST00000269305", "ENST00000445888", + "ENST00000257430", "ENST00000508376", "ENST00000288602", + "ENST00000269571", "ENST00000256078", "ENST00000384871") > > PrepareAnnotationEnsembl(mart=ensembl, annotation_path=annotation_path, + splice_matrix=FALSE, dbsnp=NULL, transcript_ids=transcript_ids, + COSMIC=FALSE) Prepare gene/transcript/protein id mapping information (ids.RData) ... done Build TranscriptDB object (txdb.sqlite) ... Warning: Ensembl will soon enforce the use of https. Ensure the 'host' argument includes "https://" Download and preprocess the 'transcripts' data frame ... OK Download and preprocess the 'chrominfo' data frame ... Error in x$.self$finalize() : attempt to apply non-function Warning: call dbDisconnect() when finished working with a connection OK Download and preprocess the 'splicings' data frame ... OK Download and preprocess the 'genes' data frame ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... Warning in call_fun_in_txdbmaker("makeTxDb", ...) : makeTxDb() has moved to the txdbmaker package. Please call txdbmaker::makeTxDb() to get rid of this warning. OK done Prepare exon annotation information (exon_anno.RData) ... done Prepare protein coding sequence (procodingseq.RData)... Error in getBM(attributes = attributes.codingseq, filters = "ensembl_peptide_id", : Invalid attribute(s): coding Please use the function 'listAttributes' to get valid attribute names Calls: PrepareAnnotationEnsembl -> getBM Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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, 2 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/customProDB.Rcheck/00check.log’ for details.