############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:customProDB.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings customProDB_1.45.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/customProDB.Rcheck’ * using R version 4.4.0 RC (2024-04-16 r86468) * 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 ‘customProDB/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘customProDB’ version ‘1.45.0’ * 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 ... WARNING Found the following significant warnings: Warning: replacing previous import ‘GenomicFeatures::makeTxDbPackage’ by ‘txdbmaker::makeTxDbPackage’ when loading ‘customProDB’ Warning: replacing previous import ‘GenomicFeatures::supportedUCSCFeatureDbTables’ by ‘txdbmaker::supportedUCSCFeatureDbTables’ when loading ‘customProDB’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromGFF’ by ‘txdbmaker::makeTxDbFromGFF’ when loading ‘customProDB’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbPackageFromBiomart’ by ‘txdbmaker::makeTxDbPackageFromBiomart’ when loading ‘customProDB’ Warning: replacing previous import ‘GenomicFeatures::supportedMiRBaseBuildValues’ by ‘txdbmaker::supportedMiRBaseBuildValues’ when loading ‘customProDB’ Warning: replacing previous import ‘GenomicFeatures::supportedUCSCFeatureDbTracks’ by ‘txdbmaker::supportedUCSCFeatureDbTracks’ when loading ‘customProDB’ Warning: replacing previous import ‘GenomicFeatures::browseUCSCtrack’ by ‘txdbmaker::browseUCSCtrack’ when loading ‘customProDB’ Warning: replacing previous import ‘GenomicFeatures::getChromInfoFromBiomart’ by ‘txdbmaker::getChromInfoFromBiomart’ when loading ‘customProDB’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromGRanges’ by ‘txdbmaker::makeTxDbFromGRanges’ when loading ‘customProDB’ Warning: replacing previous import ‘GenomicFeatures::supportedUCSCtables’ by ‘txdbmaker::supportedUCSCtables’ when loading ‘customProDB’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromBiomart’ by ‘txdbmaker::makeTxDbFromBiomart’ when loading ‘customProDB’ Warning: replacing previous import ‘GenomicFeatures::UCSCFeatureDbTableSchema’ by ‘txdbmaker::UCSCFeatureDbTableSchema’ when loading ‘customProDB’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromEnsembl’ by ‘txdbmaker::makeTxDbFromEnsembl’ when loading ‘customProDB’ Warning: replacing previous import ‘GenomicFeatures::makeTxDb’ by ‘txdbmaker::makeTxDb’ when loading ‘customProDB’ Warning: replacing previous import ‘GenomicFeatures::makeFDbPackageFromUCSC’ by ‘txdbmaker::makeFDbPackageFromUCSC’ when loading ‘customProDB’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbFromUCSC’ by ‘txdbmaker::makeTxDbFromUCSC’ when loading ‘customProDB’ Warning: replacing previous import ‘GenomicFeatures::makeTxDbPackageFromUCSC’ by ‘txdbmaker::makeTxDbPackageFromUCSC’ when loading ‘customProDB’ Warning: replacing previous import ‘GenomicFeatures::makePackageName’ by ‘txdbmaker::makePackageName’ when loading ‘customProDB’ Warning: replacing previous import ‘GenomicFeatures::makeFeatureDbFromUCSC’ by ‘txdbmaker::makeFeatureDbFromUCSC’ when loading ‘customProDB’ See ‘/home/biocbuild/bbs-3.20-bioc/meat/customProDB.Rcheck/00install.out’ for details. * 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: ‘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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed PrepareAnnotationEnsembl 4.481 0.353 12.676 * 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 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/customProDB.Rcheck/00check.log’ for details.