############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EnrichmentBrowser.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EnrichmentBrowser_2.30.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/EnrichmentBrowser.Rcheck’ * using R version 4.3.1 (2023-06-16) * 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 12.6.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘EnrichmentBrowser/DESCRIPTION’ ... OK * this is package ‘EnrichmentBrowser’ version ‘2.30.2’ * 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 ‘EnrichmentBrowser’ 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 startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: 'pathview:::parseKGML2Graph2' 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 .getGOFromBiomart: no visible binding for global variable ‘go_linkage_type’ Undefined global functions or variables: go_linkage_type * 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 ‘EnrichmentBrowser-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: getGenesets > ### Title: Definition of gene sets according to different sources > ### Aliases: getGenesets get.go.genesets get.kegg.genesets > ### parse.genesets.from.GMT showAvailableSpecies showAvailableCollections > ### writeGMT > > ### ** Examples > > > # (1) Typical usage for gene set enrichment analysis with GO: > # Biological process terms based on BioC annotation (for human) > go.gs <- getGenesets(org = "hsa", db = "go") > > # eq.: > # go.gs <- getGenesets(org = "hsa", db = "go", onto = "BP", mode = "GO.db") > # (2) Defining gene sets according to KEGG > kegg.gs <- getGenesets(org = "hsa", db = "kegg") Error in .getUrl(url, .listParser, nameColumn = 1, valueColumn = 2) : Forbidden (HTTP 403). Calls: getGenesets ... .dwnldAllKeggGS -> -> .getUrl -> stop_for_status Execution halted * 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, 2 NOTEs See ‘/Users/biocbuild/bbs-3.17-bioc/meat/EnrichmentBrowser.Rcheck/00check.log’ for details.