############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GEOquery.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GEOquery_2.78.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/GEOquery.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GEOquery/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GEOquery’ version ‘2.78.0’ * 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 ‘GEOquery’ can be installed ... OK * checking installed package size ... INFO installed size is 13.2Mb sub-directories of 1Mb or more: extdata 12.8Mb * checking package 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘R.utils’ ‘curl’ All declared Imports should be used. Package in Depends field not imported from: ‘methods’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE File ‘GEOquery/R/zzz.R’: .onLoad calls: packageStartupMessage("Setting options('download.file.method.GEOquery'='auto')") packageStartupMessage("Setting options('GEOquery.inmemory.gpl'=FALSE)") See section ‘Good practice’ in '?.onAttach'. .parseGPLTxt: no visible global function definition for ‘new’ .parseGPLWithLimits: no visible global function definition for ‘new’ .parseGSMTxt: no visible global function definition for ‘new’ .parseGSMWithLimits: no visible global function definition for ‘new’ GDS2MA: no visible global function definition for ‘new’ GDS2MA: no visible binding for global variable ‘MA’ GDS2eSet: no visible global function definition for ‘new’ browseGEOAccession: no visible global function definition for ‘browseURL’ browseWebsiteRNASeqSearch: no visible global function definition for ‘browseURL’ fastTabRead: no visible global function definition for ‘read.table’ fastTabRead: no visible global function definition for ‘read.delim’ getRNASeqData: no visible global function definition for ‘as’ parseGDS: no visible global function definition for ‘new’ parseGSE: no visible global function definition for ‘new’ parseGSEMatrix: no visible global function definition for ‘new’ parseGSEMatrix: no visible binding for global variable ‘.’ parseGSEMatrix: no visible binding for global variable ‘characteristics’ parseGSEMatrix: no visible binding for global variable ‘kvpair’ parseGSEMatrix: no visible binding for global variable ‘accession’ parseGSEMatrix: no visible binding for global variable ‘k’ parseGSEMatrix: no visible binding for global variable ‘v’ parseGSEMatrix: no visible global function definition for ‘read.table’ parseGSEMatrix: no visible global function definition for ‘as’ Undefined global functions or variables: . MA accession as browseURL characteristics k kvpair new read.delim read.table v Consider adding importFrom("methods", "as", "new") importFrom("utils", "browseURL", "read.delim", "read.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 ... NOTE Argument items with no description in Rd file 'getGEOSuppFileURL.Rd': ‘GEO’ * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': ‘GEOquery.qmd’ ‘single-cell.qmd’ Files named as vignettes but with no recognized vignette engine: ‘vignettes/GEOquery.qmd’ ‘vignettes/single-cell.qmd’ (Is a VignetteBuilder field missing?) * checking examples ... ERROR Running examples in ‘GEOquery-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: getGSEDataTables > ### Title: Get GSE data tables from GEO into R data structures. > ### Aliases: getGSEDataTables > ### Keywords: IO > > ### ** Examples > > > dfl = getGSEDataTables('GSE3494') Warning: Failed to open 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&form=xml&view=full&acc=GSE3494': The requested URL returned error: 504 Error in open.connection(x, "rb") : cannot open the connection Calls: getGSEDataTables ... read_xml.character -> read_xml.connection -> open -> open.connection Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed getGEO 4.102 0.358 5.786 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking package vignettes ... NOTE Package has ‘vignettes’ subdirectory but apparently no vignettes. Perhaps the ‘VignetteBuilder’ information is missing from the DESCRIPTION file? * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 WARNING, 4 NOTEs See ‘/Users/biocbuild/bbs-3.22-bioc/meat/GEOquery.Rcheck/00check.log’ for details.