############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:GEOquery.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GEOquery_2.75.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GEOquery.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GEOquery/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GEOquery’ version ‘2.75.0’ * 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 ... WARNING Found the following significant warnings: Warning: program compiled against libxml 212 using older 211 See ‘/home/biocbuild/bbs-3.21-bioc/meat/GEOquery.Rcheck/00install.out’ for details. * checking installed package size ... INFO installed size is 13.3Mb sub-directories of 1Mb or more: extdata 12.8Mb * 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 ...Warning: program compiled against libxml 212 using older 211 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 ... NOTE Warning: program compiled against libxml 212 using older 211 A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... NOTE Warning: program compiled against libxml 212 using older 211 It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * checking dependencies in R code ... NOTE Warning: program compiled against libxml 212 using older 211 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 ... WARNING Warning: program compiled against libxml 212 using older 211 See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... WARNING Warning: program compiled against libxml 212 using older 211 The argument of a replacement function which corresponds to the right hand side must be named ‘value’. * checking foreign function calls ... NOTE Warning: program compiled against libxml 212 using older 211 See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * 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'. Warning: program compiled against libxml 212 using older 211 .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 ... WARNING Warning: program compiled against libxml 212 using older 211 All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 * checking Rd \usage sections ... NOTE Warning: program compiled against libxml 212 using older 211 The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 getRNASeqData 6.695 0.357 27.399 getGEO 4.408 0.072 106.490 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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: 5 WARNINGs, 6 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/GEOquery.Rcheck/00check.log’ for details.