############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:GEOquery.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings GEOquery_2.69.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/GEOquery.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * checking for file ‘GEOquery/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GEOquery’ version ‘2.69.0’ * 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 ... NOTE installed size is 13.2Mb sub-directories of 1Mb or more: extdata 12.8Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License components which are templates and need '+ file LICENSE': MIT * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 ... NOTE Warning: no function found corresponding to methods exports from ‘GEOquery’ for: ‘show’ 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 startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘R.utils’ 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’ fastTabRead: no visible global function definition for ‘read.table’ fastTabRead: no visible global function definition for ‘read.delim’ 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 characteristics k kvpair new read.delim read.table v Consider adding importFrom("methods", "as", "new") importFrom("utils", "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 ... 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 getGEO 3.21 1.622 15.04 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: Error in `curl::curl_download(url, destfile, mode = mode, quiet = quiet, handle = h)`: Timeout was reached: [] Operation timed out after 120000 milliseconds with 6373376 out of 8480960 bytes received Backtrace: ▆ 1. └─GEOquery::getGEO("GSE2553", getGPL = FALSE) at test_fetch_GPL_false.R:5:4 2. └─GEOquery:::getAndParseGSEMatrices(...) 3. └─GEOquery:::downloadFile(url, destfile = destfile, mode = "wb") 4. └─base::tryCatch(...) 5. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 6. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 7. └─value[[3L]](cond) [ FAIL 5 | WARN 0 | SKIP 0 | PASS 189 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘GEOquery.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 6 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/GEOquery.Rcheck/00check.log’ for details.