Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:41 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 830/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GEOquery 2.73.2 (landing page) Sean Davis
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | ERROR | skipped | ||||||||||
To the developers/maintainers of the GEOquery package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GEOquery.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: GEOquery |
Version: 2.73.2 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GEOquery.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GEOquery_2.73.2.tar.gz |
StartedAt: 2024-08-21 01:14:47 -0400 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 01:21:22 -0400 (Wed, 21 Aug 2024) |
EllapsedTime: 394.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GEOquery.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GEOquery.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GEOquery_2.73.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/GEOquery.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'GEOquery/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'GEOquery' version '2.73.2' * 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 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 ... 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 ... 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 6.08 2.81 13.96 getRNASeqData 5.75 0.46 10.52 * 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: 3 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/GEOquery.Rcheck/00check.log' for details.
GEOquery.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL GEOquery ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'GEOquery' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GEOquery)
GEOquery.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(GEOquery) Loading required package: Biobase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) > > test_check("GEOquery") trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1000/suppl//GSE1000_RAW.tar?tool=geoquery' Content type 'application/x-tar' length 35307520 bytes (33.7 MB) ================================================== downloaded 33.7 MB trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM15nnn/GSM15789/suppl//GSM15789.cel.gz?tool=geoquery' Content type 'application/x-gzip' length 3507725 bytes (3.3 MB) ================================================== downloaded 3.3 MB trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM15nnn/GSM15789/suppl//GSM15789.cel.gz?tool=geoquery' Content type 'application/x-gzip' length 3507725 bytes (3.3 MB) ================================================== downloaded 3.3 MB [ FAIL 0 | WARN 0 | SKIP 0 | PASS 232 ] > > proc.time() user system elapsed 87.12 13.48 156.42
GEOquery.Rcheck/GEOquery-Ex.timings
name | user | system | elapsed | |
browseGEOAccession | 0 | 0 | 0 | |
browseWebsiteRNASeqSearch | 0 | 0 | 0 | |
coercion | 0.00 | 0.02 | 0.01 | |
getGEO | 6.08 | 2.81 | 13.96 | |
getGEOSuppFiles | 0.00 | 0.00 | 0.19 | |
getGEOfile | 0 | 0 | 0 | |
getGSEDataTables | 0.67 | 0.17 | 1.35 | |
getRNASeqData | 5.75 | 0.46 | 10.52 | |
searchFieldsGEO | 0.05 | 0.00 | 0.59 | |
searchGEO | 0 | 0 | 0 | |
urlForAccession | 0 | 0 | 0 | |