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This page was generated on 2024-05-20 11:32:12 -0400 (Mon, 20 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
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 821/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GEOquery 2.73.0 (landing page) Sean Davis
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | ||||||||
To the developers/maintainers of the GEOquery package: - 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: 2.73.0 |
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_2.73.0.tar.gz |
StartedAt: 2024-05-19 14:37:16 -0400 (Sun, 19 May 2024) |
EndedAt: 2024-05-19 14:38:50 -0400 (Sun, 19 May 2024) |
EllapsedTime: 94.6 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: GEOquery.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### 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_2.73.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/GEOquery.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GEOquery/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GEOquery’ version ‘2.73.0’ * 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 13.1Mb 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 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: 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 whether 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 ... ERROR Running examples in ‘GEOquery-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: getGEO > ### Title: Get a GEO object from NCBI or file > ### Aliases: getGEO > ### Keywords: IO > > ### ** Examples > > > gds <- getGEO("GDS10") HTTP error 403.File stored at: /tmp/RtmpRJsXwE/GDS10.soft.gz Error in downloadFile(myurl, destfile, mode) : Failed to download /tmp/RtmpRJsXwE/GDS10.soft.gz! Calls: getGEO -> getGEOfile -> downloadFile Execution halted * 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: nrow(res) not equivalent to 12. target is NULL, current is numeric ── Failure ('test_supp_files.R:22:5'): GSE supplemental file no-download works ── ncol(res) not equivalent to 2. target is NULL, current is numeric ── Failure ('test_supp_files.R:27:5'): GSE Supplemental file filtering works ─── ncol(res) not equivalent to 2. target is NULL, current is numeric ── Failure ('test_supp_files.R:28:5'): GSE Supplemental file filtering works ─── nrow(res) not equivalent to 4. target is NULL, current is numeric [ FAIL 16 | WARN 0 | SKIP 0 | PASS 167 ] Error: Test failures Execution halted * 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: 2 ERRORs, 6 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/GEOquery.Rcheck/00check.log’ for details.
GEOquery.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GEOquery ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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.fail
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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") [ FAIL 16 | WARN 0 | SKIP 0 | PASS 167 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_GSE.R:6:5'): empty GSE is handled correctly ──────────────────── Error in `open.connection(x, "rb")`: HTTP error 403. Backtrace: ▆ 1. └─GEOquery::getGEO("GSE11413") at test_GSE.R:6:5 2. └─GEOquery:::getAndParseGSEMatrices(...) 3. └─GEOquery:::getDirListing(sprintf(gdsurl, stub, GEO)) 4. ├─xml2::read_html(url) 5. └─xml2:::read_html.default(url) 6. ├─base::suppressWarnings(...) 7. │ └─base::withCallingHandlers(...) 8. ├─xml2::read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options) 9. └─xml2:::read_xml.character(...) 10. └─xml2:::read_xml.connection(...) 11. ├─base::open(x, "rb") 12. └─base::open.connection(x, "rb") ── Error ('test_GSE.R:15:5'): case-mismatched IDs in GSEs handled correctly ──── Error in `open.connection(x, "rb")`: HTTP error 403. Backtrace: ▆ 1. └─GEOquery::getGEO("GSE35683") at test_GSE.R:15:5 2. └─GEOquery:::getAndParseGSEMatrices(...) 3. └─GEOquery:::getDirListing(sprintf(gdsurl, stub, GEO)) 4. ├─xml2::read_html(url) 5. └─xml2:::read_html.default(url) 6. ├─base::suppressWarnings(...) 7. │ └─base::withCallingHandlers(...) 8. ├─xml2::read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options) 9. └─xml2:::read_xml.character(...) 10. └─xml2:::read_xml.connection(...) 11. ├─base::open(x, "rb") 12. └─base::open.connection(x, "rb") ── Error ('test_GSE.R:21:5'): single-sample GSE handled correctly ────────────── Error in `open.connection(x, "rb")`: HTTP error 403. Backtrace: ▆ 1. └─GEOquery::getGEO("GSE11595") at test_GSE.R:21:5 2. └─GEOquery:::getAndParseGSEMatrices(...) 3. └─GEOquery:::getDirListing(sprintf(gdsurl, stub, GEO)) 4. ├─xml2::read_html(url) 5. └─xml2:::read_html.default(url) 6. ├─base::suppressWarnings(...) 7. │ └─base::withCallingHandlers(...) 8. ├─xml2::read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options) 9. └─xml2:::read_xml.character(...) 10. └─xml2:::read_xml.connection(...) 11. ├─base::open(x, "rb") 12. └─base::open.connection(x, "rb") ── Error ('test_GSE.R:28:5'): short GSE handled correctly ────────────────────── Error in `open.connection(x, "rb")`: HTTP error 403. Backtrace: ▆ 1. └─GEOquery::getGEO("GSE34145") at test_GSE.R:28:5 2. └─GEOquery:::getAndParseGSEMatrices(...) 3. └─GEOquery:::getDirListing(sprintf(gdsurl, stub, GEO)) 4. ├─xml2::read_html(url) 5. └─xml2:::read_html.default(url) 6. ├─base::suppressWarnings(...) 7. │ └─base::withCallingHandlers(...) 8. ├─xml2::read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options) 9. └─xml2:::read_xml.character(...) 10. └─xml2:::read_xml.connection(...) 11. ├─base::open(x, "rb") 12. └─base::open.connection(x, "rb") ── Error ('test_GSE.R:47:3'): GSE with more than one value per characteristic handled ── Error in `open.connection(x, "rb")`: HTTP error 403. Backtrace: ▆ 1. └─GEOquery::getGEO("GSE71989") at test_GSE.R:47:3 2. └─GEOquery:::getAndParseGSEMatrices(...) 3. └─GEOquery:::getDirListing(sprintf(gdsurl, stub, GEO)) 4. ├─xml2::read_html(url) 5. └─xml2:::read_html.default(url) 6. ├─base::suppressWarnings(...) 7. │ └─base::withCallingHandlers(...) 8. ├─xml2::read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options) 9. └─xml2:::read_xml.character(...) 10. └─xml2:::read_xml.connection(...) 11. ├─base::open(x, "rb") 12. └─base::open.connection(x, "rb") ── Error ('test_GSE.R:55:3'): GSE has populated experimentData ───────────────── Error in `open.connection(x, "rb")`: HTTP error 403. Backtrace: ▆ 1. └─GEOquery::getGEO("GSE53986") at test_GSE.R:55:3 2. └─GEOquery:::getAndParseGSEMatrices(...) 3. └─GEOquery:::getDirListing(sprintf(gdsurl, stub, GEO)) 4. ├─xml2::read_html(url) 5. └─xml2:::read_html.default(url) 6. ├─base::suppressWarnings(...) 7. │ └─base::withCallingHandlers(...) 8. ├─xml2::read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options) 9. └─xml2:::read_xml.character(...) 10. └─xml2:::read_xml.connection(...) 11. ├─base::open(x, "rb") 12. └─base::open.connection(x, "rb") ── Error ('test_GSE.R:69:3'): GSE populates experimentData as much as possible ── Error in `open.connection(x, "rb")`: HTTP error 403. Backtrace: ▆ 1. └─GEOquery::getGEO("GSE99709") at test_GSE.R:69:3 2. └─GEOquery:::getAndParseGSEMatrices(...) 3. └─GEOquery:::getDirListing(sprintf(gdsurl, stub, GEO)) 4. ├─xml2::read_html(url) 5. └─xml2:::read_html.default(url) 6. ├─base::suppressWarnings(...) 7. │ └─base::withCallingHandlers(...) 8. ├─xml2::read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options) 9. └─xml2:::read_xml.character(...) 10. └─xml2:::read_xml.connection(...) 11. ├─base::open(x, "rb") 12. └─base::open.connection(x, "rb") ── Error ('test_GSE.R:102:3'): GSE/GPL with integer64 columns handled correctly ── Error in `open.connection(x, "rb")`: HTTP error 403. Backtrace: ▆ 1. └─GEOquery::getGEO("GSE7864") at test_GSE.R:102:3 2. └─GEOquery:::getAndParseGSEMatrices(...) 3. └─GEOquery:::getDirListing(sprintf(gdsurl, stub, GEO)) 4. ├─xml2::read_html(url) 5. └─xml2:::read_html.default(url) 6. ├─base::suppressWarnings(...) 7. │ └─base::withCallingHandlers(...) 8. ├─xml2::read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options) 9. └─xml2:::read_xml.character(...) 10. └─xml2:::read_xml.connection(...) 11. ├─base::open(x, "rb") 12. └─base::open.connection(x, "rb") ── Error ('test_fetch_GPL_false.R:5:5'): GSE without GPL works ───────────────── Error in `open.connection(x, "rb")`: HTTP error 403. Backtrace: ▆ 1. └─GEOquery::getGEO("GSE2553", getGPL = FALSE) at test_fetch_GPL_false.R:5:5 2. └─GEOquery:::getAndParseGSEMatrices(...) 3. └─GEOquery:::getDirListing(sprintf(gdsurl, stub, GEO)) 4. ├─xml2::read_html(url) 5. └─xml2:::read_html.default(url) 6. ├─base::suppressWarnings(...) 7. │ └─base::withCallingHandlers(...) 8. ├─xml2::read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options) 9. └─xml2:::read_xml.character(...) 10. └─xml2:::read_xml.connection(...) 11. ├─base::open(x, "rb") 12. └─base::open.connection(x, "rb") ── Failure ('test_supp_files.R:6:5'): GSE Supplemental files downloading works ── nrow(res) not equivalent to 1. target is NULL, current is numeric ── Failure ('test_supp_files.R:11:5'): GSM Supplemental files downloading works ── nrow(res) not equivalent to 1. target is NULL, current is numeric ── Failure ('test_supp_files.R:16:5'): GSM Supplemental files downloading to baseDir works ── nrow(res) not equivalent to 1. target is NULL, current is numeric ── Failure ('test_supp_files.R:21:5'): GSE supplemental file no-download works ── nrow(res) not equivalent to 12. target is NULL, current is numeric ── Failure ('test_supp_files.R:22:5'): GSE supplemental file no-download works ── ncol(res) not equivalent to 2. target is NULL, current is numeric ── Failure ('test_supp_files.R:27:5'): GSE Supplemental file filtering works ─── ncol(res) not equivalent to 2. target is NULL, current is numeric ── Failure ('test_supp_files.R:28:5'): GSE Supplemental file filtering works ─── nrow(res) not equivalent to 4. target is NULL, current is numeric [ FAIL 16 | WARN 0 | SKIP 0 | PASS 167 ] Error: Test failures Execution halted
GEOquery.Rcheck/GEOquery-Ex.timings
name | user | system | elapsed | |
coercion | 0.000 | 0.000 | 0.001 | |