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###
### 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_2.75.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/GEOquery.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: aarch64-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 Ventura 13.7.1
* 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 ... 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 ‘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 ... ERROR
Running examples in ‘GEOquery-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getRNASeqData
> ### Title: Get GEO RNA-seq quantifications as a SummarizedExperiment object
> ### Aliases: getRNASeqData
> 
> ### ** Examples
> 
> se <- getRNASeqData("GSE164073")
Error in getRNASeqQuantResults(accession) : No raw counts file found.
Navigate to: 
  https://ncbi.nlm.nih.gov/geo/download/?acc=GSE164073
and check if the 'RNA-Seq raw counts' link is available.
Calls: getRNASeqData -> getRNASeqQuantResults
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:
  ── Error ('test_geo_rnaseq.R:91:3'): getRNASeqQuantGenomeInfo returns correct data ──
  Error in `httr2::url_parse(url)`: `url` must be a single string, not an empty character vector.
  Backtrace:
      ▆
   1. └─GEOquery::getRNASeqQuantGenomeInfo("GSE83322") at test_geo_rnaseq.R:91:3
   2.   └─GEOquery:::urlExtractRNASeqQuantGenomeInfo(annotation_link)
   3.     └─GEOquery:::extractFilenameFromDownloadURL(url)
   4.       └─httr2::url_parse(url = url)
   5.         └─httr2:::check_string(url)
   6.           └─httr2:::stop_input_type(...)
   7.             └─rlang::abort(message, ..., call = call, arg = arg)
  
  [ FAIL 9 | WARN 1 | SKIP 0 | PASS 220 ]
  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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/GEOquery.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GEOquery
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘GEOquery’ ...
** this is package ‘GEOquery’ version ‘2.75.0’
** 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)

R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 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
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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 9 | WARN 1 | SKIP 0 | PASS 220 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_geo_rnaseq.R:18:3'): getRNAQuantRawCountsURL returns character vector ──
`result` has length 0, not length 1.
── Failure ('test_geo_rnaseq.R:27:3'): getRNAQuantAnnotationURL returns character vector ──
`result` has length 0, not length 1.
── Error ('test_geo_rnaseq.R:34:3'): readRNAQuantRawCounts returns matrix ──────
<vctrs_error_subscript_oob/vctrs_error_subscript/rlang_error/error/condition>
Error in `quants[, -1]`: Can't negate columns past the end.
ℹ Location 1 doesn't exist.
ℹ There are only 0 columns.
Backtrace:
     ▆
  1. ├─GEOquery:::readRNAQuantRawCounts(link) at test_geo_rnaseq.R:34:3
  2. │ ├─base::as.matrix(quants[, -1])
  3. │ ├─quants[, -1]
  4. │ └─tibble:::`[.tbl_df`(quants, , -1)
  5. │   └─tibble:::vectbl_as_col_location(...)
  6. │     ├─tibble:::subclass_col_index_errors(...)
  7. │     │ └─base::withCallingHandlers(...)
  8. │     └─vctrs::vec_as_location(j, n, names, missing = "error", call = call)
  9. └─vctrs (local) `<fn>`()
 10.   └─vctrs:::stop_subscript_oob(...)
 11.     └─vctrs:::stop_subscript(...)
 12.       └─rlang::abort(...)
── Failure ('test_geo_rnaseq.R:46:3'): readRNAQuantAnnotation returns data.frame ──
nrow(result) > 0 is not TRUE

`actual`:   FALSE
`expected`: TRUE 
── Failure ('test_geo_rnaseq.R:47:3'): readRNAQuantAnnotation returns data.frame ──
ncol(result) > 0 is not TRUE

`actual`:   FALSE
`expected`: TRUE 
── Error ('test_geo_rnaseq.R:52:3'): getRNASeqQuantResults returns list ────────
Error in `getRNASeqQuantResults(gse)`: No raw counts file found.
Navigate to: 
  https://ncbi.nlm.nih.gov/geo/download/?acc=GSE83322
and check if the 'RNA-Seq raw counts' link is available.
Backtrace:
    ▆
 1. └─GEOquery:::getRNASeqQuantResults(gse) at test_geo_rnaseq.R:52:3
── Error ('test_geo_rnaseq.R:62:3'): getRNASeqData returns SummarizedExperiment ──
Error in `getRNASeqQuantResults(accession)`: No raw counts file found.
Navigate to: 
  https://ncbi.nlm.nih.gov/geo/download/?acc=GSE83322
and check if the 'RNA-Seq raw counts' link is available.
Backtrace:
    ▆
 1. └─GEOquery::getRNASeqData(gse) at test_geo_rnaseq.R:62:3
 2.   └─GEOquery:::getRNASeqQuantResults(accession)
── Failure ('test_geo_rnaseq.R:80:3'): hasRNASeqQuantifications returns TRUE for GSE83322 ──
`result` is not TRUE

`actual`:   FALSE
`expected`: TRUE 
── Error ('test_geo_rnaseq.R:91:3'): getRNASeqQuantGenomeInfo returns correct data ──
Error in `httr2::url_parse(url)`: `url` must be a single string, not an empty character vector.
Backtrace:
    ▆
 1. └─GEOquery::getRNASeqQuantGenomeInfo("GSE83322") at test_geo_rnaseq.R:91:3
 2.   └─GEOquery:::urlExtractRNASeqQuantGenomeInfo(annotation_link)
 3.     └─GEOquery:::extractFilenameFromDownloadURL(url)
 4.       └─httr2::url_parse(url = url)
 5.         └─httr2:::check_string(url)
 6.           └─httr2:::stop_input_type(...)
 7.             └─rlang::abort(message, ..., call = call, arg = arg)

[ FAIL 9 | WARN 1 | SKIP 0 | PASS 220 ]
Error: Test failures
Execution halted