##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:GEOquery.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings GEOquery_2.75.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/GEOquery.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 13.3Mb
  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 ... 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 loading without being on the library search path ... 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
getRNASeqData 3.409  0.183   9.615
* 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:
   5.         └─vroom::vroom(...)
   6.           └─vroom:::vroom_(...)
  ── Error ('test_supp_files.R:15:5'): GSM Supplemental files downloading to baseDir works ──
  Error in `getGEOSuppFiles("GSM15789", baseDir = tempdir())`: Failed to download /tmp/RtmpRZtED5/GSM15789/GSM15789.cel.gz!
  Backtrace:
      ▆
   1. └─GEOquery::getGEOSuppFiles("GSM15789", baseDir = tempdir()) at test_supp_files.R:15:5
  ── Failure ('test_supp_files.R:21:5'): GSE supplemental file no-download works ──
  nrow(res) not equivalent to 12.
  1/1 mismatches
  [1] 11 - 12 == -1
  
  [ FAIL 22 | WARN 107 | SKIP 0 | PASS 46 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘GEOquery.Rmd’ using rmarkdown

Quitting from GEOquery.Rmd:106-117 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `GSMList(gse)[[1]]`:
! subscript out of bounds
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'GEOquery.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘GEOquery.Rmd’

SUMMARY: processing the following file failed:
  ‘GEOquery.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/GEOquery.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL GEOquery
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-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: x86_64-pc-linux-gnu

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

[ FAIL 22 | WARN 107 | SKIP 0 | PASS 46 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_GPL.R:9:5'): generic GPL parsing works as expected ───────────
nrow(Table(gpl)) not equivalent to 22283.
1/1 mismatches
[1] 0 - 22283 == -22283
── Failure ('test_GPL.R:10:5'): generic GPL parsing works as expected ──────────
ncol(Table(gpl)) not equivalent to 16.
1/1 mismatches
[1] 0 - 16 == -16
── Error ('test_GPL.R:17:5'): quoted GPL works ─────────────────────────────────
Error in `data.table::fread(fname, sep = "")`: File is empty: /tmp/RtmpRZtED5/file1e3fbf1afba8eb
Backtrace:
    ▆
 1. └─GEOquery::getGEO("GPL4133") at test_GPL.R:17:5
 2.   └─GEOquery::parseGEO(...)
 3.     └─GEOquery:::parseGPL(fname)
 4.       └─data.table::fread(fname, sep = "")
── Error ('test_GPL.R:23:5'): short GPL works ──────────────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `.subset2(x, i, exact = exact)`: subscript out of bounds
Backtrace:
    ▆
 1. └─GEOquery::getGEO("GPL15505") at test_GPL.R:23:5
 2.   └─GEOquery::parseGEO(...)
 3.     └─GEOquery:::parseGSEMatrix(...)
 4.       ├─data.table::fread(fname, sep = "")[[1]]
 5.       └─base::`[[.data.frame`(data.table::fread(fname, sep = ""), 1)
 6.         └─(function(x, i, exact) if (is.matrix(i)) as.matrix(x)[[i]] else .subset2(x, ...
── Error ('test_GSE.R:15:5'): case-mismatched IDs in GSEs handled correctly ────
Error in `data.table::fread(fname, sep = "")`: File is empty: /tmp/RtmpRZtED5/file1e3fbf5b27065d
Backtrace:
    ▆
 1. └─GEOquery::getGEO("GSE35683") at test_GSE.R:15:5
 2.   └─GEOquery:::getAndParseGSEMatrices(...)
 3.     └─GEOquery:::parseGSEMatrix(...)
 4.       └─data.table::fread(fname, sep = "")
── Error ('test_GSE.R:21:5'): single-sample GSE handled correctly ──────────────
<subscriptOutOfBoundsError/error/condition>
Error in `.subset2(x, i, exact = exact)`: subscript out of bounds
Backtrace:
    ▆
 1. └─GEOquery::getGEO("GSE11595") at test_GSE.R:21:5
 2.   └─GEOquery:::getAndParseGSEMatrices(...)
 3.     └─GEOquery:::parseGSEMatrix(...)
 4.       ├─data.table::fread(fname, sep = "")[[1]]
 5.       └─base::`[[.data.frame`(data.table::fread(fname, sep = ""), 1)
 6.         └─(function(x, i, exact) if (is.matrix(i)) as.matrix(x)[[i]] else .subset2(x, ...
── Error ('test_GSE.R:28:5'): short GSE handled correctly ──────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `.subset2(x, i, exact = exact)`: subscript out of bounds
Backtrace:
    ▆
 1. └─GEOquery::getGEO("GSE34145") at test_GSE.R:28:5
 2.   └─GEOquery:::getAndParseGSEMatrices(...)
 3.     └─GEOquery:::parseGSEMatrix(...)
 4.       ├─data.table::fread(fname, sep = "")[[1]]
 5.       └─base::`[[.data.frame`(data.table::fread(fname, sep = ""), 1)
 6.         └─(function(x, i, exact) if (is.matrix(i)) as.matrix(x)[[i]] else .subset2(x, ...
── Error ('test_GSE.R:34:5'): generic SOFT format GSE handled correctly ────────
Error in `data.table::fread(..., sep = "", header = FALSE)`: File is empty: /tmp/RtmpRZtED5/file1e3fbf41eeeb9c
Backtrace:
    ▆
 1. └─GEOquery::getGEO("GSE1563", GSEMatrix = FALSE) at test_GSE.R:34:5
 2.   └─GEOquery::parseGEO(...)
 3.     └─GEOquery:::parseGSE(fname, GSElimits)
 4.       └─GEOquery:::.read_lines(fname)
 5.         └─data.table::fread(..., sep = "", header = FALSE)
── Error ('test_GSE.R:47:3'): GSE with more than one value per characteristic handled ──
<subscriptOutOfBoundsError/error/condition>
Error in `.subset2(x, i, exact = exact)`: subscript out of bounds
Backtrace:
    ▆
 1. └─GEOquery::getGEO("GSE71989") at test_GSE.R:47:3
 2.   └─GEOquery:::getAndParseGSEMatrices(...)
 3.     └─GEOquery:::parseGSEMatrix(...)
 4.       ├─data.table::fread(fname, sep = "")[[1]]
 5.       └─base::`[[.data.frame`(data.table::fread(fname, sep = ""), 1)
 6.         └─(function(x, i, exact) if (is.matrix(i)) as.matrix(x)[[i]] else .subset2(x, ...
── Error ('test_GSE.R:55:3'): GSE has populated experimentData ─────────────────
Error in `parseGSEMatrix(destfile, destdir = destdir, AnnotGPL = AnnotGPL, 
    getGPL = getGPL)`: parsing failed--expected only one '!series_data_table_begin'
Backtrace:
    ▆
 1. └─GEOquery::getGEO("GSE53986") at test_GSE.R:55:3
 2.   └─GEOquery:::getAndParseGSEMatrices(...)
 3.     └─GEOquery:::parseGSEMatrix(...)
── Error ('test_GSE.R:69:3'): GSE populates experimentData as much as possible ──
Error in `data.table::fread(fname, sep = "")`: File is empty: /tmp/RtmpRZtED5/file1e3fbf1111f4e4
Backtrace:
    ▆
 1. └─GEOquery::getGEO("GSE99709") at test_GSE.R:69:3
 2.   └─GEOquery:::getAndParseGSEMatrices(...)
 3.     └─GEOquery:::parseGSEMatrix(...)
 4.       └─data.table::fread(fname, sep = "")
── Error ('test_GSE.R:102:3'): GSE/GPL with integer64 columns handled correctly ──
<subscriptOutOfBoundsError/error/condition>
Error in `.subset2(x, i, exact = exact)`: subscript out of bounds
Backtrace:
    ▆
 1. └─GEOquery::getGEO("GSE7864") at test_GSE.R:102:3
 2.   └─GEOquery:::getAndParseGSEMatrices(...)
 3.     └─GEOquery:::parseGSEMatrix(...)
 4.       ├─data.table::fread(fname, sep = "")[[1]]
 5.       └─base::`[[.data.frame`(data.table::fread(fname, sep = ""), 1)
 6.         └─(function(x, i, exact) if (is.matrix(i)) as.matrix(x)[[i]] else .subset2(x, ...
── Error ('test_GSE.R:109:3'): Test regression against issue 144 ───────────────
<subscriptOutOfBoundsError/error/condition>
Error in `.subset2(x, i, exact = exact)`: subscript out of bounds
Backtrace:
    ▆
 1. └─GEOquery::getGEO("GSE225759") at test_GSE.R:109:3
 2.   └─GEOquery:::getAndParseGSEMatrices(...)
 3.     └─GEOquery:::parseGSEMatrix(...)
 4.       ├─data.table::fread(fname, sep = "")[[1]]
 5.       └─base::`[[.data.frame`(data.table::fread(fname, sep = ""), 1)
 6.         └─(function(x, i, exact) if (is.matrix(i)) as.matrix(x)[[i]] else .subset2(x, ...
── Error ('test_GSM.R:5:5'): basic GSM works ───────────────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `.subset2(x, i, exact = exact)`: subscript out of bounds
Backtrace:
    ▆
 1. └─GEOquery::getGEO("GSM11805") at test_GSM.R:5:5
 2.   └─GEOquery::parseGEO(...)
 3.     └─GEOquery:::parseGSEMatrix(...)
 4.       ├─data.table::fread(fname, sep = "")[[1]]
 5.       └─base::`[[.data.frame`(data.table::fread(fname, sep = ""), 1)
 6.         └─(function(x, i, exact) if (is.matrix(i)) as.matrix(x)[[i]] else .subset2(x, ...
── Error ('test_fetch_GPL_false.R:5:5'): GSE without GPL works ─────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `.subset2(x, i, exact = exact)`: subscript out of bounds
Backtrace:
    ▆
 1. └─GEOquery::getGEO("GSE2553", getGPL = FALSE) at test_fetch_GPL_false.R:5:5
 2.   └─GEOquery:::getAndParseGSEMatrices(...)
 3.     └─GEOquery:::parseGSEMatrix(...)
 4.       ├─data.table::fread(fname, sep = "")[[1]]
 5.       └─base::`[[.data.frame`(data.table::fread(fname, sep = ""), 1)
 6.         └─(function(x, i, exact) if (is.matrix(i)) as.matrix(x)[[i]] else .subset2(x, ...
── Error ('test_fetch_GPL_false.R:14:5'): GDS without GPL works ────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `.subset2(x, i, exact = exact)`: subscript out of bounds
Backtrace:
    ▆
 1. └─GEOquery::getGEO("GDS10") at test_fetch_GPL_false.R:14:5
 2.   └─GEOquery::parseGEO(...)
 3.     └─GEOquery:::parseGSEMatrix(...)
 4.       ├─data.table::fread(fname, sep = "")[[1]]
 5.       └─base::`[[.data.frame`(data.table::fread(fname, sep = ""), 1)
 6.         └─(function(x, i, exact) if (is.matrix(i)) as.matrix(x)[[i]] else .subset2(x, ...
── Error ('test_geo_rnaseq.R:34:3'): readRNAQuantRawCounts returns matrix ──────
Error: Invalid argument
Backtrace:
    ▆
 1. └─GEOquery:::readRNAQuantRawCounts(link) at test_geo_rnaseq.R:34:3
 2.   └─readr::read_tsv(link, show_col_types = FALSE)
 3.     └─vroom::vroom(...)
 4.       └─vroom:::vroom_(...)
── Error ('test_geo_rnaseq.R:43:3'): readRNAQuantAnnotation returns data.frame ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': Invalid argument
Backtrace:
    ▆
 1. ├─GEOquery:::readRNAQuantAnnotation(link) at test_geo_rnaseq.R:43:3
 2. │ ├─BiocGenerics::as.data.frame(readr::read_tsv(link, show_col_types = FALSE))
 3. │ └─readr::read_tsv(link, show_col_types = FALSE)
 4. │   └─vroom::vroom(...)
 5. │     └─vroom:::vroom_(...)
 6. └─base::.handleSimpleError(`<fn>`, "Invalid argument", base::quote(NULL))
 7.   └─base (local) h(simpleError(msg, call))
── Error ('test_geo_rnaseq.R:52:3'): getRNASeqQuantResults returns list ────────
Error: Invalid argument
Backtrace:
    ▆
 1. └─GEOquery:::getRNASeqQuantResults(gse) at test_geo_rnaseq.R:52:3
 2.   └─GEOquery:::readRNAQuantRawCounts(raw_counts_link)
 3.     └─readr::read_tsv(link, show_col_types = FALSE)
 4.       └─vroom::vroom(...)
 5.         └─vroom:::vroom_(...)
── Error ('test_geo_rnaseq.R:62:3'): getRNASeqData returns SummarizedExperiment ──
Error: Invalid argument
Backtrace:
    ▆
 1. └─GEOquery::getRNASeqData(gse) at test_geo_rnaseq.R:62:3
 2.   └─GEOquery:::getRNASeqQuantResults(accession)
 3.     └─GEOquery:::readRNAQuantRawCounts(raw_counts_link)
 4.       └─readr::read_tsv(link, show_col_types = FALSE)
 5.         └─vroom::vroom(...)
 6.           └─vroom:::vroom_(...)
── Error ('test_supp_files.R:15:5'): GSM Supplemental files downloading to baseDir works ──
Error in `getGEOSuppFiles("GSM15789", baseDir = tempdir())`: Failed to download /tmp/RtmpRZtED5/GSM15789/GSM15789.cel.gz!
Backtrace:
    ▆
 1. └─GEOquery::getGEOSuppFiles("GSM15789", baseDir = tempdir()) at test_supp_files.R:15:5
── Failure ('test_supp_files.R:21:5'): GSE supplemental file no-download works ──
nrow(res) not equivalent to 12.
1/1 mismatches
[1] 11 - 12 == -1

[ FAIL 22 | WARN 107 | SKIP 0 | PASS 46 ]
Error: Test failures
Execution halted