##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:recount.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings recount_1.39.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/recount.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-11 07:46:20 UTC
* checking for file ‘recount/DESCRIPTION’ ... OK
* this is package ‘recount’ version ‘1.39.0’
* 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 ‘recount’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
coverage_matrix     4.225  0.609  14.047
expressed_regions   2.070  0.423   8.329
geo_characteristics 0.511  0.011  10.975
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 ERROR
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(find_geo("SRX110461"), "GSM836270") at test-misc.R:16:5
   2. │ └─testthat::quasi_label(enquo(object), label)
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─recount::find_geo("SRX110461")
   5.   └─rentrez::entrez_link("sra", id = uid$ids, db = "gds")
   6.     ├─base::do.call(make_entrez_query, args)
   7.     └─rentrez (local) `<fn>`(...)
   8.       └─rentrez:::entrez_check(response)
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 44 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.24-bioc/meat/recount.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL recount
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’
* installing *source* package ‘recount’ ...
** this is package ‘recount’ version ‘1.39.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (recount)

R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 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.

> ## Disable the tests if the system variable 'R_DISABLE_TESTS' is set to TRUE
> 
> flag <- as.logical(Sys.getenv("R_DISABLE_TESTS"))
> if (is.na(flag) | flag == FALSE) {
+     library("testthat")
+     test_check("recount")
+ }
Loading required package: recount
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

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

    anyMissing, rowMedians

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
trying URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata'
Content type 'binary/octet-stream' length 3130229 bytes (3.0 MB)
==================================================
downloaded 3.0 MB

trying URL 'http://duffel.rail.bio/recount/v2/SRP002001/rse_gene.Rdata'
Content type 'binary/octet-stream' length 1753074 bytes (1.7 MB)
==================================================
downloaded 1.7 MB

trying URL 'http://duffel.rail.bio/recount/v2/SRP002001/rse_exon.Rdata'
Content type 'binary/octet-stream' length 3973986 bytes (3.8 MB)
==================================================
downloaded 3.8 MB

trying URL 'http://duffel.rail.bio/recount/SRP002001/rse_jx.Rdata'
Content type 'binary/octet-stream' length 1257137 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'http://duffel.rail.bio/recount/v2/SRP002001/rse_tx.RData'
Content type 'binary/octet-stream' length 14016087 bytes (13.4 MB)
==================================================
downloaded 13.4 MB

trying URL 'http://duffel.rail.bio/recount/v2/SRP002001/counts_gene.tsv.gz'
Content type 'text/tab-separated-values' length 258000 bytes (251 KB)
==================================================
downloaded 251 KB

trying URL 'http://duffel.rail.bio/recount/v2/SRP002001/counts_exon.tsv.gz'
Content type 'text/tab-separated-values' length 435233 bytes (425 KB)
==================================================
downloaded 425 KB

trying URL 'http://duffel.rail.bio/recount/SRP002001/counts_jx.tsv.gz'
Content type 'text/tab-separated-values' length 8833 bytes
==================================================
downloaded 8833 bytes

trying URL 'http://duffel.rail.bio/recount/SRP002001/SRP002001.tsv'
Content type 'text/tab-separated-values' length 629 bytes
==================================================
downloaded 629 bytes

trying URL 'http://duffel.rail.bio/recount/v2/SRP002001/files_info.tsv'
Content type 'text/tab-separated-values' length 705 bytes
==================================================
downloaded 705 bytes

trying URL 'http://duffel.rail.bio/recount/SRP002001/bw/SRR036661.bw'
Content type 'binary/octet-stream' length 19539759 bytes (18.6 MB)
==================================================
downloaded 18.6 MB

trying URL 'http://duffel.rail.bio/recount/SRP002001/bw/mean_SRP002001.bw'
Content type 'binary/octet-stream' length 50936703 bytes (48.6 MB)
==================================================
downloaded 48.6 MB

trying URL 'http://duffel.rail.bio/recount/SRP002001/bw/mean_SRP002001.bw'
Content type 'binary/octet-stream' length 50936703 bytes (48.6 MB)
==================================================
downloaded 48.6 MB

trying URL 'http://duffel.rail.bio/recount/SRP002001/bw/SRR036661.bw'
Content type 'binary/octet-stream' length 19539759 bytes (18.6 MB)
==================================================
downloaded 18.6 MB

trying URL 'http://duffel.rail.bio/recount/SRP002001/SRP002001.tsv'
Content type 'text/tab-separated-values' length 629 bytes
==================================================
downloaded 629 bytes

trying URL 'https://github.com/leekgroup/recount-website/blob/master/metadata/metadata_clean_sra.Rdata?raw=true'
Content type 'application/octet-stream' length 2531337 bytes (2.4 MB)
==================================================
downloaded 2.4 MB

trying URL 'http://duffel.rail.bio/recount/SRP036843/SRP036843.tsv'
Content type 'text/tab-separated-values' length 1278 bytes
==================================================
downloaded 1278 bytes

trying URL 'http://duffel.rail.bio/recount/SRP029334/SRP029334.tsv'
Content type 'text/tab-separated-values' length 50296 bytes (49 KB)
==================================================
downloaded 49 KB

trying URL 'http://duffel.rail.bio/recount/SRP050563/SRP050563.tsv'
Content type 'text/tab-separated-values' length 1296 bytes
==================================================
downloaded 1296 bytes

trying URL 'http://duffel.rail.bio/recount/SRP055438/SRP055438.tsv'
Content type 'text/tab-separated-values' length 13953 bytes (13 KB)
==================================================
downloaded 13 KB

trying URL 'http://duffel.rail.bio/recount/SRP055749/SRP055749.tsv'
Content type 'text/tab-separated-values' length 4823 bytes
==================================================
downloaded 4823 bytes

trying URL 'http://duffel.rail.bio/recount/SRP058120/SRP058120.tsv'
Content type 'text/tab-separated-values' length 9768 bytes
==================================================
downloaded 9768 bytes

trying URL 'http://duffel.rail.bio/recount/SRP005342/SRP005342.tsv'
Content type 'text/tab-separated-values' length 3628 bytes
==================================================
downloaded 3628 bytes

trying URL 'http://duffel.rail.bio/recount/SRP007508/SRP007508.tsv'
Content type 'text/tab-separated-values' length 1801 bytes
==================================================
downloaded 1801 bytes

trying URL 'http://duffel.rail.bio/recount/SRP015668/SRP015668.tsv'
Content type 'text/tab-separated-values' length 11186 bytes (10 KB)
==================================================
downloaded 10 KB

trying URL 'https://github.com/leekgroup/recount-website/blob/master/metadata/metadata_clean_tcga.Rdata?raw=true'
Content type 'application/octet-stream' length 16334695 bytes (15.6 MB)
==================================================
downloaded 15.6 MB

trying URL 'https://github.com/leekgroup/recount-website/blob/master/predictions/PredictedPhenotypes_v0.0.06.rda?raw=true'
Content type 'application/octet-stream' length 548129 bytes (535 KB)
==================================================
downloaded 535 KB

Loading objects:
  PredictedPhenotypes
trying URL 'http://duffel.rail.bio/recount/v2/DRP000499/rse_gene.Rdata'
Content type 'binary/octet-stream' length 4636353 bytes (4.4 MB)
==================================================
downloaded 4.4 MB

trying URL 'http://duffel.rail.bio/recount/v2/DRP000366/files_info.tsv_fake'
Saving _problems/test-misc-16.R
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 44 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-misc.R:16:5'): Geo info ────────────────────────────────────────
Error: HTTP failure: 500
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN" "http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd"> 
<html>
<head>
<title>NCBI/eutils202 - WWW Error 500 Diagnostic</title>
<style type="text/css"> 
h1.error {color: red; font-size: 40pt}
div.diags {text-indent: 0.5in }
</style> 
</head>
<body>
<h1>Server Error</h1>


<p>Your request could not be processed due to a problem on
our Web server.  This could be a transient problem, please
try the query again.  If it doesn't clear up within a
reasonable period of time, e-mail a short description of your
query and the diagnostic information shown below to:</p>

<p>
pubmed@nlm.nih.gov - for problems with PubMed<br/>
webadmin@ncbi.nlm.nih.gov - for problems with other services<br/>
</p>

<p>Thank you for your assistance.  We will try to fix the
problem as soon as possible.
</p>
<hr/>
<p>
Diagnostic Information:</p>

<div class="diags">Error: 500</div>

<div class="diags">URL:  h t t p : / / e x t - h t t p - e u t i l s . l i n k e r d . n c b i . n l m . n i h . g o v / e n t r e z / e u t i l s / e l i n k . f c g i ? d b = g d s & a m p ; d b f r o m = s r a & a m p ; c m d = n e i g h b o r & a m p ; i d = 1 2 7 7 6 0 & a m p ; e m a i l = d a v i d . w i n t e r  4 0 g m a i l . c o m & a m p ; t o o l = r e n t r e z </div>

<div class="diags">Client: 130.14.22.22</div>

<div class="diags">Server: eutils202</div>

<div class="diags">Time: Mon May 11 03:54:54 EDT 2026</div>

 
<p>
NOTE: The above is an internal URL which may differ from the one you used to address the page.</p>
<hr/>
<p>Rev. 01/04/08</p>

</body>
</html>

Backtrace:
    ▆
 1. ├─testthat::expect_equal(find_geo("SRX110461"), "GSM836270") at test-misc.R:16:5
 2. │ └─testthat::quasi_label(enquo(object), label)
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─recount::find_geo("SRX110461")
 5.   └─rentrez::entrez_link("sra", id = uid$ids, db = "gds")
 6.     ├─base::do.call(make_entrez_query, args)
 7.     └─rentrez (local) `<fn>`(...)
 8.       └─rentrez:::entrez_check(response)

[ FAIL 1 | WARN 2 | SKIP 0 | PASS 44 ]
Error:
! Test failures.
Execution halted