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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:recount.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings recount_1.31.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/recount.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘recount/DESCRIPTION’ ... OK
* this is package ‘recount’ version ‘1.31.2’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘recount’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
* 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 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 ... NOTE
  Note: found 347 marked UTF-8 strings
* 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 ... ERROR
Running examples in ‘recount-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: coverage_matrix
> ### Title: Given a set of regions for a chromosome, compute the coverage
> ###   matrix for a given SRA study.
> ### Aliases: coverage_matrix
> 
> ### ** Examples
> 
> 
> ## Workaround for https://github.com/lawremi/rtracklayer/issues/83
> download_study("SRP002001", type = "mean")
2024-10-10 02:07:44.483355 downloading file mean_SRP002001.bw to SRP002001/bw
trying URL 'http://duffel.rail.bio/recount/SRP002001/bw/mean_SRP002001.bw'
Warning in download.file(url, method = method, ...) :
  URL 'https://recount-opendata.s3.amazonaws.com/recount2/SRP002001/bw/mean_SRP002001.bw': status was 'SSL connect error'
trying URL 'http://duffel.rail.bio/recount/SRP002001/bw/mean_SRP002001.bw'
Warning in download.file(url, method = method, ...) :
  URL 'https://recount-opendata.s3.amazonaws.com/recount2/SRP002001/bw/mean_SRP002001.bw': status was 'SSL connect error'
trying URL 'http://duffel.rail.bio/recount/SRP002001/bw/mean_SRP002001.bw'
Warning in download.file(url, method = method, ...) :
  URL 'https://recount-opendata.s3.amazonaws.com/recount2/SRP002001/bw/mean_SRP002001.bw': status was 'SSL connect error'
Error in download_retry(url = url, destfile = file.path(outdir, filename),  : 
  'download_retry()' failed:
  URL: http://duffel.rail.bio/recount/SRP002001/bw/mean_SRP002001.bw
  error: cannot open URL 'http://duffel.rail.bio/recount/SRP002001/bw/mean_SRP002001.bw'
Calls: download_study -> download_retry
Execution halted
* 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:
  "status":"ok"}
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(find_geo("SRX110461"), "GSM836270") at test-misc.R:16:5
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   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 2 | WARN 4 | SKIP 0 | PASS 19 ]
  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: 2 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/recount.Rcheck/00check.log’
for details.