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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:recount.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings recount_1.29.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/recount.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘recount/DESCRIPTION’ ... OK
* this is package ‘recount’ version ‘1.29.0’
* 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 ... 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 R 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 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
> 
> 
> if (.Platform$OS.type != "windows") {
+     ## Reading BigWig files is not supported by rtracklayer on Windows
+     ## Define expressed regions for study DRP002835, chrY
+     regions <- expressed_regions("DRP002835", "chrY",
+         cutoff = 5L,
+         maxClusterGap = 3000L
+     )
+ 
+     ## Now calculate the coverage matrix for this study
+     rse <- coverage_matrix("DRP002835", "chrY", regions)
+ 
+     ## One row per region
+     identical(length(regions), nrow(rse))
+ }
2024-01-27 06:37:50.673147 loadCoverage: loading BigWig file http://duffel.rail.bio/recount/DRP002835/bw/mean_DRP002835.bw
2024-01-27 06:37:54.688841 loadCoverage: applying the cutoff to the merged data
2024-01-27 06:37:54.71273 filterData: originally there were 57227415 rows, now there are 57227415 rows. Meaning that 0 percent was filtered.
2024-01-27 06:37:54.714941 findRegions: identifying potential segments
2024-01-27 06:37:54.717403 findRegions: segmenting information
2024-01-27 06:37:54.717667 .getSegmentsRle: segmenting with cutoff(s) 5
2024-01-27 06:37:54.72948 findRegions: identifying candidate regions
2024-01-27 06:42:54.343437 findRegions: identifying region clusters
Warning in file(file, "rt") :
  URL 'https://raw.githubusercontent.com/nellore/runs/master/gtex/hg38.sizes': status was 'Couldn't resolve host name'
Error in file(file, "rt") : 
  cannot open the connection to 'https://raw.githubusercontent.com/nellore/runs/master/gtex/hg38.sizes'
Calls: coverage_matrix -> read.table -> file
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:
      mode = "wb", ...)`: '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'
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-data.R:133:13
   2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─recount::expressed_regions("SRP002001", "chrY", cutoff = 5, outdir = tmpdir)
   5.   └─recount::download_study(...)
   6.     └─recount::download_retry(...)
  
  [ FAIL 1 | WARN 8 | SKIP 0 | PASS 48 ]
  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-3.19-bioc-mac-arm64/meat/recount.Rcheck/00check.log’
for details.