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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:recount.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings recount_1.28.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/recount.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘recount/DESCRIPTION’ ... OK
* this is package ‘recount’ version ‘1.28.0’
* 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  6.2Mb
  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 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
> 
> 
> 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))
+ }
2023-11-02 13:40:22.689352 loadCoverage: loading BigWig file http://duffel.rail.bio/recount/DRP002835/bw/mean_DRP002835.bw
2023-11-02 13:40:44.079882 loadCoverage: applying the cutoff to the merged data
2023-11-02 13:40:44.141025 filterData: originally there were 57227415 rows, now there are 57227415 rows. Meaning that 0 percent was filtered.
2023-11-02 13:40:44.147825 findRegions: identifying potential segments
2023-11-02 13:40:44.158638 findRegions: segmenting information
2023-11-02 13:40:44.159325 .getSegmentsRle: segmenting with cutoff(s) 5
2023-11-02 13:40:44.212412 findRegions: identifying candidate regions
2023-11-02 13:40:45.942684 findRegions: identifying region clusters
2023-11-02 13:40:48.751001 railMatrix: processing regions 1 to 372
2023-11-02 13:40:48.773856 railMatrix: processing file http://duffel.rail.bio/recount/DRP002835/bw/DRR028129.bw
Error in makeRestartList(...) : object 'specs' not found
Calls: coverage_matrix ... <Anonymous> -> <Anonymous> -> .rng_reset_generator -> RNGkind

 *** caught bus error ***
address 0xffffffffffff, cause 'invalid alignment'
Error in ..getNamespace(c("BiocParallel", "1.36.0"), "<unknown>") : 
  R_Reprotect: only 108 protected items, can't reprotect index 104
Calls: coverage_matrix ... .manager_recv -> .manager_recv -> .recv_any -> .recv_any -> $<-
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
Error in .manager_cleanup(manager) : bad value
Calls: coverage_matrix ... bploop -> bploop.lapply -> .bploop_impl -> .RNGstream<-
Warning: stack imbalance in '$', 64 then 62
Error in bpstop(BPPARAM) : 
  R_Reprotect: only 50 protected items, can't reprotect index 62
Calls: coverage_matrix ... bplapply -> bplapply -> .bpinit -> bpstop -> <Anonymous>
Warning: stack imbalance in 'if', 62 then 65

 *** caught segfault ***
address (nil), cause 'memory not mapped'
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/recount.Rcheck/00check.log’
for details.