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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:coMethDMR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings coMethDMR_1.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/coMethDMR.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘coMethDMR/DESCRIPTION’ ... OK
* this is package ‘coMethDMR’ version ‘1.5.0’
* 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 ‘coMethDMR’ can be installed ... OK
* checking installed package size ... OK
* 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 startup messages can be suppressed ... 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 ... NOTE
File ‘coMethDMR/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage("Checking for cached SeSAMe data.")
    packageStartupMessage("Caching SeSAMe data for 450k/EPIC arrays.")

See section ‘Good practice’ in '?.onAttach'.
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘coMethDMR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AnnotateResults
> ### Title: Annotate 'coMethDMR' Pipeline Results
> ### Aliases: AnnotateResults
> 
> ### ** Examples
> 
>    lmmResults_df <- data.frame(
+      chrom = c("chr22", "chr22", "chr22", "chr22", "chr22"),
+      start = c("39377790", "50987294", "19746156", "42470063", "43817258"),
+      end   = c("39377930", "50987527", "19746368", "42470223", "43817384"),
+      regionType = c("TSS1500", "EXON1", "ISLAND", "TSS200", "ISLAND"),
+      stringsAsFactors = FALSE
+    )
> 
>    AnnotateResults(
+      lmmRes_df = lmmResults_df,
+      arrayType = "450k"
+    )
Warning: no function found corresponding to methods exports from ‘HDF5Array’ for: ‘extract_sparse_array’, ‘is_sparse<-’
Warning: multiple methods tables found for ‘extract_array’
Warning: multiple methods tables found for ‘sparsity’
Warning: multiple methods tables found for ‘is_sparse’
Warning: multiple methods tables found for ‘write_block’
Error: objects ‘rowSums’, ‘colSums’, ‘rowMeans’, ‘colMeans’ are not exported by 'namespace:BiocGenerics'
Execution halted
* 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:
    1. ├─coMethDMR::CpGsInfoAllRegions(...) at test_CpGsInfoAllRegions.R:15:0
    2. │ └─base::lapply(...)
    3. │   └─coMethDMR (local) FUN(X[[i]], ...)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImport(...)
    6.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    7.     ├─base::namespaceImportFrom(...)
    8.     │ └─base::asNamespace(ns)
    9.     └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   10.       └─base::namespaceImportFrom(...)
   11.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  
  [ FAIL 1 | WARN 5 | SKIP 0 | PASS 8 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline.Rmd’ using ‘UTF-8’... OK
  ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline.Rmd’ using rmarkdown
Quitting from lines 181-190 (vin1_Introduction_to_coMethDMR_geneBasedPipeline.Rmd) 
Error: processing vignette 'vin1_Introduction_to_coMethDMR_geneBasedPipeline.Rmd' failed with diagnostics:
objects 'rowSums', 'colSums', 'rowMeans', 'colMeans' are not exported by 'namespace:BiocGenerics'
--- failed re-building ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline.Rmd’

--- re-building ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline.Rmd’ using rmarkdown
Quitting from lines 188-189 (vin2_BiocParallel_for_coMethDMR_geneBasedPipeline.Rmd) 
Error: processing vignette 'vin2_BiocParallel_for_coMethDMR_geneBasedPipeline.Rmd' failed with diagnostics:
objects 'rowSums', 'colSums', 'rowMeans', 'colMeans' are not exported by 'namespace:BiocGenerics'
--- failed re-building ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline.Rmd’

SUMMARY: processing the following files failed:
  ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline.Rmd’
  ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 3 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/coMethDMR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL coMethDMR
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’
* installing *source* package ‘coMethDMR’ ...
** using staged installation
** R
** data
** 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 (coMethDMR)

R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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(coMethDMR)
Checking for cached SeSAMe data.
> 
> test_check("coMethDMR")
[ FAIL 1 | WARN 5 | SKIP 0 | PASS 8 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_CpGsInfoAllRegions.R:15:1'): (code run outside of `test_that()`) ──
Error: objects 'rowSums', 'colSums', 'rowMeans', 'colMeans' are not exported by 'namespace:BiocGenerics'
Backtrace:
     ▆
  1. ├─coMethDMR::CpGsInfoAllRegions(...) at test_CpGsInfoAllRegions.R:15:0
  2. │ └─base::lapply(...)
  3. │   └─coMethDMR (local) FUN(X[[i]], ...)
  4. └─base::loadNamespace(x)
  5.   ├─base::namespaceImport(...)
  6.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
  7.     ├─base::namespaceImportFrom(...)
  8.     │ └─base::asNamespace(ns)
  9.     └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
 10.       └─base::namespaceImportFrom(...)
 11.         └─base::importIntoEnv(impenv, impnames, ns, impvars)

[ FAIL 1 | WARN 5 | SKIP 0 | PASS 8 ]
Error: Test failures
Execution halted