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### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:recountmethylation.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings recountmethylation_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/recountmethylation.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘recountmethylation/DESCRIPTION’ ... OK
* this is package ‘recountmethylation’ version ‘1.12.0’
* 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 ‘recountmethylation’ 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 loading without being on the library search path ... 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
get_fh : <anonymous>: no visible global function definition for
  ‘make_fhmatrix_autolabel’
make_si : <anonymous>: no visible global function definition for
  ‘make_hnsw_si’
query_si: no visible binding for global variable ‘v’
query_si : <anonymous>: no visible global function definition for
  ‘make_dfk_sampleid’
Undefined global functions or variables:
  make_dfk_sampleid make_fhmatrix_autolabel make_hnsw_si v
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
bactrl      12.661  0.540  13.201
gds_idat2rg  5.805  0.354   9.036
get_rmdl     0.130  0.024   5.946
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-servermatrix.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘cpg_probe_annotations.Rmd’ using ‘UTF-8’... OK
  ‘exporting_saving_data.Rmd’ using ‘UTF-8’... failed
  ‘recountmethylation_data_analyses.Rmd’ using ‘UTF-8’... failed
  ‘recountmethylation_glint.Rmd’ using ‘UTF-8’... failed
  ‘recountmethylation_pwrewas.Rmd’ using ‘UTF-8’... failed
  ‘recountmethylation_search_index.Rmd’ using ‘UTF-8’... failed
  ‘recountmethylation_users_guide.Rmd’ using ‘UTF-8’... OK
 WARNING
Errors in running code in vignettes:
when running code in ‘exporting_saving_data.Rmd’
  ...

> rg.epic <- convertArray(rg.hm450k, "IlluminaHumanMethylationEPIC")
[convertArray] Casting as IlluminaHumanMethylationEPIC
Loading required package: IlluminaHumanMethylationEPICmanifest

> ms.hm450k <- preprocessRaw(rg)

  When sourcing ‘exporting_saving_data.R’:
Error: object 'rg' not found
Execution halted
when running code in ‘recountmethylation_data_analyses.Rmd’
  ...
> opts_chunk$set(eval = FALSE, echo = TRUE, warning = FALSE, 
+     message = FALSE)

> gmdn <- "remethdb-h5se_gm_0-0-1_1590090412"

> gm <- loadHDF5SummarizedExperiment(gmdn)

  When sourcing ‘recountmethylation_data_analyses.R’:
Error: directory "remethdb-h5se_gm_0-0-1_1590090412" not found
Execution halted
when running code in ‘recountmethylation_glint.Rmd’
  ...
> glint_env <- BasiliskEnvironment(envname = env.name, 
+     pkgname = pkg.name, packages = pkgv)

> proc <- basiliskStart(glint_env)
Warning in py_initialize(config$python, config$libpython, config$pythonhome,  :
  Python 2 reached EOL on January 1, 2020. Python 2 compatability will be removed in an upcoming reticulate release.

  When sourcing ‘recountmethylation_glint.R’:
Error: PyType_GetFlags - /home/biocbuild/.cache/R/basilisk/1.14.3/recountmethylation/1.12.0/glint_env/lib/libpython2.7.so: undefined symbol: PyType_GetFlags
Execution halted
when running code in ‘recountmethylation_pwrewas.Rmd’
  ...
> lpwr <- get(load(file.path(dpath, "lpwr-results_pwrewas-example.rda")))

> revised_function_url <- paste0("https://github.com/metamaden/pwrEWAS/", 
+     "blob/master/inst/revised_functions/pwrEWAS_revised.R?raw=TRUE")

> devtools::source_url(revised_function_url)

  When sourcing ‘recountmethylation_pwrewas.R’:
Error: there is no package called ‘devtools’
Execution halted
when running code in ‘recountmethylation_search_index.Rmd’
  ...

> mdf <- md[md$blood.subgroup == "whole_blood", ]

> gsmv <- c(gsmv, mdf[sample(nrow(mdf), 20), ]$gsm)

> bval.fpath <- paste0("bval_", num.cg, ".csv")

  When sourcing ‘recountmethylation_search_index.R’:
Error: object 'num.cg' not found
Execution halted

* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/recountmethylation.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL recountmethylation
###
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘recountmethylation’ ...
** using staged installation
** R
** 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 (recountmethylation)

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

> testthat::context("Test the server matrix properties")
> 
> testthat::test_that("Properties of server matrix returned from get_rmdl 
+     and servermatrix", {
+     sm <- recountmethylation::get_servermatrix()
+     testthat::expect_true(is(sm, "matrix"))
+     testthat::expect_equal(ncol(sm), 4)
+     testthat::expect_true(is(sm[,1], "character"))
+ })
Test passed 🎉
> 
> proc.time()
   user  system elapsed 
  1.255   0.093   6.421