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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:recountmethylation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings recountmethylation_1.15.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/recountmethylation.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘recountmethylation/DESCRIPTION’ ... OK
* this is package ‘recountmethylation’ version ‘1.15.0’
* 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 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 whether 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        14.212  0.558  14.805
gds_idat2rg    6.356  0.257  18.621
gds_idatquery  1.645  0.172  13.177
get_rmdl       0.103  0.030  11.346
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-servermatrix.R’
 OK
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/recountmethylation.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL recountmethylation
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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 
  1.395   0.135  12.586