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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:recountmethylation.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings recountmethylation_1.5.5.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/recountmethylation.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'recountmethylation/DESCRIPTION' ... OK
* this is package 'recountmethylation' version '1.5.5'
* 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 whether package 'recountmethylation' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   5.1Mb
* 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 ... WARNING
'::' or ':::' imports not declared from:
  'DelayedMatrixStats' 'basilisk' 'reticulate'
Namespace in Imports field not imported from: 'IlluminaHumanMethylation450kmanifest'
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'ba.background' 'ba.biotinstaining.grn' 'ba.biotinstaining.red'
  'ba.bisulfiteconv1.grn' 'ba.bisulfiteconv1.red' 'ba.bisulfiteconv2'
  'ba.extension.grn' 'ba.extension.red' 'ba.hybridization.hi.vs.med'
  'ba.hybridization.med.vs.low' 'ba.nonpolymorphic.grn'
  'ba.nonpolymorphic.red' 'ba.restoration' 'ba.specificity1.grn'
  'ba.specificity1.red' 'ba.specificity2' 'ba.targetremoval1'
  'ba.targetremoval2' 'setup_sienv'
* 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 ... NOTE
prepare_Rd: query_si.Rd:33-35: Dropping empty section \value
* 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 ... WARNING
'library' or 'require' call not declared from: 'minfiData'
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
bactrl        11.43   0.70   12.13
get_rmdl       5.38   1.15    6.83
gds_idat2rg    5.78   0.56   18.22
gds_idatquery  1.49   0.31   14.63
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/recountmethylation.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL recountmethylation
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'recountmethylation' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'recountmethylation'
    finding HTML links ... done
    ba                                      html  
    bactrl                                  html  
    bathresh                                html  
    data_mdpost                             html  
    gds_idat2rg                             html  
    gds_idatquery                           html  
    get_crossreactive_cpgs                  html  
    get_fh                                  html  
    get_qcsignal                            html  
    get_rmdl                                html  
    get_servermatrix                        html  
    getdb                                   html  
    getrg                                   html  
    hread                                   html  
    make_si                                 html  
    matchds_1to2                            html  
    query_si                                html  
    rgse                                    html  
    servermatrix                            html  
    setup_sienv                             html  
    smfilt                                  html  
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'methylCC' is missing or broken
 done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
   1.39    0.34    2.04