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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MEAL.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MEAL_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MEAL.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MEAL/DESCRIPTION' ... OK
* this is package 'MEAL' version '1.24.0'
* 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 whether package 'MEAL' 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ':::' import not declared from: 'sva'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotRegion: no visible global function definition for
  'subsetByOverlaps'
plotRegion: no visible global function definition for 'mcols<-'
runRDA: no visible global function definition for 'rowData'
runSVA: no visible global function definition for 'resid'
runSVA: no visible global function definition for 'quantile'
Undefined global functions or variables:
  mcols<- quantile resid rowData subsetByOverlaps
Consider adding
  importFrom("stats", "quantile", "resid")
to your NAMESPACE file.
* 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 ... WARNING
Undocumented arguments in documentation object 'getProbeResults'
  'robust'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... WARNING
Found the following significant warnings:

  Warning: 'runRegionAnalysis' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
exportResults 4.15   0.29    5.52
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:

  Warning: 'runRegionAnalysis' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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: 4 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/MEAL.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/MEAL_1.24.0.tar.gz && rm -rf MEAL.buildbin-libdir && mkdir MEAL.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MEAL.buildbin-libdir MEAL_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MEAL_1.24.0.zip && rm MEAL_1.24.0.tar.gz MEAL_1.24.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  2  588k    2 15989    0     0   133k      0  0:00:04 --:--:--  0:00:04  133k
100  588k  100  588k    0     0   588k      0  0:00:01  0:00:01 --:--:--  588k

install for i386

* installing *source* package 'MEAL' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MEAL'
    finding HTML links ... done
    MEAL-defunct                            html  
    MEAL                                    html  
    computeRDAR2                            html  
    correlationMethExprs                    html  
    exportResults                           html  
    filterResults                           html  
    getGeneVals                             html  
    getProbeResults                         html  
    getRDAresults                           html  
    plotFeature                             html  
    plotRDA                                 html  
    plotRegion                              html  
    runBlockFinder                          html  
    runBumphunter                           html  
    runDMRcate                              html  
    runDiffMeanAnalysis                     html  
    runDiffVarAnalysis                      html  
    runPipeline                             html  
    runRDA                                  html  
    runRegionAnalysis                       html  
    topRDAhits                              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

install for x64

* installing *source* package 'MEAL' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MEAL' as MEAL_1.24.0.zip
* DONE (MEAL)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'MEAL' successfully unpacked and MD5 sums checked