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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MultiBaC.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MultiBaC_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MultiBaC.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 'MultiBaC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MultiBaC' version '1.4.0'
* 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 'MultiBaC' 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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Q2_plot: no visible global function definition for 'rgb'
explained_varPlot: no visible global function definition for 'rgb'
Undefined global functions or variables:
  rgb
Consider adding
  importFrom("grDevices", "rgb")
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 ... WARNING
Codoc mismatches from documentation object 'ARSyNbac':
ARSyNbac
  Code: function(mbac, batchEstimation = TRUE, filterNoise = TRUE,
                 Interaction = FALSE, Variability = 0.9, beta = 2,
                 modelName = "Model 1", showplot = TRUE)
  Docs: function(mbac, batchEstimation = TRUE, Interaction = FALSE,
                 Variability = 0.9, beta = 2, modelName = "Model 1",
                 showplot = TRUE)
  Argument names in code not in docs:
    filterNoise
  Mismatches in argument names (first 3):
    Position: 3 Code: filterNoise Docs: Interaction
    Position: 4 Code: Interaction Docs: Variability
    Position: 5 Code: Variability Docs: beta

* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
plot_pca          9.03   0.00    9.08
inner_relPlot     8.93   0.06    8.98
plot              8.91   0.00    8.92
MultiBaC          8.73   0.06    8.81
Q2_plot           8.39   0.24    8.62
explained_varPlot 8.61   0.00    8.61
ARSyNbac          7.92   0.47    8.41
batchCorrection   7.95   0.01    7.97
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
plot              12.31   0.00   12.33
explained_varPlot 12.19   0.00   12.19
inner_relPlot     11.90   0.01   11.92
plot_pca          11.21   0.00   11.21
batchCorrection   11.05   0.00   11.05
MultiBaC          10.53   0.02   10.55
Q2_plot           10.40   0.03   10.43
ARSyNbac           8.81   0.22    9.03
* 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: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/MultiBaC.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/MultiBaC_1.4.0.tar.gz && rm -rf MultiBaC.buildbin-libdir && mkdir MultiBaC.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MultiBaC.buildbin-libdir MultiBaC_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MultiBaC_1.4.0.zip && rm MultiBaC_1.4.0.tar.gz MultiBaC_1.4.0.zip
###
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                                 Dload  Upload   Total   Spent    Left  Speed

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100  102k  100  102k    0     0   452k      0 --:--:-- --:--:-- --:--:--  453k

install for i386

* installing *source* package 'MultiBaC' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MultiBaC'
    finding HTML links ... done
    A.gro                                   html  
    A.rna                                   html  
    ARSyNbac                                html  
    B.ribo                                  html  
    B.rna                                   html  
    C.par                                   html  
    C.rna                                   html  
    MultiBaC                                html  
    Q2_plot                                 html  
    batchCorrection                         html  
    batchEstPlot                            html  
    createMbac                              html  
    explained_varPlot                       html  
    genMissingOmics                         html  
    genModelList                            html  
    inner_relPlot                           html  
    multiyeast                              html  
    plot                                    html  
    plot_pca                                html  
    summary                                 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 'MultiBaC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MultiBaC' as MultiBaC_1.4.0.zip
* DONE (MultiBaC)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'MultiBaC' successfully unpacked and MD5 sums checked