##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:a4Base.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings a4Base_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/a4Base.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'a4Base/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'a4Base' version '1.38.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'JavaGD'
* 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 'a4Base' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpuqWMI4/R.INSTALL20645ee2ae7/a4Base/man/topTable-methods.Rd:113: file link 'topTable,pamClass-method' in package 'a4Classif' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpuqWMI4/R.INSTALL20645ee2ae7/a4Base/man/topTable-methods.Rd:114: file link 'topTable,rfClass-method' in package 'a4Classif' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/a4Base.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package 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 ... OK
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
spectralMap     14.52   1.03   15.54
computeLogRatio  6.84   0.22    7.33
plotLogRatio     6.07   0.08    6.16
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
spectralMap     14.41   0.92   15.33
computeLogRatio  6.09   0.19    6.30
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/a4Base.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/a4Base_1.38.0.tar.gz && rm -rf a4Base.buildbin-libdir && mkdir a4Base.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=a4Base.buildbin-libdir a4Base_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL a4Base_1.38.0.zip && rm a4Base_1.38.0.tar.gz a4Base_1.38.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  363k  100  363k    0     0  22.0M      0 --:--:-- --:--:-- --:--:-- 23.6M

install for i386

* installing *source* package 'a4Base' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'a4Base'
    finding HTML links ... done
    ExpressionSetWithComputation-class      html  
    finding level-2 HTML links ... done

    a4palette                               html  
    addQuantilesColors                      html  
    boxPlot                                 html  
    combineTwoExpressionSet                 html  
    computeLogRatio                         html  
    createExpressionSet                     html  
    filterVarInt                            html  
    heatmap.expressionSet                   html  
    histPvalue                              html  
    histpvalueplotter                       html  
    lassoReg                                html  
    limmaReg                                html  
    limmaTwoLevels                          html  
    logReg                                  html  
    nlcvTT                                  html  
    oaColors                                html  
    oaPalette                               html  
    plot1gene                               html  
    plotComb2Samples                        html  
    plotCombMultSamples                     html  
    plotCombination2genes                   html  
    plotLogRatio                            html  
    probabilitiesPlot                       html  
    probe2gene                              html  
    profilesPlot                            html  
    propDEgenes-methods                     html  
    propDEgenes                             html  
    propdegenescalculation                  html  
    replicates                              html  
    spectralMap-methods                     html  
    spectralMap                             html  
    tTest                                   html  
    topTable-methods                        html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpuqWMI4/R.INSTALL20645ee2ae7/a4Base/man/topTable-methods.Rd:113: file link 'topTable,pamClass-method' in package 'a4Classif' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpuqWMI4/R.INSTALL20645ee2ae7/a4Base/man/topTable-methods.Rd:114: file link 'topTable,rfClass-method' in package 'a4Classif' does not exist and so has been treated as a topic
    volcanoPlot-methods                     html  
    volcanoPlot                             html  
    volcanoplotter                          html  
** building package indices
** 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 'a4Base' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'a4Base' as a4Base_1.38.0.zip
* DONE (a4Base)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'a4Base' successfully unpacked and MD5 sums checked