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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ToxicoGx.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ToxicoGx_1.0.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ToxicoGx.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 'ToxicoGx/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ToxicoGx' version '1.0.1'
* 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 'ToxicoGx' 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
computeLimmaDiffExpr,ToxicoSet: no visible binding for global variable
  'cell'
Undefined global functions or variables:
  cell
* 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 ... NOTE
  Note: found 47 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/ToxicoGx.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/ToxicoGx_1.0.1.tar.gz && rm -rf ToxicoGx.buildbin-libdir && mkdir ToxicoGx.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ToxicoGx.buildbin-libdir ToxicoGx_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL ToxicoGx_1.0.1.zip && rm ToxicoGx_1.0.1.tar.gz ToxicoGx_1.0.1.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
  0 10.8M    0  5594    0     0   523k      0  0:00:21 --:--:--  0:00:21  546k
100 10.8M  100 10.8M    0     0  89.4M      0 --:--:-- --:--:-- --:--:-- 89.9M

install for i386

* installing *source* package 'ToxicoGx' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ToxicoGx'
    finding HTML links ... done
    HCC_sig                                 html  
    TGGATESsmall                            html  
    ToxicoSet-class                         html  
    ToxicoSet                               html  
    ToxicoSig                               html  
    annotation-set                          html  
    annotation                              html  
    availableTSets                          html  
    checkTSetStructure                      html  
    computeAUC                              html  
    computeICn                              html  
    computeLimmaDiffExpr-ToxicoSet-method   html  
    computeLimmaDiffExpr                    html  
    curation-set                            html  
    curation                                html  
    datasetType-set                         html  
    datasetType                             html  
    dim-ToxicoSet-method                    html  
    downloadTSet                            html  
    drugGeneResponseCurve                   html  
    drugInfo-set                            html  
    drugInfo                                html  
    drugNames-set                           html  
    drugNames                               html  
    drugPerturbationSig                     html  
    drugTimeResponseCurve                   html  
    geneDrugPerturbation                    html  
    logLogisticRegression                   html  
    mDataNames-ToxicoSet-method             html  
    name-ToxicoSet-method                   html  
    sensitivityRaw-set                      html  
    sensitivityRaw                          html  
    sensitivitySlot-set                     html  
    sensitivitySlot                         html  
    show-ToxicoSet-method                   html  
    show-ToxicoSig-method                   html  
    showSigAnnot                            html  
    sub-ToxicoSet-ANY-ANY-ANY-method        html  
    subsetTo                                html  
    summarizeMolecularProfiles              html  
    summarizeSensitivityProfiles            html  
    updateCellId                            html  
    updateDrugId                            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 'ToxicoGx' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ToxicoGx' as ToxicoGx_1.0.1.zip
* DONE (ToxicoGx)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'ToxicoGx' successfully unpacked and MD5 sums checked