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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MAGeCKFlute.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MAGeCKFlute_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/MAGeCKFlute.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 'MAGeCKFlute/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MAGeCKFlute' version '1.10.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'MAGeCKFlute' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 14.1Mb
  sub-directories of 1Mb or more:
    extdata  13.5Mb
* 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 ... NOTE
'library' or 'require' call to 'pathview' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
arrangePathview: no visible global function definition for 'pathview'
Undefined global functions or variables:
  pathview
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
enrich.ORT  7.92   0.05    8.00
TransGeneID 6.67   0.05    6.78
ReadGMT     3.75   0.02    5.08
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
TransGeneID 7.47   0.12    7.59
enrich.ORT  6.56   0.07    6.66
* 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 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/MAGeCKFlute.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/MAGeCKFlute_1.10.0.tar.gz && rm -rf MAGeCKFlute.buildbin-libdir && mkdir MAGeCKFlute.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MAGeCKFlute.buildbin-libdir MAGeCKFlute_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL MAGeCKFlute_1.10.0.zip && rm MAGeCKFlute_1.10.0.tar.gz MAGeCKFlute_1.10.0.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
100 9886k  100 9886k    0     0  45.1M      0 --:--:-- --:--:-- --:--:-- 45.3M

install for i386

* installing *source* package 'MAGeCKFlute' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MAGeCKFlute'
    finding HTML links ... done
    BarView                                 html  
    BatchRemove                             html  
    ConsistencyView                         html  
    CutoffCalling                           html  
    DensityDiffView                         html  
    DensityView                             html  
    EnrichAB                                html  
    EnrichAnalyzer                          html  
    EnrichSquare                            html  
    EnrichedFilter                          html  
    EnrichedGeneView                        html  
    EnrichedView                            html  
    FluteMLE                                html  
    FluteRRA                                html  
    HeatmapView                             html  
    IdentBarView                            html  
    IncorporateDepmap                       html  
    MAView                                  html  
    MapRatesView                            html  
    NormalizeBeta                           html  
    OmitCommonEssential                     html  
    RankView                                html  
    ReadBeta                                html  
    ReadGMT                                 html  
    ReadRRA                                 html  
    ReadsgRRA                               html  
    ResembleDepmap                          html  
    ScatterView                             html  
    Selector                                html  
    SquareView                              html  
    TransGeneID                             html  
    ViolinView                              html  
    VolcanoView                             html  
    arrangePathview                         html  
    enrich.GSE                              html  
    enrich.HGT                              html  
    enrich.ORT                              html  
    getCols                                 html  
    getGeneAnn                              html  
    getOrg                                  html  
    getOrtAnn                               html  
    gsGetter                                html  
    hclustView                              html  
    noEnrichPlot                            html  
    normalize.loess                         html  
    reexports                               html  
    retrieve_gs                             html  
    sgRankView                              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 'MAGeCKFlute' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MAGeCKFlute' as MAGeCKFlute_1.10.0.zip
* DONE (MAGeCKFlute)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'MAGeCKFlute' successfully unpacked and MD5 sums checked