Package: MAGeCKFlute

Version: 1.4.3

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MAGeCKFlute.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MAGeCKFlute_1.4.3.tar.gz

StartedAt: 2019-10-16 04:53:23 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:03:11 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 587.2 seconds

RetCode: 0

Status:  OK

CheckDir: MAGeCKFlute.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MAGeCKFlute.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MAGeCKFlute_1.4.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/MAGeCKFlute.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.4.3'
* 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 'MAGeCKFlute' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 16.5Mb
  sub-directories of 1Mb or more:
    data      5.3Mb
    doc       1.2Mb
    extdata   9.5Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File 'MAGeCKFlute/R/zzz.R':
  .onLoad calls:
    packageStartupMessage(paste(strwrap(disclaimer, 80), collapse = "\n"))

See section 'Good practice' in '?.onAttach'.

BatchRemove: no visible binding for global variable 'PC1'
BatchRemove: no visible binding for global variable 'PC2'
BatchRemove: no visible binding for global variable 'shape'
CellCycleView: no visible binding for global variable 'x'
CellCycleView: no visible binding for global variable 'y'
DensityDiffView: no visible binding for global variable 'Diff'
DensityDiffView: no visible binding for global variable '..density..'
DensityDiffView: no visible binding for global variable 'r'
DensityView: no visible binding for global variable 'value'
DensityView: no visible binding for global variable 'variable'
EnrichedFilter: no visible binding for global variable 'max_value'
EnrichedGeneView: no visible binding for global variable 'Gene'
EnrichedGeneView: no visible binding for global variable 'Term'
EnrichedGeneView: no visible binding for global variable 'Size'
EnrichedGeneView: no visible binding for global variable 'GeneScore'
EnrichedView: no visible binding for global variable 'Description'
EnrichedView: no visible binding for global variable 'size'
FluteMLE: no visible binding for global variable 'Zuber_Essential'
KeggPathwayView: no visible global function definition for 'keggConv'
KeggPathwayView: no visible binding for global variable 'rn.list'
KeggPathwayView: no visible global function definition for
  'parseKGML2Graph2'
MapRatesView: no visible binding for global variable 'count'
MapRatesView: no visible binding for global variable 'category'
MapRatesView: no visible binding for global variable 'pos'
MapRatesView: no visible binding for global variable 'percent'
NormalizeBeta: no visible binding for global variable 'Zuber_Essential'
RankView: no visible binding for global variable 'Rank'
RankView: no visible binding for global variable 'group'
RankView: no visible binding for global variable 'Gene'
ScatterView: no visible binding for global variable 'Control'
ScatterView: no visible binding for global variable 'Treatment'
ScatterView: no visible binding for global variable 'group'
Selector: no visible binding for global variable 'GeneNum'
Selector: no visible binding for global variable 'x'
Selector: no visible binding for global variable 'y'
SquareView: no visible binding for global variable 'x'
SquareView: no visible binding for global variable 'y'
SquareView: no visible binding for global variable 'group'
SquareView: no visible binding for global variable 'Gene'
ViolinView: no visible binding for global variable 'variable'
ViolinView: no visible binding for global variable 'value'
VolcanoView: no visible binding for global variable 'group'
VolcanoView: no visible binding for global variable 'color'
sgRankView: no visible global function definition for '.'
sgRankView: no visible binding for global variable 'LFC'
sgRankView: no visible binding for global variable 'Gene'
sgRankView: no visible binding for global variable 'x'
sgRankView: no visible binding for global variable 'y'
sgRankView: no visible binding for global variable 'value'
sgRankView: no visible binding for global variable 'id'
sgRankView: no visible binding for global variable 'yend'
Undefined global functions or variables:
  . ..density.. Control Description Diff Gene GeneNum GeneScore LFC PC1
  PC2 Rank Size Term Treatment Zuber_Essential category color count
  group id keggConv max_value parseKGML2Graph2 percent pos r rn.list
  shape size value variable x y yend
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
EnrichAnalyzer   17.09   0.81   20.56
enrich.ORT       16.92   0.11   17.03
EnrichedFilter   13.38   0.28   13.66
EnrichedGeneView 12.97   0.08   13.05
arrangePathview  11.41   0.59   12.81
enrich.HGT       10.86   0.05   10.91
MAView            6.57   0.65    7.25
getOrg            6.41   0.05    6.45
gsGetter          6.19   0.14    6.32
TransGeneID       5.71   0.00    5.70
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
EnrichAnalyzer   22.16   0.34   22.52
enrich.ORT       18.65   0.11   18.77
enrich.HGT       16.44   0.11   16.55
EnrichedGeneView 15.74   0.02   15.75
arrangePathview  13.63   0.42   15.19
EnrichedFilter   12.98   0.06   13.05
TransGeneID      11.67   0.00   11.67
getOrg            9.16   0.01    9.23
gsGetter          7.97   0.16    8.14
MAView            6.14   0.74    6.87
* 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-3.9-bioc/meat/MAGeCKFlute.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/MAGeCKFlute_1.4.3.tar.gz && rm -rf MAGeCKFlute.buildbin-libdir && mkdir MAGeCKFlute.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MAGeCKFlute.buildbin-libdir MAGeCKFlute_1.4.3.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL MAGeCKFlute_1.4.3.zip && rm MAGeCKFlute_1.4.3.tar.gz MAGeCKFlute_1.4.3.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 14.7M  100 14.7M    0     0  74.7M      0 --:--:-- --:--:-- --:--:-- 77.7M

install for i386

* installing *source* package 'MAGeCKFlute' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MAGeCKFlute'
    finding HTML links ... done
    BatchRemove                             html  
    CellCycleView                           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  
    KeggPathwayView                         html  
    finding level-2 HTML links ... done

    MAView                                  html  
    MapRatesView                            html  
    NormalizeBeta                           html  
    RankView                                html  
    ReadBeta                                html  
    ReadRRA                                 html  
    ReadsgRRA                               html  
    ScatterView                             html  
    Selector                                html  
    SquareView                              html  
    TransGeneID                             html  
    ViolinView                              html  
    VolcanoView                             html  
    Zuber_Essential                         html  
    arrangePathview                         html  
    countsummary                            html  
    enrich.GSE                              html  
    enrich.HGT                              html  
    enrich.ORT                              html  
    getOrg                                  html  
    gsGetter                                html  
    mle.gene_summary                        html  
    noEnrichPlot                            html  
    normalize.loess                         html  
    readGMT                                 html  
    rra.gene_summary                        html  
    rra.sgrna_summary                       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_1.4.3.zip
* DONE (MAGeCKFlute)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'MAGeCKFlute' successfully unpacked and MD5 sums checked