Package: AUCell

Version: 1.6.1

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AUCell.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings AUCell_1.6.1.tar.gz

StartedAt: 2019-10-16 02:02:00 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:07:07 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 307.2 seconds

RetCode: 0

Status:  OK

CheckDir: AUCell.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AUCell.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings AUCell_1.6.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/AUCell.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 'AUCell/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AUCell' version '1.6.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'doMC'
* 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 'AUCell' 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 ... NOTE
'library' or 'require' call to 'rbokeh' 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
AUCell_createViewerApp : : no visible global function
  definition for '%>%'
AUCell_createViewerApp : : no visible binding for global
  variable 'tsne1'
AUCell_createViewerApp : : no visible binding for global
  variable 'tsne2'
AUCell_createViewerApp : : no visible binding for global
  variable 'cell'
orderAUC: no visible global function definition for 'as.dist'
orderAUC: no visible global function definition for 'cor'
orderAUC: no visible global function definition for 'hclust'
Undefined global functions or variables:
  %>% as.dist cell cor hclust tsne1 tsne2
Consider adding
  importFrom("stats", "as.dist", "cor", "hclust")
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 ... 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 or elapsed time > 5s
                         user system elapsed
AUCell_exploreThresholds 5.52   2.03    6.88
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
AUCell_exploreThresholds 4.79   1.58    5.51
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/AUCell.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/AUCell_1.6.1.tar.gz && rm -rf AUCell.buildbin-libdir && mkdir AUCell.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AUCell.buildbin-libdir AUCell_1.6.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL AUCell_1.6.1.zip && rm AUCell_1.6.1.tar.gz AUCell_1.6.1.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
100  162k  100  162k    0     0  2993k      0 --:--:-- --:--:-- --:--:-- 3453k

install for i386

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

    AUCell_calcAUC                          html  
    AUCell_createViewerApp                  html  
    AUCell_exploreThresholds                html  
    AUCell_plotHist                         html  
    AUCell_plotTSNE                         html  
    GeneSet-methods                         html  
    aucellResults-class                     html  
    orderAUC                                html  
    plotGeneCount                           html  
    plotTsne_cellProps                      html  
    updateAucellResults                     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 'AUCell' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AUCell' as AUCell_1.6.1.zip
* DONE (AUCell)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'AUCell' successfully unpacked and MD5 sums checked

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(AUCell)
> 
> test_check("AUCell")
 min   1%   5%  10%  50% 100% 
   3    5    6    7   10   16 
 min   1%   5%  10%  50% 100% 
   3    5    6    7   10   16 
== testthat results  ===========================================================
[ OK: 39 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  24.10    6.57   27.59 

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(AUCell)
> 
> test_check("AUCell")
 min   1%   5%  10%  50% 100% 
   3    5    6    7   10   16 
 min   1%   5%  10%  50% 100% 
   3    5    6    7   10   16 
== testthat results  ===========================================================
[ OK: 39 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  22.56    4.57   23.82