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CHECK report for AUCell on tokay2

This page was generated on 2019-04-09 12:32:49 -0400 (Tue, 09 Apr 2019).

Package 92/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AUCell 1.5.5
Sara Aibar
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/AUCell
Branch: master
Last Commit: 33773fc
Last Changed Date: 2019-01-31 07:30:28 -0400 (Thu, 31 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: AUCell
Version: 1.5.5
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_1.5.5.tar.gz
StartedAt: 2019-04-09 01:10:54 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 01:15:51 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 297.2 seconds
RetCode: 0
Status:  OK  
CheckDir: AUCell.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running 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_1.5.5.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/AUCell.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.5.5'
* 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 : <anonymous>: no visible global function
  definition for '%>%'
AUCell_createViewerApp : <anonymous>: no visible binding for global
  variable 'tsne1'
AUCell_createViewerApp : <anonymous>: no visible binding for global
  variable 'tsne2'
AUCell_createViewerApp : <anonymous>: 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 4.74   1.53    6.06
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
AUCell_exploreThresholds 4.08   1.33    4.89
* 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.



Installation output

AUCell.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/AUCell_1.5.5.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_1.5.5.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL AUCell_1.5.5.zip && rm AUCell_1.5.5.tar.gz AUCell_1.5.5.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  162k  100  162k    0     0  2761k      0 --:--:-- --:--:-- --:--:-- 3121k

install for i386

* installing *source* package 'AUCell' ...
** 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_1.5.5.zip
* DONE (AUCell)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'AUCell' successfully unpacked and MD5 sums checked

Tests output

AUCell.Rcheck/tests_i386/testthat.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  21.45    6.82   24.57 

AUCell.Rcheck/tests_x64/testthat.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  21.84    3.78   22.82 

Example timings

AUCell.Rcheck/examples_i386/AUCell-Ex.timings

nameusersystemelapsed
AUCell_buildRankings1.410.401.48
AUCell_calcAUC2.120.632.41
AUCell_createViewerApp2.221.063.44
AUCell_exploreThresholds4.741.536.06
AUCell_plotHist1.370.751.48
AUCell_plotTSNE2.220.752.22
GeneSet-methods0.120.030.16
aucellResults-class1.720.721.92
orderAUC000
plotGeneCount000
plotTsne_cellProps2.010.642.02
updateAucellResults0.020.000.02

AUCell.Rcheck/examples_x64/AUCell-Ex.timings

nameusersystemelapsed
AUCell_buildRankings1.270.441.21
AUCell_calcAUC2.170.532.34
AUCell_createViewerApp2.110.502.07
AUCell_exploreThresholds4.081.334.89
AUCell_plotHist1.330.231.28
AUCell_plotTSNE1.900.441.77
GeneSet-methods0.270.000.26
aucellResults-class1.430.521.53
orderAUC000
plotGeneCount0.020.000.02
plotTsne_cellProps1.660.451.66
updateAucellResults0.010.000.01