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This page was generated on 2021-10-22 12:04:18 -0400 (Fri, 22 Oct 2021).

CHECK results for AUCell on riesling1

To the developers/maintainers of the AUCell package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AUCell.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 98/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AUCell 1.15.0  (landing page)
Sara Aibar
Snapshot Date: 2021-10-21 14:50:08 -0400 (Thu, 21 Oct 2021)
git_url: https://git.bioconductor.org/packages/AUCell
git_branch: master
git_last_commit: 82eea52
git_last_commit_date: 2021-05-19 12:30:20 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: AUCell
Version: 1.15.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AUCell.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings AUCell_1.15.0.tar.gz
StartedAt: 2021-10-21 23:59:24 -0400 (Thu, 21 Oct 2021)
EndedAt: 2021-10-22 00:02:48 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 204.3 seconds
RetCode: 0
Status:   OK  
CheckDir: AUCell.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AUCell.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings AUCell_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/AUCell.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.15.0'
* 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 ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
* 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
Namespace in Imports field not imported from: 'S4Vectors'
  All declared Imports should be used.
* 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'
plotEmb_rgb : <anonymous>: no visible global function definition for
  'rgb'
Undefined global functions or variables:
  %>% cell rgb tsne1 tsne2
Consider adding
  importFrom("grDevices", "rgb")
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 installed files from 'inst/doc' ... 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 '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: 4 NOTEs
See
  'D:/biocbuild/bbs-3.14-bioc/meat/AUCell.Rcheck/00check.log'
for details.



Installation output

AUCell.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/AUCell_1.15.0.tar.gz && rm -rf AUCell.buildbin-libdir && mkdir AUCell.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AUCell.buildbin-libdir AUCell_1.15.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL AUCell_1.15.0.zip && rm AUCell_1.15.0.tar.gz AUCell_1.15.0.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
  0 3000k    0  1137    0     0  13865      0  0:03:41 --:--:--  0:03:41 13698
100 3000k  100 3000k    0     0  3337k      0 --:--:-- --:--:-- --:--:-- 3333k

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  
    getSetNames                             html  
    orderAUC                                html  
    plotEmb_rgb                             html  
    plotGeneCount                           html  
    plotTsne_cellProps                      html  
    updateAucellResults                     html  
** building package indices
** installing vignettes
   'AUCell.Rmd' using 'UTF-8' 
** 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_1.15.0.zip
* DONE (AUCell)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'AUCell' successfully unpacked and MD5 sums checked

Tests output

AUCell.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 42 ]
> 
> proc.time()
   user  system elapsed 
  11.42    1.06   12.46 

AUCell.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 42 ]
> 
> proc.time()
   user  system elapsed 
  12.45    1.29   13.71 

Example timings

AUCell.Rcheck/examples_i386/AUCell-Ex.timings

nameusersystemelapsed
AUCell_buildRankings0.410.020.42
AUCell_calcAUC0.800.030.83
AUCell_createViewerApp1.940.932.88
AUCell_exploreThresholds1.990.032.02
AUCell_plotHist0.390.020.41
AUCell_plotTSNE0.570.040.62
GeneSet-methods0.080.020.09
aucellResults-class0.550.010.57
orderAUC000
plotGeneCount000
plotTsne_cellProps0.610.000.61
updateAucellResults0.030.000.03

AUCell.Rcheck/examples_x64/AUCell-Ex.timings

nameusersystemelapsed
AUCell_buildRankings0.390.070.45
AUCell_calcAUC1.200.011.22
AUCell_createViewerApp1.810.902.72
AUCell_exploreThresholds1.680.031.70
AUCell_plotHist0.420.000.42
AUCell_plotTSNE0.610.040.64
GeneSet-methods0.120.000.13
aucellResults-class0.550.000.54
orderAUC000
plotGeneCount000
plotTsne_cellProps1.160.011.18
updateAucellResults0.030.000.03