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CHECK report for CellMixS on tokay1

This page was generated on 2020-09-19 10:21:00 -0400 (Sat, 19 Sep 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CellMixS PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 246/1912HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CellMixS 1.5.2
Almut Lütge
Snapshot Date: 2020-09-18 14:43:25 -0400 (Fri, 18 Sep 2020)
URL: https://git.bioconductor.org/packages/CellMixS
Branch: master
Last Commit: 8bcc521
Last Changed Date: 2020-09-08 02:40:49 -0400 (Tue, 08 Sep 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CellMixS
Version: 1.5.2
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CellMixS.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings CellMixS_1.5.2.tar.gz
StartedAt: 2020-09-19 06:00:24 -0400 (Sat, 19 Sep 2020)
EndedAt: 2020-09-19 06:06:53 -0400 (Sat, 19 Sep 2020)
EllapsedTime: 389.0 seconds
RetCode: 0
Status:  OK  
CheckDir: CellMixS.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CellMixS.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings CellMixS_1.5.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/CellMixS.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CellMixS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CellMixS' version '1.5.2'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'CellMixS' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 R/sysdata.rda ... 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: OK


Installation output

CellMixS.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/CellMixS_1.5.2.tar.gz && rm -rf CellMixS.buildbin-libdir && mkdir CellMixS.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CellMixS.buildbin-libdir CellMixS_1.5.2.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL CellMixS_1.5.2.zip && rm CellMixS_1.5.2.tar.gz CellMixS_1.5.2.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 1449k  100 1449k    0     0  19.4M      0 --:--:-- --:--:-- --:--:-- 20.5M

install for i386

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

    dot-cmsCell                             html  
    dot-defineSubspace                      html  
    dot-filterKnn                           html  
    dot-filterLocMin                        html  
    dot-ldfKnn                              html  
    dot-smoothCms                           html  
    entropy                                 html  
    evalIntegration                         html  
    isi                                     html  
    ldfDiff                                 html  
    ldfSce                                  html  
    locStructure                            html  
    mixMetric                               html  
    visCluster                              html  
    visGroup                                html  
    visHist                                 html  
    visIntegration                          html  
    visMetric                               html  
    visOverview                             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 'CellMixS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CellMixS' as CellMixS_1.5.2.zip
* DONE (CellMixS)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'CellMixS' successfully unpacked and MD5 sums checked

Tests output

CellMixS.Rcheck/tests_i386/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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(CellMixS)
Loading required package: kSamples
Loading required package: SuppDists
> 
> test_check("CellMixS")
== testthat results  ===========================================================
[ OK: 81 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  30.70    1.03   31.73 

CellMixS.Rcheck/tests_x64/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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(CellMixS)
Loading required package: kSamples
Loading required package: SuppDists
> 
> test_check("CellMixS")
== testthat results  ===========================================================
[ OK: 81 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  37.20    0.60   37.81 

Example timings

CellMixS.Rcheck/examples_i386/CellMixS-Ex.timings

nameusersystemelapsed
cms1.960.182.18
entropy0.420.080.50
evalIntegration1.940.182.11
isi0.290.010.31
ldfDiff0.580.080.65
ldfSce0.400.000.41
locStructure0.690.060.75
mixMetric0.310.000.32
visCluster1.300.031.32
visGroup0.320.030.36
visHist1.450.001.45
visIntegration1.280.041.31
visMetric1.350.001.52
visOverview1.730.031.77

CellMixS.Rcheck/examples_x64/CellMixS-Ex.timings

nameusersystemelapsed
cms2.660.132.78
entropy0.590.080.67
evalIntegration3.670.033.70
isi0.690.000.69
ldfDiff1.290.031.32
ldfSce0.770.020.79
locStructure1.450.081.53
mixMetric0.640.040.69
visCluster2.750.082.83
visGroup0.750.050.79
visHist2.830.032.86
visIntegration2.190.062.25
visMetric2.650.002.66
visOverview3.720.033.75