Multiple platform build/check report for BioC 3.14 - CHECK results for diffcyt on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.2 (2021-11-01) -- "Bird Hippie"	4326
tokay2	Windows Server 2012 R2 Standard	x64	4.1.2 (2021-11-01) -- "Bird Hippie"	4075
machv2	macOS 10.14.6 Mojave	x86_64	4.1.2 (2021-11-01) -- "Bird Hippie"	4136
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

Package: diffcyt

Version: 1.14.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:diffcyt.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings diffcyt_1.14.0.tar.gz

StartedAt: 2021-12-19 17:54:07 -0500 (Sun, 19 Dec 2021)

EndedAt: 2021-12-19 18:00:32 -0500 (Sun, 19 Dec 2021)

EllapsedTime: 385.0 seconds

RetCode: 0

Status: OK

CheckDir: diffcyt.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:diffcyt.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings diffcyt_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/diffcyt.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'diffcyt/DESCRIPTION' ... OK
* this is package 'diffcyt' version '1.14.0'
* 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 'diffcyt' 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 ... NOTE
calcCounts: no visible binding for global variable 'cluster_id'
calcCounts: no visible binding for global variable 'sample_id'
calcMedians: no visible binding for global variable 'cluster_id'
calcMedians: no visible binding for global variable 'sample_id'
calcMedians: no visible binding for global variable 'value'
calcMediansByClusterMarker: no visible binding for global variable
  'cluster_id'
calcMediansByClusterMarker: no visible binding for global variable
  'marker_id'
calcMediansByClusterMarker: no visible binding for global variable
  'value'
calcMediansBySampleMarker: no visible binding for global variable
  'sample_id'
calcMediansBySampleMarker: no visible binding for global variable
  'marker_id'
calcMediansBySampleMarker: no visible binding for global variable
  'value'
Undefined global functions or variables:
  cluster_id marker_id sample_id value
* 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 (user + system) or elapsed time > 5s
            user system elapsed
diffcyt     8.46   0.45    8.91
testDA_GLMM 7.56   0.14    7.70
plotHeatmap 5.40   0.22    5.61
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
diffcyt     10.22   0.04   10.30
testDA_GLMM  9.78   0.02    9.79
plotHeatmap  6.66   0.05    6.72
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/diffcyt.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/diffcyt_1.14.0.tar.gz && rm -rf diffcyt.buildbin-libdir && mkdir diffcyt.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=diffcyt.buildbin-libdir diffcyt_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL diffcyt_1.14.0.zip && rm diffcyt_1.14.0.tar.gz diffcyt_1.14.0.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  187k  100  187k    0     0   397k      0 --:--:-- --:--:-- --:--:--  398k

install for i386

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

    calcMedians                             html  
    calcMediansByClusterMarker              html  
    calcMediansBySampleMarker               html  
    createContrast                          html  
    createDesignMatrix                      html  
    createFormula                           html  
    diffcyt                                 html  
    generateClusters                        html  
    plotHeatmap                             html  
    prepareData                             html  
    testDA_GLMM                             html  
    testDA_edgeR                            html  
    testDA_voom                             html  
    testDS_LMM                              html  
    testDS_limma                            html  
    topClusters                             html  
    topTable                                html  
    transformData                           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 'diffcyt' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'diffcyt' as diffcyt_1.14.0.zip
* DONE (diffcyt)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'diffcyt' successfully unpacked and MD5 sums checked


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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(diffcyt)
> 
> test_check("diffcyt")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
  10.50    1.09   11.57


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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(diffcyt)
> 
> test_check("diffcyt")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
   9.25    0.50    9.73

name	user	system	elapsed
calcCounts	2.16	0.16	2.31
calcMedians	1.79	0.11	1.91
calcMediansByClusterMarker	1.33	0.01	1.35
calcMediansBySampleMarker	1.14	0.02	1.15
createContrast	0	0	0
createDesignMatrix	0	0	0
createFormula	0	0	0
diffcyt	8.46	0.45	8.91
generateClusters	1.18	0.14	1.32
plotHeatmap	5.40	0.22	5.61
prepareData	0.03	0.00	0.03
testDA_GLMM	7.56	0.14	7.70
testDA_edgeR	1.27	0.03	1.30
testDA_voom	1.23	0.05	1.28
testDS_LMM	3.65	0.03	3.67
testDS_limma	1.93	0.09	2.04
topTable	3.77	0.05	3.84
transformData	0.06	0.00	0.06

name	user	system	elapsed
calcCounts	2.05	0.01	2.06
calcMedians	2.89	0.00	2.89
calcMediansByClusterMarker	1.71	0.02	1.74
calcMediansBySampleMarker	1.5	0.0	1.5
createContrast	0	0	0
createDesignMatrix	0.02	0.00	0.01
createFormula	0	0	0
diffcyt	10.22	0.04	10.30
generateClusters	1.37	0.00	1.37
plotHeatmap	6.66	0.05	6.72
prepareData	0.06	0.00	0.07
testDA_GLMM	9.78	0.02	9.79
testDA_edgeR	1.69	0.04	1.74
testDA_voom	1.66	0.02	1.67
testDS_LMM	4.69	0.00	4.69
testDS_limma	2.67	0.00	2.67
topTable	4.76	0.00	4.76
transformData	0.05	0.02	0.07

CHECK results for diffcyt on tokay2

Summary

Command output

Installation output

Tests output

Example timings