Multiple platform build/check report for BioC 3.12 - CHECK report for MetaNeighbor on tokay1

Package: MetaNeighbor

Version: 1.10.0

Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MetaNeighbor.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MetaNeighbor_1.10.0.tar.gz

StartedAt: 2021-05-06 04:26:33 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 04:30:59 -0400 (Thu, 06 May 2021)

EllapsedTime: 265.9 seconds

RetCode: 0

Status: OK

CheckDir: MetaNeighbor.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MetaNeighbor.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MetaNeighbor_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/MetaNeighbor.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MetaNeighbor/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MetaNeighbor' version '1.10.0'
* 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 'MetaNeighbor' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
* 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
MetaNeighbor : <anonymous>: no visible binding for global variable
  'cell_type'
plotDotPlot: no visible binding for global variable 'cluster'
plotDotPlot: no visible binding for global variable 'gene'
plotDotPlot: no visible binding for global variable 'cell_type'
plotDotPlot: no visible binding for global variable
  'average_expression'
plotDotPlot: no visible binding for global variable
  'percent_expressing'
Undefined global functions or variables:
  average_expression cell_type cluster gene percent_expressing
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
MetaNeighbor   30.25   1.33   31.58
plotBPlot      22.86   0.52   23.37
neighborVoting 23.00   0.23   23.23
topHits         5.19   0.17    5.36
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
MetaNeighbor   25.82   0.91   26.71
neighborVoting 15.96   0.37   16.35
plotBPlot      15.50   0.39   15.89
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/MetaNeighbor.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/MetaNeighbor_1.10.0.tar.gz && rm -rf MetaNeighbor.buildbin-libdir && mkdir MetaNeighbor.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MetaNeighbor.buildbin-libdir MetaNeighbor_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL MetaNeighbor_1.10.0.zip && rm MetaNeighbor_1.10.0.tar.gz MetaNeighbor_1.10.0.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 2631k  100 2631k    0     0  35.7M      0 --:--:-- --:--:-- --:--:-- 36.7M

install for i386

* installing *source* package 'MetaNeighbor' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MetaNeighbor'
    finding HTML links ... done
    GOhuman                                 html  
    GOmouse                                 html  
    MetaNeighbor                            html  
    MetaNeighborUS                          html  
    extendClusterSet                        html  
    extractMetaClusters                     html  
    getCellType                             html  
    getStudyId                              html  
    makeClusterGraph                        html  
    makeClusterName                         html  
    mergeSCE                                html  
    mn_data                                 html  
    neighborVoting                          html  
    plotBPlot                               html  
    plotClusterGraph                        html  
    plotDotPlot                             html  
    plotHeatmap                             html  
    plotHeatmapPretrained                   html  
    plotMetaClusters                        html  
    plotUpset                               html  
    scoreMetaClusters                       html  
    splitClusters                           html  
    splitTestClusters                       html  
    splitTrainClusters                      html  
    standardizeLabel                        html  
    subsetClusterGraph                      html  
    topHits                                 html  
    trainModel                              html  
    variableGenes                           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 'MetaNeighbor' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MetaNeighbor' as MetaNeighbor_1.10.0.zip
* DONE (MetaNeighbor)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'MetaNeighbor' successfully unpacked and MD5 sums checked


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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(MetaNeighbor)
> 
> test_check("MetaNeighbor")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
   0.43    0.09    0.51


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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(MetaNeighbor)
> 
> test_check("MetaNeighbor")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
   0.50    0.12    0.60

name	user	system	elapsed
MetaNeighbor	30.25	1.33	31.58
MetaNeighborUS	4.06	0.44	4.50
neighborVoting	23.00	0.23	23.23
plotBPlot	22.86	0.52	23.37
plotHeatmap	4.37	0.12	4.55
plotHeatmapPretrained	3.5	0.1	3.6
plotUpset	3.52	0.45	3.96
topHits	5.19	0.17	5.36
trainModel	0.89	0.06	0.96
variableGenes	1.32	0.14	1.46

name	user	system	elapsed
MetaNeighbor	25.82	0.91	26.71
MetaNeighborUS	3.98	0.19	4.18
neighborVoting	15.96	0.37	16.35
plotBPlot	15.50	0.39	15.89
plotHeatmap	2.77	0.13	2.89
plotHeatmapPretrained	3.22	0.09	3.31
plotUpset	1.72	0.16	1.87
topHits	4.08	0.11	4.19
trainModel	1.51	0.11	1.63
variableGenes	0.59	0.11	0.71

CHECK report for MetaNeighbor on tokay1

Summary

Command output

Installation output

Tests output

Example timings