Multiple platform build/check report for BioC 3.14 - CHECK results for pipeComp on machv2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
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*

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pipeComp.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pipeComp_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/pipeComp.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pipeComp/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pipeComp’ version ‘1.4.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘pipeComp’ 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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
* 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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.compileExcludedCells’ ‘.getMM’ ‘.homogenizeDEA’ ‘.runf’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
scrna_describeDatasets: no visible binding for global variable
  ‘cluster’
scrna_describeDatasets: no visible binding for global variable ‘nb’
scrna_describeDatasets : pf: no visible binding for global variable
  ‘.x’
scrna_describeDatasets : rd: no visible binding for global variable ‘y’
scrna_describeDatasets : rd: no visible binding for global variable
  ‘cluster’
scrna_evalPlot_filtering: no visible binding for global variable
  ‘max.lost’
scrna_evalPlot_filtering: no visible binding for global variable
  ‘mean_F1’
scrna_evalPlot_filtering: no visible binding for global variable ‘filt’
scrna_evalPlot_filtering: no visible binding for global variable
  ‘doubletmethod’
scrna_evalPlot_filtering: no visible binding for global variable
  ‘method’
scrna_evalPlot_overall: no visible binding for global variable
  ‘true.nbClusts’
scrna_evalPlot_overall: no visible binding for global variable ‘n_clus’
Undefined global functions or variables:
  .x cluster doubletmethod filt max.lost mean_F1 method n_clus nb
  true.nbClusts y
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
scrna_evalPlot_overall 5.376  0.039   5.421
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/pipeComp.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL pipeComp
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘pipeComp’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (pipeComp)

Tests output

Example timings

name	user	system	elapsed
PipelineDefinition-methods	0.009	0.001	0.010
PipelineDefinition	0.002	0.000	0.002
addPipelineStep	0.003	0.000	0.003
aggregatePipelineResults	0.202	0.019	0.222
buildCombMatrix	0.003	0.000	0.003
checkPipelinePackages	1.977	0.366	2.345
colCenterScale	0.002	0.000	0.002
dea_evalPlot_curve	0.675	0.060	0.735
dea_pipeline	0.003	0.001	0.003
evalHeatmap	2.307	0.026	2.340
evaluateClustering	0.010	0.002	0.011
evaluateDEA	0.042	0.001	0.042
evaluateDimRed	2.681	0.035	2.718
evaluateNorm	3.054	0.051	3.105
farthestPoint	0.006	0.001	0.008
getQualitativePalette	0	0	0
match_evaluate_multiple	0.003	0.000	0.004
mergePipelineResults	0.428	0.040	0.468
mockPipeline	0.001	0.000	0.001
parsePipNames	0.002	0.000	0.002
plotElapsed	0.533	0.003	0.537
readPipelineResults	0.116	0.020	0.136
runPipeline	0.115	0.019	0.134
scrna_evalPlot_filtering	0.422	0.005	0.429
scrna_evalPlot_overall	5.376	0.039	5.421
scrna_evalPlot_silh	0.856	0.003	0.860
scrna_pipeline	0.002	0.000	0.003

CHECK results for pipeComp on machv2

Summary

Command output

Installation output

Tests output

Example timings