Build/check report for BioC 3.17 - CHECK results for pipeComp on kunpeng1

Hostname	OS	Arch (*)	R version	Installed pkgs
kunpeng1	Linux (Ubuntu 22.04.1 LTS)	aarch64	R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"	4039
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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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:pipeComp.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings pipeComp_1.9.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/pipeComp.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘pipeComp/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pipeComp’ version ‘1.9.0’
* 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 5.618      0   7.017
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘pipeComp.Rmd’ using ‘UTF-8’... OK
  ‘pipeComp_dea.Rmd’ using ‘UTF-8’... OK
  ‘pipeComp_scRNA.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/pipeComp.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL pipeComp
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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	0.01	0.00	0.01
PipelineDefinition	0.002	0.000	0.001
addPipelineStep	0.003	0.000	0.004
aggregatePipelineResults	1.194	0.018	1.641
buildCombMatrix	0.004	0.000	0.003
checkPipelinePackages	1.253	0.152	1.926
colCenterScale	0.000	0.002	0.002
dea_evalPlot_curve	0.873	0.077	1.125
dea_pipeline	0.002	0.000	0.002
evalHeatmap	3.165	0.008	3.860
evaluateClustering	0.003	0.007	0.010
evaluateDEA	0.064	0.004	0.067
evaluateDimRed	2.273	0.016	2.672
evaluateNorm	2.689	0.004	3.272
farthestPoint	0.007	0.000	0.007
getQualitativePalette	0	0	0
match_evaluate_multiple	0.004	0.000	0.020
mergePipelineResults	2.318	0.020	2.747
mockPipeline	0.002	0.000	0.001
parsePipNames	0.002	0.000	0.002
plotElapsed	0.708	0.004	0.763
readPipelineResults	1.069	0.016	1.262
runPipeline	1.031	0.012	1.173
scrna_evalPlot_filtering	0.529	0.000	0.566
scrna_evalPlot_overall	5.618	0.000	7.017
scrna_evalPlot_silh	1.061	0.000	1.159
scrna_pipeline	0.002	0.000	0.003

CHECK results for pipeComp on kunpeng1

Summary

Command output

Installation output

Tests output

Example timings