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"	4266
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 5.435  0.068   5.504
* 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	0.006	0.003	0.011
PipelineDefinition	0.001	0.000	0.001
addPipelineStep	0.003	0.000	0.003
aggregatePipelineResults	1.118	0.061	1.295
buildCombMatrix	0.003	0.000	0.003
checkPipelinePackages	1.282	0.211	1.495
colCenterScale	0.001	0.000	0.002
dea_evalPlot_curve	0.832	0.100	0.933
dea_pipeline	0.003	0.000	0.002
evalHeatmap	3.117	0.124	3.242
evaluateClustering	0.01	0.00	0.01
evaluateDEA	0.067	0.000	0.067
evaluateDimRed	2.239	0.020	2.259
evaluateNorm	2.718	0.052	2.770
farthestPoint	0.008	0.000	0.007
getQualitativePalette	0.001	0.000	0.000
match_evaluate_multiple	0.002	0.002	0.003
mergePipelineResults	2.334	0.129	2.463
mockPipeline	0.002	0.000	0.001
parsePipNames	0.002	0.000	0.002
plotElapsed	0.718	0.000	0.718
readPipelineResults	1.085	0.012	1.097
runPipeline	1.059	0.008	1.066
scrna_evalPlot_filtering	0.52	0.00	0.52
scrna_evalPlot_overall	5.435	0.068	5.504
scrna_evalPlot_silh	1.020	0.008	1.028
scrna_pipeline	0.002	0.000	0.002

CHECK results for pipeComp on kunpeng1

Summary

Command output

Installation output

Tests output

Example timings