Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:08:16 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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

CHECK results for pipeComp on machv2


To the developers/maintainers of the pipeComp package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pipeComp.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1422/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pipeComp 1.4.0  (landing page)
Pierre-Luc Germain
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/pipeComp
git_branch: RELEASE_3_14
git_last_commit: 79b7c02
git_last_commit_date: 2021-10-26 13:00:42 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: pipeComp
Version: 1.4.0
Command: /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
StartedAt: 2022-01-20 16:25:08 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 16:32:46 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 458.5 seconds
RetCode: 0
Status:   OK  
CheckDir: pipeComp.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /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 4.1.2 (2021-11-01)
* 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 5.252  0.031    5.29
* 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

pipeComp.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL pipeComp
###
##############################################################################
##############################################################################


* 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

pipeComp.Rcheck/pipeComp-Ex.timings

nameusersystemelapsed
PipelineDefinition-methods0.0090.0010.010
PipelineDefinition0.0010.0000.002
addPipelineStep0.0040.0000.003
aggregatePipelineResults0.2010.0200.221
buildCombMatrix0.0030.0000.003
checkPipelinePackages1.9240.3752.302
colCenterScale0.0020.0010.002
dea_evalPlot_curve0.6650.0570.724
dea_pipeline0.0030.0010.003
evalHeatmap2.2580.0412.299
evaluateClustering0.0100.0020.012
evaluateDEA0.0410.0010.041
evaluateDimRed2.5790.0362.616
evaluateNorm2.8160.0452.865
farthestPoint0.0060.0010.007
getQualitativePalette0.0000.0000.001
match_evaluate_multiple0.0030.0010.004
mergePipelineResults0.3800.0320.412
mockPipeline0.0020.0000.001
parsePipNames0.0020.0000.003
plotElapsed0.5340.0020.537
readPipelineResults0.1050.0140.120
runPipeline0.1070.0150.163
scrna_evalPlot_filtering0.3830.0020.385
scrna_evalPlot_overall5.2520.0315.290
scrna_evalPlot_silh0.8670.0020.869
scrna_pipeline0.0020.0000.002