Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-23 14:06:55 -0400 (Sat, 23 Oct 2021).

CHECK results for conclus on merida1

To the developers/maintainers of the conclus package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/conclus.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 382/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
conclus 1.1.002  (landing page)
Ilyess Rachedi
Snapshot Date: 2021-10-22 14:50:11 -0400 (Fri, 22 Oct 2021)
git_url: https://git.bioconductor.org/packages/conclus
git_branch: master
git_last_commit: 9f01658
git_last_commit_date: 2021-08-31 07:26:43 -0400 (Tue, 31 Aug 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: conclus
Version: 1.1.002
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:conclus.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings conclus_1.1.002.tar.gz
StartedAt: 2021-10-23 02:18:44 -0400 (Sat, 23 Oct 2021)
EndedAt: 2021-10-23 02:31:15 -0400 (Sat, 23 Oct 2021)
EllapsedTime: 751.1 seconds
RetCode: 0
Status:   OK  
CheckDir: conclus.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:conclus.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings conclus_1.1.002.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/conclus.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘conclus/DESCRIPTION’ ... OK
* this is package ‘conclus’ version ‘1.1.002’
* 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 ‘conclus’ 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 ... 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
* 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
.retrieveClustersNumberK: no visible global function definition for
  ‘median’
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
runCONCLUS                       15.879  0.229  93.355
retrieveFromGEO                  12.297  0.243  12.555
addClustering-scRNAseq            7.692  0.159  13.758
retrieveGenesInfo-scRNAseq        5.896  0.110  13.878
normaliseCountMatrix-scRNAseq     5.424  0.149   9.358
testClustering-scRNAseq           1.358  0.042  23.081
runDBSCAN-scRNAseq                0.451  0.017  20.781
clusterCellsInternal-scRNAseq     0.358  0.017  20.965
generateTSNECoordinates-scRNAseq  0.263  0.043  27.029
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/conclus.Rcheck/00check.log’
for details.



Installation output

conclus.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL conclus
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘conclus’ ...
** using staged installation
** R
** 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 (conclus)

Tests output

conclus.Rcheck/tests/test-all.Rout


R version 4.1.1 Patched (2021-08-22 r80813) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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("conclus")
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

> test_check("conclus")
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      1       1       1       1       1       1 
The following matrix shows how many times a number of clusters 'k' has been found among the dbscan solutions :
                        1  2  3 4 5
Number of clusters k :  1  2  4 5 3
Count :                50 12 12 6 4

Statistics about number of clusters 'k' among dbscan solutions:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  1.000   1.000   1.000   1.952   3.000   5.000 

Suggested clusters number to use in clusterCellsInternal() : clusterNumber=1.[ FAIL 0 | WARN 0 | SKIP 0 | PASS 279 ]
> 
> proc.time()
   user  system elapsed 
 45.238   1.440 145.881 

Example timings

conclus.Rcheck/conclus-Ex.timings

nameusersystemelapsed
addClustering-scRNAseq 7.692 0.15913.758
calculateClustersSimilarity-scRNAseq0.0650.0010.065
clusterCellsInternal-scRNAseq 0.358 0.01720.965
conclusCacheClear000
constructors0.0230.0020.026
exportResults-scRNAseq0.1890.0230.213
generateTSNECoordinates-scRNAseq 0.263 0.04327.029
getters0.0160.0030.019
loadDataOrMatrix0.0130.0040.017
normaliseCountMatrix-scRNAseq5.4240.1499.358
plotCellHeatmap0.1550.0040.160
plotCellSimilarity-scRNAseq0.1370.0020.141
plotClusteredTSNE-scRNAseq0.6290.0100.645
plotClustersSimilarity0.0860.0010.088
plotGeneExpression-scRNAseq0.2510.0020.253
rankGenes-scRNAseq0.2330.0010.235
retrieveFromGEO12.297 0.24312.555
retrieveGenesInfo-scRNAseq 5.896 0.11013.878
retrieveTableClustersCells-scRNAseq0.0310.0000.031
retrieveTopClustersMarkers-scRNAseq0.0320.0000.032
runCONCLUS15.879 0.22993.355
runDBSCAN-scRNAseq 0.451 0.01720.781
setters0.0270.0020.029
testClustering-scRNAseq 1.358 0.04223.081