Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-11 12:04:56 -0400 (Mon, 11 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4323
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4136
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 conclus on nebbiolo2


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? 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 1.2.4  (landing page)
Ilyess Rachedi
Snapshot Date: 2022-04-10 01:55:06 -0400 (Sun, 10 Apr 2022)
git_url: https://git.bioconductor.org/packages/conclus
git_branch: RELEASE_3_14
git_last_commit: 4f3d751
git_last_commit_date: 2022-04-08 16:47:00 -0400 (Fri, 08 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  YES
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  YES
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  YES

Summary

Package: conclus
Version: 1.2.4
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:conclus.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings conclus_1.2.4.tar.gz
StartedAt: 2022-04-10 06:46:32 -0400 (Sun, 10 Apr 2022)
EndedAt: 2022-04-10 06:57:15 -0400 (Sun, 10 Apr 2022)
EllapsedTime: 642.7 seconds
RetCode: 0
Status:   OK  
CheckDir: conclus.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:conclus.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings conclus_1.2.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/conclus.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘conclus/DESCRIPTION’ ... OK
* this is package ‘conclus’ version ‘1.2.4’
* 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
retrieveFromGEO                  10.071  0.936  11.010
runCONCLUS                        9.807  0.801  83.770
retrieveGenesInfo-scRNAseq        4.960  0.449  62.876
addClustering-scRNAseq            4.775  0.317  46.825
normaliseCountMatrix-scRNAseq     2.960  0.220  14.826
testClustering-scRNAseq           0.666  0.020  14.911
runDBSCAN-scRNAseq                0.269  0.035  13.730
clusterCellsInternal-scRNAseq     0.240  0.049  13.364
generateTSNECoordinates-scRNAseq  0.195  0.028  18.301
* 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: OK


Installation output

conclus.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL conclus
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
Number of clusters k :  1  4 2 3
Count :                58 12 8 6

Statistics about number of clusters 'k' among dbscan solutions:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  1.000   1.000   1.000   1.667   2.000   4.000 

Suggested clusters number to use in clusterCellsInternal() : clusterNumber=1.[ FAIL 0 | WARN 0 | SKIP 0 | PASS 278 ]
> 
> proc.time()
   user  system elapsed 
 30.439   2.143 104.661 

Example timings

conclus.Rcheck/conclus-Ex.timings

nameusersystemelapsed
addClustering-scRNAseq 4.775 0.31746.825
calculateClustersSimilarity-scRNAseq0.0400.0120.052
clusterCellsInternal-scRNAseq 0.240 0.04913.364
conclusCacheClear0.0000.0000.001
constructors0.0140.0000.015
exportResults-scRNAseq0.1090.0080.117
generateTSNECoordinates-scRNAseq 0.195 0.02818.301
getters0.0120.0000.012
loadDataOrMatrix0.0090.0050.013
normaliseCountMatrix-scRNAseq 2.960 0.22014.826
plotCellHeatmap0.1670.0200.187
plotCellSimilarity-scRNAseq0.0810.0000.081
plotClusteredTSNE-scRNAseq0.3810.0070.389
plotClustersSimilarity0.0480.0080.056
plotGeneExpression-scRNAseq0.1760.0160.192
rankGenes-scRNAseq0.1730.0000.172
retrieveFromGEO10.071 0.93611.010
retrieveGenesInfo-scRNAseq 4.960 0.44962.876
retrieveTableClustersCells-scRNAseq0.0190.0000.020
retrieveTopClustersMarkers-scRNAseq0.0230.0000.023
runCONCLUS 9.807 0.80183.770
runDBSCAN-scRNAseq 0.269 0.03513.730
setters0.0170.0060.022
testClustering-scRNAseq 0.666 0.02014.911