Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-11-26 15:04:48 -0500 (Fri, 26 Nov 2021).

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? here for more information.
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raw results

Package 382/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
conclus 1.2.0  (landing page)
Ilyess Rachedi
Snapshot Date: 2021-11-25 04:15:05 -0500 (Thu, 25 Nov 2021)
git_url: https://git.bioconductor.org/packages/conclus
git_branch: RELEASE_3_14
git_last_commit: 6bc832f
git_last_commit_date: 2021-10-26 13:08:31 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 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: conclus
Version: 1.2.0
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_1.2.0.tar.gz
StartedAt: 2021-11-25 08:55:01 -0500 (Thu, 25 Nov 2021)
EndedAt: 2021-11-25 09:03:39 -0500 (Thu, 25 Nov 2021)
EllapsedTime: 518.3 seconds
RetCode: 0
Status:   OK  
CheckDir: conclus.Rcheck
Warnings: 0

Command output

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### Running 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_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/conclus.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.2.0’
* 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 ‘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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
runCONCLUS                       9.869  0.265  60.536
retrieveFromGEO                  9.238  0.216   9.458
addClustering-scRNAseq           5.031  0.296   9.598
retrieveGenesInfo-scRNAseq       3.296  0.060   9.165
normaliseCountMatrix-scRNAseq    3.100  0.196   6.185
testClustering-scRNAseq          0.635  0.007  15.140
runDBSCAN-scRNAseq               0.259  0.008  14.616
clusterCellsInternal-scRNAseq    0.230  0.028  13.368
generateTSNECoordinates-scRNAseq 0.154  0.058  18.049
* 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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/conclus.Rcheck/00check.log’
for details.



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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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 279 ]
> 
> proc.time()
   user  system elapsed 
 30.763   2.468  90.043 

Example timings

conclus.Rcheck/conclus-Ex.timings

nameusersystemelapsed
addClustering-scRNAseq5.0310.2969.598
calculateClustersSimilarity-scRNAseq0.0400.0000.041
clusterCellsInternal-scRNAseq 0.230 0.02813.368
conclusCacheClear000
constructors0.0150.0000.015
exportResults-scRNAseq0.0980.0200.118
generateTSNECoordinates-scRNAseq 0.154 0.05818.049
getters0.0090.0000.009
loadDataOrMatrix0.0090.0000.009
normaliseCountMatrix-scRNAseq3.1000.1966.185
plotCellHeatmap0.0950.0000.096
plotCellSimilarity-scRNAseq0.0760.0000.076
plotClusteredTSNE-scRNAseq0.3450.0200.365
plotClustersSimilarity0.0530.0000.053
plotGeneExpression-scRNAseq0.1640.0000.164
rankGenes-scRNAseq0.1360.0080.144
retrieveFromGEO9.2380.2169.458
retrieveGenesInfo-scRNAseq3.2960.0609.165
retrieveTableClustersCells-scRNAseq0.0160.0000.016
retrieveTopClustersMarkers-scRNAseq0.0230.0000.023
runCONCLUS 9.869 0.26560.536
runDBSCAN-scRNAseq 0.259 0.00814.616
setters0.0150.0000.015
testClustering-scRNAseq 0.635 0.00715.140