Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:06:22 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
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" 4137
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 tokay2


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: 2022-04-12 01:55:07 -0400 (Tue, 12 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    ERROR  skipped
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: 1.2.4
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:conclus.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings conclus_1.2.4.tar.gz
StartedAt: 2022-04-12 17:48:07 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 18:08:36 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 1228.5 seconds
RetCode: 0
Status:   OK  
CheckDir: conclus.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:conclus.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings conclus_1.2.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/conclus.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
runCONCLUS                       19.48   0.28   99.75
addClustering-scRNAseq           11.44   0.64   49.70
retrieveGenesInfo-scRNAseq        9.92   0.14   60.19
normaliseCountMatrix-scRNAseq     9.28   0.05   23.13
retrieveFromGEO                   8.68   0.58    9.53
testClustering-scRNAseq           1.00   0.02   16.79
clusterCellsInternal-scRNAseq     0.37   0.06   14.46
runDBSCAN-scRNAseq                0.28   0.01   14.69
generateTSNECoordinates-scRNAseq  0.20   0.00   18.99
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
runCONCLUS                       20.83   0.17   93.86
addClustering-scRNAseq            9.98   0.45   28.21
retrieveFromGEO                   9.98   0.19   10.17
retrieveGenesInfo-scRNAseq        9.58   0.14   21.69
normaliseCountMatrix-scRNAseq     7.31   0.06   20.86
testClustering-scRNAseq           1.00   0.04   19.94
runDBSCAN-scRNAseq                0.50   0.01   17.01
clusterCellsInternal-scRNAseq     0.33   0.03   16.45
generateTSNECoordinates-scRNAseq  0.25   0.00   22.03
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R'
 OK
** running tests for arch 'x64' ...
  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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/conclus_1.2.4.tar.gz && rm -rf conclus.buildbin-libdir && mkdir conclus.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=conclus.buildbin-libdir conclus_1.2.4.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL conclus_1.2.4.zip && rm conclus_1.2.4.tar.gz conclus_1.2.4.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0 1448k    0  5187    0     0  62930      0  0:00:23 --:--:--  0:00:23 63256
 91 1448k   91 1318k    0     0  1220k      0  0:00:01  0:00:01 --:--:-- 1220k
100 1448k  100 1448k    0     0  1255k      0  0:00:01  0:00:01 --:--:-- 1255k

install for i386

* installing *source* package 'conclus' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'conclus'
    finding HTML links ... done
    Dbscan-class                            html  
    Tsne-class                              html  
    addClustering-scRNAseq                  html  
    calculateClustersSimilarity-scRNAseq    html  
    clusterCellsInternal-scRNAseq           html  
    conclusCacheClear                       html  
    constructors                            html  
    exportResults-scRNAseq                  html  
    generateTSNECoordinates-scRNAseq        html  
    getters                                 html  
    loadDataOrMatrix                        html  
    normaliseCountMatrix-scRNAseq           html  
    plotCellHeatmap                         html  
    plotCellSimilarity-scRNAseq             html  
    plotClusteredTSNE-scRNAseq              html  
    plotClustersSimilarity                  html  
    plotGeneExpression-scRNAseq             html  
    rankGenes-scRNAseq                      html  
    retrieveFromGEO                         html  
    retrieveGenesInfo-scRNAseq              html  
    retrieveTableClustersCells-scRNAseq     html  
    retrieveTopClustersMarkers-scRNAseq     html  
    runCONCLUS                              html  
    runDBSCAN-scRNAseq                      html  
    scRNAseq-class                          html  
    setters                                 html  
    testClustering-scRNAseq                 html  
** 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

install for x64

* installing *source* package 'conclus' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'conclus' as conclus_1.2.4.zip
* DONE (conclus)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'conclus' successfully unpacked and MD5 sums checked

Tests output

conclus.Rcheck/tests_i386/test-all.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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  3 4 5
Count :                56 10 10 4 4

Statistics about number of clusters 'k' among dbscan solutions:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   1.00    1.00    1.00    1.69    2.00    5.00 

Suggested clusters number to use in clusterCellsInternal() : clusterNumber=1.[ FAIL 0 | WARN 0 | SKIP 0 | PASS 278 ]
> 
> proc.time()
   user  system elapsed 
  59.28    1.98  144.82 

conclus.Rcheck/tests_x64/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-w64-mingw32/x64 (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  3 4 5
Count :                56 10 10 4 4

Statistics about number of clusters 'k' among dbscan solutions:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   1.00    1.00    1.00    1.69    2.00    5.00 

Suggested clusters number to use in clusterCellsInternal() : clusterNumber=1.[ FAIL 0 | WARN 0 | SKIP 0 | PASS 278 ]
> 
> proc.time()
   user  system elapsed 
  50.57    1.56  145.25 

Example timings

conclus.Rcheck/examples_i386/conclus-Ex.timings

nameusersystemelapsed
addClustering-scRNAseq11.44 0.6449.70
calculateClustersSimilarity-scRNAseq0.060.060.13
clusterCellsInternal-scRNAseq 0.37 0.0614.46
conclusCacheClear000
constructors0.040.000.03
exportResults-scRNAseq0.250.050.40
generateTSNECoordinates-scRNAseq 0.20 0.0018.99
getters0.010.000.01
loadDataOrMatrix0.020.000.02
normaliseCountMatrix-scRNAseq 9.28 0.0523.13
plotCellHeatmap0.140.010.15
plotCellSimilarity-scRNAseq0.10.00.1
plotClusteredTSNE-scRNAseq0.390.020.42
plotClustersSimilarity0.060.000.06
plotGeneExpression-scRNAseq0.150.000.16
rankGenes-scRNAseq0.150.000.14
retrieveFromGEO8.680.589.53
retrieveGenesInfo-scRNAseq 9.92 0.1460.19
retrieveTableClustersCells-scRNAseq0.040.000.03
retrieveTopClustersMarkers-scRNAseq0.030.000.03
runCONCLUS19.48 0.2899.75
runDBSCAN-scRNAseq 0.28 0.0114.69
setters0.030.000.03
testClustering-scRNAseq 1.00 0.0216.79

conclus.Rcheck/examples_x64/conclus-Ex.timings

nameusersystemelapsed
addClustering-scRNAseq 9.98 0.4528.21
calculateClustersSimilarity-scRNAseq0.070.020.07
clusterCellsInternal-scRNAseq 0.33 0.0316.45
conclusCacheClear000
constructors0.030.000.03
exportResults-scRNAseq0.190.030.22
generateTSNECoordinates-scRNAseq 0.25 0.0022.03
getters0.010.000.02
loadDataOrMatrix0.020.000.01
normaliseCountMatrix-scRNAseq 7.31 0.0620.86
plotCellHeatmap0.150.020.17
plotCellSimilarity-scRNAseq0.150.000.14
plotClusteredTSNE-scRNAseq0.370.000.38
plotClustersSimilarity0.060.000.06
plotGeneExpression-scRNAseq0.190.000.19
rankGenes-scRNAseq0.250.000.25
retrieveFromGEO 9.98 0.1910.17
retrieveGenesInfo-scRNAseq 9.58 0.1421.69
retrieveTableClustersCells-scRNAseq0.030.000.03
retrieveTopClustersMarkers-scRNAseq0.050.000.05
runCONCLUS20.83 0.1793.86
runDBSCAN-scRNAseq 0.50 0.0117.01
setters0.030.000.03
testClustering-scRNAseq 1.00 0.0419.94