Back to Multiple platform build/check report for BioC 3.14
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-01-14 13:06:12 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 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? 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 1.2.0  (landing page)
Ilyess Rachedi
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
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 20.04.4 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: conclus
Version: 1.2.0
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_1.2.0.tar.gz
StartedAt: 2022-01-13 17:33:40 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 17:52:55 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 1154.7 seconds
RetCode: 0
Status:   OK  
CheckDir: conclus.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/conclus.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.2.0'
* 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 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
runCONCLUS                       24.60   0.17   79.03
addClustering-scRNAseq           13.95   0.86   18.08
retrieveGenesInfo-scRNAseq       12.80   0.08   25.96
normaliseCountMatrix-scRNAseq    10.47   0.13   18.27
retrieveFromGEO                   9.09   0.51    9.76
testClustering-scRNAseq           1.16   0.05   16.64
clusterCellsInternal-scRNAseq     0.29   0.00   14.25
generateTSNECoordinates-scRNAseq  0.28   0.00   18.24
runDBSCAN-scRNAseq                0.23   0.00   13.53
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
runCONCLUS                       20.75   0.27   98.21
addClustering-scRNAseq            9.35   0.21   26.71
retrieveFromGEO                   8.64   0.05    8.68
retrieveGenesInfo-scRNAseq        8.01   0.03   16.64
normaliseCountMatrix-scRNAseq     7.72   0.06   24.66
testClustering-scRNAseq           0.97   0.08   18.33
runDBSCAN-scRNAseq                0.44   0.03   16.07
clusterCellsInternal-scRNAseq     0.28   0.05   14.64
generateTSNECoordinates-scRNAseq  0.17   0.02   18.31
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/conclus.Rcheck/00check.log'
for details.



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_1.2.0.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_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL conclus_1.2.0.zip && rm conclus_1.2.0.tar.gz conclus_1.2.0.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
100 1447k  100 1447k    0     0  3575k      0 --:--:-- --:--:-- --:--:-- 3582k

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_1.2.0.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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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.Error in textConnection(text, encoding = "UTF-8") : 
  invalid 'text' argument
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 279 ]
> 
> proc.time()
   user  system elapsed 
  57.85    2.37  159.32 

conclus.Rcheck/tests_x64/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-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.Error in textConnection(text, encoding = "UTF-8") : 
  invalid 'text' argument
Error : Unexpected format to the list of available marts.
Please check the following URL manually, and try ?listMarts for advice.
https://www.ensembl.org:443/biomart/martservice?type=registry&requestid=biomaRt
Error in textConnection(text, encoding = "UTF-8") : 
  invalid 'text' argument
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 279 ]
> 
> proc.time()
   user  system elapsed 
  53.14    1.65  184.98 

Example timings

conclus.Rcheck/examples_i386/conclus-Ex.timings

nameusersystemelapsed
addClustering-scRNAseq13.95 0.8618.08
calculateClustersSimilarity-scRNAseq0.080.000.08
clusterCellsInternal-scRNAseq 0.29 0.0014.25
conclusCacheClear000
constructors0.020.000.02
exportResults-scRNAseq0.230.030.40
generateTSNECoordinates-scRNAseq 0.28 0.0018.24
getters0.020.000.01
loadDataOrMatrix0.030.000.03
normaliseCountMatrix-scRNAseq10.47 0.1318.27
plotCellHeatmap0.20.00.2
plotCellSimilarity-scRNAseq0.080.000.08
plotClusteredTSNE-scRNAseq0.440.000.45
plotClustersSimilarity0.060.000.07
plotGeneExpression-scRNAseq0.190.000.18
rankGenes-scRNAseq0.170.000.18
retrieveFromGEO9.090.519.76
retrieveGenesInfo-scRNAseq12.80 0.0825.96
retrieveTableClustersCells-scRNAseq0.010.000.01
retrieveTopClustersMarkers-scRNAseq0.030.000.03
runCONCLUS24.60 0.1779.03
runDBSCAN-scRNAseq 0.23 0.0013.53
setters0.030.000.04
testClustering-scRNAseq 1.16 0.0516.64

conclus.Rcheck/examples_x64/conclus-Ex.timings

nameusersystemelapsed
addClustering-scRNAseq 9.35 0.2126.71
calculateClustersSimilarity-scRNAseq0.030.030.06
clusterCellsInternal-scRNAseq 0.28 0.0514.64
conclusCacheClear000
constructors0.030.000.03
exportResults-scRNAseq0.190.010.20
generateTSNECoordinates-scRNAseq 0.17 0.0218.31
getters0.030.000.03
loadDataOrMatrix0.010.000.02
normaliseCountMatrix-scRNAseq 7.72 0.0624.66
plotCellHeatmap0.140.020.15
plotCellSimilarity-scRNAseq0.080.000.08
plotClusteredTSNE-scRNAseq0.330.030.36
plotClustersSimilarity0.030.010.04
plotGeneExpression-scRNAseq0.180.000.19
rankGenes-scRNAseq0.160.000.16
retrieveFromGEO8.640.058.68
retrieveGenesInfo-scRNAseq 8.01 0.0316.64
retrieveTableClustersCells-scRNAseq0.030.000.03
retrieveTopClustersMarkers-scRNAseq0.030.000.03
runCONCLUS20.75 0.2798.21
runDBSCAN-scRNAseq 0.44 0.0316.07
setters0.030.000.03
testClustering-scRNAseq 0.97 0.0818.33