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This page was generated on 2023-04-11 14:50:26 -0400 (Tue, 11 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
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 DuoClustering2018 on nebbiolo2


To the developers/maintainers of the DuoClustering2018 package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 103/416HostnameOS / ArchINSTALLBUILDCHECK
DuoClustering2018 1.16.0  (landing page)
Angelo Duò
Snapshot Date: 2023-04-11 07:30:01 -0400 (Tue, 11 Apr 2023)
git_url: https://git.bioconductor.org/packages/DuoClustering2018
git_branch: RELEASE_3_16
git_last_commit: 509ec27
git_last_commit_date: 2022-11-01 11:19:26 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DuoClustering2018
Version: 1.16.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:DuoClustering2018.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings DuoClustering2018_1.16.0.tar.gz
StartedAt: 2023-04-11 11:42:10 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 11:47:39 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 329.5 seconds
RetCode: 0
Status:   OK  
CheckDir: DuoClustering2018.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:DuoClustering2018.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings DuoClustering2018_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-data-experiment/meat/DuoClustering2018.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘DuoClustering2018/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DuoClustering2018’ version ‘1.16.0’
* 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 ‘DuoClustering2018’ 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 loading without being on the library search path ... 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
ari_df: no visible binding for global variable ‘cell’
plot_entropy: no visible binding for global variable ‘dataset’
plot_entropy: no visible binding for global variable ‘method’
plot_entropy: no visible binding for global variable ‘run’
plot_entropy: no visible binding for global variable ‘k’
plot_entropy: no visible binding for global variable ‘cluster’
plot_entropy: no visible binding for global variable ‘trueclass’
plot_entropy: no visible binding for global variable ‘s’
plot_entropy: no visible binding for global variable ‘s.true’
plot_entropy: no visible binding for global variable ‘est_k’
plot_entropy: no visible binding for global variable ‘sce’
plot_entropy: no visible binding for global variable ‘filtering’
plot_entropy: no visible binding for global variable ‘truenclust’
plot_entropy: no visible binding for global variable ‘entropy’
plot_entropy: no visible binding for global variable ‘ARI’
plot_entropy: no visible binding for global variable ‘s.norm’
plot_entropy: no visible binding for global variable ‘s.true.norm’
plot_entropy: no visible binding for global variable ‘ds’
plot_entropy: no visible binding for global variable ‘ds.norm’
plot_k_diff: no visible binding for global variable ‘dataset’
plot_k_diff: no visible binding for global variable ‘method’
plot_k_diff: no visible binding for global variable ‘run’
plot_k_diff: no visible binding for global variable ‘k’
plot_k_diff: no visible binding for global variable ‘cluster’
plot_k_diff: no visible binding for global variable ‘trueclass’
plot_k_diff: no visible binding for global variable ‘est_k’
plot_k_diff: no visible binding for global variable ‘elapsed’
plot_k_diff: no visible binding for global variable ‘sce’
plot_k_diff: no visible binding for global variable ‘filtering’
plot_k_diff: no visible binding for global variable ‘truenclust’
plot_k_diff: no visible binding for global variable ‘ARI’
plot_k_diff: no visible binding for global variable ‘medARI’
plot_k_diff: no visible binding for global variable ‘k_diff’
plot_k_diff: no visible binding for global variable ‘estnclust’
plot_performance: no visible binding for global variable ‘dataset’
plot_performance: no visible binding for global variable ‘method’
plot_performance: no visible binding for global variable ‘run’
plot_performance: no visible binding for global variable ‘k’
plot_performance: no visible binding for global variable ‘cluster’
plot_performance: no visible binding for global variable ‘trueclass’
plot_performance: no visible binding for global variable ‘est_k’
plot_performance: no visible binding for global variable ‘elapsed’
plot_performance: no visible binding for global variable ‘sce’
plot_performance: no visible binding for global variable ‘filtering’
plot_performance: no visible binding for global variable ‘ARI’
plot_performance: no visible binding for global variable ‘truenclust’
plot_performance: no visible binding for global variable ‘medianARI’
plot_performance: no visible binding for global variable ‘estnclust’
plot_stability: no visible binding for global variable ‘dataset’
plot_stability: no visible binding for global variable ‘method’
plot_stability: no visible binding for global variable ‘k’
plot_stability: no visible binding for global variable ‘data.wide’
plot_stability: no visible binding for global variable ‘stability’
plot_stability: no visible binding for global variable ‘truenclust’
plot_stability: no visible binding for global variable ‘sce’
plot_stability: no visible binding for global variable ‘filtering’
plot_stability: no visible binding for global variable ‘ari.stab’
plot_stability: no visible binding for global variable
  ‘median.stability’
plot_timing: no visible binding for global variable ‘dataset’
plot_timing: no visible binding for global variable ‘method’
plot_timing: no visible binding for global variable ‘run’
plot_timing: no visible binding for global variable ‘k’
plot_timing: no visible binding for global variable ‘cluster’
plot_timing: no visible binding for global variable ‘trueclass’
plot_timing: no visible binding for global variable ‘est_k’
plot_timing: no visible binding for global variable ‘elapsed’
plot_timing: no visible binding for global variable ‘sce’
plot_timing: no visible binding for global variable ‘filtering’
plot_timing: no visible binding for global variable ‘truenclust’
plot_timing: no visible binding for global variable ‘median.elapsed’
plot_timing: no visible binding for global variable ‘med.t’
plot_timing: no visible binding for global variable ‘norm.time’
plot_timing: no visible binding for global variable ‘medianelapsed’
Undefined global functions or variables:
  ARI ari.stab cell cluster data.wide dataset ds ds.norm elapsed
  entropy est_k estnclust filtering k k_diff med.t medARI
  median.elapsed median.stability medianARI medianelapsed method
  norm.time run s s.norm s.true s.true.norm sce stability trueclass
  truenclust
* 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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘combine_data_clustering.Rmd’ using ‘UTF-8’... OK
  ‘plot_performance.Rmd’ using ‘UTF-8’... OK
  ‘run_clustering.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.16-data-experiment/meat/DuoClustering2018.Rcheck/00check.log’
for details.



Installation output

DuoClustering2018.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL DuoClustering2018
###
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘DuoClustering2018’ ...
** 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
snapshotDate(): 2022-10-31
** testing if installed package can be loaded from final location
snapshotDate(): 2022-10-31
** testing if installed package keeps a record of temporary installation path
* DONE (DuoClustering2018)

Tests output


Example timings

DuoClustering2018.Rcheck/DuoClustering2018-Ex.timings

nameusersystemelapsed
clustering_summary_v12.5770.3363.101
clustering_summary_v21.7480.2482.111
duo_clustering_all_parameter_settings_v10.5920.0960.774
duo_clustering_all_parameter_settings_v20.6290.1120.828
plot_entropy2.6330.2202.942
plot_k_diff1.9040.1242.117
plot_performance1.6260.0881.824
plot_stability2.7970.2283.114
plot_timing1.8660.1562.127
sce_full_Koh4.1270.3404.574
sce_full_Kumar1.2150.1751.479
sce_full_SimKumar2.4480.3602.897
sce_full_Trapnell1.0130.0771.186
sce_full_Zhengmix2.0380.2802.406