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This page was generated on 2021-10-21 15:52:03 -0400 (Thu, 21 Oct 2021).

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 104/406HostnameOS / ArchINSTALLBUILDCHECK
DuoClustering2018 1.11.0  (landing page)
Angelo Duò
Snapshot Date: 2021-10-21 09:30:01 -0400 (Thu, 21 Oct 2021)
git_url: https://git.bioconductor.org/packages/DuoClustering2018
git_branch: master
git_last_commit: c9d35a7
git_last_commit_date: 2021-05-19 12:05:28 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DuoClustering2018
Version: 1.11.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:DuoClustering2018.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings DuoClustering2018_1.11.0.tar.gz
StartedAt: 2021-10-21 12:16:00 -0400 (Thu, 21 Oct 2021)
EndedAt: 2021-10-21 12:19:21 -0400 (Thu, 21 Oct 2021)
EllapsedTime: 201.6 seconds
RetCode: 0
Status:   OK  
CheckDir: DuoClustering2018.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:DuoClustering2018.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings DuoClustering2018_1.11.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-data-experiment/meat/DuoClustering2018.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DuoClustering2018/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DuoClustering2018’ version ‘1.11.0’
* 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 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.14-data-experiment/meat/DuoClustering2018.Rcheck/00check.log’
for details.



Installation output

DuoClustering2018.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL DuoClustering2018
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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(): 2021-10-18
** testing if installed package can be loaded from final location
snapshotDate(): 2021-10-18
** 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_v13.7810.2084.172
clustering_summary_v22.8140.1643.083
duo_clustering_all_parameter_settings_v11.5840.0361.727
duo_clustering_all_parameter_settings_v21.5910.0241.720
plot_entropy3.5960.0683.764
plot_k_diff2.6950.0442.840
plot_performance2.5090.0442.661
plot_stability3.5000.0403.661
plot_timing2.8150.0442.976
sce_full_Koh4.5490.1244.797
sce_full_Kumar1.8790.1642.152
sce_full_SimKumar3.1580.1283.407
sce_full_Trapnell1.7350.0521.894
sce_full_Zhengmix2.7050.1002.955