Package: DuoClustering2018

Version: 1.0.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:DuoClustering2018.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings DuoClustering2018_1.0.0.tar.gz

StartedAt: 2019-04-16 13:38:47 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 13:42:23 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 215.8 seconds

RetCode: 0

Status:  OK

CheckDir: DuoClustering2018.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:DuoClustering2018.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings DuoClustering2018_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-data-experiment/meat/DuoClustering2018.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.0.0’
* 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
Examples with CPU or elapsed time > 5s
                    user system elapsed
sce_full_SimKumar 11.400  0.652  14.919
sce_full_Zhengmix 10.928  0.908  12.004
* 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-3.8-data-experiment/meat/DuoClustering2018.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL DuoClustering2018
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘DuoClustering2018’ ...
** 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
snapshotDate(): 2018-10-30
* DONE (DuoClustering2018)

name	user	system	elapsed
clustering_summary_v1	1.952	0.184	2.407
clustering_summary_v2	1.712	0.176	1.966
duo_clustering_all_parameter_settings_v1	0.352	0.024	0.474
duo_clustering_all_parameter_settings_v2	0.432	0.028	0.544
plot_entropy	3.000	0.028	3.109
plot_k_diff	1.852	0.012	2.009
plot_performance	1.632	0.012	1.741
plot_stability	3.112	0.012	3.224
plot_timing	2.116	0.052	2.278
sce_full_Koh	4.296	0.176	4.784
sce_full_Kumar	0.672	0.036	0.815
sce_full_SimKumar	11.400	0.652	14.919
sce_full_Trapnell	2.256	0.180	2.809
sce_full_Zhengmix	10.928	0.908	12.004