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CHECK report for DuoClustering2018 on riesling1

This page was generated on 2021-01-11 15:59:30 -0500 (Mon, 11 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE DuoClustering2018 PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 105/385HostnameOS / ArchINSTALLBUILDCHECK
DuoClustering2018 1.9.0
Angelo Duò
Snapshot Date: 2021-01-11 09:00:09 -0500 (Mon, 11 Jan 2021)
URL: https://git.bioconductor.org/packages/DuoClustering2018
Branch: master
Last Commit: bac06f0
Last Changed Date: 2020-10-27 10:27:19 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ]

Summary

Package: DuoClustering2018
Version: 1.9.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DuoClustering2018.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings DuoClustering2018_1.9.0.tar.gz
StartedAt: 2021-01-11 11:21:24 -0500 (Mon, 11 Jan 2021)
EndedAt: 2021-01-11 11:25:59 -0500 (Mon, 11 Jan 2021)
EllapsedTime: 274.4 seconds
RetCode: 0
Status:  OK  
CheckDir: DuoClustering2018.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DuoClustering2018.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings DuoClustering2018_1.9.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/DuoClustering2018.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DuoClustering2018/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DuoClustering2018' version '1.9.0'
* 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 '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
* 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
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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
sce_full_Koh 4.41   0.21    5.69
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
sce_full_Koh          4.51   0.23    5.06
clustering_summary_v1 3.91   0.75    5.17
* 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
  'D:/biocbuild/bbs-3.13-data-experiment/meat/DuoClustering2018.Rcheck/00check.log'
for details.



Installation output

DuoClustering2018.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/DuoClustering2018_1.9.0.tar.gz && rm -rf DuoClustering2018.buildbin-libdir && mkdir DuoClustering2018.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DuoClustering2018.buildbin-libdir DuoClustering2018_1.9.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL DuoClustering2018_1.9.0.zip && rm DuoClustering2018_1.9.0.tar.gz DuoClustering2018_1.9.0.zip
###
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install for i386

* installing *source* package 'DuoClustering2018' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DuoClustering2018'
    finding HTML links ... done
    DuoClustering2018                       html  
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    ari_df                                  html  
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    clustering_summary_v1                   html  
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    clustering_summary_v2                   html  
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    duo_clustering_all_parameter_settings_v1
                                            html  
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    plot_stability                          html  
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    plot_timing                             html  
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    shannon_entropy                         html  
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** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
snapshotDate(): 2021-01-07
** testing if installed package can be loaded from final location
snapshotDate(): 2021-01-07
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'DuoClustering2018' ...
** testing if installed package can be loaded
snapshotDate(): 2021-01-07
* MD5 sums
packaged installation of 'DuoClustering2018' as DuoClustering2018_1.9.0.zip
* DONE (DuoClustering2018)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'DuoClustering2018' successfully unpacked and MD5 sums checked

Tests output


Example timings

DuoClustering2018.Rcheck/examples_i386/DuoClustering2018-Ex.timings

nameusersystemelapsed
clustering_summary_v13.600.774.80
clustering_summary_v22.990.153.47
duo_clustering_all_parameter_settings_v12.010.152.55
duo_clustering_all_parameter_settings_v21.710.172.51
plot_entropy3.530.144.03
plot_k_diff2.860.123.43
plot_performance2.840.213.39
plot_stability3.470.093.99
plot_timing2.700.163.20
sce_full_Koh4.410.215.69
sce_full_Kumar2.300.253.47
sce_full_SimKumar2.780.224.43
sce_full_Trapnell2.260.193.47
sce_full_Zhengmix2.100.162.96

DuoClustering2018.Rcheck/examples_x64/DuoClustering2018-Ex.timings

nameusersystemelapsed
clustering_summary_v13.910.755.17
clustering_summary_v22.800.303.41
duo_clustering_all_parameter_settings_v11.790.202.59
duo_clustering_all_parameter_settings_v21.930.092.66
plot_entropy3.390.133.95
plot_k_diff2.750.173.55
plot_performance2.850.123.33
plot_stability3.510.113.99
plot_timing2.60.13.1
sce_full_Koh4.510.235.06
sce_full_Kumar2.140.202.64
sce_full_SimKumar3.390.214.02
sce_full_Trapnell2.020.062.39
sce_full_Zhengmix2.640.143.15