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This page was generated on 2024-05-04 11:39:39 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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

Package 1457/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
omada 1.6.0  (landing page)
Sokratis Kariotis
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/omada
git_branch: RELEASE_3_19
git_last_commit: c092c0f
git_last_commit_date: 2024-04-30 11:44:17 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for omada on lconway


To the developers/maintainers of the omada package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/omada.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: omada
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:omada.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings omada_1.6.0.tar.gz
StartedAt: 2024-05-03 23:42:00 -0400 (Fri, 03 May 2024)
EndedAt: 2024-05-03 23:55:41 -0400 (Fri, 03 May 2024)
EllapsedTime: 820.6 seconds
RetCode: 0
Status:   OK  
CheckDir: omada.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:omada.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings omada_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/omada.Rcheck’
* using R version 4.4.0 beta (2024-04-14 r86421)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘omada/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘omada’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'pdfCluster', 'kernlab', 'fpc', 'Rcpp', 'diceR', 'ggplot2',
  'reshape', 'genieclust', 'clValid', 'glmnet', 'dplyr'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘omada’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘clValid’
A package should be listed in only one of these fields.
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 ... NOTE
Packages in Depends field not imported from:
  ‘Rcpp’ ‘dplyr’ ‘genieclust’ ‘glmnet’ ‘kernlab’ ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Index.15and28: no visible global function definition for ‘dist’
Index.15and28: no visible global function definition for ‘as.dist’
Index.sPlussMoins: no visible global function definition for ‘dist’
Index.sPlussMoins: no visible global function definition for ‘as.dist’
Index.sPlussMoins: no visible global function definition for ‘median’
Indice.cindex: no visible global function definition for ‘dist’
clusterVoting: no visible global function definition for ‘calinhara’
clusterVoting: no visible global function definition for
  ‘generalised_dunn_index’
clusterVoting: no visible global function definition for
  ‘silhouette_index’
clusterVoting: no visible global function definition for
  ‘negated_davies_bouldin_index’
clusterVoting: no visible binding for global variable ‘k’
clusterVoting: no visible binding for global variable ‘Frequency’
clusteringMethodSelection: no visible binding for global variable
  ‘value’
clusteringMethodSelection: no visible binding for global variable
  ‘methods’
featureSelection: no visible binding for global variable ‘featureSet’
featureSelection: no visible binding for global variable ‘means’
Undefined global functions or variables:
  Frequency as.dist calinhara dist featureSet generalised_dunn_index k
  means median methods negated_davies_bouldin_index silhouette_index
  value
Consider adding
  importFrom("stats", "as.dist", "dist", "median")
  importFrom("utils", "methods")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                   user system elapsed
get_feature_selection_optimal_number_of_features 47.491  0.891  48.799
get_feature_selection_scores                     43.607  0.846  44.810
plot_partition_agreement                         38.255  1.195  64.700
plot_feature_selection                           36.109  0.957  58.048
get_sample_memberships                           31.304  5.077  45.609
get_partition_agreement_scores                   32.095  3.170  44.404
get_cluster_voting_k_votes                       32.274  0.614  33.157
get_cluster_voting_metric_votes                  31.834  0.628  32.761
get_cluster_voting_memberships                   31.316  0.587  32.193
get_feature_selection_optimal_features           30.244  0.550  31.045
get_cluster_voting_scores                        28.481  0.567  29.300
plot_cluster_voting                              27.749  0.612  37.652
omada                                            22.868  5.256  33.989
get_optimal_number_of_features                   11.318  0.152  11.536
get_optimal_features                             11.122  0.191  11.424
plot_average_stabilities                         10.232  0.189  10.526
get_optimal_memberships                           9.135  0.163   9.393
get_optimal_parameter_used                        8.906  0.130   9.095
get_optimal_stability_score                       8.766  0.133   8.946
featureSelection                                  7.474  0.114   7.630
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/omada.Rcheck/00check.log’
for details.


Installation output

omada.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL omada
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘omada’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (omada)

Tests output

omada.Rcheck/tests/testthat.Rout


R version 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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(omada)
Loading required package: pdfCluster
pdfCluster 1.0-4
Loading required package: kernlab
Loading required package: fpc
Loading required package: Rcpp
Loading required package: diceR
Loading required package: ggplot2

Attaching package: 'ggplot2'

The following object is masked from 'package:kernlab':

    alpha

Loading required package: reshape
Loading required package: genieclust
Loading required package: clValid
Loading required package: cluster
Loading required package: glmnet
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:reshape':

    expand

Loaded glmnet 4.1-8
Loading required package: dplyr

Attaching package: 'dplyr'

The following object is masked from 'package:reshape':

    rename

The following object is masked from 'package:pdfCluster':

    groups

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

> 
> test_check("omada")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 38 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 38 ]
> 
> proc.time()
   user  system elapsed 
 90.807   2.210  99.632 

Example timings

omada.Rcheck/omada-Ex.timings

nameusersystemelapsed
clusterVoting3.9800.5054.515
clusteringMethodSelection1.9620.0602.040
feasibilityAnalysis1.2900.0171.314
feasibilityAnalysisDataBased3.1630.0723.256
featureSelection7.4740.1147.630
get_agreement_scores0.1750.0020.179
get_average_feature_k_stabilities4.8020.0854.923
get_average_stabilities_per_k1.0180.0121.038
get_average_stability0.9960.0071.006
get_cluster_memberships_k0.8830.1231.012
get_cluster_voting_k_votes32.274 0.61433.157
get_cluster_voting_memberships31.316 0.58732.193
get_cluster_voting_metric_votes31.834 0.62832.761
get_cluster_voting_scores28.481 0.56729.300
get_feature_selection_optimal_features30.244 0.55031.045
get_feature_selection_optimal_number_of_features47.491 0.89148.799
get_feature_selection_scores43.607 0.84644.810
get_generated_dataset3.0620.0333.124
get_internal_metric_scores0.9090.1151.034
get_max_stability1.0250.0161.051
get_metric_votes_k1.110.121.24
get_optimal_features11.122 0.19111.424
get_optimal_memberships9.1350.1639.393
get_optimal_number_of_features11.318 0.15211.536
get_optimal_parameter_used8.9060.1309.095
get_optimal_stability_score8.7660.1338.946
get_partition_agreement_scores32.095 3.17044.404
get_sample_memberships31.304 5.07745.609
get_vote_frequencies_k0.9220.1361.072
omada22.868 5.25633.989
optimalClustering0.0910.0050.097
partitionAgreement0.3520.0080.366
plot_average_stabilities10.232 0.18910.526
plot_cluster_voting27.749 0.61237.652
plot_feature_selection36.109 0.95758.048
plot_partition_agreement38.255 1.19564.700
plot_vote_frequencies1.2620.1312.494
toy_gene_memberships0.0190.0070.050
toy_genes0.0020.0030.005