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This page was generated on 2024-06-25 11:38 -0400 (Tue, 25 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4690
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4404
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4353
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 1418/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
omada 1.7.0  (landing page)
Sokratis Kariotis
Snapshot Date: 2024-06-24 14:00 -0400 (Mon, 24 Jun 2024)
git_url: https://git.bioconductor.org/packages/omada
git_branch: devel
git_last_commit: 3d3c329
git_last_commit_date: 2024-04-30 11:44:17 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  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
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for omada on nebbiolo2

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: 1.7.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:omada.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings omada_1.7.0.tar.gz
StartedAt: 2024-06-25 01:48:37 -0400 (Tue, 25 Jun 2024)
EndedAt: 2024-06-25 02:11:10 -0400 (Tue, 25 Jun 2024)
EllapsedTime: 1353.1 seconds
RetCode: 0
Status:   OK  
CheckDir: omada.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:omada.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings omada_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/omada.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘omada/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘omada’ version ‘1.7.0’
* 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 loading without being on the library search path ... 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 68.829  0.215  75.328
get_feature_selection_scores                     65.732  0.120  67.985
get_partition_agreement_scores                   51.755  0.372  52.546
plot_partition_agreement                         49.384  0.211  54.343
plot_feature_selection                           47.502  0.407  49.502
get_sample_memberships                           45.095  0.897  48.155
plot_cluster_voting                              44.221  1.525  54.512
get_cluster_voting_k_votes                       44.710  0.212  45.156
get_feature_selection_optimal_features           44.592  0.112  44.847
get_cluster_voting_metric_votes                  41.140  0.120  41.420
get_cluster_voting_scores                        40.854  0.112  41.047
get_cluster_voting_memberships                   40.785  0.176  41.138
omada                                            35.547  0.848  37.369
get_optimal_features                             15.361  0.375  15.737
plot_average_stabilities                         15.263  0.151  16.678
get_optimal_memberships                          14.735  0.300  15.036
get_optimal_number_of_features                   14.376  0.347  14.732
get_optimal_parameter_used                       13.711  0.276  15.427
get_optimal_stability_score                      13.705  0.220  14.024
featureSelection                                 10.210  0.084  10.296
get_average_feature_k_stabilities                 6.766  0.020   6.811
clusterVoting                                     5.767  0.116   5.883
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/omada.Rcheck/00check.log’
for details.


Installation output

omada.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL omada
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 1 | SKIP 0 | PASS 38 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 38 ]
> 
> proc.time()
   user  system elapsed 
138.095   1.296 159.307 

Example timings

omada.Rcheck/omada-Ex.timings

nameusersystemelapsed
clusterVoting5.7670.1165.883
clusteringMethodSelection2.2990.0522.360
feasibilityAnalysis1.9190.0201.939
feasibilityAnalysisDataBased4.0110.0884.099
featureSelection10.210 0.08410.296
get_agreement_scores0.2370.0000.237
get_average_feature_k_stabilities6.7660.0206.811
get_average_stabilities_per_k1.2860.0041.348
get_average_stability1.2340.0041.238
get_cluster_memberships_k1.1670.0921.259
get_cluster_voting_k_votes44.710 0.21245.156
get_cluster_voting_memberships40.785 0.17641.138
get_cluster_voting_metric_votes41.14 0.1241.42
get_cluster_voting_scores40.854 0.11241.047
get_feature_selection_optimal_features44.592 0.11244.847
get_feature_selection_optimal_number_of_features68.829 0.21575.328
get_feature_selection_scores65.732 0.12067.985
get_generated_dataset4.5670.0004.583
get_internal_metric_scores1.1900.0121.201
get_max_stability1.3430.0001.349
get_metric_votes_k1.0760.0521.128
get_optimal_features15.361 0.37515.737
get_optimal_memberships14.735 0.30015.036
get_optimal_number_of_features14.376 0.34714.732
get_optimal_parameter_used13.711 0.27615.427
get_optimal_stability_score13.705 0.22014.024
get_partition_agreement_scores51.755 0.37252.546
get_sample_memberships45.095 0.89748.155
get_vote_frequencies_k1.3040.0121.365
omada35.547 0.84837.369
optimalClustering0.1200.0040.124
partitionAgreement0.5020.0120.514
plot_average_stabilities15.263 0.15116.678
plot_cluster_voting44.221 1.52554.512
plot_feature_selection47.502 0.40749.502
plot_partition_agreement49.384 0.21154.343
plot_vote_frequencies1.6340.0081.668
toy_gene_memberships0.0310.0000.030
toy_genes0.0020.0000.002