Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKLMN[O]PQRSTUVWXYZ

This page was generated on 2025-09-30 12:04 -0400 (Tue, 30 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4843
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4631
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4575
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 1477/2337HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
omada 1.11.0  (landing page)
Sokratis Kariotis
Snapshot Date: 2025-09-29 13:45 -0400 (Mon, 29 Sep 2025)
git_url: https://git.bioconductor.org/packages/omada
git_branch: devel
git_last_commit: a4bccc1
git_last_commit_date: 2025-04-15 12:55:16 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 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 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


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: 1.11.0
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_1.11.0.tar.gz
StartedAt: 2025-09-29 23:03:06 -0400 (Mon, 29 Sep 2025)
EndedAt: 2025-09-29 23:17:03 -0400 (Mon, 29 Sep 2025)
EllapsedTime: 837.5 seconds
RetCode: 0
Status:   OK  
CheckDir: omada.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/omada.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘omada/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘omada’ version ‘1.11.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
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 ... OK
* 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 46.967  0.770  48.003
get_feature_selection_scores                     41.793  0.716  42.752
get_partition_agreement_scores                   29.249 12.165  68.257
plot_partition_agreement                         36.750  0.625  59.140
get_feature_selection_optimal_features           32.132  0.531  32.850
get_cluster_voting_scores                        31.849  0.548  32.622
get_cluster_voting_memberships                   31.024  0.508  31.807
get_cluster_voting_k_votes                       30.697  0.641  31.604
get_sample_memberships                           28.212  2.814  34.284
get_cluster_voting_metric_votes                  29.666  0.494  30.401
plot_feature_selection                           28.761  0.773  41.226
omada                                            24.002  2.117  27.892
plot_cluster_voting                              25.421  0.485  32.040
get_optimal_stability_score                      10.178  0.949  12.876
plot_average_stabilities                         10.467  0.154  10.679
get_optimal_number_of_features                   10.335  0.130  10.521
get_optimal_features                             10.046  0.162  10.290
get_optimal_parameter_used                        8.092  0.902  11.180
get_optimal_memberships                           7.879  0.112   8.040
featureSelection                                  7.628  0.107   7.767
get_average_feature_k_stabilities                 5.043  0.073   5.133
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/omada.Rcheck/00check.log’
for details.


Installation output

omada.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘omada’ ...
** this is package ‘omada’ version ‘1.11.0’
** 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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 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 4.1-10
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 
 95.482   2.089 127.453 

Example timings

omada.Rcheck/omada-Ex.timings

nameusersystemelapsed
clusterVoting3.9600.5684.571
clusteringMethodSelection1.6340.0501.690
feasibilityAnalysis1.2500.0141.268
feasibilityAnalysisDataBased2.7450.0962.856
featureSelection7.6280.1077.767
get_agreement_scores0.1440.0030.147
get_average_feature_k_stabilities5.0430.0735.133
get_average_stabilities_per_k0.9150.0080.924
get_average_stability0.9320.0070.944
get_cluster_memberships_k1.1300.1321.282
get_cluster_voting_k_votes30.697 0.64131.604
get_cluster_voting_memberships31.024 0.50831.807
get_cluster_voting_metric_votes29.666 0.49430.401
get_cluster_voting_scores31.849 0.54832.622
get_feature_selection_optimal_features32.132 0.53132.850
get_feature_selection_optimal_number_of_features46.967 0.77048.003
get_feature_selection_scores41.793 0.71642.752
get_generated_dataset2.9310.0192.970
get_internal_metric_scores0.8530.0990.957
get_max_stability0.9600.0110.975
get_metric_votes_k0.8720.0900.971
get_optimal_features10.046 0.16210.290
get_optimal_memberships7.8790.1128.040
get_optimal_number_of_features10.335 0.13010.521
get_optimal_parameter_used 8.092 0.90211.180
get_optimal_stability_score10.178 0.94912.876
get_partition_agreement_scores29.24912.16568.257
get_sample_memberships28.212 2.81434.284
get_vote_frequencies_k0.8630.1331.011
omada24.002 2.11727.892
optimalClustering0.0880.0030.091
partitionAgreement0.6330.0080.642
plot_average_stabilities10.467 0.15410.679
plot_cluster_voting25.421 0.48532.040
plot_feature_selection28.761 0.77341.226
plot_partition_agreement36.750 0.62559.140
plot_vote_frequencies1.9000.1413.514
toy_gene_memberships0.0170.0070.033
toy_genes0.0010.0020.003