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This page was generated on 2025-08-15 12:07 -0400 (Fri, 15 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4554
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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 1462/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
omada 1.11.0  (landing page)
Sokratis Kariotis
Snapshot Date: 2025-08-14 13:45 -0400 (Thu, 14 Aug 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
palomino8Windows 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
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 palomino8

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: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:omada.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings omada_1.11.0.tar.gz
StartedAt: 2025-08-15 05:59:15 -0400 (Fri, 15 Aug 2025)
EndedAt: 2025-08-15 06:12:06 -0400 (Fri, 15 Aug 2025)
EllapsedTime: 770.5 seconds
RetCode: 0
Status:   OK  
CheckDir: omada.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:omada.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings omada_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/omada.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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 49.56   2.39   51.97
get_feature_selection_scores                     46.59   2.70   49.30
get_feature_selection_optimal_features           34.27   1.74   36.00
plot_partition_agreement                         33.48   2.17   35.67
get_partition_agreement_scores                   33.76   1.69   35.47
get_cluster_voting_metric_votes                  32.72   1.72   34.46
plot_feature_selection                           32.22   1.73   33.97
get_cluster_voting_scores                        31.29   1.82   33.12
get_sample_memberships                           31.41   1.62   33.11
get_cluster_voting_memberships                   30.38   1.60   31.98
get_cluster_voting_k_votes                       29.26   1.39   30.66
omada                                            24.89   1.47   26.37
plot_cluster_voting                              24.25   1.19   25.44
get_optimal_number_of_features                   11.00   0.57   11.56
get_optimal_features                             10.32   0.66   10.98
plot_average_stabilities                          9.83   0.41   10.30
get_optimal_stability_score                       8.77   0.44    9.20
get_optimal_memberships                           8.69   0.43    9.13
get_optimal_parameter_used                        8.36   0.43    8.80
featureSelection                                  7.54   0.36    7.91
get_average_feature_k_stabilities                 5.29   0.20    5.50
clusterVoting                                     4.67   0.47    5.14
* 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
  'F:/biocbuild/bbs-3.22-bioc/meat/omada.Rcheck/00check.log'
for details.


Installation output

omada.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL omada
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/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 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
 105.82    7.20  119.32 

Example timings

omada.Rcheck/omada-Ex.timings

nameusersystemelapsed
clusterVoting4.670.475.14
clusteringMethodSelection1.610.111.72
feasibilityAnalysis1.560.011.58
feasibilityAnalysisDataBased3.210.213.41
featureSelection7.540.367.91
get_agreement_scores0.190.000.20
get_average_feature_k_stabilities5.290.205.50
get_average_stabilities_per_k1.150.051.19
get_average_stability1.120.001.12
get_cluster_memberships_k0.910.040.95
get_cluster_voting_k_votes29.26 1.3930.66
get_cluster_voting_memberships30.38 1.6031.98
get_cluster_voting_metric_votes32.72 1.7234.46
get_cluster_voting_scores31.29 1.8233.12
get_feature_selection_optimal_features34.27 1.7436.00
get_feature_selection_optimal_number_of_features49.56 2.3951.97
get_feature_selection_scores46.59 2.7049.30
get_generated_dataset2.970.133.09
get_internal_metric_scores1.190.151.35
get_max_stability1.250.031.28
get_metric_votes_k1.130.161.28
get_optimal_features10.32 0.6610.98
get_optimal_memberships8.690.439.13
get_optimal_number_of_features11.00 0.5711.56
get_optimal_parameter_used8.360.438.80
get_optimal_stability_score8.770.449.20
get_partition_agreement_scores33.76 1.6935.47
get_sample_memberships31.41 1.6233.11
get_vote_frequencies_k1.080.211.28
omada24.89 1.4726.37
optimalClustering0.120.000.13
partitionAgreement0.360.040.41
plot_average_stabilities 9.83 0.4110.30
plot_cluster_voting24.25 1.1925.44
plot_feature_selection32.22 1.7333.97
plot_partition_agreement33.48 2.1735.67
plot_vote_frequencies1.360.161.52
toy_gene_memberships0.020.020.06
toy_genes0.000.010.02