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### Running command:
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###   E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:omada.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings omada_1.6.0.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.19-bioc/meat/omada.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* 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 '1.6.0'
* 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 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_scores                     48.73   2.30   51.03
get_feature_selection_optimal_number_of_features 43.70   2.12   45.83
plot_partition_agreement                         40.07   2.50   45.35
get_cluster_voting_k_votes                       35.41   1.85   37.27
get_cluster_voting_memberships                   33.55   1.57   35.11
plot_feature_selection                           33.47   1.42   34.90
get_cluster_voting_scores                        32.65   1.54   34.26
get_partition_agreement_scores                   32.47   1.50   33.97
get_cluster_voting_metric_votes                  32.33   1.61   33.97
get_feature_selection_optimal_features           31.46   1.52   32.97
get_sample_memberships                           31.40   1.14   32.54
plot_cluster_voting                              24.42   1.58   26.05
omada                                            22.91   1.00   23.91
plot_average_stabilities                         11.64   0.62   12.30
get_optimal_features                             10.53   0.46   10.98
get_optimal_number_of_features                    9.81   0.27   10.08
get_optimal_parameter_used                        9.57   0.43   10.00
featureSelection                                  9.64   0.25    9.89
get_optimal_stability_score                       9.23   0.52    9.75
get_optimal_memberships                           8.53   0.37    8.91
get_average_feature_k_stabilities                 5.33   0.23    5.56
* 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
  'E:/biocbuild/bbs-3.19-bioc/meat/omada.Rcheck/00check.log'
for details.