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### Running command:
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###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:omada.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings omada_1.0.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/omada.Rcheck'
* using R version 4.2.2 (2022-10-31 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'omada/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'omada' version '1.0.0'
* 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', 'clusterCrit', '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 R 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' 'clusterCrit' '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
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'
geneSignatures: no visible global function definition for 'where'
geneSignatures: no visible binding for global variable 'features'
geneSignatures: no visible binding for global variable 'value'
geneSignatures: no visible binding for global variable 'variable'
Undefined global functions or variables:
  Frequency featureSet features k means methods value variable where
Consider adding
  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                     43.63   0.23   43.86
get_feature_selection_optimal_number_of_features 39.04   0.28   39.33
get_partition_agreement_scores                   31.04   0.22   31.25
get_cluster_voting_memberships                   29.89   0.28   30.17
get_feature_selection_optimal_features           29.88   0.21   30.07
get_cluster_voting_k_votes                       29.06   0.22   29.30
get_cluster_voting_scores                        28.85   0.14   29.00
get_signature_feature_coefs                      27.89   0.21   28.11
plot_feature_selection                           27.76   0.20   27.97
get_sample_memberships                           27.39   0.21   27.69
get_cluster_voting_metric_votes                  27.30   0.19   27.51
plot_partition_agreement                         26.45   0.11   26.61
plot_signature_feature                           25.94   0.13   26.08
plot_cluster_voting                              21.86   0.14   22.00
omada                                            20.89   0.18   21.08
get_optimal_number_of_features                   10.53   0.13   10.65
get_optimal_features                             10.20   0.00   10.20
plot_average_stabilities                          8.97   0.07    9.03
get_optimal_parameter_used                        8.89   0.01    8.91
get_optimal_memberships                           8.39   0.06    8.46
get_optimal_stability_score                       8.11   0.02    8.12
featureSelection                                  7.75   0.16    7.90
get_average_feature_k_stabilities                 5.03   0.05    5.08
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  'F:/biocbuild/bbs-3.16-bioc/meat/omada.Rcheck/00check.log'
for details.