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### Running command:
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###   /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_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/omada.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 13.0.0 (clang-1300.0.29.3)
    GNU Fortran (GCC) 12.0.1 20220312 (experimental)
* running under: macOS Monterey 12.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘omada/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘omada’ version ‘1.1.0’
* 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 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 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_optimal_number_of_features 16.753  0.307  17.062
get_feature_selection_scores                     15.389  0.349  15.740
get_signature_feature_coefs                      12.982  0.127  13.130
plot_feature_selection                           12.450  0.170  12.654
get_cluster_voting_k_votes                       11.832  0.121  11.988
get_feature_selection_optimal_features           11.744  0.203  11.949
get_partition_agreement_scores                   11.570  0.237  11.824
get_cluster_voting_metric_votes                  11.566  0.187  11.755
get_sample_memberships                           11.452  0.150  11.629
get_cluster_voting_memberships                   11.369  0.184  11.564
plot_partition_agreement                         11.257  0.213  11.472
plot_signature_feature                           10.907  0.187  11.095
get_cluster_voting_scores                        10.819  0.204  11.026
omada                                             9.285  0.122   9.422
plot_cluster_voting                               8.933  0.141   9.101
* 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
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/omada.Rcheck/00check.log’
for details.