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### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:omada.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings omada_1.9.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/omada.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘omada/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘omada’ version ‘1.9.0’
* 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 loading without being on the library search path ... 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 40.024 0.096 40.119
get_feature_selection_scores 38.381 0.035 38.416
plot_partition_agreement 29.141 0.072 29.334
get_cluster_voting_memberships 27.442 0.128 27.571
get_cluster_voting_metric_votes 27.314 0.106 27.421
plot_feature_selection 27.301 0.053 27.354
get_cluster_voting_scores 27.162 0.100 27.263
get_sample_memberships 26.962 0.090 27.097
get_cluster_voting_k_votes 26.841 0.186 27.040
get_feature_selection_optimal_features 26.851 0.097 26.948
get_partition_agreement_scores 25.828 0.017 25.846
omada 21.921 0.053 21.997
plot_cluster_voting 19.625 0.013 19.641
plot_average_stabilities 9.703 0.009 9.713
get_optimal_features 8.627 0.011 8.640
get_optimal_number_of_features 8.541 0.009 8.550
get_optimal_memberships 8.244 0.009 8.253
get_optimal_stability_score 8.003 0.011 8.014
get_optimal_parameter_used 7.300 0.006 7.305
featureSelection 6.507 0.112 6.619
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/omada.Rcheck/00check.log’
for details.