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This page was generated on 2024-05-13 11:32:09 -0400 (Mon, 13 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4378 |
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 1412/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
omada 1.7.0 (landing page) Sokratis Kariotis
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the omada package: - 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. |
Package: omada |
Version: 1.7.0 |
Command: /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_1.7.0.tar.gz |
StartedAt: 2024-05-12 21:38:42 -0400 (Sun, 12 May 2024) |
EndedAt: 2024-05-12 21:50:24 -0400 (Sun, 12 May 2024) |
EllapsedTime: 702.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: omada.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /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_1.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/omada.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘omada/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘omada’ version ‘1.7.0’ * 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 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 ... 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_optimal_number_of_features 46.520 1.748 48.415 get_feature_selection_scores 45.712 1.765 47.526 get_partition_agreement_scores 32.967 1.224 34.217 get_cluster_voting_metric_votes 32.166 1.665 33.831 get_cluster_voting_scores 31.786 1.484 33.349 get_cluster_voting_memberships 31.420 1.346 32.781 plot_partition_agreement 31.341 1.125 32.507 plot_feature_selection 30.948 1.230 32.233 get_feature_selection_optimal_features 30.401 1.455 31.859 get_cluster_voting_k_votes 30.716 1.018 31.869 get_sample_memberships 30.128 1.210 31.383 omada 24.501 0.972 25.482 plot_cluster_voting 23.337 0.920 24.332 get_optimal_number_of_features 10.797 0.290 11.113 plot_average_stabilities 9.871 0.352 10.227 get_optimal_features 9.332 0.357 9.690 get_optimal_memberships 9.413 0.272 9.689 featureSelection 8.723 0.113 8.865 get_optimal_parameter_used 8.348 0.248 8.646 get_optimal_stability_score 8.082 0.306 8.388 get_average_feature_k_stabilities 5.947 0.132 6.087 * 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 ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/omada.Rcheck/00check.log’ for details.
omada.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL omada ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘omada’ ... ** 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)
omada.Rcheck/tests/testthat.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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 4.1-8 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 87.418 3.401 90.923
omada.Rcheck/omada-Ex.timings
name | user | system | elapsed | |
clusterVoting | 4.270 | 0.432 | 4.726 | |
clusteringMethodSelection | 1.368 | 0.056 | 1.428 | |
feasibilityAnalysis | 1.072 | 0.010 | 1.086 | |
feasibilityAnalysisDataBased | 2.595 | 0.056 | 2.659 | |
featureSelection | 8.723 | 0.113 | 8.865 | |
get_agreement_scores | 0.201 | 0.006 | 0.208 | |
get_average_feature_k_stabilities | 5.947 | 0.132 | 6.087 | |
get_average_stabilities_per_k | 0.781 | 0.015 | 0.798 | |
get_average_stability | 0.754 | 0.008 | 0.766 | |
get_cluster_memberships_k | 0.974 | 0.145 | 1.123 | |
get_cluster_voting_k_votes | 30.716 | 1.018 | 31.869 | |
get_cluster_voting_memberships | 31.420 | 1.346 | 32.781 | |
get_cluster_voting_metric_votes | 32.166 | 1.665 | 33.831 | |
get_cluster_voting_scores | 31.786 | 1.484 | 33.349 | |
get_feature_selection_optimal_features | 30.401 | 1.455 | 31.859 | |
get_feature_selection_optimal_number_of_features | 46.520 | 1.748 | 48.415 | |
get_feature_selection_scores | 45.712 | 1.765 | 47.526 | |
get_generated_dataset | 2.810 | 0.082 | 2.892 | |
get_internal_metric_scores | 0.961 | 0.145 | 1.106 | |
get_max_stability | 0.715 | 0.012 | 0.727 | |
get_metric_votes_k | 1.292 | 0.159 | 1.452 | |
get_optimal_features | 9.332 | 0.357 | 9.690 | |
get_optimal_memberships | 9.413 | 0.272 | 9.689 | |
get_optimal_number_of_features | 10.797 | 0.290 | 11.113 | |
get_optimal_parameter_used | 8.348 | 0.248 | 8.646 | |
get_optimal_stability_score | 8.082 | 0.306 | 8.388 | |
get_partition_agreement_scores | 32.967 | 1.224 | 34.217 | |
get_sample_memberships | 30.128 | 1.210 | 31.383 | |
get_vote_frequencies_k | 0.978 | 0.204 | 1.182 | |
omada | 24.501 | 0.972 | 25.482 | |
optimalClustering | 0.069 | 0.003 | 0.073 | |
partitionAgreement | 0.396 | 0.019 | 0.414 | |
plot_average_stabilities | 9.871 | 0.352 | 10.227 | |
plot_cluster_voting | 23.337 | 0.920 | 24.332 | |
plot_feature_selection | 30.948 | 1.230 | 32.233 | |
plot_partition_agreement | 31.341 | 1.125 | 32.507 | |
plot_vote_frequencies | 1.067 | 0.149 | 1.217 | |
toy_gene_memberships | 0.018 | 0.006 | 0.024 | |
toy_genes | 0.001 | 0.003 | 0.004 | |