Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-30 12:04 -0400 (Tue, 30 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4843 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4631 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4575 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4576 |
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 1477/2337 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
omada 1.11.0 (landing page) Sokratis Kariotis
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the omada package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/omada.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: 1.11.0 |
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_1.11.0.tar.gz |
StartedAt: 2025-09-29 23:03:06 -0400 (Mon, 29 Sep 2025) |
EndedAt: 2025-09-29 23:17:03 -0400 (Mon, 29 Sep 2025) |
EllapsedTime: 837.5 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_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/omada.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘omada/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘omada’ version ‘1.11.0’ * 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 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 46.967 0.770 48.003 get_feature_selection_scores 41.793 0.716 42.752 get_partition_agreement_scores 29.249 12.165 68.257 plot_partition_agreement 36.750 0.625 59.140 get_feature_selection_optimal_features 32.132 0.531 32.850 get_cluster_voting_scores 31.849 0.548 32.622 get_cluster_voting_memberships 31.024 0.508 31.807 get_cluster_voting_k_votes 30.697 0.641 31.604 get_sample_memberships 28.212 2.814 34.284 get_cluster_voting_metric_votes 29.666 0.494 30.401 plot_feature_selection 28.761 0.773 41.226 omada 24.002 2.117 27.892 plot_cluster_voting 25.421 0.485 32.040 get_optimal_stability_score 10.178 0.949 12.876 plot_average_stabilities 10.467 0.154 10.679 get_optimal_number_of_features 10.335 0.130 10.521 get_optimal_features 10.046 0.162 10.290 get_optimal_parameter_used 8.092 0.902 11.180 get_optimal_memberships 7.879 0.112 8.040 featureSelection 7.628 0.107 7.767 get_average_feature_k_stabilities 5.043 0.073 5.133 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.22-bioc/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/4.5-x86_64/Resources/library’ * installing *source* package ‘omada’ ... ** this is package ‘omada’ version ‘1.11.0’ ** 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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-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 4.1-10 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 95.482 2.089 127.453
omada.Rcheck/omada-Ex.timings
name | user | system | elapsed | |
clusterVoting | 3.960 | 0.568 | 4.571 | |
clusteringMethodSelection | 1.634 | 0.050 | 1.690 | |
feasibilityAnalysis | 1.250 | 0.014 | 1.268 | |
feasibilityAnalysisDataBased | 2.745 | 0.096 | 2.856 | |
featureSelection | 7.628 | 0.107 | 7.767 | |
get_agreement_scores | 0.144 | 0.003 | 0.147 | |
get_average_feature_k_stabilities | 5.043 | 0.073 | 5.133 | |
get_average_stabilities_per_k | 0.915 | 0.008 | 0.924 | |
get_average_stability | 0.932 | 0.007 | 0.944 | |
get_cluster_memberships_k | 1.130 | 0.132 | 1.282 | |
get_cluster_voting_k_votes | 30.697 | 0.641 | 31.604 | |
get_cluster_voting_memberships | 31.024 | 0.508 | 31.807 | |
get_cluster_voting_metric_votes | 29.666 | 0.494 | 30.401 | |
get_cluster_voting_scores | 31.849 | 0.548 | 32.622 | |
get_feature_selection_optimal_features | 32.132 | 0.531 | 32.850 | |
get_feature_selection_optimal_number_of_features | 46.967 | 0.770 | 48.003 | |
get_feature_selection_scores | 41.793 | 0.716 | 42.752 | |
get_generated_dataset | 2.931 | 0.019 | 2.970 | |
get_internal_metric_scores | 0.853 | 0.099 | 0.957 | |
get_max_stability | 0.960 | 0.011 | 0.975 | |
get_metric_votes_k | 0.872 | 0.090 | 0.971 | |
get_optimal_features | 10.046 | 0.162 | 10.290 | |
get_optimal_memberships | 7.879 | 0.112 | 8.040 | |
get_optimal_number_of_features | 10.335 | 0.130 | 10.521 | |
get_optimal_parameter_used | 8.092 | 0.902 | 11.180 | |
get_optimal_stability_score | 10.178 | 0.949 | 12.876 | |
get_partition_agreement_scores | 29.249 | 12.165 | 68.257 | |
get_sample_memberships | 28.212 | 2.814 | 34.284 | |
get_vote_frequencies_k | 0.863 | 0.133 | 1.011 | |
omada | 24.002 | 2.117 | 27.892 | |
optimalClustering | 0.088 | 0.003 | 0.091 | |
partitionAgreement | 0.633 | 0.008 | 0.642 | |
plot_average_stabilities | 10.467 | 0.154 | 10.679 | |
plot_cluster_voting | 25.421 | 0.485 | 32.040 | |
plot_feature_selection | 28.761 | 0.773 | 41.226 | |
plot_partition_agreement | 36.750 | 0.625 | 59.140 | |
plot_vote_frequencies | 1.900 | 0.141 | 3.514 | |
toy_gene_memberships | 0.017 | 0.007 | 0.033 | |
toy_genes | 0.001 | 0.002 | 0.003 | |