Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-08 12:53 -0400 (Wed, 08 Oct 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" | 4854 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4641 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4586 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4584 |
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 1479/2341 | 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: 2025-10-07 20:51:59 -0400 (Tue, 07 Oct 2025) |
EndedAt: 2025-10-07 20:56:05 -0400 (Tue, 07 Oct 2025) |
EllapsedTime: 245.8 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: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.7 * 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 15.520 0.806 16.368 get_feature_selection_scores 15.269 0.875 16.164 get_cluster_voting_metric_votes 11.159 0.710 11.923 plot_partition_agreement 11.085 0.565 11.732 get_feature_selection_optimal_features 11.054 0.556 11.647 get_cluster_voting_memberships 10.954 0.621 11.593 get_partition_agreement_scores 10.737 0.589 11.330 get_cluster_voting_scores 10.477 0.666 11.166 plot_feature_selection 10.515 0.454 11.008 get_cluster_voting_k_votes 10.167 0.544 10.751 get_sample_memberships 9.913 0.553 10.466 plot_cluster_voting 7.928 0.386 8.332 omada 6.664 0.487 7.155 * 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-arm64/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: 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 4.1-10 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 31.382 1.675 33.238
omada.Rcheck/omada-Ex.timings
name | user | system | elapsed | |
clusterVoting | 1.459 | 0.201 | 1.682 | |
clusteringMethodSelection | 0.571 | 0.021 | 0.592 | |
feasibilityAnalysis | 0.296 | 0.006 | 0.301 | |
feasibilityAnalysisDataBased | 0.778 | 0.034 | 0.812 | |
featureSelection | 2.500 | 0.138 | 2.642 | |
get_agreement_scores | 0.191 | 0.006 | 0.197 | |
get_average_feature_k_stabilities | 1.864 | 0.077 | 1.943 | |
get_average_stabilities_per_k | 0.211 | 0.009 | 0.221 | |
get_average_stability | 0.203 | 0.002 | 0.205 | |
get_cluster_memberships_k | 0.322 | 0.048 | 0.371 | |
get_cluster_voting_k_votes | 10.167 | 0.544 | 10.751 | |
get_cluster_voting_memberships | 10.954 | 0.621 | 11.593 | |
get_cluster_voting_metric_votes | 11.159 | 0.710 | 11.923 | |
get_cluster_voting_scores | 10.477 | 0.666 | 11.166 | |
get_feature_selection_optimal_features | 11.054 | 0.556 | 11.647 | |
get_feature_selection_optimal_number_of_features | 15.520 | 0.806 | 16.368 | |
get_feature_selection_scores | 15.269 | 0.875 | 16.164 | |
get_generated_dataset | 0.869 | 0.030 | 0.899 | |
get_internal_metric_scores | 0.318 | 0.093 | 0.413 | |
get_max_stability | 0.204 | 0.011 | 0.215 | |
get_metric_votes_k | 0.320 | 0.059 | 0.380 | |
get_optimal_features | 4.064 | 0.108 | 4.173 | |
get_optimal_memberships | 2.694 | 0.174 | 2.878 | |
get_optimal_number_of_features | 3.613 | 0.207 | 3.820 | |
get_optimal_parameter_used | 2.862 | 0.132 | 2.996 | |
get_optimal_stability_score | 2.758 | 0.170 | 2.928 | |
get_partition_agreement_scores | 10.737 | 0.589 | 11.330 | |
get_sample_memberships | 9.913 | 0.553 | 10.466 | |
get_vote_frequencies_k | 0.315 | 0.073 | 0.389 | |
omada | 6.664 | 0.487 | 7.155 | |
optimalClustering | 0.021 | 0.001 | 0.022 | |
partitionAgreement | 0.255 | 0.010 | 0.265 | |
plot_average_stabilities | 3.656 | 0.157 | 3.825 | |
plot_cluster_voting | 7.928 | 0.386 | 8.332 | |
plot_feature_selection | 10.515 | 0.454 | 11.008 | |
plot_partition_agreement | 11.085 | 0.565 | 11.732 | |
plot_vote_frequencies | 0.379 | 0.065 | 0.447 | |
toy_gene_memberships | 0.006 | 0.002 | 0.008 | |
toy_genes | 0.001 | 0.001 | 0.002 | |