Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-16 11:39 -0400 (Thu, 16 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
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 1473/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
omada 1.10.0 (landing page) Sokratis Kariotis
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | 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: 1.10.0 |
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_1.10.0.tar.gz |
StartedAt: 2025-10-14 07:37:21 -0400 (Tue, 14 Oct 2025) |
EndedAt: 2025-10-14 07:57:26 -0400 (Tue, 14 Oct 2025) |
EllapsedTime: 1205.6 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_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/omada.Rcheck’ * using R version 4.5.1 RC (2025-06-05 r88288) * 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 ‘1.10.0’ * 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 71.932 0.639 73.059 get_feature_selection_scores 71.408 0.746 73.827 plot_partition_agreement 50.934 0.438 51.770 get_partition_agreement_scores 50.812 0.495 52.185 get_cluster_voting_memberships 48.861 0.433 50.639 get_cluster_voting_metric_votes 48.090 0.372 48.858 get_cluster_voting_k_votes 48.031 0.400 50.389 get_sample_memberships 47.368 0.426 48.560 get_cluster_voting_scores 46.952 0.381 47.680 plot_feature_selection 46.514 0.404 47.751 get_feature_selection_optimal_features 46.131 0.371 46.663 omada 38.927 0.322 40.428 plot_cluster_voting 37.669 0.322 39.100 plot_average_stabilities 17.040 0.135 17.567 get_optimal_features 16.810 0.122 17.448 get_optimal_number_of_features 14.743 0.099 15.033 get_optimal_stability_score 14.669 0.105 14.982 get_optimal_parameter_used 13.448 0.089 13.596 featureSelection 13.305 0.099 14.085 get_optimal_memberships 13.089 0.093 13.225 clusterVoting 7.731 0.469 8.636 get_average_feature_k_stabilities 7.669 0.069 7.907 get_generated_dataset 5.525 0.022 5.560 * 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-3.21-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 ‘1.10.0’ ** 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 RC (2025-06-05 r88288) -- "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 145.284 2.345 219.418
omada.Rcheck/omada-Ex.timings
name | user | system | elapsed | |
clusterVoting | 7.731 | 0.469 | 8.636 | |
clusteringMethodSelection | 3.110 | 0.059 | 3.394 | |
feasibilityAnalysis | 2.624 | 0.036 | 2.793 | |
feasibilityAnalysisDataBased | 4.717 | 0.134 | 4.891 | |
featureSelection | 13.305 | 0.099 | 14.085 | |
get_agreement_scores | 0.277 | 0.005 | 0.288 | |
get_average_feature_k_stabilities | 7.669 | 0.069 | 7.907 | |
get_average_stabilities_per_k | 1.808 | 0.009 | 1.821 | |
get_average_stability | 1.820 | 0.006 | 1.829 | |
get_cluster_memberships_k | 1.693 | 0.153 | 1.869 | |
get_cluster_voting_k_votes | 48.031 | 0.400 | 50.389 | |
get_cluster_voting_memberships | 48.861 | 0.433 | 50.639 | |
get_cluster_voting_metric_votes | 48.090 | 0.372 | 48.858 | |
get_cluster_voting_scores | 46.952 | 0.381 | 47.680 | |
get_feature_selection_optimal_features | 46.131 | 0.371 | 46.663 | |
get_feature_selection_optimal_number_of_features | 71.932 | 0.639 | 73.059 | |
get_feature_selection_scores | 71.408 | 0.746 | 73.827 | |
get_generated_dataset | 5.525 | 0.022 | 5.560 | |
get_internal_metric_scores | 1.639 | 0.077 | 1.721 | |
get_max_stability | 1.790 | 0.015 | 1.810 | |
get_metric_votes_k | 1.667 | 0.135 | 1.807 | |
get_optimal_features | 16.810 | 0.122 | 17.448 | |
get_optimal_memberships | 13.089 | 0.093 | 13.225 | |
get_optimal_number_of_features | 14.743 | 0.099 | 15.033 | |
get_optimal_parameter_used | 13.448 | 0.089 | 13.596 | |
get_optimal_stability_score | 14.669 | 0.105 | 14.982 | |
get_partition_agreement_scores | 50.812 | 0.495 | 52.185 | |
get_sample_memberships | 47.368 | 0.426 | 48.560 | |
get_vote_frequencies_k | 1.644 | 0.074 | 1.758 | |
omada | 38.927 | 0.322 | 40.428 | |
optimalClustering | 0.176 | 0.007 | 0.184 | |
partitionAgreement | 0.521 | 0.009 | 0.533 | |
plot_average_stabilities | 17.040 | 0.135 | 17.567 | |
plot_cluster_voting | 37.669 | 0.322 | 39.100 | |
plot_feature_selection | 46.514 | 0.404 | 47.751 | |
plot_partition_agreement | 50.934 | 0.438 | 51.770 | |
plot_vote_frequencies | 2.112 | 0.148 | 2.263 | |
toy_gene_memberships | 0.027 | 0.007 | 0.035 | |
toy_genes | 0.002 | 0.004 | 0.006 | |