Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-25 11:39 -0400 (Tue, 25 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4690 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4404 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4353 |
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 1418/2242 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
omada 1.7.0 (landing page) Sokratis Kariotis
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | 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: 1.7.0 |
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: 2024-06-24 21:53:13 -0400 (Mon, 24 Jun 2024) |
EndedAt: 2024-06-24 22:06:31 -0400 (Mon, 24 Jun 2024) |
EllapsedTime: 798.2 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/meat/omada.Rcheck’ * using R version 4.4.1 RC (2024-06-06 r86719) * using platform: x86_64-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 Monterey 12.7.1 * 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_scores 46.718 0.688 47.648 get_feature_selection_optimal_number_of_features 44.797 0.686 45.746 get_sample_memberships 32.099 2.478 36.262 plot_feature_selection 33.496 1.077 59.964 get_partition_agreement_scores 32.741 1.377 34.937 get_cluster_voting_k_votes 32.731 0.475 33.333 plot_partition_agreement 31.014 0.592 31.935 get_cluster_voting_scores 30.989 0.477 31.626 get_cluster_voting_memberships 30.775 0.472 31.448 get_cluster_voting_metric_votes 30.690 0.464 31.342 get_feature_selection_optimal_features 30.595 0.479 31.252 plot_cluster_voting 26.992 1.234 53.119 omada 24.329 3.410 42.463 plot_average_stabilities 12.887 0.257 26.040 get_optimal_features 9.818 0.130 9.986 get_optimal_stability_score 7.940 1.805 15.153 get_optimal_parameter_used 8.994 0.139 9.192 get_optimal_number_of_features 8.794 0.107 8.931 get_optimal_memberships 8.038 0.098 8.174 featureSelection 7.600 0.087 7.713 get_average_feature_k_stabilities 4.947 0.054 5.017 * 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/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-x86_64/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 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" Copyright (C) 2024 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 4.1-8 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 86.892 1.771 89.560
omada.Rcheck/omada-Ex.timings
name | user | system | elapsed | |
clusterVoting | 3.760 | 0.550 | 4.327 | |
clusteringMethodSelection | 1.570 | 0.046 | 1.623 | |
feasibilityAnalysis | 1.356 | 0.013 | 1.377 | |
feasibilityAnalysisDataBased | 3.091 | 0.070 | 3.173 | |
featureSelection | 7.600 | 0.087 | 7.713 | |
get_agreement_scores | 0.164 | 0.001 | 0.166 | |
get_average_feature_k_stabilities | 4.947 | 0.054 | 5.017 | |
get_average_stabilities_per_k | 0.957 | 0.009 | 0.969 | |
get_average_stability | 0.968 | 0.005 | 0.975 | |
get_cluster_memberships_k | 0.824 | 0.140 | 0.969 | |
get_cluster_voting_k_votes | 32.731 | 0.475 | 33.333 | |
get_cluster_voting_memberships | 30.775 | 0.472 | 31.448 | |
get_cluster_voting_metric_votes | 30.690 | 0.464 | 31.342 | |
get_cluster_voting_scores | 30.989 | 0.477 | 31.626 | |
get_feature_selection_optimal_features | 30.595 | 0.479 | 31.252 | |
get_feature_selection_optimal_number_of_features | 44.797 | 0.686 | 45.746 | |
get_feature_selection_scores | 46.718 | 0.688 | 47.648 | |
get_generated_dataset | 3.461 | 0.025 | 3.502 | |
get_internal_metric_scores | 1.126 | 0.078 | 1.211 | |
get_max_stability | 1.030 | 0.015 | 1.051 | |
get_metric_votes_k | 0.851 | 0.129 | 0.984 | |
get_optimal_features | 9.818 | 0.130 | 9.986 | |
get_optimal_memberships | 8.038 | 0.098 | 8.174 | |
get_optimal_number_of_features | 8.794 | 0.107 | 8.931 | |
get_optimal_parameter_used | 8.994 | 0.139 | 9.192 | |
get_optimal_stability_score | 7.940 | 1.805 | 15.153 | |
get_partition_agreement_scores | 32.741 | 1.377 | 34.937 | |
get_sample_memberships | 32.099 | 2.478 | 36.262 | |
get_vote_frequencies_k | 1.184 | 0.165 | 1.389 | |
omada | 24.329 | 3.410 | 42.463 | |
optimalClustering | 0.120 | 0.004 | 0.356 | |
partitionAgreement | 0.437 | 0.011 | 1.284 | |
plot_average_stabilities | 12.887 | 0.257 | 26.040 | |
plot_cluster_voting | 26.992 | 1.234 | 53.119 | |
plot_feature_selection | 33.496 | 1.077 | 59.964 | |
plot_partition_agreement | 31.014 | 0.592 | 31.935 | |
plot_vote_frequencies | 1.026 | 0.092 | 1.130 | |
toy_gene_memberships | 0.017 | 0.006 | 0.024 | |
toy_genes | 0.002 | 0.002 | 0.003 | |