Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-25 11:38 -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: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:omada.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings omada_1.7.0.tar.gz |
StartedAt: 2024-06-25 01:48:37 -0400 (Tue, 25 Jun 2024) |
EndedAt: 2024-06-25 02:11:10 -0400 (Tue, 25 Jun 2024) |
EllapsedTime: 1353.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: omada.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:omada.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings omada_1.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/omada.Rcheck’ * using R version 4.4.0 RC (2024-04-16 r86468) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * 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 loading without being on the library search path ... 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 68.829 0.215 75.328 get_feature_selection_scores 65.732 0.120 67.985 get_partition_agreement_scores 51.755 0.372 52.546 plot_partition_agreement 49.384 0.211 54.343 plot_feature_selection 47.502 0.407 49.502 get_sample_memberships 45.095 0.897 48.155 plot_cluster_voting 44.221 1.525 54.512 get_cluster_voting_k_votes 44.710 0.212 45.156 get_feature_selection_optimal_features 44.592 0.112 44.847 get_cluster_voting_metric_votes 41.140 0.120 41.420 get_cluster_voting_scores 40.854 0.112 41.047 get_cluster_voting_memberships 40.785 0.176 41.138 omada 35.547 0.848 37.369 get_optimal_features 15.361 0.375 15.737 plot_average_stabilities 15.263 0.151 16.678 get_optimal_memberships 14.735 0.300 15.036 get_optimal_number_of_features 14.376 0.347 14.732 get_optimal_parameter_used 13.711 0.276 15.427 get_optimal_stability_score 13.705 0.220 14.024 featureSelection 10.210 0.084 10.296 get_average_feature_k_stabilities 6.766 0.020 6.811 clusterVoting 5.767 0.116 5.883 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 5 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/omada.Rcheck/00check.log’ for details.
omada.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL omada ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 RC (2024-04-16 r86468) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 138.095 1.296 159.307
omada.Rcheck/omada-Ex.timings
name | user | system | elapsed | |
clusterVoting | 5.767 | 0.116 | 5.883 | |
clusteringMethodSelection | 2.299 | 0.052 | 2.360 | |
feasibilityAnalysis | 1.919 | 0.020 | 1.939 | |
feasibilityAnalysisDataBased | 4.011 | 0.088 | 4.099 | |
featureSelection | 10.210 | 0.084 | 10.296 | |
get_agreement_scores | 0.237 | 0.000 | 0.237 | |
get_average_feature_k_stabilities | 6.766 | 0.020 | 6.811 | |
get_average_stabilities_per_k | 1.286 | 0.004 | 1.348 | |
get_average_stability | 1.234 | 0.004 | 1.238 | |
get_cluster_memberships_k | 1.167 | 0.092 | 1.259 | |
get_cluster_voting_k_votes | 44.710 | 0.212 | 45.156 | |
get_cluster_voting_memberships | 40.785 | 0.176 | 41.138 | |
get_cluster_voting_metric_votes | 41.14 | 0.12 | 41.42 | |
get_cluster_voting_scores | 40.854 | 0.112 | 41.047 | |
get_feature_selection_optimal_features | 44.592 | 0.112 | 44.847 | |
get_feature_selection_optimal_number_of_features | 68.829 | 0.215 | 75.328 | |
get_feature_selection_scores | 65.732 | 0.120 | 67.985 | |
get_generated_dataset | 4.567 | 0.000 | 4.583 | |
get_internal_metric_scores | 1.190 | 0.012 | 1.201 | |
get_max_stability | 1.343 | 0.000 | 1.349 | |
get_metric_votes_k | 1.076 | 0.052 | 1.128 | |
get_optimal_features | 15.361 | 0.375 | 15.737 | |
get_optimal_memberships | 14.735 | 0.300 | 15.036 | |
get_optimal_number_of_features | 14.376 | 0.347 | 14.732 | |
get_optimal_parameter_used | 13.711 | 0.276 | 15.427 | |
get_optimal_stability_score | 13.705 | 0.220 | 14.024 | |
get_partition_agreement_scores | 51.755 | 0.372 | 52.546 | |
get_sample_memberships | 45.095 | 0.897 | 48.155 | |
get_vote_frequencies_k | 1.304 | 0.012 | 1.365 | |
omada | 35.547 | 0.848 | 37.369 | |
optimalClustering | 0.120 | 0.004 | 0.124 | |
partitionAgreement | 0.502 | 0.012 | 0.514 | |
plot_average_stabilities | 15.263 | 0.151 | 16.678 | |
plot_cluster_voting | 44.221 | 1.525 | 54.512 | |
plot_feature_selection | 47.502 | 0.407 | 49.502 | |
plot_partition_agreement | 49.384 | 0.211 | 54.343 | |
plot_vote_frequencies | 1.634 | 0.008 | 1.668 | |
toy_gene_memberships | 0.031 | 0.000 | 0.030 | |
toy_genes | 0.002 | 0.000 | 0.002 | |