Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1445/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
omada 1.8.0 (landing page) Sokratis Kariotis
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 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: 1.8.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:omada.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings omada_1.8.0.tar.gz |
StartedAt: 2024-12-20 04:13:55 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 04:27:15 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 800.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: omada.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:omada.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings omada_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/omada.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'omada/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'omada' version '1.8.0' * 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 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_optimal_number_of_features 49.32 2.81 52.17 get_feature_selection_scores 48.99 2.45 51.42 get_cluster_voting_scores 34.08 1.69 35.82 get_cluster_voting_memberships 33.67 1.55 40.77 plot_feature_selection 33.43 1.67 35.13 get_partition_agreement_scores 33.23 1.71 34.97 plot_partition_agreement 33.21 1.59 35.00 get_cluster_voting_k_votes 32.85 1.39 34.86 get_cluster_voting_metric_votes 31.81 1.87 33.68 get_feature_selection_optimal_features 31.41 1.66 33.08 get_sample_memberships 31.02 1.71 32.74 omada 26.31 1.31 27.69 plot_cluster_voting 25.04 1.33 26.36 get_optimal_number_of_features 11.52 0.60 12.11 get_optimal_features 11.14 0.50 11.64 plot_average_stabilities 10.53 0.69 11.26 get_optimal_stability_score 9.88 0.47 10.34 get_optimal_memberships 9.67 0.39 10.06 get_optimal_parameter_used 9.54 0.39 9.94 featureSelection 9.35 0.29 9.64 get_average_feature_k_stabilities 5.06 0.28 5.34 * 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 'F:/biocbuild/bbs-3.20-bioc/meat/omada.Rcheck/00check.log' for details.
omada.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL omada ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 107.32 7.67 127.09
omada.Rcheck/omada-Ex.timings
name | user | system | elapsed | |
clusterVoting | 4.60 | 0.36 | 4.95 | |
clusteringMethodSelection | 1.56 | 0.10 | 1.65 | |
feasibilityAnalysis | 1.41 | 0.01 | 1.43 | |
feasibilityAnalysisDataBased | 4.01 | 0.16 | 4.17 | |
featureSelection | 9.35 | 0.29 | 9.64 | |
get_agreement_scores | 0.2 | 0.0 | 0.2 | |
get_average_feature_k_stabilities | 5.06 | 0.28 | 5.34 | |
get_average_stabilities_per_k | 1.06 | 0.06 | 1.13 | |
get_average_stability | 1.07 | 0.02 | 1.07 | |
get_cluster_memberships_k | 1.04 | 0.14 | 1.19 | |
get_cluster_voting_k_votes | 32.85 | 1.39 | 34.86 | |
get_cluster_voting_memberships | 33.67 | 1.55 | 40.77 | |
get_cluster_voting_metric_votes | 31.81 | 1.87 | 33.68 | |
get_cluster_voting_scores | 34.08 | 1.69 | 35.82 | |
get_feature_selection_optimal_features | 31.41 | 1.66 | 33.08 | |
get_feature_selection_optimal_number_of_features | 49.32 | 2.81 | 52.17 | |
get_feature_selection_scores | 48.99 | 2.45 | 51.42 | |
get_generated_dataset | 3.42 | 0.17 | 3.59 | |
get_internal_metric_scores | 1.20 | 0.18 | 1.38 | |
get_max_stability | 1.17 | 0.03 | 1.20 | |
get_metric_votes_k | 1.38 | 0.12 | 1.50 | |
get_optimal_features | 11.14 | 0.50 | 11.64 | |
get_optimal_memberships | 9.67 | 0.39 | 10.06 | |
get_optimal_number_of_features | 11.52 | 0.60 | 12.11 | |
get_optimal_parameter_used | 9.54 | 0.39 | 9.94 | |
get_optimal_stability_score | 9.88 | 0.47 | 10.34 | |
get_partition_agreement_scores | 33.23 | 1.71 | 34.97 | |
get_sample_memberships | 31.02 | 1.71 | 32.74 | |
get_vote_frequencies_k | 1.14 | 0.23 | 1.37 | |
omada | 26.31 | 1.31 | 27.69 | |
optimalClustering | 0.08 | 0.00 | 0.08 | |
partitionAgreement | 0.31 | 0.00 | 0.31 | |
plot_average_stabilities | 10.53 | 0.69 | 11.26 | |
plot_cluster_voting | 25.04 | 1.33 | 26.36 | |
plot_feature_selection | 33.43 | 1.67 | 35.13 | |
plot_partition_agreement | 33.21 | 1.59 | 35.00 | |
plot_vote_frequencies | 1.45 | 0.13 | 1.93 | |
toy_gene_memberships | 0.02 | 0.01 | 0.07 | |
toy_genes | 0.00 | 0.02 | 0.01 | |