Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-15 11:47 -0400 (Thu, 15 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4420 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4413 |
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 1427/2255 | 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 | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | 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 | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: omada |
Version: 1.7.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:omada.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings omada_1.7.0.tar.gz |
StartedAt: 2024-08-15 07:22:45 -0000 (Thu, 15 Aug 2024) |
EndedAt: 2024-08-15 07:36:03 -0000 (Thu, 15 Aug 2024) |
EllapsedTime: 798.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: omada.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:omada.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings omada_1.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/omada.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * 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 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_scores 51.217 0.135 51.455 get_feature_selection_optimal_number_of_features 48.949 0.052 49.109 plot_partition_agreement 37.484 0.092 49.069 get_cluster_voting_scores 36.340 0.088 36.508 plot_feature_selection 35.616 0.032 35.725 get_partition_agreement_scores 35.410 0.084 35.578 get_feature_selection_optimal_features 35.076 0.088 35.242 get_cluster_voting_metric_votes 35.050 0.102 35.226 get_cluster_voting_memberships 34.927 0.149 35.150 get_cluster_voting_k_votes 34.798 0.212 35.087 get_sample_memberships 34.571 0.068 34.715 omada 27.380 0.052 27.493 plot_cluster_voting 25.649 0.080 25.785 plot_average_stabilities 12.739 0.051 12.819 get_optimal_features 12.320 0.064 12.409 get_optimal_number_of_features 11.062 0.014 11.098 get_optimal_parameter_used 9.657 0.028 9.705 get_optimal_memberships 9.439 0.009 9.468 get_optimal_stability_score 9.181 0.032 9.233 featureSelection 8.142 0.107 8.271 get_average_feature_k_stabilities 5.705 0.028 5.747 clusterVoting 5.581 0.148 5.742 * 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 ‘/home/biocbuild/bbs-3.20-bioc/meat/omada.Rcheck/00check.log’ for details.
omada.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL omada ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-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 2 | SKIP 0 | PASS 38 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 38 ] > > proc.time() user system elapsed 104.961 1.219 127.431
omada.Rcheck/omada-Ex.timings
name | user | system | elapsed | |
clusterVoting | 5.581 | 0.148 | 5.742 | |
clusteringMethodSelection | 1.417 | 0.028 | 1.449 | |
feasibilityAnalysis | 1.692 | 0.008 | 1.703 | |
feasibilityAnalysisDataBased | 2.891 | 0.020 | 2.918 | |
featureSelection | 8.142 | 0.107 | 8.271 | |
get_agreement_scores | 0.163 | 0.000 | 0.163 | |
get_average_feature_k_stabilities | 5.705 | 0.028 | 5.747 | |
get_average_stabilities_per_k | 1.190 | 0.016 | 1.210 | |
get_average_stability | 1.197 | 0.024 | 1.224 | |
get_cluster_memberships_k | 1.492 | 0.016 | 1.512 | |
get_cluster_voting_k_votes | 34.798 | 0.212 | 35.087 | |
get_cluster_voting_memberships | 34.927 | 0.149 | 35.150 | |
get_cluster_voting_metric_votes | 35.050 | 0.102 | 35.226 | |
get_cluster_voting_scores | 36.340 | 0.088 | 36.508 | |
get_feature_selection_optimal_features | 35.076 | 0.088 | 35.242 | |
get_feature_selection_optimal_number_of_features | 48.949 | 0.052 | 49.109 | |
get_feature_selection_scores | 51.217 | 0.135 | 51.455 | |
get_generated_dataset | 3.731 | 0.004 | 3.743 | |
get_internal_metric_scores | 1.503 | 0.000 | 1.505 | |
get_max_stability | 1.222 | 0.008 | 1.233 | |
get_metric_votes_k | 1.482 | 0.020 | 1.505 | |
get_optimal_features | 12.320 | 0.064 | 12.409 | |
get_optimal_memberships | 9.439 | 0.009 | 9.468 | |
get_optimal_number_of_features | 11.062 | 0.014 | 11.098 | |
get_optimal_parameter_used | 9.657 | 0.028 | 9.705 | |
get_optimal_stability_score | 9.181 | 0.032 | 9.233 | |
get_partition_agreement_scores | 35.410 | 0.084 | 35.578 | |
get_sample_memberships | 34.571 | 0.068 | 34.715 | |
get_vote_frequencies_k | 1.485 | 0.004 | 1.492 | |
omada | 27.380 | 0.052 | 27.493 | |
optimalClustering | 0.526 | 0.004 | 0.532 | |
partitionAgreement | 0.346 | 0.008 | 0.356 | |
plot_average_stabilities | 12.739 | 0.051 | 12.819 | |
plot_cluster_voting | 25.649 | 0.080 | 25.785 | |
plot_feature_selection | 35.616 | 0.032 | 35.725 | |
plot_partition_agreement | 37.484 | 0.092 | 49.069 | |
plot_vote_frequencies | 2.085 | 0.000 | 2.495 | |
toy_gene_memberships | 0.019 | 0.000 | 0.019 | |
toy_genes | 0.001 | 0.000 | 0.001 | |