| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-25 12:05 -0400 (Sat, 25 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 1493/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| omada 1.11.0 (landing page) Sokratis Kariotis
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | NA | NA | ||||||||||
|
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: 1.11.0 |
| 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_1.11.0.tar.gz |
| StartedAt: 2025-10-24 23:00:43 -0400 (Fri, 24 Oct 2025) |
| EndedAt: 2025-10-24 23:13:45 -0400 (Fri, 24 Oct 2025) |
| EllapsedTime: 782.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: omada.Rcheck |
| Warnings: 0 |
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### 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_1.11.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/omada.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 ‘1.11.0’
* 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 43.115 0.677 44.031
get_feature_selection_scores 42.460 0.623 43.290
get_sample_memberships 29.449 7.383 55.183
plot_partition_agreement 35.124 0.843 51.250
get_partition_agreement_scores 30.413 3.993 42.857
plot_feature_selection 31.960 0.546 44.276
get_cluster_voting_memberships 29.618 0.443 30.215
get_cluster_voting_metric_votes 29.165 0.488 29.889
get_cluster_voting_scores 28.485 0.454 29.274
get_feature_selection_optimal_features 28.308 0.481 28.973
get_cluster_voting_k_votes 27.282 0.460 27.857
omada 23.696 1.859 27.891
plot_cluster_voting 21.884 0.714 23.377
plot_average_stabilities 10.411 0.719 11.703
get_optimal_features 10.114 0.120 10.282
get_optimal_number_of_features 9.501 0.117 9.674
get_optimal_stability_score 8.931 0.112 9.088
get_optimal_memberships 8.007 0.094 8.145
featureSelection 7.873 0.086 7.985
get_optimal_parameter_used 7.831 0.101 7.980
* 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-3.22-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 ‘1.11.0’ ** 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 Patched (2025-09-10 r88807) -- "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
93.265 2.031 120.954
omada.Rcheck/omada-Ex.timings
| name | user | system | elapsed | |
| clusterVoting | 4.170 | 0.527 | 4.732 | |
| clusteringMethodSelection | 1.686 | 0.044 | 1.734 | |
| feasibilityAnalysis | 1.266 | 0.013 | 1.283 | |
| feasibilityAnalysisDataBased | 2.769 | 0.069 | 2.846 | |
| featureSelection | 7.873 | 0.086 | 7.985 | |
| get_agreement_scores | 0.157 | 0.004 | 0.161 | |
| get_average_feature_k_stabilities | 4.264 | 0.060 | 4.341 | |
| get_average_stabilities_per_k | 0.860 | 0.006 | 0.870 | |
| get_average_stability | 0.843 | 0.004 | 0.851 | |
| get_cluster_memberships_k | 0.815 | 0.103 | 0.922 | |
| get_cluster_voting_k_votes | 27.282 | 0.460 | 27.857 | |
| get_cluster_voting_memberships | 29.618 | 0.443 | 30.215 | |
| get_cluster_voting_metric_votes | 29.165 | 0.488 | 29.889 | |
| get_cluster_voting_scores | 28.485 | 0.454 | 29.274 | |
| get_feature_selection_optimal_features | 28.308 | 0.481 | 28.973 | |
| get_feature_selection_optimal_number_of_features | 43.115 | 0.677 | 44.031 | |
| get_feature_selection_scores | 42.460 | 0.623 | 43.290 | |
| get_generated_dataset | 2.838 | 0.016 | 2.865 | |
| get_internal_metric_scores | 0.821 | 0.069 | 0.895 | |
| get_max_stability | 0.934 | 0.016 | 0.958 | |
| get_metric_votes_k | 0.839 | 0.115 | 0.960 | |
| get_optimal_features | 10.114 | 0.120 | 10.282 | |
| get_optimal_memberships | 8.007 | 0.094 | 8.145 | |
| get_optimal_number_of_features | 9.501 | 0.117 | 9.674 | |
| get_optimal_parameter_used | 7.831 | 0.101 | 7.980 | |
| get_optimal_stability_score | 8.931 | 0.112 | 9.088 | |
| get_partition_agreement_scores | 30.413 | 3.993 | 42.857 | |
| get_sample_memberships | 29.449 | 7.383 | 55.183 | |
| get_vote_frequencies_k | 0.901 | 0.284 | 1.285 | |
| omada | 23.696 | 1.859 | 27.891 | |
| optimalClustering | 0.084 | 0.005 | 0.088 | |
| partitionAgreement | 0.348 | 0.005 | 0.353 | |
| plot_average_stabilities | 10.411 | 0.719 | 11.703 | |
| plot_cluster_voting | 21.884 | 0.714 | 23.377 | |
| plot_feature_selection | 31.960 | 0.546 | 44.276 | |
| plot_partition_agreement | 35.124 | 0.843 | 51.250 | |
| plot_vote_frequencies | 1.344 | 0.099 | 2.450 | |
| toy_gene_memberships | 0.018 | 0.006 | 0.053 | |
| toy_genes | 0.001 | 0.003 | 0.009 | |