| Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-12-15 12:08 -0500 (Mon, 15 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4882 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4673 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4607 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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 1.12.0 (landing page) Sokratis Kariotis
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / 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. |
| Package: omada |
| Version: 1.12.0 |
| 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_1.12.0.tar.gz |
| StartedAt: 2025-12-13 16:17:53 -0500 (Sat, 13 Dec 2025) |
| EndedAt: 2025-12-13 16:33:03 -0500 (Sat, 13 Dec 2025) |
| EllapsedTime: 910.9 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_1.12.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/omada.Rcheck’
* using R version 4.5.2 Patched (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘omada/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘omada’ version ‘1.12.0’
* 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 41.961 1.046 53.995
get_feature_selection_scores 41.691 1.079 54.936
plot_feature_selection 31.757 0.737 43.395
plot_partition_agreement 31.214 0.702 43.788
get_partition_agreement_scores 29.792 0.717 38.490
get_sample_memberships 29.806 0.656 39.707
get_cluster_voting_k_votes 29.367 0.711 42.157
get_feature_selection_optimal_features 28.934 0.724 39.500
get_cluster_voting_scores 28.187 0.695 40.390
get_cluster_voting_metric_votes 27.900 0.621 40.369
get_cluster_voting_memberships 26.782 0.697 37.342
omada 23.579 0.542 33.280
plot_cluster_voting 22.415 0.544 31.145
get_optimal_number_of_features 10.743 0.173 13.539
get_optimal_features 10.675 0.197 13.358
plot_average_stabilities 10.633 0.206 14.656
get_optimal_stability_score 9.211 0.151 11.911
get_optimal_memberships 8.818 0.172 11.813
get_optimal_parameter_used 7.669 0.156 9.763
featureSelection 6.702 0.139 9.425
clusterVoting 4.211 0.463 6.682
get_average_feature_k_stabilities 4.272 0.090 5.976
feasibilityAnalysisDataBased 3.822 0.096 5.543
* 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-arm64/Resources/library’ * installing *source* package ‘omada’ ... ** this is package ‘omada’ version ‘1.12.0’ ** 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 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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 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
87.130 2.274 123.237
omada.Rcheck/omada-Ex.timings
| name | user | system | elapsed | |
| clusterVoting | 4.211 | 0.463 | 6.682 | |
| clusteringMethodSelection | 1.668 | 0.057 | 2.421 | |
| feasibilityAnalysis | 1.140 | 0.019 | 1.632 | |
| feasibilityAnalysisDataBased | 3.822 | 0.096 | 5.543 | |
| featureSelection | 6.702 | 0.139 | 9.425 | |
| get_agreement_scores | 0.127 | 0.010 | 0.190 | |
| get_average_feature_k_stabilities | 4.272 | 0.090 | 5.976 | |
| get_average_stabilities_per_k | 0.785 | 0.008 | 1.096 | |
| get_average_stability | 0.830 | 0.016 | 1.269 | |
| get_cluster_memberships_k | 0.906 | 0.130 | 1.443 | |
| get_cluster_voting_k_votes | 29.367 | 0.711 | 42.157 | |
| get_cluster_voting_memberships | 26.782 | 0.697 | 37.342 | |
| get_cluster_voting_metric_votes | 27.900 | 0.621 | 40.369 | |
| get_cluster_voting_scores | 28.187 | 0.695 | 40.390 | |
| get_feature_selection_optimal_features | 28.934 | 0.724 | 39.500 | |
| get_feature_selection_optimal_number_of_features | 41.961 | 1.046 | 53.995 | |
| get_feature_selection_scores | 41.691 | 1.079 | 54.936 | |
| get_generated_dataset | 3.035 | 0.038 | 3.959 | |
| get_internal_metric_scores | 0.911 | 0.114 | 1.256 | |
| get_max_stability | 0.793 | 0.022 | 1.109 | |
| get_metric_votes_k | 0.935 | 0.134 | 1.364 | |
| get_optimal_features | 10.675 | 0.197 | 13.358 | |
| get_optimal_memberships | 8.818 | 0.172 | 11.813 | |
| get_optimal_number_of_features | 10.743 | 0.173 | 13.539 | |
| get_optimal_parameter_used | 7.669 | 0.156 | 9.763 | |
| get_optimal_stability_score | 9.211 | 0.151 | 11.911 | |
| get_partition_agreement_scores | 29.792 | 0.717 | 38.490 | |
| get_sample_memberships | 29.806 | 0.656 | 39.707 | |
| get_vote_frequencies_k | 0.928 | 0.113 | 1.606 | |
| omada | 23.579 | 0.542 | 33.280 | |
| optimalClustering | 0.091 | 0.005 | 0.108 | |
| partitionAgreement | 0.279 | 0.012 | 0.437 | |
| plot_average_stabilities | 10.633 | 0.206 | 14.656 | |
| plot_cluster_voting | 22.415 | 0.544 | 31.145 | |
| plot_feature_selection | 31.757 | 0.737 | 43.395 | |
| plot_partition_agreement | 31.214 | 0.702 | 43.788 | |
| plot_vote_frequencies | 1.133 | 0.133 | 1.842 | |
| toy_gene_memberships | 0.019 | 0.007 | 0.040 | |
| toy_genes | 0.001 | 0.004 | 0.009 | |