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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (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 1445/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
omada 1.8.0  (landing page)
Sokratis Kariotis
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/omada
git_branch: RELEASE_3_20
git_last_commit: 8b5b5fd
git_last_commit_date: 2024-10-29 11:13:51 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for omada on merida1

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.

raw results


Summary

Package: omada
Version: 1.8.0
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_1.8.0.tar.gz
StartedAt: 2024-12-20 07:05:14 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 07:26:03 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 1248.7 seconds
RetCode: 0
Status:   OK  
CheckDir: omada.Rcheck
Warnings: 0

Command output

##############################################################################
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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_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/omada.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* 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 ‘1.8.0’
* 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 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 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 75.216  0.748  77.154
get_feature_selection_scores                     72.795  0.756  77.174
plot_partition_agreement                         53.253  0.679  88.976
plot_feature_selection                           50.273  0.498  52.486
get_cluster_voting_scores                        50.190  0.528  51.907
get_feature_selection_optimal_features           50.111  0.497  51.463
get_sample_memberships                           49.966  0.577  52.592
get_cluster_voting_k_votes                       49.890  0.552  51.434
get_partition_agreement_scores                   49.824  0.539  51.972
get_cluster_voting_memberships                   49.564  0.509  50.912
get_cluster_voting_metric_votes                  48.566  0.529  49.455
omada                                            39.851  0.408  42.022
plot_cluster_voting                              37.430  0.364  38.618
plot_average_stabilities                         17.064  0.148  17.852
get_optimal_features                             16.623  0.175  16.922
get_optimal_number_of_features                   16.610  0.132  17.247
get_optimal_parameter_used                       14.378  0.134  15.367
get_optimal_memberships                          14.266  0.153  14.621
get_optimal_stability_score                      13.770  0.109  14.447
featureSelection                                 12.797  0.153  13.096
clusterVoting                                     7.545  0.768   8.534
get_average_feature_k_stabilities                 7.760  0.067   7.898
get_generated_dataset                             5.661  0.027   5.745
* 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
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/omada.Rcheck/00check.log’
for details.


Installation output

omada.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL omada
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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)

Tests output

omada.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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 4.1-8
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 
150.917   2.032 200.348 

Example timings

omada.Rcheck/omada-Ex.timings

nameusersystemelapsed
clusterVoting7.5450.7688.534
clusteringMethodSelection2.4330.0562.513
feasibilityAnalysis2.7630.0292.978
feasibilityAnalysisDataBased4.4810.1104.750
featureSelection12.797 0.15313.096
get_agreement_scores0.2850.0060.300
get_average_feature_k_stabilities7.7600.0677.898
get_average_stabilities_per_k1.9240.0121.949
get_average_stability1.9430.0071.987
get_cluster_memberships_k1.6800.1421.833
get_cluster_voting_k_votes49.890 0.55251.434
get_cluster_voting_memberships49.564 0.50950.912
get_cluster_voting_metric_votes48.566 0.52949.455
get_cluster_voting_scores50.190 0.52851.907
get_feature_selection_optimal_features50.111 0.49751.463
get_feature_selection_optimal_number_of_features75.216 0.74877.154
get_feature_selection_scores72.795 0.75677.174
get_generated_dataset5.6610.0275.745
get_internal_metric_scores1.6430.1361.788
get_max_stability1.9490.0101.999
get_metric_votes_k1.6530.1211.788
get_optimal_features16.623 0.17516.922
get_optimal_memberships14.266 0.15314.621
get_optimal_number_of_features16.610 0.13217.247
get_optimal_parameter_used14.378 0.13415.367
get_optimal_stability_score13.770 0.10914.447
get_partition_agreement_scores49.824 0.53951.972
get_sample_memberships49.966 0.57752.592
get_vote_frequencies_k1.6770.0951.970
omada39.851 0.40842.022
optimalClustering0.1900.0090.207
partitionAgreement0.5550.0050.581
plot_average_stabilities17.064 0.14817.852
plot_cluster_voting37.430 0.36438.618
plot_feature_selection50.273 0.49852.486
plot_partition_agreement53.253 0.67988.976
plot_vote_frequencies2.0550.0954.365
toy_gene_memberships0.0280.0070.067
toy_genes0.0020.0040.006