Federico Marini
| Snapshot Date: 2025-04-21 13:40 -0400 (Mon, 21 Apr 2025) |
| git_url: https://git.bioconductor.org/packages/GeneTonic |
| git_branch: RELEASE_3_21 |
| git_last_commit: b49ba54 |
| git_last_commit_date: 2025-04-15 11:54:19 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-04-22 13:16 -0400 (Tue, 22 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4831 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4553 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4570 |
| 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 825/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneTonic 3.2.0 (landing page) Federico Marini
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the GeneTonic package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeneTonic.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: GeneTonic |
| Version: 3.2.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeneTonic_3.2.0.tar.gz |
| StartedAt: 2025-04-21 20:54:11 -0400 (Mon, 21 Apr 2025) |
| EndedAt: 2025-04-21 21:06:12 -0400 (Mon, 21 Apr 2025) |
| EllapsedTime: 721.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneTonic.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeneTonic_3.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/GeneTonic.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* 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 ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘3.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 38 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 ‘GeneTonic’ 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 ... OK
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 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
gs_mds 7.653 0.413 8.128
GeneTonic 6.760 0.264 7.087
ggs_graph 6.298 0.198 6.550
gs_upset 6.238 0.209 6.510
summarize_ggs_hubgenes 5.917 0.228 6.194
ggs_backbone 5.587 0.215 5.866
gs_scores 5.387 0.201 5.634
gs_heatmap 5.307 0.214 5.571
gs_dendro 5.248 0.221 5.515
signature_volcano 4.850 0.196 5.088
* 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: OK
GeneTonic.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GeneTonic ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘GeneTonic’ ... ** this is package ‘GeneTonic’ version ‘3.2.0’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (GeneTonic)
GeneTonic.Rcheck/tests/testthat.Rout
R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
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(GeneTonic)
Welcome to GeneTonic v3.2.0
If you use GeneTonic in your work, please cite:
GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data
Federico Marini, Annekathrin Ludt, Jan Linke, Konstantin Strauch
BMC Bioinformatics, 2021 - https://doi.org/10.1186/s12859-021-04461-5
and/or (if adopting the series of protocols as a whole)
Interactive and Reproducible Workflows for Exploring and Modeling RNA-seq Data with pcaExplorer, ideal, and GeneTonic
Annekathrin Ludt, Arsenij Ustjanzew, Harald Binder, Konstantin Strauch, Federico Marini
Current Protocols, 2022 - https://doi.org/10.1002/cpz1.411
>
> test_check("GeneTonic")
--- Loading packages...
- Done!
--- Generating objects for the testing setup...
using counts and average transcript lengths from tximeta
'select()' returned 1:many mapping between keys and columns
estimating size factors
using 'avgTxLength' from assays(dds), correcting for library size
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
- Done!
--- Running enrichGO...
--- Running gseGO...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).
preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
Found 500 gene sets in `topGOtableResult` object.
Converting for usage in GeneTonic...
- Done!
---------------------------------
----- GeneTonicList object ------
---------------------------------
----- dds object -----
Providing an expression object (as DESeqDataset) of 17806 features over 24 samples
----- res_de object -----
Providing a DE result object (as DESeqResults), 17806 features tested, 1024 found as DE
Upregulated: 652
Downregulated: 372
----- res_enrich object -----
Providing an enrichment result object, 200 reported
----- annotation_obj object -----
Providing an annotation object of 58294 features with information on 2 identifier types
--- Test setup script completed!
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[ FAIL 0 | WARN 0 | SKIP 0 | PASS 264 ]
>
> proc.time()
user system elapsed
203.916 11.808 186.876
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 6.760 | 0.264 | 7.087 | |
| GeneTonicList | 3.158 | 0.167 | 3.343 | |
| check_colors | 0.010 | 0.001 | 0.011 | |
| checkup_GeneTonic | 3.997 | 0.145 | 4.170 | |
| checkup_gtl | 4.071 | 0.157 | 4.259 | |
| cluster_markov | 0.105 | 0.004 | 0.111 | |
| create_jaccard_matrix | 1.484 | 0.114 | 1.606 | |
| create_kappa_matrix | 3.745 | 0.250 | 4.016 | |
| create_upsetdata | 0.038 | 0.040 | 0.079 | |
| deprecated | 0 | 0 | 0 | |
| deseqresult2df | 0.119 | 0.003 | 0.121 | |
| distill_enrichment | 4.487 | 0.197 | 4.713 | |
| enhance_table | 4.392 | 0.155 | 4.590 | |
| enrichment_map | 4.185 | 0.123 | 4.380 | |
| export_for_iSEE | 3.548 | 0.133 | 3.725 | |
| export_to_sif | 0.067 | 0.013 | 0.081 | |
| gene_plot | 4.441 | 0.145 | 4.638 | |
| geneinfo_2_html | 0.008 | 0.001 | 0.009 | |
| get_aggrscores | 3.907 | 0.153 | 4.084 | |
| get_expression_values | 3.160 | 0.114 | 3.296 | |
| ggs_backbone | 5.587 | 0.215 | 5.866 | |
| ggs_graph | 6.298 | 0.198 | 6.550 | |
| go_2_html | 0.025 | 0.001 | 0.027 | |
| gs_alluvial | 3.143 | 0.216 | 3.377 | |
| gs_dendro | 5.248 | 0.221 | 5.515 | |
| gs_fuzzyclustering | 0.861 | 0.038 | 0.905 | |
| gs_heatmap | 5.307 | 0.214 | 5.571 | |
| gs_horizon | 4.486 | 0.136 | 4.653 | |
| gs_mds | 7.653 | 0.413 | 8.128 | |
| gs_radar | 3.015 | 0.223 | 3.267 | |
| gs_scores | 5.387 | 0.201 | 5.634 | |
| gs_scoresheat | 4.352 | 0.192 | 4.588 | |
| gs_simplify | 1.190 | 0.061 | 1.268 | |
| gs_summary_heat | 4.108 | 0.158 | 4.294 | |
| gs_summary_overview | 3.189 | 0.155 | 3.373 | |
| gs_summary_overview_pair | 3.109 | 0.135 | 3.267 | |
| gs_upset | 6.238 | 0.209 | 6.510 | |
| gs_volcano | 4.567 | 0.151 | 4.755 | |
| happy_hour | 3.061 | 0.156 | 3.249 | |
| map2color | 0.014 | 0.003 | 0.018 | |
| overlap_coefficient | 0.001 | 0.000 | 0.000 | |
| overlap_jaccard_index | 0.000 | 0.000 | 0.001 | |
| shake_davidResult | 0.010 | 0.001 | 0.012 | |
| shake_enrichResult | 1.610 | 0.058 | 1.679 | |
| shake_enrichrResult | 0.063 | 0.003 | 0.066 | |
| shake_fgseaResult | 0.124 | 0.010 | 0.135 | |
| shake_gprofilerResult | 0.098 | 0.010 | 0.109 | |
| shake_gsenrichResult | 2.763 | 0.114 | 2.899 | |
| shake_topGOtableResult | 0.007 | 0.008 | 0.014 | |
| signature_volcano | 4.850 | 0.196 | 5.088 | |
| styleColorBar_divergent | 0.279 | 0.068 | 0.355 | |
| summarize_ggs_hubgenes | 5.917 | 0.228 | 6.194 | |