Federico Marini
| Snapshot Date: 2025-11-13 13:40 -0500 (Thu, 13 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/GeneTonic |
| git_branch: devel |
| git_last_commit: 0340f38 |
| git_last_commit_date: 2025-10-29 10:56:40 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-14 11:35 -0500 (Fri, 14 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4825 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4547 |
| 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 824/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneTonic 3.5.0 (landing page) Federico Marini
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | 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: 3.5.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings GeneTonic_3.5.0.tar.gz |
| StartedAt: 2025-11-13 23:51:54 -0500 (Thu, 13 Nov 2025) |
| EndedAt: 2025-11-14 00:04:32 -0500 (Fri, 14 Nov 2025) |
| EllapsedTime: 758.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneTonic.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings GeneTonic_3.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/GeneTonic.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘3.5.0’
* 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 loading without being on the library search path ... 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'deprecated.Rd':
‘[mosdef:create_link_genecards]{mosdef::create_link_GeneCards()}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 8.629 0.030 8.659
gs_upset 8.181 0.413 8.594
gene_plot 7.669 0.178 7.847
GeneTonic 7.136 0.336 7.474
gs_scores 6.193 0.854 7.048
signature_volcano 6.479 0.254 6.735
ggs_backbone 6.476 0.159 6.635
gs_heatmap 6.289 0.018 6.309
export_for_iSEE 5.678 0.091 5.771
summarize_ggs_hubgenes 5.545 0.199 5.744
gs_dendro 5.267 0.045 5.313
gs_summary_heat 4.480 0.750 5.232
ggs_graph 5.008 0.120 5.128
gs_scoresheat 4.625 0.413 5.039
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/GeneTonic.Rcheck/00check.log’
for details.
GeneTonic.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL GeneTonic ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘GeneTonic’ ... ** this is package ‘GeneTonic’ version ‘3.5.0’ ** 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 Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(GeneTonic)
Welcome to GeneTonic v3.5.0
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 1 | SKIP 1 | PASS 262 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1):
[ FAIL 0 | WARN 1 | SKIP 1 | PASS 262 ]
>
> proc.time()
user system elapsed
198.938 7.886 176.351
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 7.136 | 0.336 | 7.474 | |
| GeneTonicList | 2.979 | 0.103 | 3.082 | |
| check_colors | 0.007 | 0.001 | 0.008 | |
| checkup_GeneTonic | 3.840 | 0.162 | 4.001 | |
| checkup_gtl | 4.002 | 0.140 | 4.143 | |
| cluster_markov | 0.102 | 0.001 | 0.103 | |
| create_jaccard_matrix | 1.281 | 0.021 | 1.302 | |
| create_kappa_matrix | 4.876 | 0.040 | 4.915 | |
| create_upsetdata | 0.032 | 0.047 | 0.080 | |
| deprecated | 0 | 0 | 0 | |
| deseqresult2df | 0.143 | 0.005 | 0.148 | |
| distill_enrichment | 3.536 | 0.048 | 3.583 | |
| enhance_table | 4.392 | 0.068 | 4.460 | |
| enrichment_map | 3.142 | 0.073 | 3.215 | |
| export_for_iSEE | 5.678 | 0.091 | 5.771 | |
| export_to_sif | 0.050 | 0.000 | 0.051 | |
| gene_plot | 7.669 | 0.178 | 7.847 | |
| geneinfo_2_html | 0.016 | 0.000 | 0.016 | |
| get_aggrscores | 4.665 | 0.175 | 4.840 | |
| get_expression_values | 2.274 | 0.053 | 2.327 | |
| ggs_backbone | 6.476 | 0.159 | 6.635 | |
| ggs_graph | 5.008 | 0.120 | 5.128 | |
| go_2_html | 0.022 | 0.002 | 0.024 | |
| gs_alluvial | 3.179 | 0.099 | 3.287 | |
| gs_dendro | 5.267 | 0.045 | 5.313 | |
| gs_fuzzyclustering | 0.942 | 0.003 | 0.946 | |
| gs_heatmap | 6.289 | 0.018 | 6.309 | |
| gs_horizon | 4.876 | 0.085 | 4.961 | |
| gs_mds | 8.629 | 0.030 | 8.659 | |
| gs_radar | 3.196 | 0.039 | 3.236 | |
| gs_scores | 6.193 | 0.854 | 7.048 | |
| gs_scoresheat | 4.625 | 0.413 | 5.039 | |
| gs_simplify | 1.115 | 0.161 | 1.276 | |
| gs_summary_heat | 4.480 | 0.750 | 5.232 | |
| gs_summary_overview | 3.571 | 0.062 | 3.633 | |
| gs_summary_overview_pair | 3.342 | 0.141 | 3.483 | |
| gs_upset | 8.181 | 0.413 | 8.594 | |
| gs_volcano | 3.919 | 0.086 | 4.005 | |
| happy_hour | 3.196 | 0.153 | 3.349 | |
| map2color | 0.012 | 0.002 | 0.014 | |
| overlap_coefficient | 0.000 | 0.000 | 0.001 | |
| overlap_jaccard_index | 0.000 | 0.000 | 0.001 | |
| shake_davidResult | 0.010 | 0.000 | 0.011 | |
| shake_enrichResult | 1.792 | 0.068 | 1.860 | |
| shake_enrichrResult | 0.042 | 0.004 | 0.048 | |
| shake_fgseaResult | 0.119 | 0.002 | 0.121 | |
| shake_gprofilerResult | 0.084 | 0.007 | 0.092 | |
| shake_gsenrichResult | 1.850 | 0.081 | 1.931 | |
| shake_topGOtableResult | 0.005 | 0.002 | 0.007 | |
| signature_volcano | 6.479 | 0.254 | 6.735 | |
| styleColorBar_divergent | 0.203 | 0.012 | 0.218 | |
| summarize_ggs_hubgenes | 5.545 | 0.199 | 5.744 | |