Federico Marini
| Snapshot Date: 2025-11-04 13:40 -0500 (Tue, 04 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 Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-05 11:32 -0500 (Wed, 05 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" | 4818 |
| 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 824/2323 | 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 | | ||||||||
|
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: 2025-11-04 23:39:33 -0500 (Tue, 04 Nov 2025) |
| EndedAt: 2025-11-04 23:51:58 -0500 (Tue, 04 Nov 2025) |
| EllapsedTime: 745.0 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 8.650 0.380 9.030
gs_upset 8.106 0.323 8.430
gs_summary_heat 7.898 0.446 8.344
GeneTonic 6.404 0.638 7.044
gs_heatmap 6.405 0.543 6.949
signature_volcano 6.435 0.226 6.663
ggs_backbone 6.161 0.137 6.298
gs_scores 5.587 0.369 5.958
gs_dendro 5.699 0.098 5.797
summarize_ggs_hubgenes 5.430 0.111 5.543
gs_horizon 5.024 0.391 5.415
* 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 0 | PASS 262 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 262 ]
>
> proc.time()
user system elapsed
196.766 9.798 176.200
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 6.404 | 0.638 | 7.044 | |
| GeneTonicList | 2.791 | 0.147 | 2.939 | |
| check_colors | 0.006 | 0.001 | 0.008 | |
| checkup_GeneTonic | 3.784 | 0.278 | 4.062 | |
| checkup_gtl | 3.943 | 0.169 | 4.115 | |
| cluster_markov | 0.092 | 0.000 | 0.094 | |
| create_jaccard_matrix | 1.198 | 0.032 | 1.231 | |
| create_kappa_matrix | 4.699 | 0.226 | 4.924 | |
| create_upsetdata | 0.026 | 0.047 | 0.075 | |
| deprecated | 0 | 0 | 0 | |
| deseqresult2df | 0.135 | 0.004 | 0.141 | |
| distill_enrichment | 3.265 | 0.061 | 3.328 | |
| enhance_table | 4.132 | 0.087 | 4.221 | |
| enrichment_map | 2.948 | 0.070 | 3.018 | |
| export_for_iSEE | 4.366 | 0.248 | 4.615 | |
| export_to_sif | 0.020 | 0.002 | 0.023 | |
| gene_plot | 4.615 | 0.076 | 4.691 | |
| geneinfo_2_html | 0.008 | 0.000 | 0.008 | |
| get_aggrscores | 3.758 | 0.123 | 3.881 | |
| get_expression_values | 2.121 | 0.047 | 2.167 | |
| ggs_backbone | 6.161 | 0.137 | 6.298 | |
| ggs_graph | 4.799 | 0.111 | 4.909 | |
| go_2_html | 0.022 | 0.000 | 0.021 | |
| gs_alluvial | 3.027 | 0.115 | 3.141 | |
| gs_dendro | 5.699 | 0.098 | 5.797 | |
| gs_fuzzyclustering | 0.98 | 0.05 | 1.03 | |
| gs_heatmap | 6.405 | 0.543 | 6.949 | |
| gs_horizon | 5.024 | 0.391 | 5.415 | |
| gs_mds | 8.65 | 0.38 | 9.03 | |
| gs_radar | 3.086 | 0.136 | 3.222 | |
| gs_scores | 5.587 | 0.369 | 5.958 | |
| gs_scoresheat | 4.351 | 0.118 | 4.469 | |
| gs_simplify | 1.097 | 0.027 | 1.124 | |
| gs_summary_heat | 7.898 | 0.446 | 8.344 | |
| gs_summary_overview | 3.945 | 0.088 | 4.034 | |
| gs_summary_overview_pair | 3.416 | 0.065 | 3.481 | |
| gs_upset | 8.106 | 0.323 | 8.430 | |
| gs_volcano | 3.676 | 0.111 | 3.788 | |
| happy_hour | 3.119 | 0.079 | 3.198 | |
| map2color | 0.010 | 0.003 | 0.014 | |
| overlap_coefficient | 0.001 | 0.000 | 0.001 | |
| overlap_jaccard_index | 0.000 | 0.001 | 0.001 | |
| shake_davidResult | 0.009 | 0.000 | 0.010 | |
| shake_enrichResult | 1.852 | 0.060 | 1.912 | |
| shake_enrichrResult | 0.048 | 0.002 | 0.051 | |
| shake_fgseaResult | 0.124 | 0.000 | 0.124 | |
| shake_gprofilerResult | 0.087 | 0.005 | 0.093 | |
| shake_gsenrichResult | 1.873 | 0.047 | 1.921 | |
| shake_topGOtableResult | 0.007 | 0.000 | 0.008 | |
| signature_volcano | 6.435 | 0.226 | 6.663 | |
| styleColorBar_divergent | 0.187 | 0.016 | 0.209 | |
| summarize_ggs_hubgenes | 5.430 | 0.111 | 5.543 | |