| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-13 11:34 -0400 (Fri, 13 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4819 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences" | 4049 |
| 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 839/2360 | 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 | ERROR | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| See other builds for GeneTonic in R Universe. | ||||||||||||||
|
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: /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_3.5.0.tar.gz |
| StartedAt: 2026-03-12 18:41:49 -0400 (Thu, 12 Mar 2026) |
| EndedAt: 2026-03-12 18:47:34 -0400 (Thu, 12 Mar 2026) |
| EllapsedTime: 345.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GeneTonic.Rcheck |
| Warnings: NA |
##############################################################################
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###
### 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_3.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/GeneTonic.Rcheck’
* using R Under development (unstable) (2026-03-01 r89506)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Sonoma 14.8.3
* using session charset: UTF-8
* current time: 2026-03-12 22:41:49 UTC
* using option ‘--no-vignettes’
* 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 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-gs_shaker.R:23:3'): Converting from clusterProfiler ────────────
Error in `shake_enrichResult(ego_IFNg_vs_naive)`: Provided object must be of class `enrichResult`
Backtrace:
▆
1. └─GeneTonic::shake_enrichResult(ego_IFNg_vs_naive) at test-gs_shaker.R:23:3
[ FAIL 1 | WARN 1 | SKIP 1 | PASS 254 ]
Error:
! Test failures.
Warning message:
In clusterProfiler::bitr(gene, fromType = keyType, toType = "ENTREZID", :
2.44% of input gene IDs are fail to map...
Execution halted
* 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: 1 ERROR, 1 NOTE
See
‘/Users/biocbuild/bbs-3.23-bioc/meat/GeneTonic.Rcheck/00check.log’
for details.
GeneTonic.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GeneTonic ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/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.fail
R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
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...
'select()' returned 1:1 mapping between keys and columns
No gene sets have size between 10 and 500 ...
--> return NULL...
--- Running gseGO...
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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Saving _problems/test-gs_shaker-23.R
[ FAIL 1 | WARN 1 | SKIP 1 | PASS 254 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1):
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-gs_shaker.R:23:3'): Converting from clusterProfiler ────────────
Error in `shake_enrichResult(ego_IFNg_vs_naive)`: Provided object must be of class `enrichResult`
Backtrace:
▆
1. └─GeneTonic::shake_enrichResult(ego_IFNg_vs_naive) at test-gs_shaker.R:23:3
[ FAIL 1 | WARN 1 | SKIP 1 | PASS 254 ]
Error:
! Test failures.
Warning message:
In clusterProfiler::bitr(gene, fromType = keyType, toType = "ENTREZID", :
2.44% of input gene IDs are fail to map...
Execution halted
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 2.396 | 0.073 | 2.498 | |
| GeneTonicList | 1.708 | 0.046 | 1.796 | |
| check_colors | 0.003 | 0.001 | 0.003 | |
| checkup_GeneTonic | 1.184 | 0.062 | 1.312 | |
| checkup_gtl | 2.146 | 0.049 | 2.223 | |
| cluster_markov | 0.039 | 0.002 | 0.042 | |
| create_jaccard_matrix | 0.501 | 0.024 | 0.554 | |
| create_kappa_matrix | 1.429 | 0.149 | 1.620 | |
| create_upsetdata | 0.014 | 0.014 | 0.031 | |
| deprecated | 0 | 0 | 0 | |
| deseqresult2df | 0.065 | 0.002 | 0.078 | |
| distill_enrichment | 1.833 | 0.061 | 1.978 | |
| enhance_table | 1.637 | 0.068 | 1.754 | |
| enrichment_map | 1.734 | 0.055 | 1.822 | |
| export_for_iSEE | 1.811 | 0.058 | 1.885 | |
| export_to_sif | 0.011 | 0.001 | 0.011 | |
| gene_plot | 1.424 | 0.052 | 1.492 | |
| geneinfo_2_html | 0.003 | 0.001 | 0.003 | |
| get_aggrscores | 1.791 | 0.050 | 1.882 | |
| get_expression_values | 0.900 | 0.038 | 0.955 | |
| ggs_backbone | 3.059 | 0.095 | 3.189 | |
| ggs_graph | 1.912 | 0.085 | 2.065 | |
| go_2_html | 0.007 | 0.000 | 0.008 | |
| gs_alluvial | 1.295 | 0.070 | 1.417 | |
| gs_dendro | 2.236 | 0.101 | 2.412 | |
| gs_fuzzyclustering | 0.374 | 0.037 | 0.423 | |
| gs_heatmap | 1.993 | 0.095 | 2.130 | |
| gs_horizon | 2.045 | 0.074 | 2.162 | |
| gs_mds | 2.907 | 0.223 | 3.236 | |
| gs_radar | 1.865 | 0.084 | 2.071 | |
| gs_scores | 1.720 | 0.081 | 1.838 | |
| gs_scoresheat | 2.233 | 0.090 | 2.364 | |
| gs_simplify | 0.403 | 0.030 | 0.440 | |
| gs_summary_heat | 1.297 | 0.088 | 1.412 | |
| gs_summary_overview | 1.401 | 0.073 | 1.533 | |
| gs_summary_overview_pair | 1.928 | 0.082 | 2.063 | |
| gs_upset | 2.623 | 0.091 | 2.827 | |
| gs_volcano | 1.991 | 0.063 | 2.135 | |
| happy_hour | 1.893 | 0.077 | 2.032 | |
| map2color | 0.006 | 0.003 | 0.008 | |
| overlap_coefficient | 0.000 | 0.000 | 0.001 | |
| overlap_jaccard_index | 0 | 0 | 0 | |
| shake_davidResult | 0.004 | 0.000 | 0.005 | |
| shake_enrichResult | 0.800 | 0.022 | 0.874 | |
| shake_enrichrResult | 0.024 | 0.001 | 0.029 | |
| shake_fgseaResult | 0.056 | 0.001 | 0.061 | |
| shake_gprofilerResult | 0.046 | 0.001 | 0.048 | |
| shake_gsenrichResult | 0.818 | 0.027 | 0.853 | |
| shake_topGOtableResult | 0.004 | 0.002 | 0.006 | |
| signature_volcano | 2.155 | 0.086 | 2.297 | |
| styleColorBar_divergent | 0.088 | 0.011 | 0.101 | |
| summarize_ggs_hubgenes | 2.146 | 0.129 | 2.345 | |