| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-31 12:05 -0400 (Fri, 31 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| 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 834/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneTonic 3.4.0 (landing page) Federico Marini
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | ERROR | 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: 3.4.0 |
| 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_3.4.0.tar.gz |
| StartedAt: 2025-10-30 19:54:59 -0400 (Thu, 30 Oct 2025) |
| EndedAt: 2025-10-30 19:59:21 -0400 (Thu, 30 Oct 2025) |
| EllapsedTime: 262.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GeneTonic.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### 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_3.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/GeneTonic.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘3.4.0’
* 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 ... ERROR
Running examples in ‘GeneTonic-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gs_upset
> ### Title: Upset plot for genesets
> ### Aliases: gs_upset
>
> ### ** Examples
>
> library("macrophage")
> library("DESeq2")
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: ‘generics’
The following objects are masked from ‘package:base’:
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:utils’:
findMatches
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Seqinfo
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: ‘MatrixGenerics’
The following objects are masked from ‘package:matrixStats’:
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: ‘Biobase’
The following object is masked from ‘package:MatrixGenerics’:
rowMedians
The following objects are masked from ‘package:matrixStats’:
anyMissing, rowMedians
> library("org.Hs.eg.db")
Loading required package: AnnotationDbi
> library("AnnotationDbi")
>
> # dds object
> data("gse", package = "macrophage")
> dds_macrophage <- DESeqDataSet(gse, design = ~ line + condition)
using counts and average transcript lengths from tximeta
> rownames(dds_macrophage) <- substr(rownames(dds_macrophage), 1, 15)
> dds_macrophage <- estimateSizeFactors(dds_macrophage)
using 'avgTxLength' from assays(dds), correcting for library size
>
> # annotation object
> anno_df <- data.frame(
+ gene_id = rownames(dds_macrophage),
+ gene_name = mapIds(org.Hs.eg.db,
+ keys = rownames(dds_macrophage),
+ column = "SYMBOL",
+ keytype = "ENSEMBL"
+ ),
+ stringsAsFactors = FALSE,
+ row.names = rownames(dds_macrophage)
+ )
'select()' returned 1:many mapping between keys and columns
>
> # res object
> data(res_de_macrophage, package = "GeneTonic")
> res_de <- res_macrophage_IFNg_vs_naive
>
> # res_enrich object
> data(res_enrich_macrophage, package = "GeneTonic")
> res_enrich <- shake_topGOtableResult(topgoDE_macrophage_IFNg_vs_naive)
Found 500 gene sets in `topGOtableResult` object.
Converting for usage in GeneTonic...
> res_enrich <- get_aggrscores(res_enrich, res_de, anno_df)
> gs_upset(res_enrich,
+ n_gs = 10
+ )
Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.
ℹ The deprecated feature was likely used in the ComplexUpset package.
Please report the issue at
<https://github.com/krassowski/complex-upset/issues>.
Warning: themes$intersections_matrix is not a valid theme.
Please use `theme()` to construct themes.
Warning: `legend.margin` must be specified using `margin()`
ℹ For the old behavior use `legend.spacing`
Warning: themes$intersections_matrix is not a valid theme.
Please use `theme()` to construct themes.
Warning: selected_theme is not a valid theme.
Please use `theme()` to construct themes.
Warning: `legend.margin` must be specified using `margin()`
ℹ For the old behavior use `legend.spacing`
Warning: selected_theme is not a valid theme.
Please use `theme()` to construct themes.
Warning: themes$overall_sizes is not a valid theme.
Please use `theme()` to construct themes.
Warning: `legend.margin` must be specified using `margin()`
ℹ For the old behavior use `legend.spacing`
Warning: themes$overall_sizes is not a valid theme.
Please use `theme()` to construct themes.
Error in `plot_theme()`:
! The `axis.title.x` theme element must be a <element_text> object.
Backtrace:
▆
1. ├─base (local) `<fn>`(x)
2. └─patchwork:::print.patchwork(x)
3. └─patchwork:::build_patchwork(plot, plot$layout$guides %||% "auto")
4. └─base::lapply(x$plots, plot_table, guides = guides)
5. ├─patchwork (local) FUN(X[[i]], ...)
6. └─patchwork:::plot_table.ggplot(X[[i]], ...)
7. └─ggplot2::ggplotGrob(x)
8. ├─ggplot2::ggplot_gtable(ggplot_build(x))
9. │ └─ggplot2:::attach_plot_env(data@plot@plot_env)
10. │ └─base::options(ggplot2_plot_env = env)
11. ├─ggplot2::ggplot_build(x)
12. └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
13. └─ggplot2:::plot_theme(plot)
14. └─ggplot2:::check_theme(theme)
15. └─base::mapply(...)
16. └─ggplot2 (local) `<fn>`(...)
17. └─cli::cli_abort(...)
18. └─rlang::abort(...)
Execution halted
* 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: 1 ERROR, 1 NOTE
See
‘/Users/biocbuild/bbs-3.22-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/4.5-arm64/Resources/library’ * installing *source* package ‘GeneTonic’ ... ** this is package ‘GeneTonic’ version ‘3.4.0’ ** 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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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 v3.4.0
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 34 | SKIP 0 | PASS 262 ]
[ FAIL 0 | WARN 34 | SKIP 0 | PASS 262 ]
>
> proc.time()
user system elapsed
85.519 5.213 74.605
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 2.792 | 0.069 | 2.864 | |
| GeneTonicList | 1.612 | 0.053 | 1.667 | |
| check_colors | 0.003 | 0.000 | 0.003 | |
| checkup_GeneTonic | 1.614 | 0.049 | 1.664 | |
| checkup_gtl | 1.597 | 0.045 | 1.642 | |
| cluster_markov | 0.036 | 0.001 | 0.037 | |
| create_jaccard_matrix | 0.432 | 0.031 | 0.462 | |
| create_kappa_matrix | 1.182 | 0.095 | 1.277 | |
| create_upsetdata | 0.013 | 0.013 | 0.026 | |
| deprecated | 0 | 0 | 0 | |
| deseqresult2df | 0.061 | 0.001 | 0.062 | |
| distill_enrichment | 1.713 | 0.071 | 1.785 | |
| enhance_table | 1.938 | 0.052 | 1.990 | |
| enrichment_map | 1.549 | 0.050 | 1.599 | |
| export_for_iSEE | 1.690 | 0.037 | 1.728 | |
| export_to_sif | 0.010 | 0.001 | 0.010 | |
| gene_plot | 1.856 | 0.045 | 1.901 | |
| geneinfo_2_html | 0.003 | 0.000 | 0.003 | |
| get_aggrscores | 1.655 | 0.056 | 1.712 | |
| get_expression_values | 0.872 | 0.040 | 0.917 | |
| ggs_backbone | 2.291 | 0.098 | 2.396 | |
| ggs_graph | 1.787 | 0.080 | 1.892 | |
| go_2_html | 0.007 | 0.001 | 0.008 | |
| gs_alluvial | 1.710 | 0.069 | 1.782 | |
| gs_dendro | 2.029 | 0.097 | 2.134 | |
| gs_fuzzyclustering | 0.323 | 0.041 | 0.370 | |
| gs_heatmap | 2.410 | 0.104 | 2.532 | |
| gs_horizon | 1.428 | 0.057 | 1.491 | |
| gs_mds | 3.056 | 0.303 | 3.366 | |
| gs_radar | 1.226 | 0.123 | 1.362 | |
| gs_scores | 1.609 | 0.133 | 1.752 | |
| gs_scoresheat | 2.110 | 0.100 | 2.211 | |
| gs_simplify | 0.350 | 0.024 | 0.377 | |
| gs_summary_heat | 1.284 | 0.055 | 1.366 | |
| gs_summary_overview | 1.843 | 0.056 | 1.900 | |
| gs_summary_overview_pair | 1.267 | 0.046 | 1.315 | |