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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GeneTonic_3.3.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/GeneTonic.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘3.3.3’
* 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 ... 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
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
gs_mds        9.499  0.020   9.547
ggs_graph     7.780  0.028   7.828
gs_heatmap    7.554  0.020   7.593
ggs_backbone  7.064  0.027   7.116
GeneTonic     6.659  0.191   6.874
gs_scores     6.531  0.080   6.628
enhance_table 6.218  0.068   6.306
gs_dendro     5.854  0.064   5.932
gene_plot     5.576  0.016   5.606
gs_scoresheat 5.399  0.012   5.425
* 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/GeneTonic.Rcheck/00check.log’
for details.