Federico Marini
| Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/GeneTonic |
| git_branch: RELEASE_3_18 |
| git_last_commit: c3f7778 |
| git_last_commit_date: 2023-10-24 11:19:17 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:37:45 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 810/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneTonic 2.6.0 (landing page) Federico Marini
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 2.6.0 |
| 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_2.6.0.tar.gz |
| StartedAt: 2024-04-16 03:12:31 -0400 (Tue, 16 Apr 2024) |
| EndedAt: 2024-04-16 03:30:05 -0400 (Tue, 16 Apr 2024) |
| EllapsedTime: 1054.2 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_2.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/GeneTonic.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘2.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 R 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 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 ... OK
* 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
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, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, 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: GenomeInfoDb
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
+ )
Error in `plot_theme()`:
! The `legend.text.align` theme element is not defined in the element
hierarchy.
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:::ggplot_gtable.ggplot_built(ggplot_build(x))
10. └─ggplot2:::plot_theme(plot)
11. └─ggplot2:::validate_theme(theme)
12. └─base::mapply(...)
13. └─ggplot2 (local) `<fn>`(...)
14. └─cli::cli_abort(...)
15. └─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 in ‘inst/doc’ ... 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
See
‘/Users/biocbuild/bbs-3.18-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/4.3-x86_64/Resources/library’ * installing *source* package ‘GeneTonic’ ... ** 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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)
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)
>
> 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...
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, 928 found as DE
Upregulated: 599
Downregulated: 329
----- 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 10 | SKIP 0 | PASS 264 ]
[ FAIL 0 | WARN 10 | SKIP 0 | PASS 264 ]
>
> proc.time()
user system elapsed
343.956 14.204 334.408
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 9.003 | 0.390 | 9.992 | |
| GeneTonicList | 6.140 | 0.210 | 7.086 | |
| check_colors | 0.018 | 0.004 | 0.022 | |
| checkup_GeneTonic | 6.268 | 0.203 | 6.836 | |
| checkup_gtl | 6.089 | 0.185 | 6.626 | |
| cluster_markov | 0.175 | 0.006 | 0.190 | |
| create_jaccard_matrix | 2.265 | 0.135 | 2.632 | |
| create_kappa_matrix | 6.125 | 0.346 | 7.131 | |
| create_upsetdata | 0.090 | 0.127 | 0.221 | |
| deseqresult2df | 0.250 | 0.008 | 0.268 | |
| distill_enrichment | 6.847 | 0.199 | 7.495 | |
| enhance_table | 8.416 | 0.186 | 8.991 | |
| enrichment_map | 5.996 | 0.150 | 6.213 | |
| export_for_iSEE | 7.081 | 0.171 | 7.378 | |
| export_to_sif | 0.039 | 0.003 | 0.042 | |
| gene_plot | 8.097 | 0.200 | 8.618 | |
| geneinfo_2_html | 0.015 | 0.001 | 0.017 | |
| get_aggrscores | 5.190 | 0.139 | 5.598 | |
| get_expression_values | 3.742 | 0.134 | 4.070 | |
| ggs_backbone | 11.109 | 0.377 | 12.212 | |
| ggs_graph | 11.189 | 0.317 | 12.443 | |
| go_2_html | 0.048 | 0.001 | 0.056 | |
| gs_alluvial | 6.431 | 0.346 | 7.597 | |
| gs_dendro | 8.593 | 0.242 | 9.174 | |
| gs_fuzzyclustering | 1.692 | 0.136 | 2.009 | |
| gs_heatmap | 10.518 | 0.261 | 11.402 | |
| gs_horizon | 7.355 | 0.200 | 7.953 | |
| gs_mds | 12.609 | 0.576 | 13.735 | |
| gs_radar | 5.463 | 0.304 | 6.116 | |
| gs_scores | 9.961 | 0.258 | 10.544 | |
| gs_scoresheat | 7.942 | 0.186 | 8.489 | |
| gs_simplify | 2.865 | 0.115 | 3.151 | |
| gs_summary_heat | 6.465 | 0.186 | 6.901 | |
| gs_summary_overview | 5.922 | 0.136 | 6.324 | |
| gs_summary_overview_pair | 5.699 | 0.162 | 6.098 | |