Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-03-20 11:45 -0400 (Thu, 20 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4777
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4458
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 817/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneTonic 3.1.2  (landing page)
Federico Marini
Snapshot Date: 2025-03-19 13:40 -0400 (Wed, 19 Mar 2025)
git_url: https://git.bioconductor.org/packages/GeneTonic
git_branch: devel
git_last_commit: f1af392
git_last_commit_date: 2025-01-09 16:20:19 -0400 (Thu, 09 Jan 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for GeneTonic on kjohnson3

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.

raw results


Summary

Package: GeneTonic
Version: 3.1.2
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_3.1.2.tar.gz
StartedAt: 2025-03-19 19:34:40 -0400 (Wed, 19 Mar 2025)
EndedAt: 2025-03-19 19:39:02 -0400 (Wed, 19 Mar 2025)
EllapsedTime: 262.0 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneTonic.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_3.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/GeneTonic.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘3.1.2’
* 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 ... 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 ... OK
* 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: OK


Installation output

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 ‘3.1.2’
** 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)

Tests output

GeneTonic.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"
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 v3.1.2

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 0 | SKIP 0 | PASS 264 ]
> 
> proc.time()
   user  system elapsed 
 83.666   5.171  70.019 

Example timings

GeneTonic.Rcheck/GeneTonic-Ex.timings

nameusersystemelapsed
GeneTonic2.6160.0662.698
GeneTonicList1.1380.0571.201
check_colors0.0030.0010.003
checkup_GeneTonic1.5810.0501.632
checkup_gtl1.5700.0461.621
cluster_markov0.0320.0010.033
create_jaccard_matrix0.4470.0340.485
create_kappa_matrix1.0720.1761.248
create_upsetdata0.0130.0120.025
deprecated000
deseqresult2df0.0610.0030.064
distill_enrichment1.6900.0551.758
enhance_table1.8800.0511.933
enrichment_map1.6360.0551.692
export_for_iSEE1.6780.0441.725
export_to_sif0.0090.0010.009
gene_plot1.7510.0431.795
geneinfo_2_html0.0030.0000.003
get_aggrscores1.6190.0541.674
get_expression_values1.3220.0341.356
ggs_backbone1.7920.0741.868
ggs_graph2.2430.0852.379
go_2_html0.0070.0000.007
gs_alluvial1.2270.0761.311
gs_dendro2.0470.0992.150
gs_fuzzyclustering0.3140.0370.351
gs_heatmap2.3300.0922.424
gs_horizon1.3100.0511.361
gs_mds2.9260.1823.155
gs_radar1.2150.0711.293
gs_scores1.6590.0841.765
gs_scoresheat2.0690.0742.151
gs_simplify0.3420.0380.388
gs_summary_heat1.2340.0491.289
gs_summary_overview1.7540.0731.833
gs_summary_overview_pair1.2340.0651.327
gs_upset2.6070.0972.725
gs_volcano1.3300.0551.434
happy_hour1.2230.0581.357
map2color0.0060.0010.007
overlap_coefficient0.0000.0010.000
overlap_jaccard_index000
shake_davidResult0.0040.0000.006
shake_enrichResult0.7920.0220.846
shake_enrichrResult0.0240.0010.024
shake_fgseaResult0.0520.0010.056
shake_gprofilerResult0.0400.0020.052
shake_gsenrichResult1.3090.0501.397
shake_topGOtableResult0.0030.0000.003
signature_volcano1.9440.0972.049
styleColorBar_divergent0.0860.0110.097
summarize_ggs_hubgenes1.9060.1012.016