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This page was generated on 2024-06-21 13:21 -0400 (Fri, 21 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4690
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4404
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4353
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 795/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneTonic 2.9.0  (landing page)
Federico Marini
Snapshot Date: 2024-06-20 14:00 -0400 (Thu, 20 Jun 2024)
git_url: https://git.bioconductor.org/packages/GeneTonic
git_branch: devel
git_last_commit: 9473081
git_last_commit_date: 2024-04-30 11:20:41 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  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 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for GeneTonic on nebbiolo2

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: 2.9.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GeneTonic_2.9.0.tar.gz
StartedAt: 2024-06-20 23:25:26 -0400 (Thu, 20 Jun 2024)
EndedAt: 2024-06-20 23:35:08 -0400 (Thu, 20 Jun 2024)
EllapsedTime: 582.1 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneTonic.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GeneTonic_2.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/GeneTonic.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘2.9.0’
* 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 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 ... 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
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
gs_mds                 7.037  0.119   7.157
gs_heatmap             6.582  0.100   6.682
ggs_backbone           5.681  0.187   5.868
GeneTonic              5.518  0.280   5.799
ggs_graph              5.637  0.129   5.766
gs_upset               5.513  0.051   5.566
summarize_ggs_hubgenes 5.332  0.075   5.409
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

GeneTonic.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL GeneTonic
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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)

Tests output

GeneTonic.Rcheck/tests/testthat.Rout


R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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...
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 
180.842   8.807 158.408 

Example timings

GeneTonic.Rcheck/GeneTonic-Ex.timings

nameusersystemelapsed
GeneTonic5.5180.2805.799
GeneTonicList4.2370.1764.413
check_colors0.0090.0000.009
checkup_GeneTonic3.6360.0883.724
checkup_gtl3.3860.1483.534
cluster_markov0.0810.0030.084
create_jaccard_matrix0.7810.0690.850
create_kappa_matrix3.0840.0363.120
create_upsetdata0.0320.0070.040
deseqresult2df0.1410.0010.141
distill_enrichment3.8280.1874.016
enhance_table3.7090.0483.758
enrichment_map3.5320.0363.569
export_for_iSEE3.0690.0523.120
export_to_sif0.0210.0010.023
gene_plot4.0810.1254.205
geneinfo_2_html0.0060.0000.006
get_aggrscores2.7760.0402.815
get_expression_values2.8150.0592.875
ggs_backbone5.6810.1875.868
ggs_graph5.6370.1295.766
go_2_html0.0190.0000.019
gs_alluvial3.6610.0993.762
gs_dendro3.9800.0674.048
gs_fuzzyclustering0.890.000.89
gs_heatmap6.5820.1006.682
gs_horizon3.2820.0733.353
gs_mds7.0370.1197.157
gs_radar2.9780.0753.053
gs_scores4.7860.0404.825
gs_scoresheat4.7840.1004.884
gs_simplify0.9760.0000.976
gs_summary_heat3.0400.0523.092
gs_summary_overview4.0530.1444.198
gs_summary_overview_pair2.9690.0453.013
gs_upset5.5130.0515.566
gs_volcano3.4540.0713.525
happy_hour3.5850.0483.633
map2color0.0100.0020.012
overlap_coefficient000
overlap_jaccard_index0.0000.0000.001
shake_davidResult0.0080.0000.009
shake_enrichResult1.6340.0401.674
shake_enrichrResult0.0490.0000.049
shake_fgseaResult0.1190.0000.120
shake_gprofilerResult0.1600.0010.160
shake_gsenrichResult1.6070.0561.663
shake_topGOtableResult0.0060.0020.007
signature_volcano4.8430.0844.927
styleColorBar_divergent0.2080.0000.208
summarize_ggs_hubgenes5.3320.0755.409