Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:06:08 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

CHECK results for GeneTonic on lconway


To the developers/maintainers of the GeneTonic package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 773/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneTonic 2.2.0  (landing page)
Federico Marini
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/GeneTonic
git_branch: RELEASE_3_16
git_last_commit: cbc0a9f
git_last_commit_date: 2022-11-01 11:21:18 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GeneTonic
Version: 2.2.0
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_2.2.0.tar.gz
StartedAt: 2023-04-10 20:22:23 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 20:31:01 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 518.5 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_2.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/GeneTonic.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘2.2.0’
* 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 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                 6.110  0.458   6.586
GeneTonic              6.143  0.227   6.403
summarize_ggs_hubgenes 6.119  0.245   6.398
gs_upset               5.958  0.175   6.150
gs_heatmap             5.543  0.186   5.744
signature_volcano      5.497  0.193   5.710
ggs_backbone           5.419  0.226   5.673
ggs_graph              5.356  0.241   5.618
gs_scores              4.965  0.330   5.387
gene_plot              4.980  0.208   5.253
* 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: 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/4.2/Resources/library’
* installing *source* package ‘GeneTonic’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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:     329
Downregulated:   599

----- 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 4 | SKIP 0 | PASS 258 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 258 ]
> 
> proc.time()
   user  system elapsed 
192.718  15.653 160.215 

Example timings

GeneTonic.Rcheck/GeneTonic-Ex.timings

nameusersystemelapsed
GeneTonic6.1430.2276.403
GeneTonicList3.6820.1723.872
check_colors0.0070.0010.008
checkup_GeneTonic3.6510.1313.795
checkup_gtl3.6290.1663.820
cluster_markov0.0900.0040.095
create_jaccard_matrix0.7690.0650.844
create_kappa_matrix2.7830.4413.233
create_upsetdata0.0340.0350.070
deseqresult2df0.1380.0030.141
distill_enrichment3.9650.1724.155
enhance_table4.0560.1334.211
enrichment_map3.7740.1483.939
export_for_iSEE4.1310.1594.330
export_to_sif0.0200.0020.022
gene_plot4.9800.2085.253
geneinfo_2_html0.0060.0010.007
get_aggrscores3.5400.1163.667
get_expression_values3.0140.1483.221
ggs_backbone5.4190.2265.673
ggs_graph5.3560.2415.618
go_2_html0.0190.0000.020
gs_alluvial3.6000.1773.785
gs_dendro4.4800.2424.736
gs_fuzzyclustering0.7370.0660.807
gs_heatmap5.5430.1865.744
gs_horizon4.0910.2384.343
gs_mds6.1100.4586.586
gs_radar3.7030.2553.971
gs_scores4.9650.3305.387
gs_scoresheat3.9940.2064.216
gs_simplify1.0110.0351.054
gs_summary_heat3.9600.1934.179
gs_summary_overview3.4890.1263.631
gs_summary_overview_pair4.0140.2514.299
gs_upset5.9580.1756.150
gs_volcano3.2720.1143.398
happy_hour3.6500.1413.800
map2color0.0110.0080.020
overlap_coefficient0.0000.0000.001
overlap_jaccard_index000
shake_davidResult0.0130.0010.014
shake_enrichResult1.7020.0421.751
shake_enrichrResult0.0550.0020.058
shake_fgseaResult0.1390.0030.143
shake_gprofilerResult0.0800.0020.085
shake_gsenrichResult1.8250.0631.898
shake_topGOtableResult0.0070.0010.008
signature_volcano5.4970.1935.710
styleColorBar_divergent0.2150.0350.251
summarize_ggs_hubgenes6.1190.2456.398