Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-05-16 11:05:00 -0400 (Mon, 16 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4379
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4153
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4220
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 nebbiolo1


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 760/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneTonic 2.0.0  (landing page)
Federico Marini
Snapshot Date: 2022-05-15 13:55:12 -0400 (Sun, 15 May 2022)
git_url: https://git.bioconductor.org/packages/GeneTonic
git_branch: RELEASE_3_15
git_last_commit: f15fe5f
git_last_commit_date: 2022-04-26 12:02:24 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GeneTonic
Version: 2.0.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings GeneTonic_2.0.0.tar.gz
StartedAt: 2022-05-15 19:40:14 -0400 (Sun, 15 May 2022)
EndedAt: 2022-05-15 19:49:02 -0400 (Sun, 15 May 2022)
EllapsedTime: 528.0 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneTonic.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings GeneTonic_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/GeneTonic.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘2.0.0’
* 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
GeneTonic              6.815  0.237   7.054
gs_mds                 6.686  0.076   6.761
ggs_backbone           6.398  0.144   6.544
gs_heatmap             6.179  0.100   6.279
summarize_ggs_hubgenes 6.025  0.110   6.135
ggs_graph              5.930  0.148   6.078
signature_volcano      5.837  0.068   5.905
gs_scores              5.656  0.140   5.796
gs_upset               5.488  0.092   5.580
gs_scoresheat          5.233  0.108   5.342
gs_dendro              5.008  0.064   5.073
* 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:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL GeneTonic
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 1 | SKIP 0 | PASS 255 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 255 ]
> 
> proc.time()
   user  system elapsed 
200.886  11.702 161.718 

Example timings

GeneTonic.Rcheck/GeneTonic-Ex.timings

nameusersystemelapsed
GeneTonic6.8150.2377.054
GeneTonicList3.7440.2033.948
check_colors0.0090.0000.009
checkup_GeneTonic3.7910.1123.902
checkup_gtl2.9840.0773.062
cluster_markov0.0860.0000.086
create_jaccard_matrix0.7640.0080.771
create_kappa_matrix3.1620.0513.214
create_upsetdata0.0430.0470.091
deseqresult2df0.1550.0050.158
distill_enrichment4.1950.1874.383
enhance_table4.0120.1484.160
enrichment_map3.1460.0443.190
export_for_iSEE4.0470.1044.151
export_to_sif0.0220.0000.022
gene_plot4.1370.0764.214
geneinfo_2_html0.0080.0000.008
get_aggrscores4.1510.0924.243
get_expression_values2.4510.0802.531
ggs_backbone6.3980.1446.544
ggs_graph5.9300.1486.078
go_2_html0.020.000.02
gs_alluvial3.9610.1204.082
gs_dendro5.0080.0645.073
gs_fuzzyclustering0.7550.0280.783
gs_heatmap6.1790.1006.279
gs_horizon4.1770.0644.241
gs_mds6.6860.0766.761
gs_radar3.2970.1043.402
gs_scores5.6560.1405.796
gs_scoresheat5.2330.1085.342
gs_simplify1.0510.0011.051
gs_summary_heat4.3290.1074.437
gs_summary_overview3.6520.0683.720
gs_summary_overview_pair4.3820.1004.483
gs_upset5.4880.0925.580
gs_volcano4.1500.0524.203
happy_hour3.5580.1323.690
map2color0.0100.0020.012
overlap_coefficient000
overlap_jaccard_index000
shake_davidResult0.0090.0000.009
shake_enrichResult1.6670.0321.699
shake_enrichrResult0.0380.0030.044
shake_fgseaResult0.1090.0030.113
shake_gprofilerResult0.0750.0040.081
shake_gsenrichResult1.6900.0441.733
shake_topGOtableResult0.0070.0000.006
signature_volcano5.8370.0685.905
styleColorBar_divergent0.2120.0120.224
summarize_ggs_hubgenes6.0250.1106.135