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CHECK report for GeneTonic on merida1

This page was generated on 2021-05-06 12:35:05 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the GeneTonic package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 705/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneTonic 1.2.0  (landing page)
Federico Marini
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/GeneTonic
Branch: RELEASE_3_12
Last Commit: 6b41744
Last Changed Date: 2020-10-27 11:53:11 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: GeneTonic
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneTonic_1.2.0.tar.gz
StartedAt: 2021-05-06 02:04:31 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 02:13:45 -0400 (Thu, 06 May 2021)
EllapsedTime: 553.8 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneTonic.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneTonic_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/GeneTonic.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.2.0’
* 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        8.485  0.354   8.856
ggs_graph     7.891  0.189   8.094
gs_heatmap    7.025  0.144   7.186
GeneTonic     6.622  0.250   6.880
gs_scoresheat 6.390  0.176   6.639
gs_scores     6.206  0.136   6.356
gs_dendro     5.854  0.183   6.046
gs_horizon    5.023  0.086   5.115
* 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GeneTonic
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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...
Found 500 gene sets in `topGOtableResult` object.
Converting for usage in GeneTonic...
- Done!
--- Test setup script completed!
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 173 ]
> 
> proc.time()
   user  system elapsed 
155.544   6.978 163.093 

Example timings

GeneTonic.Rcheck/GeneTonic-Ex.timings

nameusersystemelapsed
GeneTonic6.6220.2506.880
check_colors0.0110.0020.014
checkup_GeneTonic4.3120.1454.461
cluster_markov0.1060.0040.110
create_jaccard_matrix1.3250.0651.392
create_kappa_matrix3.7040.3974.110
deseqresult2df0.2210.0210.244
distill_enrichment4.7770.1324.913
enhance_table4.5510.1464.702
enrichment_map4.1400.1034.247
export_for_iSEE4.7490.1054.860
export_to_sif0.0190.0010.019
gene_plot4.6050.1114.729
geneinfo_2_html0.0080.0000.008
get_aggrscores4.4410.0834.534
get_expression_values3.6400.1123.763
ggs_graph7.8910.1898.094
go_2_html0.0290.0030.032
gs_alluvial3.8840.1784.071
gs_dendro5.8540.1836.046
gs_heatmap7.0250.1447.186
gs_horizon5.0230.0865.115
gs_mds8.4850.3548.856
gs_radar4.6780.2424.942
gs_scores6.2060.1366.356
gs_scoresheat6.3900.1766.639
gs_simplify1.7780.0441.824
gs_summary_heat3.9150.1074.025
gs_summary_overview3.9580.1014.064
gs_summary_overview_pair4.7280.0924.827
gs_volcano3.8780.1023.987
happy_hour3.4730.0913.569
map2color0.0120.0020.015
overlap_coefficient0.0000.0010.000
overlap_jaccard_index0.0000.0000.001
shake_davidResult0.0130.0010.014
shake_enrichResult1.9280.0391.973
shake_enrichrResult0.0720.0020.074
shake_fgseaResult0.2030.0030.207
shake_gprofilerResult0.1190.0040.123
shake_topGOtableResult0.0070.0010.008
styleColorBar_divergent0.3190.0370.357