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CHECK report for GeneTonic on malbec1

This page was generated on 2021-05-06 12:27:42 -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: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings GeneTonic_1.2.0.tar.gz
StartedAt: 2021-05-06 01:52:24 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 02:01:27 -0400 (Thu, 06 May 2021)
EllapsedTime: 543.2 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneTonic.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings GeneTonic_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/GeneTonic.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘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        9.192  0.068   9.275
ggs_graph     9.144  0.104   9.254
gs_scoresheat 7.800  0.096   7.908
gs_heatmap    7.752  0.072   7.852
GeneTonic     7.636  0.172   7.904
gs_dendro     6.656  0.032   6.694
gs_scores     5.880  0.068   5.961
gs_radar      5.264  0.068   5.360
gs_horizon    5.076  0.016   5.110
* 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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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL GeneTonic
###
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* installing to library ‘/home/biocbuild/bbs-3.12-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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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...
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 
154.420   1.924 156.872 

Example timings

GeneTonic.Rcheck/GeneTonic-Ex.timings

nameusersystemelapsed
GeneTonic7.6360.1727.904
check_colors0.0160.0000.016
checkup_GeneTonic3.9760.1204.102
cluster_markov0.0840.0000.084
create_jaccard_matrix0.940.000.94
create_kappa_matrix4.1360.0204.158
deseqresult2df0.2480.0000.251
distill_enrichment4.8240.0684.896
enhance_table4.7080.0764.788
enrichment_map3.9920.0244.026
export_for_iSEE4.2920.0604.353
export_to_sif0.020.000.02
gene_plot4.2520.0484.303
geneinfo_2_html0.0080.0000.007
get_aggrscores4.7600.0564.824
get_expression_values4.0920.0524.152
ggs_graph9.1440.1049.254
go_2_html0.0200.0000.024
gs_alluvial3.8280.0604.061
gs_dendro6.6560.0326.694
gs_heatmap7.7520.0727.852
gs_horizon5.0760.0165.110
gs_mds9.1920.0689.275
gs_radar5.2640.0685.360
gs_scores5.8800.0685.961
gs_scoresheat7.8000.0967.908
gs_simplify1.5520.0001.556
gs_summary_heat4.5840.0404.635
gs_summary_overview4.1520.0204.176
gs_summary_overview_pair4.5120.0524.568
gs_volcano3.9040.0843.996
happy_hour4.0640.0244.095
map2color0.0160.0000.017
overlap_coefficient0.0000.0000.001
overlap_jaccard_index000
shake_davidResult0.0200.0000.026
shake_enrichResult1.9960.0242.022
shake_enrichrResult0.0560.0000.062
shake_fgseaResult0.1560.0000.155
shake_gprofilerResult0.0960.0000.103
shake_topGOtableResult0.0040.0000.007
styleColorBar_divergent0.3160.0120.393