Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:05:24 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 nebbiolo2


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 739/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneTonic 1.6.4  (landing page)
Federico Marini
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/GeneTonic
git_branch: RELEASE_3_14
git_last_commit: c9ee95b
git_last_commit_date: 2022-03-24 08:30:47 -0400 (Thu, 24 Mar 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GeneTonic
Version: 1.6.4
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings GeneTonic_1.6.4.tar.gz
StartedAt: 2022-04-12 07:33:22 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 07:41:53 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 510.5 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneTonic.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings GeneTonic_1.6.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/GeneTonic.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.6.4’
* 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                 7.368  0.036   7.405
GeneTonic              6.984  0.296   7.280
gs_scores              6.543  0.132   6.675
summarize_ggs_hubgenes 6.532  0.048   6.580
gs_heatmap             6.381  0.136   6.517
ggs_graph              6.075  0.153   6.227
ggs_backbone           5.810  0.076   5.888
gs_scoresheat          5.201  0.120   5.322
signature_volcano      5.172  0.040   5.212
* 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-3.14-bioc/R/bin/R CMD INSTALL GeneTonic
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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 4.1.3 (2022-03-10) -- "One Push-Up"
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!
--- Test setup script completed!

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[ FAIL 0 | WARN 1 | SKIP 0 | PASS 243 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 243 ]
> 
> proc.time()
   user  system elapsed 
194.873   8.985 159.147 

Example timings

GeneTonic.Rcheck/GeneTonic-Ex.timings

nameusersystemelapsed
GeneTonic6.9840.2967.280
GeneTonic_list4.0270.1204.147
check_colors0.0080.0000.008
checkup_GeneTonic4.0670.0924.158
checkup_gtl3.2170.0443.260
cluster_markov0.0790.0000.078
create_jaccard_matrix1.5460.0601.607
create_kappa_matrix2.4900.0712.562
deseqresult2df0.1310.0020.133
distill_enrichment3.3060.0783.384
enhance_table4.0300.1154.146
enrichment_map3.9080.1054.012
export_for_iSEE4.7970.0914.889
export_to_sif0.0250.0010.025
gene_plot4.1730.1354.309
geneinfo_2_html0.0070.0010.007
get_aggrscores3.8650.1113.977
get_expression_values3.1440.0453.189
ggs_backbone5.8100.0765.888
ggs_graph6.0750.1536.227
go_2_html0.0190.0010.020
gs_alluvial4.2620.1364.398
gs_dendro4.8860.1004.986
gs_fuzzyclustering0.720.000.72
gs_heatmap6.3810.1366.517
gs_horizon4.7150.0444.759
gs_mds7.3680.0367.405
gs_radar3.3600.0763.437
gs_scores6.5430.1326.675
gs_scoresheat5.2010.1205.322
gs_simplify0.9930.0000.994
gs_summary_heat3.8940.0763.970
gs_summary_overview3.5410.0403.581
gs_summary_overview_pair4.0990.0324.131
gs_volcano3.9450.0283.973
happy_hour3.1770.0323.209
map2color0.0130.0000.013
overlap_coefficient000
overlap_jaccard_index0.0010.0000.001
shake_davidResult0.0110.0000.011
shake_enrichResult2.7120.1032.816
shake_enrichrResult0.0420.0000.043
shake_fgseaResult0.1170.0000.116
shake_gprofilerResult0.0750.0030.079
shake_gsenrichResult1.7890.0041.794
shake_topGOtableResult0.0060.0000.005
signature_volcano5.1720.0405.212
styleColorBar_divergent0.1990.0110.211
summarize_ggs_hubgenes6.5320.0486.580