Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-26 13:08:04 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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 machv2


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? here 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 1.6.1  (landing page)
Federico Marini
Snapshot Date: 2022-01-25 01:55:07 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/GeneTonic
git_branch: RELEASE_3_14
git_last_commit: c8bf092
git_last_commit_date: 2021-12-01 18:02:34 -0500 (Wed, 01 Dec 2021)
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    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GeneTonic
Version: 1.6.1
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_1.6.1.tar.gz
StartedAt: 2022-01-25 13:21:47 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 13:35:32 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 825.0 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_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/GeneTonic.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.6.1’
* 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
ggs_backbone             11.499  0.312  11.917
gs_mds                   11.296  0.484  11.802
gs_heatmap               11.266  0.185  11.475
ggs_graph                10.087  0.225  10.322
gs_scores                 9.783  0.190   9.987
summarize_ggs_hubgenes    9.716  0.179   9.918
gs_scoresheat             9.075  0.210   9.312
GeneTonic                 8.481  0.307   8.801
gs_dendro                 8.205  0.180   8.405
signature_volcano         7.888  0.200   8.105
export_for_iSEE           7.831  0.135   8.012
enhance_table             6.494  0.200   6.696
gs_summary_overview       6.501  0.129   6.643
gene_plot                 6.510  0.112   6.628
gs_alluvial               6.183  0.250   6.440
gs_horizon                6.126  0.137   6.267
distill_enrichment        6.114  0.147   6.268
gs_volcano                5.949  0.166   6.123
gs_summary_heat           5.908  0.168   6.102
enrichment_map            5.775  0.133   5.947
GeneTonic_list            5.664  0.178   5.846
checkup_GeneTonic         5.662  0.167   5.833
happy_hour                5.659  0.136   5.813
checkup_gtl               5.566  0.141   5.715
gs_radar                  5.416  0.276   5.697
get_aggrscores            5.563  0.099   5.672
gs_summary_overview_pair  5.205  0.108   5.321
* 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/4.1/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 4.1.2 (2021-11-01) -- "Bird Hippie"
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...
--- 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 
331.417  16.970 275.536 

Example timings

GeneTonic.Rcheck/GeneTonic-Ex.timings

nameusersystemelapsed
GeneTonic8.4810.3078.801
GeneTonic_list5.6640.1785.846
check_colors0.0150.0020.018
checkup_GeneTonic5.6620.1675.833
checkup_gtl5.5660.1415.715
cluster_markov0.1440.0040.149
create_jaccard_matrix1.6270.0861.720
create_kappa_matrix4.4280.4034.837
deseqresult2df0.2100.0050.216
distill_enrichment6.1140.1476.268
enhance_table6.4940.2006.696
enrichment_map5.7750.1335.947
export_for_iSEE7.8310.1358.012
export_to_sif0.0280.0010.030
gene_plot6.5100.1126.628
geneinfo_2_html0.0130.0010.015
get_aggrscores5.5630.0995.672
get_expression_values4.8220.1534.980
ggs_backbone11.499 0.31211.917
ggs_graph10.087 0.22510.322
go_2_html0.0440.0010.045
gs_alluvial6.1830.2506.440
gs_dendro8.2050.1808.405
gs_fuzzyclustering1.2320.0581.295
gs_heatmap11.266 0.18511.475
gs_horizon6.1260.1376.267
gs_mds11.296 0.48411.802
gs_radar5.4160.2765.697
gs_scores9.7830.1909.987
gs_scoresheat9.0750.2109.312
gs_simplify2.5310.0702.620
gs_summary_heat5.9080.1686.102
gs_summary_overview6.5010.1296.643
gs_summary_overview_pair5.2050.1085.321
gs_volcano5.9490.1666.123
happy_hour5.6590.1365.813
map2color0.0140.0020.017
overlap_coefficient0.0010.0010.001
overlap_jaccard_index0.0000.0000.001
shake_davidResult0.0190.0010.020
shake_enrichResult2.9540.0423.001
shake_enrichrResult0.0890.0030.094
shake_fgseaResult0.2020.0040.206
shake_gprofilerResult0.1410.0060.147
shake_gsenrichResult2.8650.0572.924
shake_topGOtableResult0.0090.0010.010
signature_volcano7.8880.2008.105
styleColorBar_divergent0.2840.0360.322
summarize_ggs_hubgenes9.7160.1799.918