Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-05-18 12:08:13 -0400 (Wed, 18 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" 4154
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 merida1


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: 2022-05-17 13:55:01 -0400 (Tue, 17 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: /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_2.0.0.tar.gz
StartedAt: 2022-05-18 02:36:18 -0400 (Wed, 18 May 2022)
EndedAt: 2022-05-18 02:52:08 -0400 (Wed, 18 May 2022)
EllapsedTime: 949.3 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_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/GeneTonic.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘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
gs_mds                   12.817  0.706  13.597
ggs_backbone             12.729  0.285  13.143
gs_heatmap               11.295  0.160  11.488
ggs_graph                11.084  0.194  11.364
summarize_ggs_hubgenes   10.845  0.182  11.106
GeneTonic                 9.378  0.335   9.729
gs_upset                  9.418  0.161   9.602
gs_scoresheat             8.778  0.197   9.004
gs_dendro                 8.457  0.209   8.691
signature_volcano         8.354  0.164   8.540
gs_scores                 8.218  0.215   8.480
gs_horizon                7.153  0.136   7.319
gene_plot                 6.986  0.142   7.193
gs_summary_overview       6.858  0.149   7.114
export_for_iSEE           6.835  0.149   6.991
enhance_table             6.736  0.194   6.945
distill_enrichment        6.565  0.223   6.795
gs_alluvial               6.291  0.180   6.489
create_kappa_matrix       6.023  0.403   6.434
enrichment_map            6.248  0.168   6.423
happy_hour                6.184  0.121   6.318
GeneTonicList             6.034  0.198   6.238
checkup_GeneTonic         6.030  0.193   6.240
get_aggrscores            5.901  0.122   6.038
gs_radar                  5.786  0.187   6.137
gs_volcano                5.737  0.116   5.868
gs_summary_overview_pair  5.747  0.104   6.124
gs_summary_heat           5.598  0.109   5.860
checkup_gtl               5.280  0.129   5.418
* 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/4.2/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 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 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!
---------------------------------
----- 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 
362.081  18.781 305.282 

Example timings

GeneTonic.Rcheck/GeneTonic-Ex.timings

nameusersystemelapsed
GeneTonic9.3780.3359.729
GeneTonicList6.0340.1986.238
check_colors0.0140.0020.015
checkup_GeneTonic6.0300.1936.240
checkup_gtl5.2800.1295.418
cluster_markov0.1650.0030.168
create_jaccard_matrix2.1110.0912.212
create_kappa_matrix6.0230.4036.434
create_upsetdata0.0610.0310.091
deseqresult2df0.2410.0030.243
distill_enrichment6.5650.2236.795
enhance_table6.7360.1946.945
enrichment_map6.2480.1686.423
export_for_iSEE6.8350.1496.991
export_to_sif0.0370.0020.039
gene_plot6.9860.1427.193
geneinfo_2_html0.0120.0000.013
get_aggrscores5.9010.1226.038
get_expression_values3.7510.1313.891
ggs_backbone12.729 0.28513.143
ggs_graph11.084 0.19411.364
go_2_html0.0450.0000.045
gs_alluvial6.2910.1806.489
gs_dendro8.4570.2098.691
gs_fuzzyclustering1.4780.0431.522
gs_heatmap11.295 0.16011.488
gs_horizon7.1530.1367.319
gs_mds12.817 0.70613.597
gs_radar5.7860.1876.137
gs_scores8.2180.2158.480
gs_scoresheat8.7780.1979.004
gs_simplify2.6380.0552.738
gs_summary_heat5.5980.1095.860
gs_summary_overview6.8580.1497.114
gs_summary_overview_pair5.7470.1046.124
gs_upset9.4180.1619.602
gs_volcano5.7370.1165.868
happy_hour6.1840.1216.318
map2color0.0170.0020.020
overlap_coefficient000
overlap_jaccard_index0.0010.0010.001
shake_davidResult0.0190.0010.021
shake_enrichResult2.8760.0362.915
shake_enrichrResult0.0940.0020.096
shake_fgseaResult0.2380.0020.240
shake_gprofilerResult0.2210.0380.260
shake_gsenrichResult2.9170.0412.966
shake_topGOtableResult0.0110.0010.012
signature_volcano8.3540.1648.540
styleColorBar_divergent0.3580.0370.400
summarize_ggs_hubgenes10.845 0.18211.106