Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-11 14:43 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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

Package 820/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneTonic 2.8.0  (landing page)
Federico Marini
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/GeneTonic
git_branch: RELEASE_3_19
git_last_commit: dd4c5de
git_last_commit_date: 2024-04-30 11:20:41 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for GeneTonic on kjohnson3

To the developers/maintainers of the GeneTonic package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: GeneTonic
Version: 2.8.0
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_2.8.0.tar.gz
StartedAt: 2024-06-10 16:39:12 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 16:55:48 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 995.2 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_2.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/GeneTonic.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘2.8.0’
* 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 code 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 whether startup messages can be suppressed ... 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
GeneTonic                8.986  0.247  14.898
summarize_ggs_hubgenes   8.016  0.281  12.587
ggs_backbone             7.533  0.268  11.709
ggs_graph                7.452  0.236  11.318
gs_mds                   7.391  0.197  11.497
gs_heatmap               7.336  0.188  11.282
gs_upset                 6.590  0.171  10.116
gs_alluvial              6.192  0.189   8.915
enhance_table            6.028  0.178   9.606
gs_dendro                5.701  0.156   9.172
signature_volcano        5.433  0.192   8.591
gs_volcano               5.367  0.152   8.624
gs_horizon               5.367  0.130   7.553
gs_scoresheat            5.065  0.186   7.797
gs_scores                5.025  0.162   7.913
gs_summary_overview_pair 5.003  0.143   7.707
gs_radar                 4.928  0.210   7.656
distill_enrichment       4.973  0.149   7.641
export_for_iSEE          4.971  0.118   7.078
get_aggrscores           4.771  0.135   7.543
enrichment_map           4.707  0.124   6.071
GeneTonicList            4.595  0.136   7.265
checkup_gtl              4.560  0.126   6.922
checkup_GeneTonic        4.498  0.134   6.816
gene_plot                3.898  0.133   5.516
gs_summary_overview      3.757  0.129   5.641
create_kappa_matrix      3.719  0.142   5.867
get_expression_values    3.727  0.116   5.763
gs_summary_heat          3.693  0.139   6.018
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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/4.4-arm64/Resources/library’
* installing *source* package ‘GeneTonic’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

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, 1024 found as DE
Upregulated:     652
Downregulated:   372

----- 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 0 | SKIP 0 | PASS 264 ]
> 
> proc.time()
   user  system elapsed 
215.344   8.904 295.407 

Example timings

GeneTonic.Rcheck/GeneTonic-Ex.timings

nameusersystemelapsed
GeneTonic 8.986 0.24714.898
GeneTonicList4.5950.1367.265
check_colors0.0090.0020.014
checkup_GeneTonic4.4980.1346.816
checkup_gtl4.5600.1266.922
cluster_markov0.1020.0070.169
create_jaccard_matrix0.8550.0571.329
create_kappa_matrix3.7190.1425.867
create_upsetdata0.0360.0290.087
deseqresult2df0.1770.0070.289
distill_enrichment4.9730.1497.641
enhance_table6.0280.1789.606
enrichment_map4.7070.1246.071
export_for_iSEE4.9710.1187.078
export_to_sif0.0340.0030.039
gene_plot3.8980.1335.516
geneinfo_2_html0.0070.0010.009
get_aggrscores4.7710.1357.543
get_expression_values3.7270.1165.763
ggs_backbone 7.533 0.26811.709
ggs_graph 7.452 0.23611.318
go_2_html0.0200.0010.022
gs_alluvial6.1920.1898.915
gs_dendro5.7010.1569.172
gs_fuzzyclustering0.8090.0291.303
gs_heatmap 7.336 0.18811.282
gs_horizon5.3670.1307.553
gs_mds 7.391 0.19711.497
gs_radar4.9280.2107.656
gs_scores5.0250.1627.913
gs_scoresheat5.0650.1867.797
gs_simplify1.1950.0381.924
gs_summary_heat3.6930.1396.018
gs_summary_overview3.7570.1295.641
gs_summary_overview_pair5.0030.1437.707
gs_upset 6.590 0.17110.116
gs_volcano5.3670.1528.624
happy_hour3.2900.1204.643
map2color0.0140.0030.016
overlap_coefficient0.0010.0000.001
overlap_jaccard_index000
shake_davidResult0.0140.0020.023
shake_enrichResult1.9220.0482.693
shake_enrichrResult0.0640.0040.093
shake_fgseaResult0.2430.0040.405
shake_gprofilerResult0.1080.0070.174
shake_gsenrichResult1.9920.0663.088
shake_topGOtableResult0.0080.0020.021
signature_volcano5.4330.1928.591
styleColorBar_divergent0.2520.0360.413
summarize_ggs_hubgenes 8.016 0.28112.587