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This page was generated on 2024-05-15 13:46:32 -0400 (Wed, 15 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4663
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4480
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 791/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneTonic 2.9.0  (landing page)
Federico Marini
Snapshot Date: 2024-05-13 14:05:07 -0400 (Mon, 13 May 2024)
git_url: https://git.bioconductor.org/packages/GeneTonic
git_branch: devel
git_last_commit: 9473081
git_last_commit_date: 2024-04-30 11:20:41 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson1macOS 13.6.6 Ventura / arm64see weekly results here

CHECK results for GeneTonic on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: GeneTonic
Version: 2.8.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings GeneTonic_2.8.0.tar.gz
StartedAt: 2024-05-09 07:41:51 -0000 (Thu, 09 May 2024)
EndedAt: 2024-05-09 07:53:30 -0000 (Thu, 09 May 2024)
EllapsedTime: 698.2 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneTonic.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings GeneTonic_2.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GeneTonic.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* 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 loading without being on the library search path ... 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
gs_upset               8.777  0.064   8.859
gs_heatmap             8.134  0.112   8.262
gs_mds                 8.050  0.048   8.115
ggs_backbone           7.728  0.115   7.859
summarize_ggs_hubgenes 7.726  0.063   7.805
ggs_graph              7.324  0.096   7.435
signature_volcano      7.093  0.064   7.171
GeneTonic              6.373  0.207   6.598
enhance_table          6.436  0.104   6.553
export_for_iSEE        6.350  0.040   6.402
gs_scoresheat          6.111  0.008   6.132
gs_scores              5.960  0.024   5.997
gs_horizon             5.586  0.032   5.630
gs_summary_overview    5.355  0.060   5.426
gs_dendro              5.327  0.020   5.357
distill_enrichment     5.183  0.059   5.252
gs_alluvial            5.010  0.080   5.099
gs_radar               5.048  0.040   5.098
* 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:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL GeneTonic
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 
234.328   8.772 209.428 

Example timings

GeneTonic.Rcheck/GeneTonic-Ex.timings

nameusersystemelapsed
GeneTonic6.3730.2076.598
GeneTonicList4.8100.0804.899
check_colors0.0110.0000.011
checkup_GeneTonic4.8100.1164.935
checkup_gtl4.9020.0524.964
cluster_markov0.0970.0120.110
create_jaccard_matrix1.1120.0201.134
create_kappa_matrix3.8240.0353.867
create_upsetdata0.0290.0120.042
deseqresult2df0.1670.0000.168
distill_enrichment5.1830.0595.252
enhance_table6.4360.1046.553
enrichment_map4.8670.0204.896
export_for_iSEE6.3500.0406.402
export_to_sif0.0280.0000.028
gene_plot4.7350.0644.808
geneinfo_2_html0.0080.0000.008
get_aggrscores4.7560.1004.865
get_expression_values2.7630.0282.796
ggs_backbone7.7280.1157.859
ggs_graph7.3240.0967.435
go_2_html0.0350.0000.035
gs_alluvial5.0100.0805.099
gs_dendro5.3270.0205.357
gs_fuzzyclustering0.9990.0001.001
gs_heatmap8.1340.1128.262
gs_horizon5.5860.0325.630
gs_mds8.0500.0488.115
gs_radar5.0480.0405.098
gs_scores5.9600.0245.997
gs_scoresheat6.1110.0086.132
gs_simplify1.5100.0031.517
gs_summary_heat4.1330.0484.189
gs_summary_overview5.3550.0605.426
gs_summary_overview_pair4.0610.0204.090
gs_upset8.7770.0648.859
gs_volcano4.3030.0204.332
happy_hour3.8850.0323.926
map2color0.0120.0000.011
overlap_coefficient0.0010.0000.001
overlap_jaccard_index0.0010.0000.000
shake_davidResult0.0130.0000.014
shake_enrichResult2.0090.0282.041
shake_enrichrResult0.1440.0000.146
shake_fgseaResult0.1330.0000.133
shake_gprofilerResult0.0960.0000.099
shake_gsenrichResult1.9070.0161.927
shake_topGOtableResult0.0080.0000.007
signature_volcano7.0930.0647.171
styleColorBar_divergent0.2420.0040.250
summarize_ggs_hubgenes7.7260.0637.805