Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-05-16 11:06:14 -0400 (Mon, 16 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" 4153
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 palomino3


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: 2022-05-15 13:55:12 -0400 (Sun, 15 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: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneTonic.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings GeneTonic_2.0.0.tar.gz
StartedAt: 2022-05-16 00:00:01 -0400 (Mon, 16 May 2022)
EndedAt: 2022-05-16 00:16:01 -0400 (Mon, 16 May 2022)
EllapsedTime: 959.7 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneTonic.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneTonic.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings GeneTonic_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/GeneTonic.Rcheck'
* using R version 4.2.0 (2022-04-22 ucrt)
* using platform: x86_64-w64-mingw32 (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 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           7.32   0.25   17.66
GeneTonic              7.03   0.28   25.98
gs_mds                 7.01   0.30    7.32
gs_heatmap             6.87   0.16    8.36
ggs_graph              5.92   0.17    6.09
signature_volcano      5.44   0.22    5.67
summarize_ggs_hubgenes 5.36   0.26    5.62
gs_upset               5.12   0.12    5.25
* 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:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL GeneTonic
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-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 4.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 2 | SKIP 0 | PASS 255 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 255 ]
> 
> proc.time()
   user  system elapsed 
 137.59    9.42  544.11 

Example timings

GeneTonic.Rcheck/GeneTonic-Ex.timings

nameusersystemelapsed
GeneTonic 7.03 0.2825.98
GeneTonicList3.530.153.68
check_colors0.000.020.01
checkup_GeneTonic3.800.163.96
checkup_gtl2.780.092.87
cluster_markov0.100.000.16
create_jaccard_matrix0.820.060.89
create_kappa_matrix2.460.192.64
create_upsetdata0.060.000.06
deseqresult2df0.150.000.14
distill_enrichment3.780.113.97
enhance_table3.780.113.89
enrichment_map3.530.053.58
export_for_iSEE3.840.093.93
export_to_sif0.020.000.02
gene_plot3.860.083.94
geneinfo_2_html0.010.000.01
get_aggrscores3.520.173.69
get_expression_values2.980.113.09
ggs_backbone 7.32 0.2517.66
ggs_graph5.920.176.09
go_2_html0.030.000.04
gs_alluvial3.740.204.78
gs_dendro4.810.104.90
gs_fuzzyclustering0.600.040.64
gs_heatmap6.870.168.36
gs_horizon3.560.063.62
gs_mds7.010.307.32
gs_radar3.330.173.55
gs_scores4.390.134.54
gs_scoresheat4.140.174.31
gs_simplify0.950.000.96
gs_summary_heat3.690.233.92
gs_summary_overview3.190.163.34
gs_summary_overview_pair3.910.194.09
gs_upset5.120.125.25
gs_volcano3.310.113.42
happy_hour3.050.113.16
map2color0.020.000.01
overlap_coefficient000
overlap_jaccard_index000
shake_davidResult0.010.000.02
shake_enrichResult1.660.111.76
shake_enrichrResult0.060.000.94
shake_fgseaResult0.110.000.11
shake_gprofilerResult0.110.022.95
shake_gsenrichResult1.940.062.00
shake_topGOtableResult0.010.000.02
signature_volcano5.440.225.67
styleColorBar_divergent0.180.030.64
summarize_ggs_hubgenes5.360.265.62