Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-22 11:05:52 -0500 (Sat, 22 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
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 nebbiolo1


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 736/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneTonic 1.7.2  (landing page)
Federico Marini
Snapshot Date: 2022-01-21 13:55:18 -0500 (Fri, 21 Jan 2022)
git_url: https://git.bioconductor.org/packages/GeneTonic
git_branch: master
git_last_commit: cd1b0b1
git_last_commit_date: 2022-01-19 06:01:20 -0500 (Wed, 19 Jan 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    NA    NA  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'AnnotationDbi' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GeneTonic
Version: 1.7.2
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings GeneTonic_1.7.2.tar.gz
StartedAt: 2022-01-21 19:19:25 -0500 (Fri, 21 Jan 2022)
EndedAt: 2022-01-21 19:27:51 -0500 (Fri, 21 Jan 2022)
EllapsedTime: 506.5 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneTonic.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings GeneTonic_1.7.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/GeneTonic.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘1.7.2’
* 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
GeneTonic              6.985  0.196   7.183
gs_mds                 6.909  0.052   6.961
ggs_backbone           6.632  0.144   6.780
ggs_graph              6.091  0.068   6.158
gs_heatmap             5.634  0.112   5.746
gs_scoresheat          5.580  0.048   5.629
summarize_ggs_hubgenes 5.572  0.052   5.624
* 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:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL GeneTonic
###
##############################################################################
##############################################################################


* installing to library ‘/home/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 Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
198.179  11.532 159.975 

Example timings

GeneTonic.Rcheck/GeneTonic-Ex.timings

nameusersystemelapsed
GeneTonic6.9850.1967.183
GeneTonic_list4.2480.4444.694
check_colors0.0070.0040.011
checkup_GeneTonic3.8440.5924.437
checkup_gtl2.9340.0442.978
cluster_markov0.0900.0000.091
create_jaccard_matrix0.7670.0120.779
create_kappa_matrix3.1150.0163.131
deseqresult2df0.1530.0000.153
distill_enrichment3.9350.0884.022
enhance_table4.2850.0644.349
enrichment_map3.8040.1033.906
export_for_iSEE3.8960.0643.960
export_to_sif0.0210.0000.020
gene_plot4.0500.0684.118
geneinfo_2_html0.0070.0000.007
get_aggrscores3.6040.0683.672
get_expression_values2.9660.0483.014
ggs_backbone6.6320.1446.780
ggs_graph6.0910.0686.158
go_2_html0.0220.0000.022
gs_alluvial3.8240.0883.912
gs_dendro4.5910.0964.688
gs_fuzzyclustering0.7040.0120.716
gs_heatmap5.6340.1125.746
gs_horizon3.2900.0683.359
gs_mds6.9090.0526.961
gs_radar3.0200.0843.105
gs_scores4.5120.0484.560
gs_scoresheat5.5800.0485.629
gs_simplify1.0390.0001.039
gs_summary_heat3.3570.0683.426
gs_summary_overview4.0370.0484.085
gs_summary_overview_pair3.0540.0643.118
gs_volcano3.3920.0243.417
happy_hour3.7760.0643.840
map2color0.0140.0000.013
overlap_coefficient0.0000.0000.001
overlap_jaccard_index0.0000.0000.001
shake_davidResult0.0100.0000.011
shake_enrichResult1.7170.0161.732
shake_enrichrResult0.0480.0040.055
shake_fgseaResult0.1220.0040.126
shake_gprofilerResult0.0850.0000.088
shake_gsenrichResult1.6800.0481.728
shake_topGOtableResult0.0060.0000.006
signature_volcano4.8500.0644.914
styleColorBar_divergent0.2190.0120.231
summarize_ggs_hubgenes5.5720.0525.624