Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-21 11:07:36 -0500 (Fri, 21 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 riesling1


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: 2022-01-20 13:55:17 -0500 (Thu, 20 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    OK    OK  
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: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneTonic.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings GeneTonic_1.7.2.tar.gz
StartedAt: 2022-01-20 18:57:48 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 19:05:48 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 479.7 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneTonic.Rcheck
Warnings: 0

Command output

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


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/GeneTonic.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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       5.84   0.38    6.22
ggs_backbone 5.06   0.55    5.68
ggs_graph    4.88   0.37    5.25
GeneTonic    4.63   0.50    5.12
* 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:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL GeneTonic
###
##############################################################################
##############################################################################


* installing to library 'D:/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
  converting help for package 'GeneTonic'
    finding HTML links ... done
    GeneTonic-pkg                           html  
    GeneTonic                               html  
    GeneTonic_list                          html  
    check_colors                            html  
    checkup_GeneTonic                       html  
    checkup_gtl                             html  
    cluster_markov                          html  
    create_jaccard_matrix                   html  
    create_kappa_matrix                     html  
    describe_gtl                            html  
    deseqresult2df                          html  
    distill_enrichment                      html  
    dot-check_pandoc                        html  
    enhance_table                           html  
    enrichment_map                          html  
    enrichr_output_macrophage               html  
    export_for_iSEE                         html  
    finding level-2 HTML links ... done

    export_to_sif                           html  
    fgseaRes                                html  
    gene_plot                               html  
    geneinfo_2_html                         html  
    get_aggrscores                          html  
    get_expression_values                   html  
    ggs_backbone                            html  
    ggs_graph                               html  
    go_2_html                               html  
    gostres_macrophage                      html  
    gs_alluvial                             html  
    gs_dendro                               html  
    gs_fuzzyclustering                      html  
    gs_heatmap                              html  
    gs_horizon                              html  
    gs_mds                                  html  
    gs_radar                                html  
    gs_scores                               html  
    gs_scoresheat                           html  
    gs_simplify                             html  
    gs_summary_heat                         html  
    gs_summary_overview                     html  
    gs_summary_overview_pair                html  
    gs_volcano                              html  
    happy_hour                              html  
    map2color                               html  
    overlap_coefficient                     html  
    overlap_jaccard_index                   html  
    res_macrophage_IFNg_vs_naive            html  
    shake_davidResult                       html  
    shake_enrichResult                      html  
    shake_enrichrResult                     html  
    shake_fgseaResult                       html  
    shake_gprofilerResult                   html  
    shake_gsenrichResult                    html  
    shake_topGOtableResult                  html  
    signature_volcano                       html  
    styleColorBar_divergent                 html  
    summarize_ggs_hubgenes                  html  
    topgoDE_macrophage_IFNg_vs_naive        html  
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'miRLAB' is missing or broken
 done

Tests output

GeneTonic.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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!
--- Test setup script completed!

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[ FAIL 0 | WARN 2 | SKIP 0 | PASS 243 ]
> 
> proc.time()
   user  system elapsed 
 119.95   12.01  163.17 

Example timings

GeneTonic.Rcheck/GeneTonic-Ex.timings

nameusersystemelapsed
GeneTonic4.630.505.12
GeneTonic_list2.750.393.15
check_colors000
checkup_GeneTonic3.280.463.74
checkup_gtl2.710.373.07
cluster_markov0.060.000.07
create_jaccard_matrix0.690.140.83
create_kappa_matrix2.280.612.89
deseqresult2df0.130.000.13
distill_enrichment3.390.443.82
enhance_table2.470.382.85
enrichment_map3.250.433.69
export_for_iSEE3.000.323.31
export_to_sif0.020.000.02
gene_plot2.950.393.34
geneinfo_2_html0.020.000.02
get_aggrscores2.790.283.08
get_expression_values2.270.262.53
ggs_backbone5.060.555.68
ggs_graph4.880.375.25
go_2_html0.010.000.02
gs_alluvial3.210.383.61
gs_dendro3.640.344.00
gs_fuzzyclustering0.550.020.56
gs_heatmap4.560.314.84
gs_horizon2.740.283.02
gs_mds5.840.386.22
gs_radar2.340.332.70
gs_scores3.360.403.76
gs_scoresheat3.940.304.24
gs_simplify0.780.030.81
gs_summary_heat2.420.232.66
gs_summary_overview3.020.363.37
gs_summary_overview_pair2.460.272.72
gs_volcano2.620.192.81
happy_hour2.770.373.14
map2color000
overlap_coefficient000
overlap_jaccard_index000
shake_davidResult0.020.000.01
shake_enrichResult1.310.191.50
shake_enrichrResult0.050.000.05
shake_fgseaResult0.090.000.09
shake_gprofilerResult0.050.020.06
shake_gsenrichResult1.300.091.40
shake_topGOtableResult000
signature_volcano4.110.304.40
styleColorBar_divergent0.200.010.22
summarize_ggs_hubgenes4.220.424.64