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###
### 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_1.7.3.tar.gz
###
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* 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 '1.7.3'
* 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 ... ERROR
Running examples in 'GeneTonic-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggs_backbone
> ### Title: Extract the backbone for the gene-geneset graph
> ### Aliases: ggs_backbone
> 
> ### ** Examples
> 
> library("macrophage")
> library("DESeq2")
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> library("org.Hs.eg.db")
Loading required package: AnnotationDbi
> library("AnnotationDbi")
> 
> # dds object
> data("gse", package = "macrophage")
> dds_macrophage <- DESeqDataSet(gse, design = ~ line + condition)
using counts and average transcript lengths from tximeta
> rownames(dds_macrophage) <- substr(rownames(dds_macrophage), 1, 15)
> dds_macrophage <- estimateSizeFactors(dds_macrophage)
using 'avgTxLength' from assays(dds), correcting for library size
> 
> # annotation object
> anno_df <- data.frame(
+   gene_id = rownames(dds_macrophage),
+   gene_name = mapIds(org.Hs.eg.db,
+     keys = rownames(dds_macrophage),
+     column = "SYMBOL",
+     keytype = "ENSEMBL"
+   ),
+   stringsAsFactors = FALSE,
+   row.names = rownames(dds_macrophage)
+ )
'select()' returned 1:many mapping between keys and columns
> 
> # res object
> data(res_de_macrophage, package = "GeneTonic")
> res_de <- res_macrophage_IFNg_vs_naive
> 
> # res_enrich object
> data(res_enrich_macrophage, package = "GeneTonic")
> res_enrich <- shake_topGOtableResult(topgoDE_macrophage_IFNg_vs_naive)
Found 500 gene sets in `topGOtableResult` object.
Converting for usage in GeneTonic...
> res_enrich <- get_aggrscores(res_enrich, res_de, anno_df)
> 
> ggs_bbg <- ggs_backbone(res_enrich,
+   res_de,
+   anno_df,
+   n_gs = 50,
+   bb_on = "genesets",
+   color_graph = TRUE,
+   color_by_geneset = "z_score"
+ )
This matrix object is being treated as an unweighted bipartite network of 50 agents and 319 artifacts.
Error in backbone::backbone.extract(bbobj, alpha = bb_extract_alpha, fwer = bb_extract_fwer) : 
  unused argument (fwer = bb_extract_fwer)
Calls: ggs_backbone
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Converting for usage in GeneTonic...
  - Done!
  --- Test setup script completed!
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 232 ]
  
  == Failed tests ================================================================
  -- Error (test-ggs_graph.R:78:3): Backbone functionality up and running --------
  Error in `backbone::backbone.extract(bbobj, alpha = bb_extract_alpha, fwer = bb_extract_fwer)`: unused argument (fwer = bb_extract_fwer)
  Backtrace:
      x
   1. \-GeneTonic::ggs_backbone(...) at test-ggs_graph.R:78:2
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 232 ]
  Error: Test failures
  Execution halted
* 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: 2 ERRORs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/GeneTonic.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL GeneTonic
###
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* 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 'GeomxTools' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'psygenet2r' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'systemPipeTools' is missing or broken
 done

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!
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 232 ]

== Failed tests ================================================================
-- Error (test-ggs_graph.R:78:3): Backbone functionality up and running --------
Error in `backbone::backbone.extract(bbobj, alpha = bb_extract_alpha, fwer = bb_extract_fwer)`: unused argument (fwer = bb_extract_fwer)
Backtrace:
    x
 1. \-GeneTonic::ggs_backbone(...) at test-ggs_graph.R:78:2

[ FAIL 1 | WARN 2 | SKIP 0 | PASS 232 ]
Error: Test failures
Execution halted