Running ‘testthat.R’ [89s/264s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(RCPA)
  Loading required package: tidyr
  
  Attaching package: 'tidyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  Loading required package: dplyr
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  Loading required package: ggplot2
  Setting options('download.file.method.GEOquery'='auto')
  Setting options('GEOquery.inmemory.gpl'=FALSE)
  Warning message:
  replacing previous import 'S4Arrays::read_block' by 'DelayedArray::read_block' when loading 'SummarizedExperiment' 
  > 
  > test_check("RCPA")
  
  Attaching package: 'limma'
  
  The following object is masked from 'package:RCPA':
  
      plotMA
  
  converting counts to integer mode
  using supplied model matrix
  estimating size factors
  estimating dispersions
  gene-wise dispersion estimates
  mean-dispersion relationship
  -- note: fitType='parametric', but the dispersion trend was not well captured by the
     function: y = a/x + b, and a local regression fit was automatically substituted.
     specify fitType='local' or 'mean' to avoid this message next time.
  final dispersion estimates
  fitting model and testing
  converting counts to integer mode
  using supplied model matrix
  estimating size factors
  estimating dispersions
  gene-wise dispersion estimates
  mean-dispersion relationship
  -- note: fitType='parametric', but the dispersion trend was not well captured by the
     function: y = a/x + b, and a local regression fit was automatically substituted.
     specify fitType='local' or 'mean' to avoid this message next time.
  final dispersion estimates
  fitting model and testing
  converting counts to integer mode
  using supplied model matrix
  estimating size factors
  estimating dispersions
  gene-wise dispersion estimates
  mean-dispersion relationship
  -- note: fitType='parametric', but the dispersion trend was not well captured by the
     function: y = a/x + b, and a local regression fit was automatically substituted.
     specify fitType='local' or 'mean' to avoid this message next time.
  final dispersion estimates
  fitting model and testing
  converting counts to integer mode
  using supplied model matrix
  estimating size factors
  estimating dispersions
  gene-wise dispersion estimates
  mean-dispersion relationship
  -- note: fitType='parametric', but the dispersion trend was not well captured by the
     function: y = a/x + b, and a local regression fit was automatically substituted.
     specify fitType='local' or 'mean' to avoid this message next time.
  final dispersion estimates
  fitting model and testing
  converting counts to integer mode
  using supplied model matrix
  estimating size factors
  estimating dispersions
  gene-wise dispersion estimates
  mean-dispersion relationship
  -- note: fitType='parametric', but the dispersion trend was not well captured by the
     function: y = a/x + b, and a local regression fit was automatically substituted.
     specify fitType='local' or 'mean' to avoid this message next time.
  final dispersion estimates
  fitting model and testing
  converting counts to integer mode
  using supplied model matrix
  estimating size factors
  estimating dispersions
  gene-wise dispersion estimates
  mean-dispersion relationship
  -- note: fitType='parametric', but the dispersion trend was not well captured by the
     function: y = a/x + b, and a local regression fit was automatically substituted.
     specify fitType='local' or 'mean' to avoid this message next time.
  final dispersion estimates
  fitting model and testing
  converting counts to integer mode
  using supplied model matrix
  estimating size factors
  estimating dispersions
  gene-wise dispersion estimates
  mean-dispersion relationship
  -- note: fitType='parametric', but the dispersion trend was not well captured by the
     function: y = a/x + b, and a local regression fit was automatically substituted.
     specify fitType='local' or 'mean' to avoid this message next time.
  final dispersion estimates
  fitting model and testing
  converting counts to integer mode
  using supplied model matrix
  estimating size factors
  estimating dispersions
  gene-wise dispersion estimates
  mean-dispersion relationship
  -- note: fitType='parametric', but the dispersion trend was not well captured by the
     function: y = a/x + b, and a local regression fit was automatically substituted.
     specify fitType='local' or 'mean' to avoid this message next time.
  final dispersion estimates
  fitting model and testing
  Loading required package: AnnotationDbi
  Loading required package: stats4
  Loading required package: BiocGenerics
  
  Attaching package: 'BiocGenerics'
  
  The following object is masked from 'package:limma':
  
      plotMA
  
  The following object is masked from 'package:RCPA':
  
      plotMA
  
  The following objects are masked from 'package:dplyr':
  
      combine, intersect, setdiff, union
  
  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, aperm, 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
  
  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")'.
  
  Loading required package: IRanges
  Loading required package: S4Vectors
  
  Attaching package: 'S4Vectors'
  
  The following objects are masked from 'package:dplyr':
  
      first, rename
  
  The following object is masked from 'package:tidyr':
  
      expand
  
  The following object is masked from 'package:utils':
  
      findMatches
  
  The following objects are masked from 'package:base':
  
      I, expand.grid, unname
  
  
  Attaching package: 'IRanges'
  
  The following objects are masked from 'package:dplyr':
  
      collapse, desc, slice
  
  
  Attaching package: 'AnnotationDbi'
  
  The following object is masked from 'package:dplyr':
  
      select
  
  Loading required package: org.Hs.eg.db
  
  
  Loading required package: MatrixGenerics
  Loading required package: matrixStats
  
  Attaching package: 'matrixStats'
  
  The following objects are masked from 'package:Biobase':
  
      anyMissing, rowMedians
  
  The following object is masked from 'package:dplyr':
  
      count
  
  
  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
  
  The following object is masked from 'package:Biobase':
  
      rowMedians
  
  Loading required package: GenomicRanges
  Loading required package: GenomeInfoDb
  Loading 'meta' package (version 6.2-1).
  Type 'help(meta)' for a brief overview.
  Readers of 'Meta-Analysis with R (Use R!)' should install
  older version of 'meta' package: https://tinyurl.com/dt4y5drs
  [ FAIL 1 | WARN 4 | SKIP 71 | PASS 122 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (71)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-plot-pathway-network.R:2:1'): (code run outside of `test_that()`) ──
  <packageNotFoundError/error/condition>
  Error in `library(RCyjs)`: there is no package called 'RCyjs'
  Backtrace:
      ▆
   1. └─base::library(RCyjs) at test-plot-pathway-network.R:2:0
  
  [ FAIL 1 | WARN 4 | SKIP 71 | PASS 122 ]
  Error: Test failures
  Execution halted