Running ‘run_test_lmQCM.R’ [6s/7s]
Running the tests in ‘tests/run_test_lmQCM.R’ failed.
Complete output:
  > library(lmQCM)
  Loading required package: genefilter
  Loading required package: Biobase
  Loading required package: BiocGenerics
  Loading required package: parallel
  
  Attaching package: 'BiocGenerics'
  
  The following objects are masked from 'package:parallel':
  
      clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
      clusterExport, clusterMap, parApply, parCapply, parLapply,
      parLapplyLB, parRapply, parSapply, parSapplyLB
  
  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, which.max, which.min
  
  Welcome to Bioconductor
  
      Vignettes contain introductory material; view with
      'browseVignettes()'. To cite Bioconductor, see
      'citation("Biobase")', and for packages 'citation("pkgname")'.
  
  Loading required package: progress
    Package lmQCM 0.2.1 loaded.
  
  ==========================================================================
  
   If you benefit from this package, please cite:
   
   Zhang, Jie & Huang, Kun (2014) 
   Normalized ImQCM: An Algorithm for Detecting Weak Quasi-Cliques
   in Weighted Graph with Applications in Gene Co-Expression Module
   Discovery in Cancers. Cancer informatics, 13, CIN-S14021.
  
  ==========================================================================
  
  
  > library(Biobase)
  > data(sample.ExpressionSet)
  > data = assayData(sample.ExpressionSet)$exprs
  > lmQCM(data)
  Calculating massive correlation coefficient ...
  Number of Maximum Edges: 154
   Calculation Finished.
   64 Modules before merging.
   5 Modules remain after merging.
  Error in svd(XNorm, LINPACK = FALSE) : 
    the LINPACK argument has been defunct since R 3.1.0
  Calls: lmQCM -> svd
  Execution halted