Running 'test.haplo.cc.R' [25s]
  Running 'test.haplo.em.R' [27s]
  Comparing 'test.haplo.em.Rout' to 'test.haplo.em.Rout.save' ... OK
  Running 'test.haplo.power.R' [6s]
  Comparing 'test.haplo.power.Rout' to 'test.haplo.power.Rout.save' ... OK
Running the tests in 'tests/test.haplo.cc.R' failed.
Complete output:
  > #$Author: sinnwell $
  > #$Date: 2011/12/05 20:53:27 $
  > #$Header: /projects/genetics/cvs/cvsroot/haplo.stats/test/test.haplo.cc.R,v 1.1 2011/12/05 20:53:27 sinnwell Exp $
  > #$Locker:  $
  > #$Log: test.haplo.cc.R,v $
  > #Revision 1.1  2011/12/05 20:53:27  sinnwell
  > #changed from .q to .R, to work with R check
  > #
  > #
  > #library(genetics) or library(haplo.stats) for R
  > 
  > ## package: haplo.stats
  > ## test script: haplo.cc
  > 
  > ## settings
  > verbose=TRUE
  > options(width=140)
  > require(haplo.stats)
  Loading required package: haplo.stats
  > tmp <- Sys.setlocale("LC_ALL", "C")
  > tmp <- Sys.getlocale()
  > 
  > 
  > # Jason Sinnwell, created 3/2004, updated 9/2014
  > # Mayo Clinic, Biostatistics
  > 
  >   if(verbose) cat("setting up data...\n")
  setting up data...
  >   
  >   label <- c("DQB","DRB","B")
  > 
  >   if(exists("is.R") && is.function(is.R) && is.R()) data(hla.demo)
  >   y.bin <- 1*(hla.demo$resp.cat=="low")
  > 
  >   geno <- as.matrix(hla.demo[,c(17,18,21:24)])
  > 
  >   # commented code was to check data that goes into haplo.cc
  >   # and gets pasted together in the huge data.frame.
  >   
  >  # sink(file="results.haplo.cc.txt")  
  > 
  >   seed <- c(17, 53, 1, 40, 37, 0, 62, 56, 5, 52, 12, 1)
  >   set.seed(seed)
  > 
  > #  group.hla <- haplo.group(y.bin, geno, miss.val=0, locus.label=label,
  > #                         control=haplo.em.control(n.try=1))
  > #  set.seed(seed)
  >   if(verbose) cat("hla data \n")
  hla data 
  >   cc.hla <- haplo.cc(y.bin, geno, miss.val=0,locus.label=label, 
  +                      control=haplo.glm.control(haplo.min.count=8,
  +                        em.c=haplo.em.control()))
  Error in svd(x, LINPACK = FALSE) : 
    the LINPACK argument has been defunct since R 3.1.0
  Calls: haplo.cc -> haplo.score -> Ginv -> svd
  Execution halted