Running ‘test_io.R’ [0s/0s]
  Running ‘test_mapqtl_io.R’ [2s/3s]
  Comparing ‘test_mapqtl_io.Rout’ to ‘test_mapqtl_io.Rout.save’ ... OK
  Running ‘test_qtl.R’ [0s/0s]
  Running ‘test_scanonevar.R’ [5s/6s]
  Comparing ‘test_scanonevar.Rout’ to ‘test_scanonevar.Rout.save’ ... OK
  Running ‘test_tidyIO.R’ [0s/1s]
  Comparing ‘test_tidyIO.Rout’ to ‘test_tidyIO.Rout.save’ ... OK
  Running ‘testaugmentation.R’ [1s/2s]
  Running ‘testthat.R’ [18s/22s]
Running the tests in ‘tests/test_io.R’ failed.
Complete output:
  > ######################################################################
  > #
  > # TestIO/input.R
  > #
  > # copyright (c) 2002, Karl W Broman
  > # last modified Feb, 2002
  > # first written Feb, 2002
  > #
  > #     This program is free software; you can redistribute it and/or
  > #     modify it under the terms of the GNU General Public License,
  > #     version 3, as published by the Free Software Foundation.
  > # 
  > #     This program is distributed in the hope that it will be useful,
  > #     but without any warranty; without even the implied warranty of
  > #     merchantability or fitness for a particular purpose.  See the GNU
  > #     General Public License, version 3, for more details.
  > # 
  > #     A copy of the GNU General Public License, version 3, is available
  > #     at http://www.r-project.org/Licenses/GPL-3
  > #
  > # This file contains code for testing the cross IO in R/qtl.
  > #
  > # Needed input files:
  > #
  > #    gen.txt, map.txt, phe.txt    [Karl's format]
  > #    listeria.raw, listeria.map   [mapmaker format]
  > #    listeria.raw, listeria2.map  [mapmaker format; no marker pos]
  > #    listeria.csv                 [csv format] 
  > #    listeria2.csv                [csv format; no marker pos] 
  > #
  > ######################################################################
  > 
  > library(qtl)
  > 
  > ##############################
  > # Reading
  > ##############################
  > # Read CSV format
  > csv <- read.cross("csv", "", "listeria.csv")
   --Read the following data:
  	 120  individuals
  	 133  markers
  	 1  phenotypes
   --Cross type: f2 
  Warning message:
  In fixXgeno.f2(cross, alleles) :*** buffer overflow detected ***: terminated
  Aborted
Running the tests in ‘tests/test_qtl.R’ failed.
Complete output:
  > ######################################################################
  > #
  > # test_qtl.R
  > #
  > # copyright (c) 2009, Karl W Broman, Pjotr Prins
  > # first written July 2009
  > #
  > #     This program is free software; you can redistribute it and/or
  > #     modify it under the terms of the GNU General Public License,
  > #     version 3, as published by the Free Software Foundation.
  > #
  > #     This program is distributed in the hope that it will be useful,
  > #     but without any warranty; without even the implied warranty of
  > #     merchantability or fitness for a particular purpose.  See the GNU
  > #     General Public License, version 3, for more details.
  > #
  > #     A copy of the GNU General Public License, version 3, is available
  > #     at http://www.r-project.org/Licenses/GPL-3
  > #
  > # Some basic regression/integration testing for some of the QTL mapping routines
  > #
  > # You can run it with:
  > #
  > #   R --no-save --no-restore --no-readline --slave < ./tests/test_qtl.R 
  > 
  > ######################################################################
  > 
  > library(qtl)
  > 
  > version = mqm_version()
  > cat("R/qtl=",version$RQTL)
  R/qtl= 1.74> cat("R-MQM=",version$RMQM)
  R-MQM= 0.90-pre1> cat("MQM=",version$MQM)
  MQM= 0.90-pre1> 
  > 
  > data(listeria)
  > if (nind(listeria)!=120) stop("Number of individuals incorrect")
  > 
  > # ---- a quick test of standard R/qtl scanone
  > mr = scanone(listeria, method='mr')
  Warning message:
  In checkcovar(cross, pheno.col, addcovar, intcovar, perm.strata,  :*** buffer overflow detected ***: terminated
  Aborted