Running 'test_io.R' [167s]
  Running 'test_mapqtl_io.R' [171s]
  Running 'test_qtl.R' [5s]
  Running 'test_scanonevar.R' [6s]
  Comparing 'test_scanonevar.Rout' to 'test_scanonevar.Rout.save' ... OK
  Running 'test_tidyIO.R' [161s]
  Running 'testaugmentation.R' [2s]
  Running 'testthat.R' [178s]
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) :
     --Assuming that all individuals are female.
  
  > csv2 <- read.cross("csv", "", "listeria2.csv", estimate=FALSE)
   --Read the following data:
  	 120  individuals
  	 133  markers
  	 1  phenotypes
   --Cross type: f2 
  Warning message:
  In fixXgeno.f2(cross, alleles) :
     --Assuming that all individuals are female.
  
  > 
  > # Read mapmaker format
  > mm <- read.cross("mm", "", "listeria.raw", "listeria.map")
   --Read the following data:
  	Type of cross:          f2 
  	Number of individuals:  120 
  	Number of markers:      133 
  	Number of phenotypes:   1 
   --Cross type: f2 
  Warning message:
  In fixXgeno.f2(cross, alleles) :
     --Assuming that all individuals are female.
  
  > mm2 <- read.cross("mm", "", "listeria.raw", "listeria2.map", estimate=FALSE)
   --Read the following data:
  	Type of cross:          f2 
  	Number of individuals:  120 
  	Number of markers:      133 
  	Number of phenotypes:   1 
   --Cross type: f2 
  Warning message:
  In fixXgeno.f2(cross, alleles) :
     --Assuming that all individuals are female.
  
  > 
  > ##############################
  > # Writing
  > ##############################
  > # Write in CSV format
  > write.cross(csv, "csv", filestem="junk1")
  > csv3 <- read.cross("csv", "", "junk1.csv", genotypes=c("AA","AB","BB","not BB","not AA"))
   --Read the following data:
  	 120  individuals
  	 133  markers
  	 3  phenotypes
   --Cross type: f2 
  > comparecrosses(csv, csv3)
  	Crosses are identical.
  > 
  > # Write in mapmaker format
  > write.cross(csv, "mm", filestem="junk2")
  > 
  > # Cleanup
  > unlink("junk1.csv")
  > unlink("junk2.raw")
  > unlink("junk2.prep")
  > 
  > proc.time()
     user  system elapsed 
     0.59    0.23    0.81 
Running the tests in 'tests/test_mapqtl_io.R' failed.
Complete output:
  > # test input/output in mapqtl format
  > 
  > library(qtl)
  > data(fake.4way)
  > 
  > write.cross(fake.4way, "mapqtl", "fake_4way_mapqtl")
  > 
  > x <- read.cross("mapqtl", "", genfile="fake_4way_mapqtl.loc",
  +                 phefile="fake_4way_mapqtl.qua",
  +                 mapfile="fake_4way_mapqtl_female.map")
   --Read the following data:
  	Number of individuals:  250 
  	Number of markers:  157 
  	Number of phenotypes:  2 
   --Cross type: 4way 
  > 
  > x <- replace.map(x, pull.map(fake.4way))
  > 
  > comparecrosses(x, fake.4way)
  	Crosses are identical.
  > 
  > proc.time()
     user  system elapsed 
     2.42    0.31    2.71 
Running the tests in 'tests/test_tidyIO.R' failed.
Complete output:
  > library(qtl)
  > data(hyper)
  > 
  > # write to tidy format
  > write.cross(hyper, "tidy", "hyper_tidy")
  > 
  > # read back in
  > x <- read.cross("tidy", "", genfile="hyper_tidy_gen.csv",
  +                 mapfile="hyper_tidy_map.csv", phefile="hyper_tidy_phe.csv",
  +                 genotypes=c("BB", "BA", "AA"))
   --Read the following data:
  	 250  individuals
  	 174  markers
  	 2  phenotypes
   --Cross type: bc 
  > 
  > # compare results
  > comparecrosses(x, hyper)
  	Crosses are identical.
  > 
  > proc.time()
     user  system elapsed 
     0.45    0.10    0.54 
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("qtl")
  Loading required package: qtl
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 51 ]
  > 
  > proc.time()
     user  system elapsed 
    20.56    0.98   21.54