[Genabel-commits] r823 - in pkg/GenABEL: R inst/unitTests src src/GAlib
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Dec 7 11:33:34 CET 2011
Author: yurii
Date: 2011-12-07 11:33:34 +0100 (Wed, 07 Dec 2011)
New Revision: 823
Removed:
pkg/GenABEL/R/bartlett.R
pkg/GenABEL/src/GAlib/bartlett_test.cpp
pkg/GenABEL/src/GAlib/bartlett_test.h
Modified:
pkg/GenABEL/inst/unitTests/report.html
pkg/GenABEL/inst/unitTests/report.txt
pkg/GenABEL/inst/unitTests/reportSummary.txt
pkg/GenABEL/inst/unitTests/runit.descriptives.trait.R
pkg/GenABEL/src/Makevars
Log:
make sure all is in sync
Deleted: pkg/GenABEL/R/bartlett.R
===================================================================
--- pkg/GenABEL/R/bartlett.R 2011-12-07 10:29:51 UTC (rev 822)
+++ pkg/GenABEL/R/bartlett.R 2011-12-07 10:33:34 UTC (rev 823)
@@ -1,92 +0,0 @@
-#=====================================================================================
-#
-# Filename: R/bartlett.R
-#
-# Description: Bartlett's test of variance homogeneity
-#
-# Version: 1.0
-# Created:
-# Revision: none
-#
-#
-# Author: Maksim V. Struchalin
-# Company: ErasmusMC, Epidemiology, The Netherlands.
-# Email: m.struchalin at erasmusmc.nl
-#
-#=====================================================================================
-
-
-"bartlett" <-
-function(trait, data, analysis_type) {#, trait.type = "gaussian") {
-
-
-#if(class(data) != "gwaa.data" && class(data) != "snp.data")
-# {
-# stop("Wrong data class: data input parameter must be \"gwaa.data\" or \"snp.data\"")
-# }
-
-#class_formula <- class(formula)
-
-#if(class_formula != "formula" || class_formula != "numeric" || class_formula != "integer" || class_formula != "double")
-# {
-# stop("Wrong formula class: formula must have one of the following types: \"formula\", \"numeric\", \"integer\", \"double\"")
-# }
-
-#if(class(data) == "snp.data" && class(formula) == "formula" )
-# {
-# stop("Wrong types of input parameters. data can not have type \"snp.data\" and formula - \"formula\" ")
-# }
-
-#if(class(trait.type) != "character")
-# {
-# stop("Wrong types of trait.type. It must be \"character\".")
-# }
-
-
-#if(class(trait.type) != "gaussian")
-# {
-# stop("error: gaussian is only support")
-# }
-
-
-
-
-
-
-
-if(length(trait) != data at gtdata@nids)
- {
- stop("Length of trait does not match to ids amount")
- }
-
-
-
-is_trait_na <- is.na(trait)
-
-
-trait[is_trait_na] <- 0
-
-
-is_trait_na <- as.integer(is_trait_na)
-
-
-
-
-print("start calculating")
-
-retrun_val <- .C("bartlett_test_R", as.raw(data at gtdata@gtps), as.integer(data at gtdata@nids), as.integer(data at gtdata@nsnps),
- as.double(trait), as.integer(is_trait_na),
- chi2 = double(data at gtdata@nsnps), analysis_type)
-
-
-chi2 <- retrun_val$chi2
-
-
-print("all snps done")
-
-chi2[chi2 == -1] <- NA
-
-
-return(chi2)
-
-}
Modified: pkg/GenABEL/inst/unitTests/report.html
===================================================================
--- pkg/GenABEL/inst/unitTests/report.html 2011-12-07 10:29:51 UTC (rev 822)
+++ pkg/GenABEL/inst/unitTests/report.html 2011-12-07 10:33:34 UTC (rev 823)
@@ -1,11 +1,11 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
"http://www.w3.org/TR/html4/transitional.dtd">
-<html><head><title>RUNIT TEST PROTOCOL--Mon Dec 5 23:16:08 2011</title>
+<html><head><title>RUNIT TEST PROTOCOL--Tue Dec 6 13:20:55 2011</title>
</head>
-<body><h1 TRUE>RUNIT TEST PROTOCOL--Mon Dec 5 23:16:08 2011</h1>
+<body><h1 TRUE>RUNIT TEST PROTOCOL--Tue Dec 6 13:20:55 2011</h1>
<p>Number of test functions: 18</p>
<p>Number of errors: 0</p>
-<p>Number of failures: 0</p>
+<p style=color:red>Number of failures: 2</p>
<hr>
<h3 TRUE>1 Test suite</h3>
<table border="1" width="60%" >
@@ -17,28 +17,47 @@
<tr><td><a href="#GenABEL unit testing">GenABEL unit testing</a></td>
<td>18</td>
<td>0</td>
-<td>0</td>
+<td bgcolor="red">2</td>
</tr>
</table>
<hr>
+<h3 TRUE>Failures</h3>
+<table border="1" width="100%" >
+<tr><th width="30%">Test suite : test function</th>
+<th width="70%">message</th>
+</tr>
+<tr><td><a href="#GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.exports.R_test.exports">GenABEL unit testing : test.exports</a></td>
+<td>Error in checkIdentical(xBack[, sameCode], dta[, sameCode]) : FALSE
+</td>
+</tr>
+<tr><td><a href="#GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.polylik.R_test.polylik">GenABEL unit testing : test.polylik</a></td>
+<td>Error in checkEquals(h2htNew$pgresidualY, h2htOld$pgresidualY) :
+ Mean relative difference: 1.756053e-08
+</td>
+</tr>
+</table>
+<hr>
<h3 TRUE>Details</h3>
<p><a name="GenABEL unit testing"><h5 TRUE>Test Suite: GenABEL unit testing</h5>
-</a>Test function regexp: ^test.+<br/>Test file regexp: ^runit.+\.[rR]$<br/>Involved directory:<br/>/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests<br/><ul><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.convert.snp.R">Test file: runit.convert.snp.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.convert.snp.R_test.convert.snp">test.convert.snp: (4 checks) ... OK (0.9 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.convert.snp.ped.R">Test file: runit.convert.snp.ped.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.convert.snp.ped.R_test.convert.snp.ped">test.convert.snp.ped: (0 checks) ... OK (0.01 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.descriptives.trait.R">Test file: runit.descriptives.trait.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.descriptives.trait.R_test.descriptives.trait">test.descriptives.trait: (1 checks) ... OK (0.37 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.exports.R">Test file: runit.exports.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.exports.R_test.exports">test.exports: (169 checks) ... OK (3.07 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.findRelatives.R">Test file: runit.findRelatives.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.findRelatives.R_test.findRelatives">test.findRelatives: (10 checks) ... OK (55.56 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.impute2xxx.R">Test file: runit.impute2xxx.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.impute2xxx.R_test.impute2databel">test.impute2databel: (23 checks) ... OK (0.57 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.impute2xxx_large.R">Test file: runit.impute2xxx_large.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.impute2xxx_large.R_test.impute2xxx_large">test.impute2xxx_large: (0 checks) ... OK (0 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.iterator.R">Test file: runit.iterator.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.iterator.R_test.qtscore">test.qtscore: (0 checks) ... OK (0 seconds)<br/></a></li><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.iterator.R_test.summary_snp_data">test.summary_snp_data: (3 checks) ... OK (3.96 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.mach2databel.R">Test file: runit.mach2databel.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.mach2databel.R_test.mach2databel">test.mach2databel: (8 checks) ... OK (0.13 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.merge.R">Test file: runit.merge.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.merge.R_test.merge.bug1641">test.merge.bug1641: (0 checks) ... OK (0.19 seconds)<br/></a></li><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.merge.R_test.merge.bug1676">test.merge.bug1676: (2 checks) ... OK (0.18 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.mmscore.R">Test file: runit.mmscore.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.mmscore.R_test.exports">test.exports: (1 checks) ... OK (0.69 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.polygenic.R">Test file: runit.polygenic.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.polygenic.R_test.polygenic.Bug1322">test.polygenic.Bug1322: (2 checks) ... OK (1.12 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.polylik.R">Test file: runit.polylik.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.polylik.R_test.polylik">test.polylik: (6 checks) ... OK (7.3 seconds)<br/></a></li></ul></li></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.recodeChromosome.R">Test file: runit.recodeChromosome.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.recodeChromosome.R_test.recodeChromosome">test.recodeChromosome: (8 checks) ... OK (0.13 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.sortmap.internal.R">Test file: runit.sortmap.internal.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.sortmap.internal.R_test.sortmap.internal.bug1673">test.sortmap.internal.bug1673: (1 checks) ... OK (0 seconds)<br/></a></li></ul></li><li><a href="/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.strandModify.R">Test file: runit.strandModify.R</a><ul><li><a name="GenABEL unit testing__Users_yuryaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.strandModify.R_test.strandModify">test.strandModify: (2 checks) ... OK (0.05 seconds)<br/></a></li></ul></li></ul><hr>
+</a>Test function regexp: ^test.+<br/>Test file regexp: ^runit.+\.[rR]$<br/>Involved directory:<br/>/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests<br/><ul><li><a href="/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.convert.snp.ped.R">Test file: runit.convert.snp.ped.R</a><ul><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.convert.snp.ped.R_test.convert.snp.ped">test.convert.snp.ped: (0 checks) ... OK (0.12 seconds)<br/></a></li></ul></li><li><a href="/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.convert.snp.R">Test file: runit.convert.snp.R</a><ul><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.convert.snp.R_test.convert.snp">test.convert.snp: (4 checks) ... OK (1.49 seconds)<br/></a></li></ul></li><li><a href="/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.descriptives.trait.R">Test file: runit.descriptives.trait.R</a><ul><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.descriptives.trait.R_test.descriptives.trait">test.descriptives.trait: (1 checks) ... OK (0.43 seconds)<br/></a></li></ul></li><li><a href="/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.exports.R">Test file: runit.exports.R</a><ul><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.exports.R_test.exports"><u style=color:red>test.exports: FAILURE !! (check number 8) </u></a>Error in checkIdentical(xBack[, sameCode], dta[, sameCode]) : FALSE
+<br/></li></ul></li><li><a href="/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.findRelatives.R">Test file: runit.findRelatives.R</a><ul><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.findRelatives.R_test.findRelatives">test.findRelatives: (10 checks) ... OK (45.05 seconds)<br/></a></li></ul></li><li><a href="/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.impute2xxx_large.R">Test file: runit.impute2xxx_large.R</a><ul><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.impute2xxx_large.R_test.impute2xxx_large">test.impute2xxx_large: (0 checks) ... OK (0.03 seconds)<br/></a></li></ul></li><li><a href="/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.impute2xxx.R">Test file: runit.impute2xxx.R</a><ul><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.impute2xxx.R_test.impute2databel">test.impute2databel: (23 checks) ... OK (1.15 seconds)<br/></a></li></ul></li><li><a href="/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.iterator.R">Test file: runit.iterator.R</a><ul><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.iterator.R_test.qtscore">test.qtscore: (0 checks) ... OK (0 seconds)<br/></a></li><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.iterator.R_test.summary_snp_data">test.summary_snp_data: (3 checks) ... OK (8.34 seconds)<br/></a></li></ul></li><li><a href="/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.mach2databel.R">Test file: runit.mach2databel.R</a><ul><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.mach2databel.R_test.mach2databel">test.mach2databel: (8 checks) ... OK (0.97 seconds)<br/></a></li></ul></li><li><a href="/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.merge.R">Test file: runit.merge.R</a><ul><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.merge.R_test.merge.bug1641">test.merge.bug1641: (0 checks) ... OK (0.17 seconds)<br/></a></li><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.merge.R_test.merge.bug1676">test.merge.bug1676: (2 checks) ... OK (0.2 seconds)<br/></a></li></ul></li><li><a href="/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.mmscore.R">Test file: runit.mmscore.R</a><ul><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.mmscore.R_test.exports">test.exports: (1 checks) ... OK (0.65 seconds)<br/></a></li></ul></li><li><a href="/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.polygenic.R">Test file: runit.polygenic.R</a><ul><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.polygenic.R_test.polygenic.Bug1322">test.polygenic.Bug1322: (2 checks) ... OK (1.05 seconds)<br/></a></li></ul></li><li><a href="/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.polylik.R">Test file: runit.polylik.R</a><ul><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.polylik.R_test.polylik"><u style=color:red>test.polylik: FAILURE !! (check number 4) </u></a>Error in checkEquals(h2htNew$pgresidualY, h2htOld$pgresidualY) :
+ Mean relative difference: 1.756053e-08
+<br/></li></ul></li></li><li><a href="/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.recodeChromosome.R">Test file: runit.recodeChromosome.R</a><ul><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.recodeChromosome.R_test.recodeChromosome">test.recodeChromosome: (8 checks) ... OK (0.19 seconds)<br/></a></li></ul></li><li><a href="/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.sortmap.internal.R">Test file: runit.sortmap.internal.R</a><ul><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.sortmap.internal.R_test.sortmap.internal.bug1673">test.sortmap.internal.bug1673: (1 checks) ... OK (0 seconds)<br/></a></li></ul></li><li><a href="/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.strandModify.R">Test file: runit.strandModify.R</a><ul><li><a name="GenABEL unit testing__home_yurii_yuriiaulchenko_eclipse_workspace_genabel_pkg_GenABEL_tests_.._inst_unitTests_runit.strandModify.R_test.strandModify">test.strandModify: (2 checks) ... OK (0.05 seconds)<br/></a></li></ul></li></ul><hr>
<table border="0" width="80%" >
<tr><th>Name</th>
<th>Value</th>
</tr>
<tr><td>platform</td>
-<td>x86_64-apple-darwin9.8.0</td>
+<td>x86_64-unknown-linux-gnu</td>
</tr>
<tr><td>arch</td>
<td>x86_64</td>
</tr>
<tr><td>os</td>
-<td>darwin9.8.0</td>
+<td>linux-gnu</td>
</tr>
<tr><td>system</td>
-<td>x86_64, darwin9.8.0</td>
+<td>x86_64, linux-gnu</td>
</tr>
<tr><td>status</td>
<td>Under development (unstable)</td>
@@ -47,31 +66,31 @@
<td>2</td>
</tr>
<tr><td>minor</td>
-<td>14.0</td>
+<td>15.0</td>
</tr>
<tr><td>year</td>
<td>2011</td>
</tr>
<tr><td>month</td>
-<td>06</td>
+<td>12</td>
</tr>
<tr><td>day</td>
-<td>30</td>
+<td>04</td>
</tr>
<tr><td>svn rev</td>
-<td>56238</td>
+<td>57813</td>
</tr>
<tr><td>language</td>
<td>R</td>
</tr>
<tr><td>version.string</td>
-<td>R version 2.14.0 Under development (unstable) (2011-06-30 r56238)</td>
+<td>R Under development (unstable) (2011-12-04 r57813)</td>
</tr>
<tr><td>host</td>
-<td>Yury-Aulchenkos-MacBook-Pro.local</td>
+<td>debian</td>
</tr>
<tr><td>compiler</td>
-<td>NA</td>
+<td>g++</td>
</tr>
</table>
</body>
Modified: pkg/GenABEL/inst/unitTests/report.txt
===================================================================
--- pkg/GenABEL/inst/unitTests/report.txt 2011-12-07 10:29:51 UTC (rev 822)
+++ pkg/GenABEL/inst/unitTests/report.txt 2011-12-07 10:33:34 UTC (rev 823)
@@ -1,12 +1,15 @@
-RUNIT TEST PROTOCOL -- Mon Dec 5 23:16:08 2011
+RUNIT TEST PROTOCOL -- Tue Dec 6 13:20:55 2011
***********************************************
Number of test functions: 18
Number of errors: 0
-Number of failures: 0
+Number of failures: 2
1 Test Suite :
-GenABEL unit testing - 18 test functions, 0 errors, 0 failures
+GenABEL unit testing - 18 test functions, 0 errors, 2 failures
+FAILURE in test.exports: Error in checkIdentical(xBack[, sameCode], dta[, sameCode]) : FALSE
+FAILURE in test.polylik: Error in checkEquals(h2htNew$pgresidualY, h2htOld$pgresidualY) :
+ Mean relative difference: 1.756053e-08
@@ -16,54 +19,57 @@
Test function regexp: ^test.+
Test file regexp: ^runit.+\.[rR]$
Involved directory:
-/Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests
+/home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests
---------------------------
-Test file: /Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.convert.snp.R
-test.convert.snp: (4 checks) ... OK (0.9 seconds)
+Test file: /home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.convert.snp.ped.R
+test.convert.snp.ped: (0 checks) ... OK (0.12 seconds)
---------------------------
-Test file: /Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.convert.snp.ped.R
-test.convert.snp.ped: (0 checks) ... OK (0.01 seconds)
+Test file: /home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.convert.snp.R
+test.convert.snp: (4 checks) ... OK (1.49 seconds)
---------------------------
-Test file: /Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.descriptives.trait.R
-test.descriptives.trait: (1 checks) ... OK (0.37 seconds)
+Test file: /home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.descriptives.trait.R
+test.descriptives.trait: (1 checks) ... OK (0.43 seconds)
---------------------------
-Test file: /Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.exports.R
-test.exports: (169 checks) ... OK (3.07 seconds)
+Test file: /home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.exports.R
+test.exports: FAILURE !! (check number 8)
+Error in checkIdentical(xBack[, sameCode], dta[, sameCode]) : FALSE
---------------------------
-Test file: /Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.findRelatives.R
-test.findRelatives: (10 checks) ... OK (55.56 seconds)
+Test file: /home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.findRelatives.R
+test.findRelatives: (10 checks) ... OK (45.05 seconds)
---------------------------
-Test file: /Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.impute2xxx.R
-test.impute2databel: (23 checks) ... OK (0.57 seconds)
+Test file: /home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.impute2xxx_large.R
+test.impute2xxx_large: (0 checks) ... OK (0.03 seconds)
---------------------------
-Test file: /Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.impute2xxx_large.R
-test.impute2xxx_large: (0 checks) ... OK (0 seconds)
+Test file: /home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.impute2xxx.R
+test.impute2databel: (23 checks) ... OK (1.15 seconds)
---------------------------
-Test file: /Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.iterator.R
+Test file: /home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.iterator.R
test.qtscore: (0 checks) ... OK (0 seconds)
-test.summary_snp_data: (3 checks) ... OK (3.96 seconds)
+test.summary_snp_data: (3 checks) ... OK (8.34 seconds)
---------------------------
-Test file: /Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.mach2databel.R
-test.mach2databel: (8 checks) ... OK (0.13 seconds)
+Test file: /home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.mach2databel.R
+test.mach2databel: (8 checks) ... OK (0.97 seconds)
---------------------------
-Test file: /Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.merge.R
-test.merge.bug1641: (0 checks) ... OK (0.19 seconds)
-test.merge.bug1676: (2 checks) ... OK (0.18 seconds)
+Test file: /home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.merge.R
+test.merge.bug1641: (0 checks) ... OK (0.17 seconds)
+test.merge.bug1676: (2 checks) ... OK (0.2 seconds)
---------------------------
-Test file: /Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.mmscore.R
-test.exports: (1 checks) ... OK (0.69 seconds)
+Test file: /home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.mmscore.R
+test.exports: (1 checks) ... OK (0.65 seconds)
---------------------------
-Test file: /Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.polygenic.R
-test.polygenic.Bug1322: (2 checks) ... OK (1.12 seconds)
+Test file: /home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.polygenic.R
+test.polygenic.Bug1322: (2 checks) ... OK (1.05 seconds)
---------------------------
-Test file: /Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.polylik.R
-test.polylik: (6 checks) ... OK (7.3 seconds)
+Test file: /home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.polylik.R
+test.polylik: FAILURE !! (check number 4)
+Error in checkEquals(h2htNew$pgresidualY, h2htOld$pgresidualY) :
+ Mean relative difference: 1.756053e-08
---------------------------
-Test file: /Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.recodeChromosome.R
-test.recodeChromosome: (8 checks) ... OK (0.13 seconds)
+Test file: /home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.recodeChromosome.R
+test.recodeChromosome: (8 checks) ... OK (0.19 seconds)
---------------------------
-Test file: /Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.sortmap.internal.R
+Test file: /home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.sortmap.internal.R
test.sortmap.internal.bug1673: (1 checks) ... OK (0 seconds)
---------------------------
-Test file: /Users/yuryaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.strandModify.R
+Test file: /home/yurii/yuriiaulchenko/eclipse_workspace/genabel/pkg/GenABEL/tests/../inst/unitTests/runit.strandModify.R
test.strandModify: (2 checks) ... OK (0.05 seconds)
Modified: pkg/GenABEL/inst/unitTests/reportSummary.txt
===================================================================
--- pkg/GenABEL/inst/unitTests/reportSummary.txt 2011-12-07 10:29:51 UTC (rev 822)
+++ pkg/GenABEL/inst/unitTests/reportSummary.txt 2011-12-07 10:33:34 UTC (rev 823)
@@ -1,9 +1,12 @@
-RUNIT TEST PROTOCOL -- Mon Dec 5 23:16:08 2011
+RUNIT TEST PROTOCOL -- Tue Dec 6 13:20:55 2011
***********************************************
Number of test functions: 18
Number of errors: 0
-Number of failures: 0
+Number of failures: 2
1 Test Suite :
-GenABEL unit testing - 18 test functions, 0 errors, 0 failures
+GenABEL unit testing - 18 test functions, 0 errors, 2 failures
+FAILURE in test.exports: Error in checkIdentical(xBack[, sameCode], dta[, sameCode]) : FALSE
+FAILURE in test.polylik: Error in checkEquals(h2htNew$pgresidualY, h2htOld$pgresidualY) :
+ Mean relative difference: 1.756053e-08
Modified: pkg/GenABEL/inst/unitTests/runit.descriptives.trait.R
===================================================================
--- pkg/GenABEL/inst/unitTests/runit.descriptives.trait.R 2011-12-07 10:29:51 UTC (rev 822)
+++ pkg/GenABEL/inst/unitTests/runit.descriptives.trait.R 2011-12-07 10:33:34 UTC (rev 823)
@@ -43,4 +43,4 @@
attach(phdata(test))
descriptives.trait(data=test, by = bt)
detach(phdata(test))
-}
\ No newline at end of file
+}
Deleted: pkg/GenABEL/src/GAlib/bartlett_test.cpp
===================================================================
--- pkg/GenABEL/src/GAlib/bartlett_test.cpp 2011-12-07 10:29:51 UTC (rev 822)
+++ pkg/GenABEL/src/GAlib/bartlett_test.cpp 2011-12-07 10:33:34 UTC (rev 823)
@@ -1,108 +0,0 @@
-//#include <memory>
-#include <list>
-#include <cmath>
-#include <iostream>
-#include <stdio.h>
-#include <stdlib.h>
-#include "bartlett_test.h"
-
-
-using namespace std;
-
-extern "C" {
-
-
-
-//_____________________________________________________________
-// Bartlett test for homogeneity in variances
-//http://en.wikipedia.org/wiki/Bartlett%27s_test
-//retrun test chi2 or -1 in case of a problem
-
-double bartlett_test(std::list<my_small_vector> * samples)
- {
-
- unsigned sample_amount = samples->size();
- if(sample_amount <= 1) {std::cout<<"error: bartlett_test: only one sample found\n"; return -1;}
-
- std::list<my_small_vector>::const_iterator it;
-
-
-// double * variances = new double[sample_amount]
-// double * n = new double[sample_amount];
-
- double Sp2=0;
- double sum_ni_1lnSi2 = 0; //sum( (n_i-1)*ln(Si2) )
- double sum_1__n_1=0;
- double N=0;
- double var_i=0;
-
-
- for(it=samples->begin(); it!=samples->end(); ++it)
- {
- if(it->number <= 1) {std::cout<<"error: bartlett_test: one of the sample has 1 element only\n"; return -1;}
- N += it->number;
-
- var_i = var(*it);
- if(var_i > -1.E-32 && var_i < 1.E-32) {std::cout<<"error: bartlett_test: one of the sample has too small variance\n"; return -1;}
-
- sum_ni_1lnSi2 += (it->number - 1)*log(var_i);
-
- sum_1__n_1 += 1./(it->number-1.);
-
- Sp2 += (it->number - 1)*var_i;
- }
-
- Sp2 = Sp2/(N-sample_amount);
-
-
- double X2 = ((N - sample_amount)*log(Sp2) - sum_ni_1lnSi2)/(1 + (sum_1__n_1-1/(N-sample_amount))/(3*(sample_amount-1)) );
-
- return X2;
- }
-
-
-
-
-
-//_____________________________________________________________
-
-
-double var(my_small_vector vec)
- {
- double sum = 0;
- double mean = get_mean(vec);
-
- if(vec.number <= 1) {std::cout<<"error: var: sample has not more than one element\n"; exit(1);}
-
- for(unsigned i=0; i<vec.number ; i++)
- {
- sum += (vec.vector[i]-mean)*(vec.vector[i]-mean);
- }
-
- return sum/(vec.number-1);
- }
-
-//_____________________________________________________________
-
-
-
-//_____________________________________________________________
-// returun mean of the array or exit(1) in case of problem
-
-double get_mean(my_small_vector vec)
- {
- double mean =0;
-
- if(vec.number == 0) {std::cout<<"error: get_mean: sample does not have any element\n"; exit(1);}
-
- for(unsigned i=0; i<vec.number ; i++)
- {
- mean += vec.vector[i];
- }
-
- return mean/vec.number;
- }
-//_____________________________________________________________
-
-
-}
Deleted: pkg/GenABEL/src/GAlib/bartlett_test.h
===================================================================
--- pkg/GenABEL/src/GAlib/bartlett_test.h 2011-12-07 10:29:51 UTC (rev 822)
+++ pkg/GenABEL/src/GAlib/bartlett_test.h 2011-12-07 10:33:34 UTC (rev 823)
@@ -1,38 +0,0 @@
-#ifndef SMV_BARTLETT_TEST_H
-#define SMV_BARTLETT_TEST_H
-
-
-#include <list>
-
-extern "C" {
-
-
-class my_small_vector
- {
-
- public:
- my_small_vector(double * vector_, unsigned long number_)
- {
- vector=vector_;
- number=number_;
- }
-// ~my_small_vector(void)
-// {
-// delete[] vector;
-// }
-
- double * vector;
- unsigned long number; //amount of cells in vector
-};
-
-
-
-double bartlett_test(std::list<my_small_vector> * samples);
-
-double get_mean(my_small_vector vec);
-double var(my_small_vector vec);
-
-
-}
-
-#endif
Modified: pkg/GenABEL/src/Makevars
===================================================================
--- pkg/GenABEL/src/Makevars 2011-12-07 10:29:51 UTC (rev 822)
+++ pkg/GenABEL/src/Makevars 2011-12-07 10:33:34 UTC (rev 823)
@@ -6,4 +6,4 @@
rm -f ../configure.Rout ../.RData *.c* *.h* *.o *.uxf ../R/.RData
clean:
- rm -f *.o *.so *.dll Makedeps
\ No newline at end of file
+ rm -f *.o *.so *.dll Makedeps
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