[Genabel-commits] r807 - in pkg/ProbABEL: . examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Dec 2 18:24:58 CET 2011
Author: lckarssen
Date: 2011-12-02 18:24:57 +0100 (Fri, 02 Dec 2011)
New Revision: 807
Added:
pkg/ProbABEL/examples/Makefile.am
Modified:
pkg/ProbABEL/Makefile.am
pkg/ProbABEL/configure.ac
pkg/ProbABEL/examples/
pkg/ProbABEL/examples/example_bt.sh
pkg/ProbABEL/examples/example_mms.sh
pkg/ProbABEL/examples/example_qt.sh
Log:
Added the test scripts from the example directory to the Makefile. Now running
make check
or
make distcheck
will run these checks.
Modified: pkg/ProbABEL/Makefile.am
===================================================================
--- pkg/ProbABEL/Makefile.am 2011-12-02 15:56:55 UTC (rev 806)
+++ pkg/ProbABEL/Makefile.am 2011-12-02 17:24:57 UTC (rev 807)
@@ -1,62 +1,4 @@
## Process this file with automake to produce Makefile.in
AUTOMAKE_OPTIONS = foreign
-SUBDIRS = src doc
-
-examplefiles = \
- examples/height_ngp2_robust_int1_over_domin.out.txt.save \
- examples/test.prob.fvi examples/mmscore_gen.prob.fvd \
- examples/test.map examples/mldose.IDS \
- examples/impute_with_missing.mlinfo \
- examples/height_ngp2_robust_int1_recess.out.txt.save \
- examples/height_ngp2_2df.out.txt.save examples/mmscore_gen.mlprob \
- examples/mmscore_gen.mlinfo \
- examples/height_ngp2_robust_recess.out.txt.save \
- examples/example_cox.sh examples/test.mlprob examples/test.prob.fvd \
- examples/impute_with_missing_robust_int1_add.out.txt.save \
- examples/test.mlinfo examples/regression_add.out.txt.save \
- examples/height_ngp2_robust_add.out.txt.save \
- examples/mmscore_gen.dose.fvi \
- examples/impute_with_missing_allcov_add.out.txt.save \
- examples/example_bt.sh examples/height_ngp2_int1_recess.out.txt.save \
- examples/example_qt.sh examples/coxph_data.txt \
- examples/height_ngp2_robust_int1_domin.out.txt.save \
- examples/height_ngp2_allcov_2df.out.txt.save \
- examples/impute_with_missing_int1_add.out.txt.save \
- examples/mmscore_gen.mldose examples/example_mms.sh \
- examples/height_ngp2_recess.out.txt.save \
- examples/height_ngp2_over_domin.out.txt.save \
- examples/height_ngp2_int1_domin.out.txt.save \
- examples/height_ngp2_allcov_domin.out.txt.save \
- examples/height_ngp2_robust_over_domin.out.txt.save \
- examples/height_ngp2_robust_int1_add.out.txt.save \
- examples/height_int1_add.out.txt.save \
- examples/height_allcov_add.out.txt.save \
- examples/impute_with_missing_base_add.out.txt.save \
- examples/example_all.sh examples/height_base_add.out.txt.save \
- examples/height_ngp2_int1_over_domin.out.txt.save \
- examples/height_robust_add.out.txt.save examples/test.mldose \
- examples/height_ngp2_allcov_add.out.txt.save \
- examples/mmscore_InvSigma_aj.sex.age.dat \
- examples/height_ngp2_robust_int1_2df.out.txt.save \
- examples/mmscore_gen.dose.fvd examples/mmscore.R \
- examples/test.dose.fvd examples/height_ngp2_domin.out.txt.save \
- examples/test.dose.fvi \
- examples/impute_with_missing_robust_add.out.txt.save \
- examples/allheight.txt examples/mmscore_add.out.txt.save \
- examples/coxph.out.txt_add.out.txt.save examples/mmscore_pheno.PHE \
- examples/height_ngp2_robust_2df.out.txt.save \
- examples/height_ngp2_int1_add.out.txt.save \
- examples/mmscore_gen.prob.fvi \
- examples/height_robust_int1_add.out.txt.save \
- examples/logist.out.txt_add.out.txt.save \
- examples/height_ngp2_allcov_recess.out.txt.save \
- examples/impute_with_missing.PHE \
- examples/height_ngp2_allcov_over_domin.out.txt.save \
- examples/height_ngp2_add.out.txt.save examples/logist_data.txt \
- examples/height_ngp2_int1_2df.out.txt.save \
- examples/impute_with_missing_add.out.txt.save \
- examples/height_ngp2_robust_domin.out.txt.save examples/height.txt
-
-exampledir = $(pkgdatadir)/examples
-dist_example_DATA = $(examplefiles)
+SUBDIRS = src doc examples
Modified: pkg/ProbABEL/configure.ac
===================================================================
--- pkg/ProbABEL/configure.ac 2011-12-02 15:56:55 UTC (rev 806)
+++ pkg/ProbABEL/configure.ac 2011-12-02 17:24:57 UTC (rev 807)
@@ -55,6 +55,7 @@
Makefile
src/Makefile
doc/Makefile
+ examples/Makefile
])
# Create output files
AC_OUTPUT
Property changes on: pkg/ProbABEL/examples
___________________________________________________________________
Added: svn:ignore
+ Makefile.in
Added: pkg/ProbABEL/examples/Makefile.am
===================================================================
--- pkg/ProbABEL/examples/Makefile.am (rev 0)
+++ pkg/ProbABEL/examples/Makefile.am 2011-12-02 17:24:57 UTC (rev 807)
@@ -0,0 +1,102 @@
+## Process this file with automake to produce Makefile.in
+
+AUTOMAKE_OPTIONS = foreign color-tests
+
+examplefiles = height_ngp2_robust_int1_over_domin.out.txt.save \
+ test.prob.fvi mmscore_gen.prob.fvd test.map mldose.IDS \
+ impute_with_missing.mlinfo \
+ height_ngp2_robust_int1_recess.out.txt.save \
+ height_ngp2_2df.out.txt.save mmscore_gen.mlprob mmscore_gen.mlinfo \
+ height_ngp2_robust_recess.out.txt.save example_cox.sh test.mlprob \
+ test.prob.fvd impute_with_missing_robust_int1_add.out.txt.save \
+ test.mlinfo regression_add.out.txt.save \
+ height_ngp2_robust_add.out.txt.save mmscore_gen.dose.fvi \
+ impute_with_missing_allcov_add.out.txt.save example_bt.sh \
+ height_ngp2_int1_recess.out.txt.save example_qt.sh coxph_data.txt \
+ height_ngp2_robust_int1_domin.out.txt.save \
+ height_ngp2_allcov_2df.out.txt.save \
+ impute_with_missing_int1_add.out.txt.save mmscore_gen.mldose \
+ example_mms.sh height_ngp2_recess.out.txt.save \
+ height_ngp2_over_domin.out.txt.save \
+ height_ngp2_int1_domin.out.txt.save \
+ height_ngp2_allcov_domin.out.txt.save \
+ height_ngp2_robust_over_domin.out.txt.save \
+ height_ngp2_robust_int1_add.out.txt.save height_int1_add.out.txt.save \
+ height_allcov_add.out.txt.save \
+ impute_with_missing_base_add.out.txt.save example_all.sh \
+ height_base_add.out.txt.save height_ngp2_int1_over_domin.out.txt.save \
+ height_robust_add.out.txt.save test.mldose \
+ height_ngp2_allcov_add.out.txt.save mmscore_InvSigma_aj.sex.age.dat \
+ height_ngp2_robust_int1_2df.out.txt.save mmscore_gen.dose.fvd \
+ mmscore.R test.dose.fvd height_ngp2_domin.out.txt.save test.dose.fvi \
+ impute_with_missing_robust_add.out.txt.save allheight.txt \
+ mmscore_add.out.txt.save coxph.out.txt_add.out.txt.save \
+ mmscore_pheno.PHE height_ngp2_robust_2df.out.txt.save \
+ height_ngp2_int1_add.out.txt.save mmscore_gen.prob.fvi \
+ height_robust_int1_add.out.txt.save logist.out.txt_add.out.txt.save \
+ height_ngp2_allcov_recess.out.txt.save impute_with_missing.PHE \
+ height_ngp2_allcov_over_domin.out.txt.save \
+ height_ngp2_add.out.txt.save logist_data.txt \
+ height_ngp2_int1_2df.out.txt.save \
+ impute_with_missing_add.out.txt.save \
+ height_ngp2_robust_domin.out.txt.save height.txt
+
+exampledir = $(pkgdatadir)
+dist_example_DATA = $(examplefiles)
+
+TESTS_ENVIRONMENT = sh
+check_SCRIPTS = example_bt.sh example_qt.sh example_mms.sh
+TESTS = $(check_SCRIPTS)
+
+cleanfiles_bt = logist_add.out.txt logist_fv_add.out.txt
+
+cleanfiles_qt = height_base_add.out.txt height_base_fv_add.out.txt \
+height_allcov_add.out.txt height_allcov_fv_add.out.txt \
+height_int1_add.out.txt height_int1_fv_add.out.txt \
+height_robust_add.out.txt height_robust_fv_add.out.txt \
+height_robust_int1_add.out.txt height_robust_int1_fv_add.out.txt \
+height_ngp2_add.out.txt height_ngp2_fv_add.out.txt \
+height_ngp2_domin.out.txt height_ngp2_fv_domin.out.txt \
+height_ngp2_over_domin.out.txt height_ngp2_fv_over_domin.out.txt \
+height_ngp2_recess.out.txt height_ngp2_fv_recess.out.txt \
+height_ngp2_2df.out.txt height_ngp2_fv_2df.out.txt \
+height_ngp2_allcov_add.out.txt height_ngp2_allcov_fv_add.out.txt \
+height_ngp2_allcov_domin.out.txt height_ngp2_allcov_fv_domin.out.txt \
+height_ngp2_allcov_over_domin.out.txt \
+height_ngp2_allcov_fv_over_domin.out.txt \
+height_ngp2_allcov_recess.out.txt height_ngp2_allcov_fv_recess.out.txt \
+height_ngp2_allcov_recess.out.txt height_ngp2_allcov_fv_recess.out.txt \
+height_ngp2_int1_add.out.txt height_ngp2_int1_fv_add.out.txt \
+height_ngp2_int1_domin.out.txt height_ngp2_int1_fv_domin.out.txt \
+height_ngp2_int1_over_domin.out.txt \
+height_ngp2_int1_fv_over_domin.out.txt height_ngp2_int1_recess.out.txt \
+height_ngp2_int1_fv_recess.out.txt height_ngp2_int1_2df.out.txt \
+height_ngp2_int1_fv_2df.out.txt height_ngp2_robust_add.out.txt \
+height_ngp2_robust_fv_add.out.txt height_ngp2_robust_domin.out.txt \
+height_ngp2_robust_fv_domin.out.txt \
+height_ngp2_robust_over_domin.out.txt \
+height_ngp2_robust_fv_over_domin.out.txt \
+height_ngp2_robust_recess.out.txt height_ngp2_robust_fv_recess.out.txt \
+height_ngp2_robust_2df.out.txt height_ngp2_robust_fv_2df.out.txt \
+height_ngp2_robust_int1_add.out.txt \
+height_ngp2_robust_int1_fv_add.out.txt \
+height_ngp2_robust_int1_domin.out.txt \
+height_ngp2_robust_int1_fv_domin.out.txt \
+height_ngp2_robust_int1_over_domin.out.txt \
+height_ngp2_robust_int1_fv_over_domin.out.txt \
+height_ngp2_robust_int1_recess.out.txt \
+height_ngp2_robust_int1_fv_recess.out.txt \
+height_ngp2_robust_int1_2df.out.txt \
+height_ngp2_robust_int1_fv_2df.out.txt \
+height_ngp2_allcov_fv_2df.out.txt height_ngp2_robust_fv_add.out.txt \
+height_ngp2_allcov_2df.out.txt
+
+cleanfiles_mms = mmscore_add.out.txt mmscore_fv_add.out.txt \
+mmscore_prob_fv_over_domin.out.txt mmscore_prob_fv_domin.out.txt \
+mmscore_prob_over_domin.out.txt mmscore_prob_fv_add.out.txt \
+mmscore_prob_fv_recess.out.txt mmscore_prob_domin.out.txt \
+mmscore_prob_recess.out.txt mmscore_prob_add.out.txt \
+mmscore_prob_2df.out.txt mmscore_prob_fv_2df.out.txt
+
+
+CLEANFILES = $(cleanfiles_bt) $(cleanfiles_qt) $(cleanfiles_mms)
Modified: pkg/ProbABEL/examples/example_bt.sh
===================================================================
--- pkg/ProbABEL/examples/example_bt.sh 2011-12-02 15:56:55 UTC (rev 806)
+++ pkg/ProbABEL/examples/example_bt.sh 2011-12-02 17:24:57 UTC (rev 807)
@@ -1,5 +1,9 @@
echo "analysing BT"
-../bin/palogist -p logist_data.txt -d test.mldose -i test.mlinfo -m test.map -c 19 -o logist
-../bin/palogist -p logist_data.txt -d test.dose.fvi -i test.mlinfo -m test.map -c 19 -o logist_fv
+if [ -z ${srcdir} ]; then
+ srcdir="."
+fi
+
+../src/palogist -p ${srcdir}/logist_data.txt -d ${srcdir}/test.mldose -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 -o logist
+../src/palogist -p ${srcdir}/logist_data.txt -d ${srcdir}/test.dose.fvi -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 -o logist_fv
+
diff logist_add.out.txt logist_fv_add.out.txt
-
Modified: pkg/ProbABEL/examples/example_mms.sh
===================================================================
--- pkg/ProbABEL/examples/example_mms.sh 2011-12-02 15:56:55 UTC (rev 806)
+++ pkg/ProbABEL/examples/example_mms.sh 2011-12-02 17:24:57 UTC (rev 807)
@@ -1,7 +1,15 @@
echo "analysis using MMSCORE"
-../bin/palinear -p mmscore_pheno.PHE -i mmscore_gen.mlinfo -d mmscore_gen.mldose --sep="," -o mmscore --mmscore mmscore_InvSigma_aj.sex.age.dat
-../bin/palinear -p mmscore_pheno.PHE -i mmscore_gen.mlinfo -d mmscore_gen.dose.fvi --sep="," -o mmscore_fv --mmscore mmscore_InvSigma_aj.sex.age.dat
+if [ -z ${srcdir} ]; then
+ srcdir="."
+fi
+
+../src/palinear -p ${srcdir}/mmscore_pheno.PHE -i ${srcdir}/mmscore_gen.mlinfo -d ${srcdir}/mmscore_gen.mldose --sep="," -o mmscore --mmscore ${srcdir}/mmscore_InvSigma_aj.sex.age.dat
+../src/palinear -p ${srcdir}/mmscore_pheno.PHE -i ${srcdir}/mmscore_gen.mlinfo -d ${srcdir}/mmscore_gen.dose.fvi --sep="," -o mmscore_fv --mmscore ${srcdir}/mmscore_InvSigma_aj.sex.age.dat
+
diff mmscore_add.out.txt mmscore_fv_add.out.txt
-../bin/palinear -p mmscore_pheno.PHE -i mmscore_gen.mlinfo -d mmscore_gen.mlprob --ngpreds=2 --sep="," -o mmscore_prob --mmscore mmscore_InvSigma_aj.sex.age.dat
-../bin/palinear -p mmscore_pheno.PHE -i mmscore_gen.mlinfo -d mmscore_gen.prob.fvi --ngpreds=2 --sep="," -o mmscore_prob_fv --mmscore mmscore_InvSigma_aj.sex.age.dat
+
+../src/palinear -p ${srcdir}/mmscore_pheno.PHE -i ${srcdir}/mmscore_gen.mlinfo -d ${srcdir}/mmscore_gen.mlprob --ngpreds=2 --sep="," -o mmscore_prob --mmscore ${srcdir}/mmscore_InvSigma_aj.sex.age.dat
+../src/palinear -p ${srcdir}/mmscore_pheno.PHE -i ${srcdir}/mmscore_gen.mlinfo -d ${srcdir}/mmscore_gen.prob.fvi --ngpreds=2 --sep="," -o mmscore_prob_fv --mmscore ${srcdir}/mmscore_InvSigma_aj.sex.age.dat
+
+diff mmscore_prob_add.out.txt mmscore_prob_fv_add.out.txt
Modified: pkg/ProbABEL/examples/example_qt.sh
===================================================================
--- pkg/ProbABEL/examples/example_qt.sh 2011-12-02 15:56:55 UTC (rev 806)
+++ pkg/ProbABEL/examples/example_qt.sh 2011-12-02 17:24:57 UTC (rev 807)
@@ -1,33 +1,42 @@
echo "analysing QT"
+if [ -z ${srcdir} ]; then
+ srcdir="."
+fi
echo "base analysis"
-../bin/palinear -p height.txt -d test.mldose -i test.mlinfo -m test.map -c 19 -o height_base
-../bin/palinear -p height.txt -d test.dose.fvi -i test.mlinfo -m test.map -c 19 -o height_base_fv
+../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.mldose -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 -o height_base
+../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.dose.fvi -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 -o height_base_fv
+
diff height_base_add.out.txt height_base_fv_add.out.txt
echo "Option --allcov"
-../bin/palinear -p height.txt -d test.mldose -i test.mlinfo -m test.map -c 19 --allcov -o height_allcov
-../bin/palinear -p height.txt -d test.dose.fvi -i test.mlinfo -m test.map -c 19 --allcov -o height_allcov_fv
+../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.mldose -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --allcov -o height_allcov
+../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.dose.fvi -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --allcov -o height_allcov_fv
+
diff height_allcov_add.out.txt height_allcov_fv_add.out.txt
echo "Option --interaction=1"
-../bin/palinear -p height.txt -d test.mldose -i test.mlinfo -m test.map -c 19 --interaction=1 -o height_int1
-../bin/palinear -p height.txt -d test.dose.fvi -i test.mlinfo -m test.map -c 19 --interaction=1 -o height_int1_fv
+../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.mldose -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --interaction=1 -o height_int1
+../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.dose.fvi -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --interaction=1 -o height_int1_fv
+
diff height_int1_add.out.txt height_int1_fv_add.out.txt
echo "Option --robust"
-../bin/palinear -p height.txt -d test.mldose -i test.mlinfo -m test.map -c 19 --robust -o height_robust
-../bin/palinear -p height.txt -d test.dose.fvi -i test.mlinfo -m test.map -c 19 --robust -o height_robust_fv
+../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.mldose -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --robust -o height_robust
+../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.dose.fvi -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --robust -o height_robust_fv
+
diff height_robust_add.out.txt height_robust_fv_add.out.txt
echo "Option --robust --interaction=1"
-../bin/palinear -p height.txt -d test.mldose -i test.mlinfo -m test.map -c 19 --robust --interaction=1 -o height_robust_int1
-../bin/palinear -p height.txt -d test.dose.fvi -i test.mlinfo -m test.map -c 19 --robust --interaction=1 -o height_robust_int1_fv
+../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.mldose -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --robust --interaction=1 -o height_robust_int1
+../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.dose.fvi -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --robust --interaction=1 -o height_robust_int1_fv
+
diff height_robust_int1_add.out.txt height_robust_int1_fv_add.out.txt
echo "Option --ngp=2, mlprob file"
-../bin/palinear -p height.txt -d test.mlprob -i test.mlinfo -m test.map -c 19 --ngp=2 -o height_ngp2
-../bin/palinear -p height.txt -d test.prob.fvi -i test.mlinfo -m test.map -c 19 --ngp=2 -o height_ngp2_fv
+../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.mlprob -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --ngp=2 -o height_ngp2
+../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.prob.fvi -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --ngp=2 -o height_ngp2_fv
+
diff height_ngp2_add.out.txt height_ngp2_fv_add.out.txt
diff height_ngp2_domin.out.txt height_ngp2_fv_domin.out.txt
diff height_ngp2_over_domin.out.txt height_ngp2_fv_over_domin.out.txt
@@ -35,8 +44,9 @@
diff height_ngp2_2df.out.txt height_ngp2_fv_2df.out.txt
echo "Option --ngp=2 --allcov"
-../bin/palinear -p height.txt -d test.mlprob -i test.mlinfo -m test.map -c 19 --ngp=2 --allcov -o height_ngp2_allcov
-../bin/palinear -p height.txt -d test.prob.fvi -i test.mlinfo -m test.map -c 19 --ngp=2 --allcov -o height_ngp2_allcov_fv
+../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.mlprob -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --ngp=2 --allcov -o height_ngp2_allcov
+../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.prob.fvi -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --ngp=2 --allcov -o height_ngp2_allcov_fv
+
diff height_ngp2_allcov_add.out.txt height_ngp2_allcov_fv_add.out.txt
diff height_ngp2_allcov_domin.out.txt height_ngp2_allcov_fv_domin.out.txt
diff height_ngp2_allcov_over_domin.out.txt height_ngp2_allcov_fv_over_domin.out.txt
@@ -44,8 +54,9 @@
diff height_ngp2_allcov_2df.out.txt height_ngp2_allcov_fv_2df.out.txt
echo "Option --ngp=2 --interaction=1"
-../bin/palinear -p height.txt -d test.mlprob -i test.mlinfo -m test.map -c 19 --ngp=2 --interaction=1 -o height_ngp2_int1
-../bin/palinear -p height.txt -d test.prob.fvi -i test.mlinfo -m test.map -c 19 --ngp=2 --interaction=1 -o height_ngp2_int1_fv
+../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.mlprob -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --ngp=2 --interaction=1 -o height_ngp2_int1
+../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.prob.fvi -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --ngp=2 --interaction=1 -o height_ngp2_int1_fv
+
diff height_ngp2_int1_add.out.txt height_ngp2_int1_fv_add.out.txt
diff height_ngp2_int1_domin.out.txt height_ngp2_int1_fv_domin.out.txt
diff height_ngp2_int1_over_domin.out.txt height_ngp2_int1_fv_over_domin.out.txt
@@ -53,8 +64,9 @@
diff height_ngp2_int1_2df.out.txt height_ngp2_int1_fv_2df.out.txt
echo "Option --ngp=2 --robust"
-../bin/palinear -p height.txt -d test.mlprob -i test.mlinfo -m test.map -c 19 --ngp=2 --robust -o height_ngp2_robust
-../bin/palinear -p height.txt -d test.prob.fvi -i test.mlinfo -m test.map -c 19 --ngp=2 --robust -o height_ngp2_robust_fv
+../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.mlprob -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --ngp=2 --robust -o height_ngp2_robust
+../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.prob.fvi -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --ngp=2 --robust -o height_ngp2_robust_fv
+
diff height_ngp2_robust_add.out.txt height_ngp2_robust_fv_add.out.txt
diff height_ngp2_robust_domin.out.txt height_ngp2_robust_fv_domin.out.txt
diff height_ngp2_robust_over_domin.out.txt height_ngp2_robust_fv_over_domin.out.txt
@@ -62,11 +74,11 @@
diff height_ngp2_robust_2df.out.txt height_ngp2_robust_fv_2df.out.txt
echo "Option --ngp=2 --robust --interaction=1"
-../bin/palinear -p height.txt -d test.mlprob -i test.mlinfo -m test.map -c 19 --ngp=2 --robust --interaction=1 -o height_ngp2_robust_int1
-../bin/palinear -p height.txt -d test.prob.fvi -i test.mlinfo -m test.map -c 19 --ngp=2 --robust --interaction=1 -o height_ngp2_robust_int1_fv
+../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.mlprob -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --ngp=2 --robust --interaction=1 -o height_ngp2_robust_int1
+../src/palinear -p ${srcdir}/height.txt -d ${srcdir}/test.prob.fvi -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 --ngp=2 --robust --interaction=1 -o height_ngp2_robust_int1_fv
+
diff height_ngp2_robust_int1_add.out.txt height_ngp2_robust_int1_fv_add.out.txt
diff height_ngp2_robust_int1_domin.out.txt height_ngp2_robust_int1_fv_domin.out.txt
diff height_ngp2_robust_int1_over_domin.out.txt height_ngp2_robust_int1_fv_over_domin.out.txt
diff height_ngp2_robust_int1_recess.out.txt height_ngp2_robust_int1_fv_recess.out.txt
diff height_ngp2_robust_int1_2df.out.txt height_ngp2_robust_int1_fv_2df.out.txt
-
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