[Genabel-commits] r808 - pkg/ProbABEL/examples

[noreply at r-forge.r-project.org]

Author: lckarssen
Date: 2011-12-05 10:36:40 +0100 (Mon, 05 Dec 2011)
New Revision: 808

Modified:
   pkg/ProbABEL/examples/Makefile.am
   pkg/ProbABEL/examples/example_cox.sh
Log:
Added the Cox tests to 'make check' for ProbABEL.
However, since the test took more than 48 minutes on my laptop I commented it. 



Modified: pkg/ProbABEL/examples/Makefile.am
===================================================================
--- pkg/ProbABEL/examples/Makefile.am	2011-12-02 17:24:57 UTC (rev 807)
+++ pkg/ProbABEL/examples/Makefile.am	2011-12-05 09:36:40 UTC (rev 808)
@@ -41,11 +41,13 @@
  impute_with_missing_add.out.txt.save					\
  height_ngp2_robust_domin.out.txt.save height.txt
 
-exampledir = $(pkgdatadir)
+exampledir = $(pkgdatadir)/examples
 dist_example_DATA = $(examplefiles)
 
 TESTS_ENVIRONMENT = sh
 check_SCRIPTS = example_bt.sh example_qt.sh example_mms.sh
+# example_cox.sh: don't run this test. It takes several hours...
+
 TESTS = $(check_SCRIPTS)
 
 cleanfiles_bt = logist_add.out.txt logist_fv_add.out.txt
@@ -98,5 +100,6 @@
 mmscore_prob_recess.out.txt mmscore_prob_add.out.txt			\
 mmscore_prob_2df.out.txt mmscore_prob_fv_2df.out.txt
 
+cleanfiles_cox = coxph_add.out.txt coxph_fv_add.out.txt
 
-CLEANFILES = $(cleanfiles_bt) $(cleanfiles_qt) $(cleanfiles_mms)
+CLEANFILES = $(cleanfiles_bt) $(cleanfiles_qt) $(cleanfiles_mms) $(cleanfiles_cox)

Modified: pkg/ProbABEL/examples/example_cox.sh
===================================================================
--- pkg/ProbABEL/examples/example_cox.sh	2011-12-02 17:24:57 UTC (rev 807)
+++ pkg/ProbABEL/examples/example_cox.sh	2011-12-05 09:36:40 UTC (rev 808)
@@ -1,4 +1,9 @@
 echo "analysing Cox model"
-../bin/pacoxph -p coxph_data.txt -d test.mldose -i test.mlinfo -m test.map -c 19 -o coxph
-../bin/pacoxph -p coxph_data.txt -d test.dose.fvi -i test.mlinfo -m test.map -c 19 -o coxph_fv
+if [ -z ${srcdir} ]; then
+    srcdir="."
+fi
+
+../src/pacoxph -p ${srcdir}/coxph_data.txt -d ${srcdir}/test.mldose -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 -o coxph
+../src/pacoxph -p ${srcdir}/coxph_data.txt -d ${srcdir}/test.dose.fvi -i ${srcdir}/test.mlinfo -m ${srcdir}/test.map -c 19 -o coxph_fv
+
 diff coxph_add.out.txt coxph_fv_add.out.txt