Add test/README: shell file self-documented

diff --git a/.gitignore b/.gitignore
index 3a96875..d52ee00 100644 (file)
--- a/.gitignore
+++ b/.gitignore
@@ -5,6 +5,7 @@
 #ignore temporary files
 *~
 *.swp
 #ignore temporary files
 *~
 *.swp

+*.Rout

 
 #ignore R session files + RStudio files
 .Rhistory
 
 #ignore R session files + RStudio files
 .Rhistory

diff --git a/pkg/DESCRIPTION b/pkg/DESCRIPTION
index 5a8bc18..d3841a7 100644 (file)
--- a/pkg/DESCRIPTION
+++ b/pkg/DESCRIPTION
@@ -28,4 +28,4 @@ Suggests:
 URL: http://git.auder.net/?p=valse.git
 License: MIT + file LICENSE
 VignetteBuilder: knitr
 URL: http://git.auder.net/?p=valse.git
 License: MIT + file LICENSE
 VignetteBuilder: knitr

-RoxygenNote: 5.0.1
+RoxygenNote: 6.0.1

diff --git a/test/Makefile b/test/Makefile
index 26d9bc6..0fa1189 100644 (file)
--- a/test/Makefile
+++ b/test/Makefile
@@ -1,11 +1,11 @@
 CC = gcc
 CFLAGS = -g -std=gnu99 -Wno-implicit-function-declaration
 CC = gcc
 CFLAGS = -g -std=gnu99 -Wno-implicit-function-declaration

-LDFLAGS = -lm -lgsl -lcblas -lgomp
+LDFLAGS = -lm -lgsl -lcblas

 TEST_LDFLAGS = -L. libvalse_core.so
 LIB = libvalse_core.so
 TEST_LDFLAGS = -L. libvalse_core.so
 LIB = libvalse_core.so

-LIB_SRC = $(wildcard ../sources/*.c)
+LIB_SRC = $(wildcard ../pkg/src/sources/*.c)

 LIB_OBJ = $(LIB_SRC:.c=.o)
 LIB_OBJ = $(LIB_SRC:.c=.o)

-INCLUDES = -I../sources
+INCLUDES = -I../pkg/src/sources

 TESTS = test.EMGLLF test.EMGrank test.constructionModelesLassoMLE test.EMGrank\
         test.constructionModelesLassoRank test.selectionTotale
 
 TESTS = test.EMGLLF test.EMGrank test.constructionModelesLassoMLE test.EMGrank\
         test.constructionModelesLassoRank test.selectionTotale
 


@@ -33,7 +33,7 @@ test.selectionTotale: $(LIB) test.selectionTotale.o test_utils.o
        $(CC) -fPIC -o $@ -c $< $(CFLAGS) $(INCLUDES)
 
 clean:
        $(CC) -fPIC -o $@ -c $< $(CFLAGS) $(INCLUDES)
 
 clean:

-       rm -f *.o ../sources/*.o ../adapters/*.o
+       rm -f *.o ../pkg/src/sources/*.o ../pkg/src/adapters/*.o

 
 cclean: clean
        rm -f *.so $(TESTS)
 
 cclean: clean
        rm -f *.so $(TESTS)

diff --git a/test/README b/test/README
new file mode 100644 (file)
index 0000000..32fcb6d
--- /dev/null
+++ b/test/README
@@ -0,0 +1,30 @@
+#!/bin/sh
+
+#Testing procedure for EMGLLF (inside this folder):
+
+#0) Install current version of the package
+    # Should be library(roxygen2);roxygenize('.'), but roxygen2 6.0.1 bug
+    # ==> temporary workaround with devtools + document()
+    echo "setwd('../pkg');library(devtools);document()" | R --slave
+    R CMD INSTALL ../pkg
+
+#1) Generate data using R versions of EMGLLF/EMGrank (slow, but trusted)
+    cd generate_test_data/
+    echo "source('generateRunSaveTest_EMGLLF.R');\
+      # I'm happy with default values - feel free to give args
+      generateRunSaveTest_EMGLLF() "\
+      | R --slave
+
+#2) Compile test C code
+               # Next line might be required sometimes, to destroy all .o and .so
+    make cclean
+               # Next line compile the test into an executable named "test.EMGLLF"
+    make test.EMGLLF
+
+#3) Run it!
+    # Fingers crossed, hoping everything is alright
+    ./test.EMGLLF
+               # Ask valgrind (generally better idea ;) )
+               valgrind ./test.EMGLLF
+
+#For EMGrank: same procedure, just change EMGLLF to EMGrank everwhere.