[Genabel-commits] r1248 - in pkg/ProbABEL: . doc examples src tests

Thu Jun 13 20:44:51 CEST 2013

Author: lckarssen
Date: 2013-06-13 20:44:51 +0200 (Thu, 13 Jun 2013)
New Revision: 1248

Modified:
   pkg/ProbABEL/configure.ac
   pkg/ProbABEL/doc/INSTALL
   pkg/ProbABEL/doc/Makefile.am
   pkg/ProbABEL/examples/Makefile.am
   pkg/ProbABEL/src/Makefile.am
   pkg/ProbABEL/tests/Makefile.am
Log:
Add --disable options to ./configure so that building of pacoxph, palinear or palogist can be disabled for those who are compiling from source. So if you only need the pacoxph module run:
 ./configure --disable-palinear --disable-palogist
By default all three binaries are built. Disabling one of these will also make sore that the corresponding examples and man pages are not run/installed. 


Modified: pkg/ProbABEL/configure.ac
===================================================================

--- pkg/ProbABEL/configure.ac	2013-06-13 18:41:09 UTC (rev 1247)
+++ pkg/ProbABEL/configure.ac	2013-06-13 18:44:51 UTC (rev 1248)
@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.67])
-AC_INIT(ProbABEL, 0.3.0, genabel-devel at r-forge.wu-wien.ac.at)
+AC_INIT(ProbABEL, 0.4.0-beta, genabel-devel at r-forge.wu-wien.ac.at)
 AM_INIT_AUTOMAKE([silent-rules])
 AM_SILENT_RULES
 AC_CONFIG_SRCDIR([src/data.h])
@@ -109,7 +109,28 @@
 
 AM_CONDITIONAL([HAVE_PDFLATEX], test -n "$PDFLATEX")
 
-# Since pacoxph is buggy it needs to be enabled explixitly
+# Building of each of the three modules can be disabled on request
+AC_ARG_ENABLE([palinear],
+    [AS_HELP_STRING([--disable-palinear], [disable building the palinear program])],
+    [palinear=no],
+    [palinear=yes])
+
+if test "x$palinear" = "xyes"; then
+   AC_MSG_NOTICE([building of palinear is enabled])
+fi
+AM_CONDITIONAL([BUILD_palinear], test "x$palinear" = "xyes")
+
+AC_ARG_ENABLE([palogist],
+    [AS_HELP_STRING([--disable-palogist], [disable building the palogist program])],
+    [palogist=no],
+    [palogist=yes])
+
+if test "x$palogist" = "xyes"; then
+   AC_MSG_NOTICE([building of palogist is enabled])
+fi
+
+AM_CONDITIONAL([BUILD_palogist], test "x$palogist" = "xyes")
+
 AC_ARG_ENABLE([pacoxph],
     [AS_HELP_STRING([--disable-pacoxph], [disable building the pacoxph program])],
     [pacoxph=no],

Modified: pkg/ProbABEL/doc/INSTALL
===================================================================
--- pkg/ProbABEL/doc/INSTALL	2013-06-13 18:41:09 UTC (rev 1247)
+++ pkg/ProbABEL/doc/INSTALL	2013-06-13 18:44:51 UTC (rev 1248)
@@ -56,15 +56,17 @@
   to install ProbABEL in that subdirectory. Instead of using
   /usr/local/ as install root directory, it installs in /some/subdirectory.
 
-  The pacoxph binary will not be built by default because it is too
-  buggy at present. If you want to build and install it anyway use the
-  --enable function of ./configure:
-./configure --enable-pacoxph
+  ProbABEL consists of three main programs: palinear, palogist and
+  pacoxph. Building of each of these programs can be disabled by
+  adding a --disable- option to configure, for example:
+./configure --disable-palinear
 
   Another commonly used option is --enable-silent-rules, this reduces
   the output (sometimes considered to be noise) of the make step:
 ./configure --enable-silent-rules
 
+
+* Options for developers
   To generate a .tar.gz package for distribution run:
 ./configure
 make dist
@@ -110,8 +112,8 @@
   running 'make install' the whole directory structure can be zipped
   easily):
 ./configure --host=i686-w64-mingw32 --build=i686-linux-gnu \
-	    --prefix=/tmp/PA --sysconfdir=/tmp/PA/ \
-	    --datarootdir=/tmp/PA --docdir=/tmp/PA/doc
+            --prefix=/tmp/PA --sysconfdir=/tmp/PA/ \
+            --datarootdir=/tmp/PA --docdir=/tmp/PA/doc
 
   The --host option sets the type of the host the programs will be run
   on, the --build option sets the type of machine you are building the

Modified: pkg/ProbABEL/doc/Makefile.am
===================================================================
--- pkg/ProbABEL/doc/Makefile.am	2013-06-13 18:41:09 UTC (rev 1247)
+++ pkg/ProbABEL/doc/Makefile.am	2013-06-13 18:44:51 UTC (rev 1248)
@@ -6,7 +6,17 @@
  test.mlinfo test_regression.R COPYING LICENSE INSTALL ChangeLog	\
  TODO
 
-man_MANS = palinear.1 palogist.1 pacoxph.1
+man_MANS =
+if BUILD_palinear
+man_MANS += palinear.1
+endif
+if BUILD_palogist
+man_MANS += palogist.1
+endif
+if BUILD_pacoxph
+man_MANS += pacoxph.1
+endif
+
 EXTRA_DIST = $(man_MANS)
 
 if HAVE_PDFLATEX
@@ -26,8 +36,8 @@
 .aux.pdf:
 	@echo === Making PDF ===
 	$(PDFLATEX) $(srcdir)/$(MANTEXSRC)
-	@while ( grep "Rerun to " 			\
-		$(MANNAME).log  ); do		\
+	@while ( grep "Rerun to "			\
+		$(MANNAME).log  ); do			\
 		echo '** Re-running LaTeX **';		\
 		$(PDFLATEX) $(srcdir)/$(MANTEXSRC);	\
 	done

Modified: pkg/ProbABEL/examples/Makefile.am
===================================================================
--- pkg/ProbABEL/examples/Makefile.am	2013-06-13 18:41:09 UTC (rev 1247)
+++ pkg/ProbABEL/examples/Makefile.am	2013-06-13 18:44:51 UTC (rev 1248)
@@ -45,7 +45,13 @@
 dist_example_DATA = $(examplefiles)
 
 TESTS_ENVIRONMENT = bash
-check_SCRIPTS = example_bt.sh example_qt.sh example_mms.sh
+check_SCRIPTS =
+if BUILD_palinear
+check_SCRIPTS += example_qt.sh example_mms.sh
+endif
+if BUILD_palogist
+check_SCRIPTS += example_bt.sh
+endif
 if BUILD_pacoxph
 check_SCRIPTS +=  example_cox.sh
 endif

Modified: pkg/ProbABEL/src/Makefile.am
===================================================================
--- pkg/ProbABEL/src/Makefile.am	2013-06-13 18:41:09 UTC (rev 1247)
+++ pkg/ProbABEL/src/Makefile.am	2013-06-13 18:44:51 UTC (rev 1248)
@@ -30,12 +30,19 @@
  include/R_ext/Print.h include/R_ext/Random.h include/R_ext/Utils.h	\
  include/R_ext/RS.h
 
-bin_PROGRAMS = palinear palogist extract-snp
+bin_PROGRAMS = extract-snp
+if BUILD_palinear
+bin_PROGRAMS += palinear
+endif
+
+if BUILD_palogist
+bin_PROGRAMS += palogist
+endif
+
 if BUILD_pacoxph
 ## Extra files for pacoxph
 COXBASE = coxfit2 chinv2 cholesky2 chsolve2 dmatrix
 COXSRC = $(COXBASE:=.c)
-
 bin_PROGRAMS += pacoxph
 endif
 

Modified: pkg/ProbABEL/tests/Makefile.am
===================================================================
--- pkg/ProbABEL/tests/Makefile.am	2013-06-13 18:41:09 UTC (rev 1247)
+++ pkg/ProbABEL/tests/Makefile.am	2013-06-13 18:44:51 UTC (rev 1248)
@@ -2,7 +2,8 @@
 
 AUTOMAKE_OPTIONS = foreign color-tests
 
-tests_files = check_probabel.pl_chunk.sh check_dose_input.sh
+#tests_files = check_probabel.pl_chunk.sh check_dose_input.sh
+tests_files =  check_dose_input.sh
 verified_results = verified_results/height_add.out.txt	\
  verified_results/height_ngp2_add.out.txt			\
  verified_results/height_ngp2_2df.out.txt			\
@@ -36,8 +37,10 @@
 testsdir = $(pkgdatadir)/tests
 dist_tests_DATA = $(tests_files) $(verified_results)
 
-TESTS_ENVIRONMENT = sh
+TESTS_ENVIRONMENT = bash
+if BUILD_palinear
 check_SCRIPTS = $(tests_files)
+endif
 
 TESTS = $(check_SCRIPTS)
 

