[Genabel-commits] r741 - in branches/ProbABEL/autotools-integration/ProbABEL: . src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jun 22 17:20:44 CEST 2011
Author: lckarssen
Date: 2011-06-22 17:20:44 +0200 (Wed, 22 Jun 2011)
New Revision: 741
Added:
branches/ProbABEL/autotools-integration/ProbABEL/Makefile.am
branches/ProbABEL/autotools-integration/ProbABEL/configure.ac
branches/ProbABEL/autotools-integration/ProbABEL/src/Makefile.am
Removed:
branches/ProbABEL/autotools-integration/ProbABEL/Makefile
Log:
In the ProbABEL autotools integration branch:
- Removed the old Makefile
- Added configure.ac that servers as input for auto(re)conf
- Added the Makefile.am files needed by automake to generate the final Makefiles.
Deleted: branches/ProbABEL/autotools-integration/ProbABEL/Makefile
===================================================================
--- branches/ProbABEL/autotools-integration/ProbABEL/Makefile 2011-06-21 21:03:41 UTC (rev 740)
+++ branches/ProbABEL/autotools-integration/ProbABEL/Makefile 2011-06-22 15:20:44 UTC (rev 741)
@@ -1,51 +0,0 @@
-VERSION = 0.1-9e
-SRCDIR = src
-BINDIR = bin
-DOCDIR = doc
-LINREG = $(BINDIR)/palinear
-LOGREG = $(BINDIR)/palogist
-COXREG = $(BINDIR)/pacoxph
-EXECUTABLES = $(LOGREG) $(LINREG) $(COXREG)
-
-REGFILES = $(SRCDIR)/data.h $(SRCDIR)/mematrix.h $(SRCDIR)/reg1.h $(SRCDIR)/usage.h $(SRCDIR)/main.cpp
-COXBASE = $(SRCDIR)/chinv2 $(SRCDIR)/cholesky2 $(SRCDIR)/chsolve2 $(SRCDIR)/dmatrix $(SRCDIR)/coxfit2
-COXSRC = $(COXBASE:=.c)
-COXOBJ = $(COXBASE:=.o)
-
-CPP = g++
-CFLAGS = -I $(SRCDIR)/include -O2
-
-all: $(EXECUTABLES) doc
- cp $(SRCDIR)/extIDS.pl $(BINDIR)/.
- cp $(SRCDIR)/prepare_data.R $(BINDIR)/.
- cp $(SRCDIR)/probabel.pl $(BINDIR)/probabel.pl_example
- cp $(SRCDIR)/probabel_config.cfg $(BINDIR)/probabel_config.cfg_example
-
-$(LINREG): $(REGFILES)
- $(CPP) $(CFLAGS) -DLINEAR $(SRCDIR)/main.cpp $(SRCDIR)/fvlib/*.cpp -o $(LINREG)
-
-$(LOGREG): $(REGFILES)
- $(CPP) $(CFLAGS) -DLOGISTIC $(SRCDIR)/main.cpp $(SRCDIR)/fvlib/*.cpp -o $(LOGREG)
-
-$(COXREG): $(COXSRC) $(REGFILES)
- $(CPP) $(CFLAGS) -DCOXPH $(COXSRC) $(SRCDIR)/main.cpp $(SRCDIR)/fvlib/*.cpp -o $(COXREG)
-
-doc:
- $(MAKE) -C $(DOCDIR)/
-
-clean: clean_doc
- rm -f $(BINDIR)/* $(SRCDIR)/*~ $(SRCDIR)/*.o *.zip *.tar.gz examples/*.out.txt examples/*out
- $(MAKE) clean -C $(DOCDIR)/
-
-clean_doc:
- $(MAKE) clean_doc -C $(DOCDIR)/
-
-linux_distrib: clean
- cd .. ; tar -czvf ProbABEL_$(VERSION).tar.gz ProbABEL
-
-win_distrib: all
- cd .. ; zip -r9 ProbABEL_$(VERSION)_win.zip ProbABEL
-
-distrib: linux_distrib clean win_distrib clean
-
-.PHONY: distrib linux_distrib win_distrib clean clean_doc doc
Added: branches/ProbABEL/autotools-integration/ProbABEL/Makefile.am
===================================================================
--- branches/ProbABEL/autotools-integration/ProbABEL/Makefile.am (rev 0)
+++ branches/ProbABEL/autotools-integration/ProbABEL/Makefile.am 2011-06-22 15:20:44 UTC (rev 741)
@@ -0,0 +1,66 @@
+AUTOMAKE_OPTIONS = foreign
+SUBDIRS = src
+
+docfiles = doc/ProbABEL_manual.pdf doc/ProbABEL_manual.tex \
+ doc/QuickStart.txt doc/short_coxph_data.txt doc/short_height.out.csv \
+ doc/short_height.txt doc/short_logist_data.txt doc/test_regression.R \
+ doc/COPYING doc/LICENSE doc/INSTALL doc/CHANGES.LOG doc/TODO
+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
+
+dist_doc_DATA = $(docfiles)
+
+exampledir = $(pkgdatadir)/examples
+dist_example_DATA = $(examplefiles)
Added: branches/ProbABEL/autotools-integration/ProbABEL/configure.ac
===================================================================
--- branches/ProbABEL/autotools-integration/ProbABEL/configure.ac (rev 0)
+++ branches/ProbABEL/autotools-integration/ProbABEL/configure.ac 2011-06-22 15:20:44 UTC (rev 741)
@@ -0,0 +1,34 @@
+# -*- Autoconf -*-
+# Process this file with autoconf to produce a configure script.
+
+AC_PREREQ([2.67])
+AC_INIT(ProbABEL, 0.1-9e, genabel-devel at r-forge.wu-wien.ac.at)
+AM_INIT_AUTOMAKE(ProbABEL, 0.1-9e)
+AC_CONFIG_SRCDIR([src/data.h])
+AC_CONFIG_HEADERS([src/config.h])
+
+# Checks for programs.
+AC_PROG_CXX
+AC_PROG_CC
+AM_PROG_CC_C_O
+AC_PROG_INSTALL
+AC_PROG_LN_S
+
+# Checks for libraries.
+
+# Checks for header files.
+AC_FUNC_ALLOCA
+AC_CHECK_HEADERS([float.h inttypes.h libintl.h limits.h stddef.h stdint.h stdlib.h string.h sys/param.h wchar.h wctype.h])
+
+# Checks for typedefs, structures, and compiler characteristics.
+AC_HEADER_STDBOOL
+AC_C_INLINE
+AC_TYPE_OFF_T
+AC_TYPE_SIZE_T
+
+# Checks for library functions.
+AC_FUNC_ERROR_AT_LINE
+AC_FUNC_MALLOC
+AC_CHECK_FUNCS([pow putenv sqrt strdup strncasecmp])
+
+AC_OUTPUT(Makefile src/Makefile)
Added: branches/ProbABEL/autotools-integration/ProbABEL/src/Makefile.am
===================================================================
--- branches/ProbABEL/autotools-integration/ProbABEL/src/Makefile.am (rev 0)
+++ branches/ProbABEL/autotools-integration/ProbABEL/src/Makefile.am 2011-06-22 15:20:44 UTC (rev 741)
@@ -0,0 +1,46 @@
+AM_CXXFLAGS = -I include -O2
+AM_CFLAGS = -I include -O2
+AM_LDFLAGS =
+
+## Using wildcards in these lists doesn't work. Also GNU make's ($wildcard,) doesn't
+## work. It gives warning message about portability, but in the end doesn't work,
+## I tried :-).
+REGFILES = data.h mematrix.h reg1.h usage.h main.cpp version.h mematri1.h
+
+COXBASE = chinv2 cholesky2 chsolve2 dmatrix
+COXSRC = $(COXBASE:=.c) coxfit2.c
+
+FVSRC = fvlib/AbstractMatrix.cpp fvlib/CastUtils.cpp \
+ fvlib/convert_util.cpp fvlib/FileVector.cpp fvlib/FilteredMatrix.cpp \
+ fvlib/frutil.cpp fvlib/Logger.cpp fvlib/RealHandlerWrapper.cpp \
+ fvlib/ReusableFileHandle.cpp fvlib/Transposer.cpp
+FVHEADERS = fvlib/AbstractMatrix.h fvlib/CastUtils.h fvlib/const.h \
+ fvlib/convert_util.h fvlib/FileVector.h fvlib/frutil.h \
+ fvlib/frversion.h fvlib/Logger.h fvlib/Transposer.h \
+ fvlib/ReusableFileHandle.h fvlib/RealHandlerWrapper.h \
+ fvlib/FilteredMatrix.h
+
+bin_PROGRAMS = palinear palogist
+#pacoxph
+
+palinear_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS)
+palinear_CXXFLAGS = -DLINEAR
+
+palogist_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS)
+palogist_CXXFLAGS = -DLOGISTIC
+
+# pacoxph_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS) $(COXSRC)
+# pacoxph_CXXFLAGS = -DCOXPH -I include
+# pacoxph_CFLAGS = -DCOXPH -I include
+
+bin_SCRIPTS = probabel.pl extIDS.pl
+
+## Old Makefile rules
+# palinear: $(REGFILES)
+# $(CXX) $(CXXFLAGS) -DLINEAR main.cpp $(FVSRC) -o $@
+
+# palogist: $(REGFILES)
+# $(CPP) $(CFLAGS) -DLOGISTIC main.cpp fvlib/*.cpp -o $(LOGREG)
+
+# pacoxph: $(COXSRC) $(REGFILES)
+# $(CPP) $(CFLAGS) -DCOXPH $(COXSRC) main.cpp fvlib/*.cpp -o $(COXREG)
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