[Genabel-commits] r1416 - in branches/filevector-lib/ProbABEL: . src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Nov 22 15:32:59 CET 2013
Author: lckarssen
Date: 2013-11-22 15:32:58 +0100 (Fri, 22 Nov 2013)
New Revision: 1416
Removed:
branches/filevector-lib/ProbABEL/src/fvlib
Modified:
branches/filevector-lib/ProbABEL/configure.ac
branches/filevector-lib/ProbABEL/src/Makefile.am
branches/filevector-lib/ProbABEL/src/command_line_settings.cpp
branches/filevector-lib/ProbABEL/src/coxph_data.cpp
branches/filevector-lib/ProbABEL/src/data.cpp
branches/filevector-lib/ProbABEL/src/extract-snp.cpp
branches/filevector-lib/ProbABEL/src/gendata.cpp
branches/filevector-lib/ProbABEL/src/gendata.h
branches/filevector-lib/ProbABEL/src/regdata.cpp
Log:
First steps towards using ProbABEL with a separate libfilevector (in the filevector-lib branch).
- Remove the fvlib directory from ProbABEL
- Change the #include statements for the filevector headers to <filevector/..>
This works when following the following steps (and requires the pkg-config tool):
- For libfilevector:
./configure --prefix=/tmp/fvlib/
make
make install
- For ProbABEL:
# Tell pkg-config where to find the information for libfilevector
export PKG_CONFIG_PATH="$PKG_CONFIG_PATH;/tmp/fvlib/lib/pkgconfig/"
./configure --prefix=/tmp/pa
make
# Tell the system where to find libfilevector (since it was installed in a non-standard path)
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH;/tmp/fvlib/lib"
make check
Modified: branches/filevector-lib/ProbABEL/configure.ac
===================================================================
--- branches/filevector-lib/ProbABEL/configure.ac 2013-11-22 13:27:19 UTC (rev 1415)
+++ branches/filevector-lib/ProbABEL/configure.ac 2013-11-22 14:32:58 UTC (rev 1416)
@@ -35,6 +35,8 @@
#Tell compiler to build not R version of filevector
CXXFLAGS+=" -D_NOT_R_FILEVECTOR"
+PKG_CHECK_MODULES([LIBDEPS], [filevector-0.1 >= 0.1.0])
+CXXFLAGS+=" $LIBDEPS_CFLAGS $LIBDEPS_LIBS"
# Since most of our code is in C++, set that language as the default
# for the subsequent checks
Modified: branches/filevector-lib/ProbABEL/src/Makefile.am
===================================================================
--- branches/filevector-lib/ProbABEL/src/Makefile.am 2013-11-22 13:27:19 UTC (rev 1415)
+++ branches/filevector-lib/ProbABEL/src/Makefile.am 2013-11-22 14:32:58 UTC (rev 1416)
@@ -12,15 +12,17 @@
EIGENFILES = eigen_mematrix.h eigen_mematrix.cpp
## Filevector files:
-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
+# 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
+FVSRC=
+FVHEADERS=
## R headers, used by pacoxph
RHEADERS = include/R.h include/Rmath.h include/R_ext/Arith.h \
@@ -30,7 +32,11 @@
include/R_ext/Print.h include/R_ext/Random.h include/R_ext/Utils.h \
include/R_ext/RS.h
+AM_CPPFLAGS = $(LIBDEPS_CFLAGS)
+
bin_PROGRAMS = extract-snp
+extract_snp_LDADD = $(LIBDEPS_LIBS)
+
if BUILD_palinear
bin_PROGRAMS += palinear
endif
@@ -49,6 +55,7 @@
palinear_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS)
palinear_CXXFLAGS = -DLINEAR $(AM_CXXFLAGS)
palinear_CPPFLAGS = $(AM_CPPFLAGS)
+palinear_LDADD = $(LIBDEPS_LIBS)
if WITH_EIGEN
palinear_SOURCES += $(EIGENFILES)
palinear_CXXFLAGS += -DEIGEN
@@ -57,6 +64,7 @@
palogist_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS)
palogist_CXXFLAGS = -DLOGISTIC $(AM_CXXFLAGS)
palogist_CPPFLAGS = $(AM_CPPFLAGS)
+palogist_LDADD = $(LIBDEPS_LIBS)
if WITH_EIGEN
palogist_SOURCES += $(EIGENFILES)
palogist_CXXFLAGS += -DEIGEN
@@ -67,6 +75,7 @@
pacoxph_CXXFLAGS = -DCOXPH -I $(top_srcdir)/src/include $(AM_CXXFLAGS)
pacoxph_CPPFLAGS = $(AM_CPPFLAGS)
pacoxph_CFLAGS = -DCOXPH -I $(top_srcdir)/src/include $(AM_CFLAGS)
+pacoxph_LDADD = $(LIBDEPS_LIBS)
if WITH_EIGEN
pacoxph_SOURCES += $(EIGENFILES)
pacoxph_CXXFLAGS += -DEIGEN
Modified: branches/filevector-lib/ProbABEL/src/command_line_settings.cpp
===================================================================
--- branches/filevector-lib/ProbABEL/src/command_line_settings.cpp 2013-11-22 13:27:19 UTC (rev 1415)
+++ branches/filevector-lib/ProbABEL/src/command_line_settings.cpp 2013-11-22 14:32:58 UTC (rev 1416)
@@ -18,7 +18,7 @@
#if HAVE_CONFIG_H
#include "config.h"
#endif
-#include "fvlib/FileVector.h"
+#include <filevector/FileVector.h>
using std::cout;
using std::cerr;
Modified: branches/filevector-lib/ProbABEL/src/coxph_data.cpp
===================================================================
--- branches/filevector-lib/ProbABEL/src/coxph_data.cpp 2013-11-22 13:27:19 UTC (rev 1415)
+++ branches/filevector-lib/ProbABEL/src/coxph_data.cpp 2013-11-22 14:32:58 UTC (rev 1416)
@@ -12,15 +12,15 @@
}
// #include "reg1.h"
-#include "fvlib/AbstractMatrix.h"
-#include "fvlib/CastUtils.h"
-#include "fvlib/const.h"
-#include "fvlib/convert_util.h"
-#include "fvlib/FileVector.h"
-#include "fvlib/frutil.h"
-#include "fvlib/frversion.h"
-#include "fvlib/Logger.h"
-#include "fvlib/Transposer.h"
+#include <filevector/AbstractMatrix.h>
+#include <filevector/CastUtils.h>
+#include <filevector/const.h>
+#include <filevector/convert_util.h>
+#include <filevector/FileVector.h>
+#include <filevector/frutil.h>
+#include <filevector/frversion.h>
+#include <filevector/Logger.h>
+#include <filevector/Transposer.h>
// compare for sort of times
int cmpfun(const void *a, const void *b)
Modified: branches/filevector-lib/ProbABEL/src/data.cpp
===================================================================
--- branches/filevector-lib/ProbABEL/src/data.cpp 2013-11-22 13:27:19 UTC (rev 1415)
+++ branches/filevector-lib/ProbABEL/src/data.cpp 2013-11-22 14:32:58 UTC (rev 1416)
@@ -2,15 +2,15 @@
#include <sstream>
#include <fstream>
-#include "fvlib/AbstractMatrix.h"
-#include "fvlib/CastUtils.h"
-#include "fvlib/const.h"
-#include "fvlib/convert_util.h"
-#include "fvlib/FileVector.h"
-#include "fvlib/frutil.h"
-#include "fvlib/frversion.h"
-#include "fvlib/Logger.h"
-#include "fvlib/Transposer.h"
+#include <filevector/AbstractMatrix.h>
+#include <filevector/CastUtils.h>
+#include <filevector/const.h>
+#include <filevector/convert_util.h>
+#include <filevector/FileVector.h>
+#include <filevector/frutil.h>
+#include <filevector/frversion.h>
+#include <filevector/Logger.h>
+#include <filevector/Transposer.h>
#include "phedata.h"
#include "gendata.h"
#include "data.h"
Modified: branches/filevector-lib/ProbABEL/src/extract-snp.cpp
===================================================================
--- branches/filevector-lib/ProbABEL/src/extract-snp.cpp 2013-11-22 13:27:19 UTC (rev 1415)
+++ branches/filevector-lib/ProbABEL/src/extract-snp.cpp 2013-11-22 14:32:58 UTC (rev 1416)
@@ -31,9 +31,9 @@
using std::cerr;
using std::endl;
-#include "fvlib/Logger.h"
-#include "fvlib/FileVector.h"
-#include "fvlib/CastUtils.h"
+#include <filevector/Logger.h>
+#include <filevector/FileVector.h>
+#include <filevector/CastUtils.h>
void info(char *program_name)
Deleted: branches/filevector-lib/ProbABEL/src/fvlib
===================================================================
--- branches/filevector-lib/ProbABEL/src/fvlib 2013-11-22 13:27:19 UTC (rev 1415)
+++ branches/filevector-lib/ProbABEL/src/fvlib 2013-11-22 14:32:58 UTC (rev 1416)
@@ -1 +0,0 @@
-link ../../filevector/fvlib
\ No newline at end of file
Modified: branches/filevector-lib/ProbABEL/src/gendata.cpp
===================================================================
--- branches/filevector-lib/ProbABEL/src/gendata.cpp 2013-11-22 13:27:19 UTC (rev 1415)
+++ branches/filevector-lib/ProbABEL/src/gendata.cpp 2013-11-22 14:32:58 UTC (rev 1416)
@@ -7,7 +7,7 @@
#include <string>
#include <errno.h>
#include "gendata.h"
-#include "fvlib/FileVector.h"
+#include <filevector/FileVector.h>
#if EIGEN
#include "eigen_mematrix.h"
#include "eigen_mematrix.cpp"
Modified: branches/filevector-lib/ProbABEL/src/gendata.h
===================================================================
--- branches/filevector-lib/ProbABEL/src/gendata.h 2013-11-22 13:27:19 UTC (rev 1415)
+++ branches/filevector-lib/ProbABEL/src/gendata.h 2013-11-22 14:32:58 UTC (rev 1416)
@@ -8,7 +8,7 @@
#ifndef GENDATA_H_
#define GENDATA_H_
#include <string>
-#include "fvlib/FileVector.h"
+#include <filevector/FileVector.h>
#if EIGEN
#include "eigen_mematrix.h"
Modified: branches/filevector-lib/ProbABEL/src/regdata.cpp
===================================================================
--- branches/filevector-lib/ProbABEL/src/regdata.cpp 2013-11-22 13:27:19 UTC (rev 1415)
+++ branches/filevector-lib/ProbABEL/src/regdata.cpp 2013-11-22 14:32:58 UTC (rev 1416)
@@ -5,15 +5,15 @@
* Author: mkooyman
*/
-#include "fvlib/AbstractMatrix.h"
-#include "fvlib/CastUtils.h"
-#include "fvlib/const.h"
-#include "fvlib/convert_util.h"
-#include "fvlib/FileVector.h"
-#include "fvlib/frutil.h"
-#include "fvlib/frversion.h"
-#include "fvlib/Logger.h"
-#include "fvlib/Transposer.h"
+#include <filevector/AbstractMatrix.h>
+#include <filevector/CastUtils.h>
+#include <filevector/const.h>
+#include <filevector/convert_util.h>
+#include <filevector/FileVector.h>
+#include <filevector/frutil.h>
+#include <filevector/frversion.h>
+#include <filevector/Logger.h>
+#include <filevector/Transposer.h>
#include "regdata.h"
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