From eee5fe536591e96af67ad4bcd417d6c8b89e26bb Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Tue, 19 Jan 2016 14:25:03 +0100
Subject: Allow out-of-tree builds

---
 build/linux/Makefile.in | 67 +++++++++++++++++++++++++++----------------------
 1 file changed, 37 insertions(+), 30 deletions(-)

diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in
index 01ef527..90f8801 100644
--- a/build/linux/Makefile.in
+++ b/build/linux/Makefile.in
@@ -21,7 +21,10 @@ all: $(TARGETS)
 prefix=@prefix@
 exec_prefix=@exec_prefix@
 
-VPATH=../..
+srcdir=@srcdir@
+abs_top_builddir=@abs_top_builddir@
+
+VPATH=$(srcdir)/../..
 
 CPPFLAGS=@SAVED_CPPFLAGS@
 CXXFLAGS=@SAVED_CXXFLAGS@
@@ -29,7 +32,7 @@ NVCCFLAGS=@SAVED_NVCCFLAGS@
 LDFLAGS=@SAVED_LDFLAGS@
 LIBS=@SAVED_LIBS@
 
-CPPFLAGS+=-I../.. -I../../include -I../../lib/include
+CPPFLAGS+=-I$(srcdir)/../.. -I$(srcdir)/../../include -I$(srcdir)/../../lib/include
 CXXFLAGS+=-g -O3 -Wall -Wshadow
 LIBS+=-lpthread
 LDFLAGS+=-g
@@ -38,7 +41,7 @@ CPPFLAGS+=@CPPFLAGS_OS@
 
 ifeq ($(cuda),yes)
 CPPFLAGS  += @CPPFLAGS_CUDA@ -DASTRA_CUDA
-NVCCFLAGS += @NVCCFLAGS_EXTRA@ @CPPFLAGS_CUDA@ -I../.. -I../../include -DASTRA_CUDA
+NVCCFLAGS += @NVCCFLAGS_EXTRA@ @CPPFLAGS_CUDA@ -I$(srcdir)/../.. -I$(srcdir)/../../include -DASTRA_CUDA
 LDFLAGS   += @LDFLAGS_CUDA@
 LIBS      += -lcudart -lcufft
 NVCC       = @NVCC@
@@ -59,7 +62,7 @@ CPPFLAGS += -DASTRA_PYTHON -I$(PYINCDIR)
 PYCPPFLAGS  = $(CPPFLAGS)
 PYCPPFLAGS  += -I../include
 PYLDFLAGS = $(LDFLAGS)
-PYLDFLAGS   += -L../build/linux/.libs
+PYLDFLAGS   += -L$(abs_top_builddir)/.libs
 LIBS		+= -l$(PYLIBVER)
 LDFLAGS += -L$(PYLIBDIR)
 endif
@@ -78,6 +81,7 @@ MKDIR=mkdir -p
 CXX=@CXX@
 LD=@CXX@
 SHELL=@SHELL@
+INSTALL_SH=$(SHELL) $(srcdir)/install-sh
 
 ifeq ($(matlab),yes)
 MEXFLAGS  = -cxx
@@ -264,12 +268,12 @@ endif
 
 ifeq ($(python),yes)
 py: libastra.la
-	cd ../../python; CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py install \
+	cd $(srcdir)/../../python; CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py install \
 	--install-base=./finalbuild --install-headers=./finalbuild --install-purelib=./finalbuild \
 	--install-platlib=./finalbuild --install-scripts=./finalbuild --install-data=./finalbuild
 
 python-root-install: libastra.la
-	cd ../../python; CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py install
+	cd $(srcdir)/../../python; CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py install
 
 endif
 
@@ -331,33 +335,33 @@ clean:
 	rm -f $(addsuffix /*.d,$(DEPDIRS))
 	rm -f $(addsuffix /*,$(LIBDIRS))
 	rm -f $(TEST_OBJECTS) test.bin
-	rm -fr ../../python/finalbuild/
-	rm -fr ../../python/build/
-	rm -f ../../python/astra/*.cpp
-	rm -f ../../python/astra/*.c
+	rm -fr $(srcdir)/../../python/finalbuild/
+	rm -fr $(srcdir)/../../python/build/
+	rm -f $(srcdir)/../../python/astra/*.cpp
+	rm -f $(srcdir)/../../python/astra/*.c
 
 distclean: clean
-	rm -f config.guess config.sub ltmain.sh libtool install-sh
+	rm -f $(srcdir)/config.guess $(srcdir)/config.sub $(srcdir)/ltmain.sh libtool $(srcdir)/install-sh
 	rm -f config.log config.status
-	rm -f aclocal.m4
-	rm -rf autom4te.cache
-	rm -f configure Makefile
+	rm -f $(srcdir)/aclocal.m4
+	rm -rf $(srcdir)/autom4te.cache
+	rm -f $(srcdir)/configure Makefile
 
 install: install-libraries install-matlab install-python
 
 install-libraries: libastra.la
-	./install-sh -m 755 -d @libdir@
-	./libtool --mode=install ./install-sh -m 644 libastra.la @libdir@
+	$(INSTALL_SH) -m 755 -d @libdir@
+	./libtool --mode=install $(INSTALL_SH) -m 644 libastra.la @libdir@
 	./libtool --mode=finish @libdir@
 
 ifeq ($(matlab),yes)
 # TODO: This install location doesn't work well for /usr or /usr/local
 install-matlab: $(MATLAB_MEX)
-	./install-sh -m 755 -d @prefix@/matlab
-	./install-sh -m 755 -d @prefix@/matlab/mex
-	./install-sh -m 755 -d @prefix@/matlab/tools
-	./install-sh -m 644 $(MATLAB_MEX) @prefix@/matlab/mex
-	./install-sh -m 644 ../../matlab/tools/*.m @prefix@/matlab/tools
+	$(INSTALL_SH) -m 755 -d @prefix@/matlab
+	$(INSTALL_SH) -m 755 -d @prefix@/matlab/mex
+	$(INSTALL_SH) -m 755 -d @prefix@/matlab/tools
+	$(INSTALL_SH) -m 644 $(MATLAB_MEX) @prefix@/matlab/mex
+	$(INSTALL_SH) -m 644 $(srcdir)/../../matlab/tools/*.m @prefix@/matlab/tools
 # TODO: docs
 else
 install-matlab:
@@ -366,11 +370,11 @@ endif
 ifeq ($(python),yes)
 # TODO: This install location doesn't work well for /usr or /usr/local
 install-python: py
-	./install-sh -m 755 -d @prefix@/python
-	./install-sh -m 755 -d @prefix@/python/astra
-	./install-sh -m 644 ../../python/finalbuild/astra/*.so @prefix@/python/astra
-	./install-sh -m 644 ../../python/finalbuild/astra/*.py @prefix@/python/astra
-	./install-sh -m 644 ../../python/finalbuild/*.egg-info @prefix@/python/
+	$(INSTALL_SH) -m 755 -d @prefix@/python
+	$(INSTALL_SH) -m 755 -d @prefix@/python/astra
+	$(INSTALL_SH) -m 644 $(srcdir)/../../python/finalbuild/astra/*.so @prefix@/python/astra
+	$(INSTALL_SH) -m 644 $(srcdir)/../../python/finalbuild/astra/*.py @prefix@/python/astra
+	$(INSTALL_SH) -m 644 $(srcdir)/../../python/finalbuild/*.egg-info @prefix@/python/
 	@echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
 	@echo "To use ASTRA in Python, add @prefix@/python/ to your PYTHONPATH"
 	@echo "and @libdir@ to your LD_LIBRARY_PATH."
@@ -381,18 +385,21 @@ install-python:
 endif
 
 
-Makefile: Makefile.in config.status
+Makefile: $(srcdir)/Makefile.in config.status
 	CONFIG_HEADERS= CONFIG_LINKS= CONFIG_FILES=$@ $(SHELL) ./config.status
 
-config.status: configure
+config.status: $(srcdir)/configure
 	@echo "configure script has changed. Re-running it with last parameters"
 	$(SHELL) ./config.status --recheck
 
-configure: configure.ac
+$(srcdir)/configure: $(srcdir)/configure.ac
 	@echo "configure.ac has been changed. Regenerating configure script"
-	$(SHELL) ./autogen.sh
+	cd $(srcdir) && $(SHELL) ./autogen.sh
 
 .PHONY: all mex test clean distclean install install-libraries
 
 # don't remove intermediate files:
 .SECONDARY:
+
+# disable all implicit built-in rules
+.SUFFIXES:
-- 
cgit v1.2.3


From 61d95e4d4cabcc1da959ccf68588895862ec64c5 Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Tue, 19 Jan 2016 15:54:08 +0100
Subject: Place Python build/temporary files in build directory

This also allows out-of-tree builds for Python.
---
 build/linux/Makefile.in | 21 ++++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in
index 90f8801..4f99db2 100644
--- a/build/linux/Makefile.in
+++ b/build/linux/Makefile.in
@@ -268,12 +268,15 @@ endif
 
 ifeq ($(python),yes)
 py: libastra.la
-	cd $(srcdir)/../../python; CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py install \
-	--install-base=./finalbuild --install-headers=./finalbuild --install-purelib=./finalbuild \
-	--install-platlib=./finalbuild --install-scripts=./finalbuild --install-data=./finalbuild
+	$(MKDIR) python/build
+	$(MKDIR) python/finalbuild
+	cd $(srcdir)/../../python; CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py build --build-base=$(abs_top_builddir)/python/build install \
+	--install-base=$(abs_top_builddir)/python/finalbuild --install-headers=$(abs_top_builddir)/python/finalbuild --install-purelib=$(abs_top_builddir)/python/finalbuild \
+	--install-platlib=$(abs_top_builddir)/python/finalbuild --install-scripts=$(abs_top_builddir)/python/finalbuild --install-data=$(abs_top_builddir)/python/finalbuild
 
 python-root-install: libastra.la
-	cd $(srcdir)/../../python; CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py install
+	$(MKDIR) python/build
+	cd $(srcdir)/../../python; CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py build --build-base=$(abs_top_builddir)/python/build install
 
 endif
 
@@ -335,8 +338,8 @@ clean:
 	rm -f $(addsuffix /*.d,$(DEPDIRS))
 	rm -f $(addsuffix /*,$(LIBDIRS))
 	rm -f $(TEST_OBJECTS) test.bin
-	rm -fr $(srcdir)/../../python/finalbuild/
-	rm -fr $(srcdir)/../../python/build/
+	rm -fr python/finalbuild/
+	rm -fr python/build/
 	rm -f $(srcdir)/../../python/astra/*.cpp
 	rm -f $(srcdir)/../../python/astra/*.c
 
@@ -372,9 +375,9 @@ ifeq ($(python),yes)
 install-python: py
 	$(INSTALL_SH) -m 755 -d @prefix@/python
 	$(INSTALL_SH) -m 755 -d @prefix@/python/astra
-	$(INSTALL_SH) -m 644 $(srcdir)/../../python/finalbuild/astra/*.so @prefix@/python/astra
-	$(INSTALL_SH) -m 644 $(srcdir)/../../python/finalbuild/astra/*.py @prefix@/python/astra
-	$(INSTALL_SH) -m 644 $(srcdir)/../../python/finalbuild/*.egg-info @prefix@/python/
+	$(INSTALL_SH) -m 644 python/finalbuild/astra/*.so @prefix@/python/astra
+	$(INSTALL_SH) -m 644 python/finalbuild/astra/*.py @prefix@/python/astra
+	$(INSTALL_SH) -m 644 python/finalbuild/*.egg-info @prefix@/python/
 	@echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
 	@echo "To use ASTRA in Python, add @prefix@/python/ to your PYTHONPATH"
 	@echo "and @libdir@ to your LD_LIBRARY_PATH."
-- 
cgit v1.2.3


From 2d2be13aa9dcfc77afed1dbe52c78e5dce5a04fa Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Tue, 19 Jan 2016 17:06:57 +0100
Subject: Fail when python six module is not found

---
 build/linux/configure.ac | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build/linux/configure.ac b/build/linux/configure.ac
index 684a4c5..354bccc 100644
--- a/build/linux/configure.ac
+++ b/build/linux/configure.ac
@@ -213,7 +213,7 @@ assert(LooseVersion(Cython.__version__)>=LooseVersion("0.13"))
   fi
   AC_MSG_RESULT(yes)
   AC_MSG_CHECKING(for six module)
-  ASTRA_TRY_PYTHON([import six])
+  ASTRA_TRY_PYTHON([import six],,HAVEPYTHON=no)
   if test x$HAVEPYTHON = xno; then
     AC_MSG_RESULT(no)
     AC_MSG_ERROR(You need the six module to use the ASTRA toolbox in Python)
-- 
cgit v1.2.3


From 5c33826855a8d88889cdbbfc78b27c86549715d5 Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Wed, 20 Jan 2016 13:02:36 +0100
Subject: Add check for scipy

The module matrix_c.pyx uses it.
---
 build/linux/configure.ac | 7 +++++++
 python/conda/meta.yaml   | 1 +
 2 files changed, 8 insertions(+)

diff --git a/build/linux/configure.ac b/build/linux/configure.ac
index 354bccc..5a04509 100644
--- a/build/linux/configure.ac
+++ b/build/linux/configure.ac
@@ -219,6 +219,13 @@ assert(LooseVersion(Cython.__version__)>=LooseVersion("0.13"))
     AC_MSG_ERROR(You need the six module to use the ASTRA toolbox in Python)
   fi
   AC_MSG_RESULT(yes)
+  AC_MSG_CHECKING(for scipy module)
+  ASTRA_TRY_PYTHON([import scipy],,HAVEPYTHON=no)
+  if test x$HAVEPYTHON = xno; then
+    AC_MSG_RESULT(no)
+    AC_MSG_ERROR(You need the scipy module to use the ASTRA toolbox in Python)
+  fi
+  AC_MSG_RESULT(yes)
 fi
 
 AC_SUBST(HAVEPYTHON)
diff --git a/python/conda/meta.yaml b/python/conda/meta.yaml
index 41250dc..7e4679b 100644
--- a/python/conda/meta.yaml
+++ b/python/conda/meta.yaml
@@ -21,6 +21,7 @@ requirements:
     - python
     - cython >=0.13
     - numpy
+    - scipy
     - six
 
   run:
-- 
cgit v1.2.3


From 5e3bcf20be6188331c856d9d8854fb931b2abba7 Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Wed, 20 Jan 2016 14:34:00 +0100
Subject: Avoid incorrect include dirs when building python modules

---
 build/linux/Makefile.in | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in
index 4f99db2..c165d37 100644
--- a/build/linux/Makefile.in
+++ b/build/linux/Makefile.in
@@ -32,7 +32,6 @@ NVCCFLAGS=@SAVED_NVCCFLAGS@
 LDFLAGS=@SAVED_LDFLAGS@
 LIBS=@SAVED_LIBS@
 
-CPPFLAGS+=-I$(srcdir)/../.. -I$(srcdir)/../../include -I$(srcdir)/../../lib/include
 CXXFLAGS+=-g -O3 -Wall -Wshadow
 LIBS+=-lpthread
 LDFLAGS+=-g
@@ -59,7 +58,7 @@ PYLIBDIR = $(shell $(PYTHON) -c 'from distutils.sysconfig import get_config_var;
 PYINCDIR = $(shell $(PYTHON) -c 'from distutils.sysconfig import get_python_inc; import six; six.print_(get_python_inc())')
 PYLIBVER = `basename $(PYINCDIR)`
 CPPFLAGS += -DASTRA_PYTHON -I$(PYINCDIR)
-PYCPPFLAGS  = $(CPPFLAGS)
+PYCPPFLAGS  := $(CPPFLAGS)
 PYCPPFLAGS  += -I../include
 PYLDFLAGS = $(LDFLAGS)
 PYLDFLAGS   += -L$(abs_top_builddir)/.libs
@@ -67,6 +66,10 @@ LIBS		+= -l$(PYLIBVER)
 LDFLAGS += -L$(PYLIBDIR)
 endif
 
+# This is below where PYCPPFLAGS copies CPPFLAGS.  The python code is built
+# from a different directory, so these relative includes would be wrong.
+CPPFLAGS+=-I$(srcdir)/../.. -I$(srcdir)/../../include -I$(srcdir)/../../lib/include
+
 BOOST_CPPFLAGS=
 BOOST_LDFLAGS=
 
-- 
cgit v1.2.3


From 29c5c86e56697286a92031aaa9fdd903b3bcc426 Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Wed, 20 Jan 2016 16:18:05 +0100
Subject: Use nvcc's -MT option

---
 build/linux/Makefile.in | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in
index c165d37..12c9e2b 100644
--- a/build/linux/Makefile.in
+++ b/build/linux/Makefile.in
@@ -303,10 +303,8 @@ ifeq ($(cuda),yes)
 	@$(MKDIR) $(*D)/.libs
 	@$(MKDIR) $(*D)/$(DEPDIR)
 	@$(NVCC) $(NVCCFLAGS) -c $(<) -Xcompiler -fPIC -DPIC -o $(*D)/.libs/$(*F).o >/dev/null 2>&1
-	@# Generate a .d file, and change the target name in it from .o to .lo
-	@$(NVCC) $(NVCCFLAGS) -M $(<) -odir $(*D) -o $(*D)/$(DEPDIR)/$(*F).d2
-	@sed '1s/\.o :/.lo :/' < $(*D)/$(DEPDIR)/$(*F).d2 > $(*D)/$(DEPDIR)/$(*F).d
-	@rm -f $(*D)/$(DEPDIR)/$(*F).d2
+	@# Generate a .d file, with target name $*.lo
+	@$(NVCC) $(NVCCFLAGS) -M $(<) -MT $(*F).lo -odir $(*D) -o $(*D)/$(DEPDIR)/$(*F).d
 	@# Generate a fake libtool .lo file
 	@echo "# $*.lo - a libtool object file" > $*.lo
 	@echo "# Generated by" `./libtool --version | head -n 1` >> $*.lo
-- 
cgit v1.2.3


From b428366389ecdad457fb04e13857902e11585881 Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Wed, 20 Jan 2016 16:18:08 +0100
Subject: Try to improve nvcc dependency file generation

We now append empty targets for all dependencies listed in the .d
file generated by nvcc. This mimics the behaviour of gcc's -MP option,
and prevents deleted header files from breaking the build.
---
 build/linux/Makefile.in | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in
index 12c9e2b..f556066 100644
--- a/build/linux/Makefile.in
+++ b/build/linux/Makefile.in
@@ -305,6 +305,9 @@ ifeq ($(cuda),yes)
 	@$(NVCC) $(NVCCFLAGS) -c $(<) -Xcompiler -fPIC -DPIC -o $(*D)/.libs/$(*F).o >/dev/null 2>&1
 	@# Generate a .d file, with target name $*.lo
 	@$(NVCC) $(NVCCFLAGS) -M $(<) -MT $(*F).lo -odir $(*D) -o $(*D)/$(DEPDIR)/$(*F).d
+	@# Generate empty targets for all dependencies listed in the .d file.
+	@# This mimics gcc's -MP option.
+	@for x in `cat $(*D)/$(DEPDIR)/$(*F).d`; do if test a$$x != a: -a a$$x != a\\; then echo -e "\n$$x:\n" >> $(*D)/$(DEPDIR)/$(*F).d; fi; done
 	@# Generate a fake libtool .lo file
 	@echo "# $*.lo - a libtool object file" > $*.lo
 	@echo "# Generated by" `./libtool --version | head -n 1` >> $*.lo
-- 
cgit v1.2.3


From 8fecf27e5eba5e89d9212c2235e957a64e58ec22 Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Wed, 20 Jan 2016 16:38:01 +0100
Subject: Don't build cuda non-PIC object if static libs are disabled

This significantly speeds up builds since we usually pass disable-static to
libtool.
---
 build/linux/Makefile.in | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in
index f556066..8398e35 100644
--- a/build/linux/Makefile.in
+++ b/build/linux/Makefile.in
@@ -295,14 +295,18 @@ libastra.la: $(ALL_OBJECTS)
 	$(MKDIR) $(*D)/$(DEPDIR)
 	./libtool --mode=compile --tag=CXX $(CXX) -Wp,-MMD,"$(*D)/$(DEPDIR)/$(*F).d",-MQ,"$@",-MP $(CXXFLAGS) $(CPPFLAGS) -c $(<) -o $*.o
 
+gen_static_libs := `./libtool --features | grep -q 'disable static' && echo no || echo yes`
+
 ifeq ($(cuda),yes)
 %.lo: %.cu
 	@# Behave like libtool: compile both a PIC and a non-PIC object file
 	@$(MKDIR) $(*D)
-	$(NVCC) $(NVCCFLAGS) -c $(<) -o $*.o
 	@$(MKDIR) $(*D)/.libs
 	@$(MKDIR) $(*D)/$(DEPDIR)
-	@$(NVCC) $(NVCCFLAGS) -c $(<) -Xcompiler -fPIC -DPIC -o $(*D)/.libs/$(*F).o >/dev/null 2>&1
+	$(NVCC) $(NVCCFLAGS) -c $(<) -Xcompiler -fPIC -DPIC -o $(*D)/.libs/$(*F).o
+ifeq ($(gen_static_libs),yes)
+	@$(NVCC) $(NVCCFLAGS) -c $(<) -o $*.o >/dev/null 2>&1
+endif
 	@# Generate a .d file, with target name $*.lo
 	@$(NVCC) $(NVCCFLAGS) -M $(<) -MT $(*F).lo -odir $(*D) -o $(*D)/$(DEPDIR)/$(*F).d
 	@# Generate empty targets for all dependencies listed in the .d file.
@@ -319,7 +323,11 @@ ifeq ($(cuda),yes)
 	@echo "pic_object='.libs/$(*F).o'" >> $*.lo
 	@echo >> $*.lo
 	@echo "# Name of the non-PIC object." >> $*.lo
+ifeq ($(gen_static_libs),yes)
 	@echo "non_pic_object='$(*F).o'" >> $*.lo
+else
+	@echo "non_pic_object=none" >> $*.lo
+endif
 	@# Remove generated .linkinfo file
 	@rm -f $(*F).linkinfo
 endif
-- 
cgit v1.2.3


From 2b0177d66197cb613eed2dabe463b9486428a3e3 Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Thu, 21 Jan 2016 11:12:32 +0100
Subject: Fix file permissions

---
 matlab/mex/astra_mex_direct_c.cpp | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 mode change 100755 => 100644 matlab/mex/astra_mex_direct_c.cpp

diff --git a/matlab/mex/astra_mex_direct_c.cpp b/matlab/mex/astra_mex_direct_c.cpp
old mode 100755
new mode 100644
-- 
cgit v1.2.3


From 6a7eaf9c8fee52e01e7a48cd7e4630453c033655 Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Thu, 21 Jan 2016 11:29:53 +0100
Subject: Fix VPATH problem with older autoconf versions

---
 build/linux/Makefile.in  | 2 +-
 build/linux/configure.ac | 6 ++++++
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in
index 8398e35..3018674 100644
--- a/build/linux/Makefile.in
+++ b/build/linux/Makefile.in
@@ -24,7 +24,7 @@ exec_prefix=@exec_prefix@
 srcdir=@srcdir@
 abs_top_builddir=@abs_top_builddir@
 
-VPATH=$(srcdir)/../..
+VPATH=@VPATH_SRCDIR@/../..
 
 CPPFLAGS=@SAVED_CPPFLAGS@
 CXXFLAGS=@SAVED_CXXFLAGS@
diff --git a/build/linux/configure.ac b/build/linux/configure.ac
index 5a04509..630b08d 100644
--- a/build/linux/configure.ac
+++ b/build/linux/configure.ac
@@ -243,6 +243,12 @@ esac
 
 AC_SUBST(CPPFLAGS_OS)
 
+# For some reason, some older versions of autoconf produce a config.status
+# that disables all lines looking like VPATH=@srcdir@
+# (More recent autoconf fixes the too broad matching there.)
+# We use a different variable name as a workaround.
+VPATH_SRCDIR="$srcdir"
+AC_SUBST(VPATH_SRCDIR)
 
 # TODO:
 
-- 
cgit v1.2.3