first commit

Author: gitlim

3rd/atk-1.32.0.tar.bz2

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+                                             
+Copyright (C) 2012 Joseph Lim <[email protected]>
+Copyright (C) 2012 Pablo Arbelaez <[email protected]>
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU Affero General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU Affero General Public License for more details.
+
+You should have received a copy of the GNU Affero General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.

3rd/cairo-1.8.0.tar.gz

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+TEXTON SVM
+==========
+
+Experimental Evaluation of Support Vector Machine-based and Correlation-based Approaches to Automatic Particle Selection
+Pablo Arbelaez, Bong-Gyoon Han, Dieter Typke, Joseph J. Lim, Robert M. Glaeser, Jitendra Malik.
+Journal of Structural Biology 2011. doi:10.1016/j.jsb.2011.05.017.
+

3rd/gettext-0.14.3.tar.gz

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+set -e
+
+TMP_DIR=`readlink -f $0`
+TEXTONSVM_DIR=`dirname $TMP_DIR`
+
+# LIBTIFF
+cd $TEXTONSVM_DIR/3rd
+unzip $TEXTONSVM_DIR/3rd/tiff-3.9.4.zip
+cd tiff-3.9.4
+./configure --prefix=$TEXTONSVM_DIR/tools/libtiff
+make
+make install
+
+# gettext
+#cd $TEXTONSVM_DIR/3rd
+#tar -xvf gettext-0.14.3.tar.gz
+#cd gettext-0.14.3
+#./configure --prefix=$TEXTONSVM_DIR/tools/gettext
+#make
+#make install
+
+# glib
+PKG_CONFIG_PATH=
+LD_LIBRARY_PATH=$TEXTONSVM_DIR/tools/libtiff/lib
+cd $TEXTONSVM_DIR/3rd
+tar -xvf glib-2.21.5.tar.gz
+cd glib-2.21.5
+./configure --prefix=$TEXTONSVM_DIR/tools/glib
+make
+make install
+
+
+# pixman
+PKG_CONFIG_PATH=$PKG_CONFIG_PATH:$TEXTONSVM_DIR/tools/glib/lib/pkgconfig
+LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$TEXTONSVM_DIR/tools/glib/lib
+PATH=$PATH:$TEXTONSVM_DIR/tools/glib/bin
+export PKG_CONFIG_PATH LD_LIBRARY_PATH PATH
+cd $TEXTONSVM_DIR/3rd
+tar -xvf pixman-0.12.0.tar.gz
+cd pixman-0.12.0
+./configure --prefix=$TEXTONSVM_DIR/tools/pixman --disable-gtk
+make
+make install
+
+# cairo
+PKG_CONFIG_PATH=$PKG_CONFIG_PATH:$TEXTONSVM_DIR/tools/pixman/lib/pkgconfig
+LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$TEXTONSVM_DIR/tools/pixman/lib
+export PKG_CONFIG_PATH LD_LIBRARY_PATH
+cd $TEXTONSVM_DIR/3rd
+tar -xvf cairo-1.8.0.tar.gz
+cd cairo-1.8.0
+./configure --prefix=$TEXTONSVM_DIR/tools/cairo
+#--disable-png --enable-svg=no
+make
+make install
+
+# pango
+PKG_CONFIG_PATH=$PKG_CONFIG_PATH:$TEXTONSVM_DIR/tools/cairo/lib/pkgconfig
+LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$TEXTONSVM_DIR/tools/cairo/lib
+export PKG_CONFIG_PATH LD_LIBRARY_PATH
+cd $TEXTONSVM_DIR/3rd
+tar -xvf pango-1.28.0.tar.gz
+cd pango-1.28.0
+./configure --prefix=$TEXTONSVM_DIR/tools/pango
+make
+make install
+
+# atk
+PKG_CONFIG_PATH=$PKG_CONFIG_PATH:$TEXTONSVM_DIR/tools/pango/lib/pkgconfig
+LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$TEXTONSVM_DIR/tools/pango/lib
+export PKG_CONFIG_PATH LD_LIBRARY_PATH
+cd $TEXTONSVM_DIR/3rd
+tar -xvf $TEXTONSVM_DIR/3rd/atk-1.32.0.tar.bz2
+cd atk-1.32.0
+./configure --prefix=$TEXTONSVM_DIR/tools/atk
+make
+make install
+
+# gtk
+PKG_CONFIG_PATH=$PKG_CONFIG_PATH:$TEXTONSVM_DIR/tools/atk/lib/pkgconfig
+LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$TEXTONSVM_DIR/tools/atk/lib
+export PKG_CONFIG_PATH LD_LIBRARY_PATH
+cd $TEXTONSVM_DIR/3rd
+tar -xvf $TEXTONSVM_DIR/3rd/gtk+-2.18.0.tar.gz
+cd gtk+-2.18.0
+./configure --prefix=$TEXTONSVM_DIR/tools/gtk --without-libpng
+make
+make install
+
+# gtkimageview
+PKG_CONFIG_PATH=$PKG_CONFIG_PATH:$TEXTONSVM_DIR/tools/gtk/lib/pkgconfig
+LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$TEXTONSVM_DIR/tools/gtk/lib
+export PKG_CONFIG_PATH LD_LIBRARY_PATH
+cd $TEXTONSVM_DIR/3rd
+tar -xvf $TEXTONSVM_DIR/3rd/gtkimageview-1.6.4.tar.gz
+cd gtkimageview-1.6.4
+./configure --prefix=$TEXTONSVM_DIR/tools/gtkimageview
+make
+make install
+
+
+# textonsvm_setup
+cd $TEXTONSVM_DIR
+echo 'TEXTONSVM_DIR='$TEXTONSVM_DIR >> textonsvm_setup
+
+filename="textonsvm_setup.tmp"
+while read line
+do
+	echo $line >> textonsvm_setup
+done <$filename
+
+# final make
+cd $TEXTONSVM_DIR
+source ./textonsvm_setup
+cd src
+make

3rd/glib-2.21.5.tar.gz

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+.PHONY: all
+all:
+ifdef TEXTONSVM_BIN_DIR
+	make -C input
+	make -C output
+	make -C backend
+	make -C "backend/textonsvm"
+else
+	@echo ERROR: TEXTONSVM_BIN_DIR is not initialized. Check [TEXTONSVM_DIR/textonsvm_setup];
+	@exit 2;
+endif
+
+.PHONY: clean
+clean:
+	make -r -C input clean
+	make -r -C output clean
+	make -r -C backend clean
+	make -r -C "backend/textonsvm" clean

3rd/gtk+-2.18.0.tar.gz

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+include Rules.make
+
+.PHONY: default
+default: all
+ 
+.PHONY: all
+all: src test
+
+.PHONY: world
+world: all check_world
+
+.PHONY: src
+src:
+	@$(MAKE) -r -C $(src_dir) all
+        
+.PHONY: test
+test: src
+	@$(MAKE) -r -C $(test_dir) all
+
+.PHONY: test_results
+test_results:
+	@$(MAKE) -r -C $(test_dir) test_results_all
+
+.PHONY: test_results_world
+test_results_world: test
+	@$(MAKE) -r -C $(test_dir) test_results_all
+
+.PHONY: check
+check:
+	@$(MAKE) -r -C $(test_dir) check_all
+
+.PHONY: check_world
+check_world: test_results_world
+	@$(MAKE) -r -C $(test_dir) check_all
+
+.PHONY: matlab
+matlab:
+	@$(MAKE) -r -C $(matlab_dir) all
+
+.PHONY: doc
+doc:
+	@$(MAKE) -r -C $(doc_dir) all
+
+.PHONY: doc_clean
+doc_clean:
+	@$(MAKE) -r -C $(doc_dir) clean_all
+
+.PHONY: clean
+clean:
+	@$(MAKE) -r -C $(src_dir) clean_all
+	@$(MAKE) -r -C $(test_dir) clean_all
+	@$(MAKE) -r -C $(matlab_dir) clean_all

3rd/gtkimageview-1.6.4.tar.gz

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+#############################################################################
+# Project directory structure.
+#############################################################################
+
+# build scripts directory
+build_scripts_dir := scripts/build
+
+# directory layout
+bin_dir     := bin
+depend_dir  := depend
+include_dir := include
+src_dir     := src
+test_dir    := test
+matlab_dir  := matlab
+doc_dir     := doc
+
+#############################################################################
+# C++ compilation settings.
+#############################################################################
+
+# compiler
+CXX := g++
+
+# compilation settings - libraries to link
+CXX_LINK := -ljpeg -lpng
+
+# compilation settings - warning flags
+CXX_WARN_BASIC := -ansi -Wall -Wno-long-long
+CXX_WARN_EXTRA := -Wundef -Wpointer-arith -Wold-style-cast \
+                  -Woverloaded-virtual -Wsign-promo
+CXX_WARN  := $(CXX_WARN_BASIC) $(CXX_WARN_EXTRA)
+
+# compilation settings - build flags
+CXX_BUILD := -pthread -fexceptions -fPIC -O3 -rdynamic
+
+# compilation settings - all flags
+CXX_FLAGS := $(CXX_WARN) $(CXX_BUILD)
+
+# compilation settings - linker flags
+CXX_LDFLAGS := $(CXX_FLAGS) $(CXX_LINK)
+
+#############################################################################
+# Matlab mex file compilation settings (only used if building mex files).
+#############################################################################
+
+# matlab mex file compilation settings - matlab path
+MATLAB_PATH := /usr/local/matlab/matlab-r2007a
+
+# matlab mex file compilation settings - matlab architecture (32-bit machines)
+#MATLAB_ARCH := glnx86
+#MEX_EXTN := mexglx
+
+# matlab mex file compilation settings - matlab architecture (64-bit machines)
+MATLAB_ARCH := glnxa64
+MEX_EXTN := mexa64
+
+# matlab mex file compilation settings - include path for mex header files
+MEX_INCLUDE_PATH := $(MATLAB_PATH)/extern/include
+
+# matlab mex file compilation settings - libraries to link
+MEX_LINK := $(CXX_LINK) -lmx -lmex -lmat
+
+# matlab mex file compilation settings - warning flags
+MEX_WARN := $(CXX_WARN)
+
+# matlab mex file compilation settings - build flags
+MEX_BUILD := $(CXX_BUILD) -DMATLAB_MEX_FILE -D_GNU_SOURCE -DNDEBUG
+
+# matlab mex file compilation settings - all flags
+MEX_FLAGS := $(MEX_WARN) $(MEX_BUILD)
+
+# matlab mex file compilation settings - linker flags
+MEX_LDFLAGS := \
+   $(MEX_FLAGS) -shared \
+   -Wl,--version-script,"$(MATLAB_PATH)/extern/lib/$(MATLAB_ARCH)/mexFunction.map" \
+   -Wl,--rpath-link,"$(MATLAB_PATH)/bin/$(MATLAB_ARCH)" \
+   -L"$(MATLAB_PATH)/bin/$(MATLAB_ARCH)" $(MEX_LINK)
+
+#############################################################################
+# Documentation build settings (only used if generating documentation).
+#############################################################################
+
+# doxygen c++ source code documentation generator
+DOXYGEN := doxygen