sci-biology/mosaik: Version bump to 2.2.30

* EAPI=6
* Make build system verbose
* Honour CPPFLAGS and LDFLAGS
* Handle LFS properly
* Fix -Werror=format-security errors

Package-Manager: portage-2.3.0

3 files changed, 320 insertions, 0 deletions

diff --git a/sci-biology/mosaik/files/mosaik-2.2.30-Wformat-security.patch b/sci-biology/mosaik/files/mosaik-2.2.30-Wformat-security.patch
new file mode 100644
index 000000000000..9f7271860229
--- /dev/null
+++ b/sci-biology/mosaik/files/mosaik-2.2.30-Wformat-security.patch
@@ -0,0 +1,84 @@
+- Fix incorrect printf format specifier (-Wformat)
+* fann.c: In function ‘fann_print_connections’:
+* fann.c:889:11: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long int’ [-Wformat=]
+*     printf("L %3d / N %4d %s\n", layer_it - ann->first_layer,
+
+- Fix erroneous memset call
+* md5.c: In function ‘MD5Final’:
+* md5.c:152:26: warning: argument to ‘sizeof’ in ‘memset’ call is the same expression as the destination; did you mean to dereference it? [-Wsizeof-pointer-memaccess]
+*      memset(ctx, 0, sizeof(ctx));        /* In case it's sensitive */
+
+--- a/fann-2.1.0/fann.c
++++ b/fann-2.1.0/fann.c
+@@ -886,7 +886,7 @@
+ 					neurons[ann->connections[i] - ann->first_layer->first_neuron] = (char)('A' + value);
+ 				}
+ 			}
+-			printf("L %3d / N %4d %s\n", layer_it - ann->first_layer,
++			printf("L %3ld / N %4ld %s\n", layer_it - ann->first_layer,
+ 				   neuron_it - ann->first_layer->first_neuron, neurons);
+ 		}
+ 	}
+@@ -987,12 +987,12 @@
+ 	{
+ 		if(ann->network_type == FANN_NETTYPE_SHORTCUT)
+ 		{
+-			printf("  Hidden layer                       :%4d neurons, 0 bias\n",
++			printf("  Hidden layer                       :%4ld neurons, 0 bias\n",
+ 				   layer_it->last_neuron - layer_it->first_neuron);
+ 		}
+ 		else
+ 		{
+-			printf("  Hidden layer                       :%4d neurons, 1 bias\n",
++			printf("  Hidden layer                       :%4ld neurons, 1 bias\n",
+ 				   layer_it->last_neuron - layer_it->first_neuron - 1);
+ 		}
+ 	}
+--- a/fann-2.1.0/fann_io.c
++++ b/fann-2.1.0/fann_io.c
+@@ -174,7 +174,7 @@
+ #endif
+ 
+ 	/* Save network parameters */
+-	fprintf(conf, "num_layers=%u\n", ann->last_layer - ann->first_layer);
++	fprintf(conf, "num_layers=%ld\n", ann->last_layer - ann->first_layer);
+ 	fprintf(conf, "learning_rate=%f\n", ann->learning_rate);
+ 	fprintf(conf, "connection_rate=%f\n", ann->connection_rate);
+ 	fprintf(conf, "network_type=%u\n", ann->network_type);
+@@ -236,7 +236,7 @@
+ 	for(layer_it = ann->first_layer; layer_it != ann->last_layer; layer_it++)
+ 	{
+ 		/* the number of neurons in the layers (in the last layer, there is always one too many neurons, because of an unused bias) */
+-		fprintf(conf, "%u ", layer_it->last_neuron - layer_it->first_neuron);
++		fprintf(conf, "%ld ", layer_it->last_neuron - layer_it->first_neuron);
+ 	}
+ 	fprintf(conf, "\n");
+ 
+@@ -316,14 +316,14 @@
+ 		if(save_as_fixed)
+ 		{
+ 			/* save the connection "(source weight) " */
+-			fprintf(conf, "(%u, %d) ",
++			fprintf(conf, "(%ld, %d) ",
+ 					connected_neurons[i] - first_neuron,
+ 					(int) floor((weights[i] * fixed_multiplier) + 0.5));
+ 		}
+ 		else
+ 		{
+ 			/* save the connection "(source weight) " */
+-			fprintf(conf, "(%u, " FANNPRINTF ") ", connected_neurons[i] - first_neuron, weights[i]);
++			fprintf(conf, "(%ld, " FANNPRINTF ") ", connected_neurons[i] - first_neuron, weights[i]);
+ 		}
+ #else
+ 		/* save the connection "(source weight) " */
+--- a/CommonSource/Utilities/md5.c
++++ b/CommonSource/Utilities/md5.c
+@@ -149,7 +149,7 @@
+     MD5Transform(ctx->buf, (uint32 *) ctx->in);
+     byteReverse((unsigned char *) ctx->buf, 4);
+     memcpy(digest, ctx->buf, 16);
+-    memset(ctx, 0, sizeof(ctx));        /* In case it's sensitive */
++    memset(ctx, 0, sizeof(*ctx));        /* In case it's sensitive */
+ }
+ 
+ 
diff --git a/sci-biology/mosaik/files/mosaik-2.2.30-fix-build-system.patch b/sci-biology/mosaik/files/mosaik-2.2.30-fix-build-system.patch
new file mode 100644
index 000000000000..00a9bec3ae4d
--- /dev/null
+++ b/sci-biology/mosaik/files/mosaik-2.2.30-fix-build-system.patch
@@ -0,0 +1,226 @@
+- Make build system verbose by default, as required by Gentoo policy
+  See also: https://bugs.gentoo.org/show_bug.cgi?id=429308
+- Remove CFLAGS and CXXFLAGS defaults
+- Fix order of flags and honour CPPFLAGS for LFS support
+  and LDFLAGS for --as-needed, respectively
+
+--- a/CommonSource/DataStructures/Makefile
++++ b/CommonSource/DataStructures/Makefile
+@@ -22,7 +22,7 @@
+ 
+ $(BUILT_OBJECTS): $(SOURCES)
+ 	@echo "  * compiling" $(*F).cpp
+-	@$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+ 
+ clean:
+ 	@echo "Cleaning up."
+--- a/CommonSource/ExternalReadFormats/Makefile
++++ b/CommonSource/ExternalReadFormats/Makefile
+@@ -22,7 +22,7 @@
+ 
+ $(BUILT_OBJECTS): $(SOURCES)
+ 	@echo "  * compiling" $(*F).cpp
+-	@$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+ 
+ clean:
+ 	@echo "Cleaning up."
+--- a/CommonSource/MosaikReadFormat/Makefile
++++ b/CommonSource/MosaikReadFormat/Makefile
+@@ -22,7 +22,7 @@
+ 
+ $(BUILT_OBJECTS): $(SOURCES)
+ 	@echo "  * compiling" $(*F).cpp
+-	@$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+ 
+ clean:
+ 	@echo "Cleaning up."
+--- a/CommonSource/PairwiseAlignment/Makefile
++++ b/CommonSource/PairwiseAlignment/Makefile
+@@ -26,11 +26,11 @@
+ 
+ $(BUILT_OBJECTS): $(SOURCES)
+ 	@echo "  * compiling" $(*F).cpp
+-	@$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+ 
+ $(CBUILT_OBJECTS): $(CSOURCES)
+ 	@echo "  * compiling" $(*F).c
+-	@$(CC) -c -o $@ $(*F).c -O3 $(PLATFORM_FLAGS) $(INCLUDES)
++	$(CC) $(CFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).c
+ 
+ clean:
+ 	@echo "Cleaning up."
+--- a/CommonSource/Utilities/Makefile
++++ b/CommonSource/Utilities/Makefile
+@@ -48,11 +48,11 @@
+ 
+ $(BUILT_OBJECTS): $(SOURCES)
+ 	@echo "  * compiling" $(*F).cpp
+-	@$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+ 
+ $(CBUILT_OBJECTS): $(CSOURCES)
+ 	@echo "  * compiling" $(*F).c
+-	@$(CC) -c -o $@ $(*F).c -O3 -w -DSQLITE_OMIT_LOAD_EXTENSION $(PLATFORM_FLAGS) $(INCLUDES)
++	$(CC) $(CFLAGS) $(CPPFLAGS) -DSQLITE_OMIT_LOAD_EXTENSION $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).c
+ 
+ clean:
+ 	@echo "Cleaning up."
+--- a/fann-2.1.0/Makefile
++++ b/fann-2.1.0/Makefile
+@@ -12,7 +12,7 @@
+ 
+ $(CBUILT_OBJECTS): $(CSOURCES)
+ 	@echo "  * compiling" $(*F).c
+-	@$(CC) -c -o $@ $(*F).c -O3 $(PLATFORM_FLAGS) -I$(INCLUDES) 
++	$(CC) $(CFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) -I$(INCLUDES) -c -o $@ $(*F).c
+ 
+ clean:
+ 	@echo "Cleaning up."
+--- a/Makefile
++++ b/Makefile
+@@ -4,8 +4,8 @@
+ # ==========================
+ 
+ # define our object and binary directories
+-export OBJ_DIR = ../obj
+-export BIN_DIR = ../bin
++export OBJ_DIR = ./obj
++export BIN_DIR = ./bin
+ 
+ # define our common source directories
+ export ASSEMBLY_DIR = CommonSource/AssemblyFormats
+@@ -16,20 +16,6 @@
+ export PAIRWISE_DIR = CommonSource/PairwiseAlignment
+ export UTILITIES_DIR = CommonSource/Utilities
+ 
+-# define some default flags
+-FLAGS = -Wall -Wno-char-subscripts -ansi -O3
+-#FLAGS = -Wall -Wno-char-subscripts -ansi -g -D VERBOSE_DEBUG #gdb debugging
+-#FLAGS = -Wall -Wno-char-subscripts -ansi -O3 -D VERBOSE_DEBUG #enables verbose debugging
+-CFLAGS =
+-CXXFLAGS =
+-#CXXFLAGS = -ansi -pedantic -Wextra -Weffc++
+-CFLAGS += $(FLAGS)
+-CXXFLAGS += $(FLAGS)
+-export CFLAGS
+-export CXXFLAGS
+-#export LDFLAGS = -Wl
+-export CXX ?= g++
+-
+ # define our platform
+ export BLD_PLATFORM ?= linux
+ include includes/$(BLD_PLATFORM).inc
+--- a/MosaikAligner/Makefile
++++ b/MosaikAligner/Makefile
+@@ -68,11 +68,11 @@
+ 
+ $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
+ 	@echo "  * linking $(PROGRAM)"
+-	@$(CXX) $(LDFLAGS) $(CXXFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS)
+ 
+ $(BUILT_OBJECTS): $(SOURCES)
+ 	@echo "  * compiling" $(*F).cpp
+-	@$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+ 
+ $(EXT_OBJECTS):
+ 	@$(MAKE) --no-print-directory -C $(TD)$(DATA_STRUCT_DIR)
+--- a/MosaikBuild/Makefile
++++ b/MosaikBuild/Makefile
+@@ -26,11 +26,11 @@
+ 
+ $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
+ 	@echo "  * linking $(PROGRAM)"
+-	@$(CXX) $(LDFLAGS) $(CXXFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS)
+ 
+ $(BUILT_OBJECTS): $(SOURCES)
+ 	@echo "  * compiling" $(*F).cpp
+-	@$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+ 
+ $(EXT_OBJECTS):
+ 	@$(MAKE) --no-print-directory -C $(TD)$(DATA_STRUCT_DIR)
+--- a/MosaikJump/Makefile
++++ b/MosaikJump/Makefile
+@@ -26,11 +26,11 @@
+ 
+ $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
+ 	@echo "  * linking $(PROGRAM)"
+-	@$(CXX) $(LDFLAGS) $(CXXFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS)
+ 
+ $(BUILT_OBJECTS): $(SOURCES)
+ 	@echo "  * compiling" $(*F).cpp
+-	@$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+ 
+ $(EXT_OBJECTS):
+ 	@$(MAKE) --no-print-directory -C $(TD)$(MOSAIKREAD_DIR)
+--- a/MosaikText/Makefile
++++ b/MosaikText/Makefile
+@@ -26,11 +26,11 @@
+ 
+ $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
+ 	@echo "  * linking $(PROGRAM)"
+-	@$(CXX) $(LDFLAGS) $(CXXFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS)
+ 
+ $(BUILT_OBJECTS): $(SOURCES)
+ 	@echo "  * compiling" $(*F).cpp
+-	@$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+ 
+ $(EXT_OBJECTS):
+ 	@$(MAKE) --no-print-directory -C $(TD)$(MOSAIKREAD_DIR)
+--- a/networkFile/retrainCode/attachXC/Makefile
++++ b/networkFile/retrainCode/attachXC/Makefile
+@@ -3,12 +3,11 @@
+ # (c) 2012 Wan-Ping Lee
+ # ==========================
+ 
+-FLAGS = -Wall -O3
+ 
+ 
+ all: xc_pe.cpp xc_se.cpp
+-	@$(CXX) $(FLAGS) xc_pe.cpp -o xc_pe
+-	@$(CXX) $(FLAGS) xc_se.cpp -o xc_se
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) xc_pe.cpp -o xc_pe
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) xc_se.cpp -o xc_se
+ 
+ .PHONY: all
+ 
+--- a/networkFile/retrainCode/trainNetwork/Makefile
++++ b/networkFile/retrainCode/trainNetwork/Makefile
+@@ -5,8 +5,6 @@
+ 
+ OBJ_DIR = ./obj
+ 
+-FLAGS =  -Wall -O3
+-CFLAGS = -O3
+ FANN=../../../fann-2.1.0
+ 
+ SOURCES = sam_parser_float.cpp parameter_parser_float.cpp mq_train_float.cpp
+@@ -15,12 +13,12 @@
+ all: $(FANN)/floatfann.c $(SOURCES)
+ 	@test -d $(OBJ_DIR) || mkdir $(OBJ_DIR)
+ 	@echo "  * compiling ......"
+-	@$(CC) $(CFLAGS) -c -o $(OBJ_DIR)/floatfann.o $(FANN)/floatfann.c -I$(FANN)/include
+-	@$(CXX) -c $(FLAGS) -o $(OBJ_DIR)/sam_parser_float.o sam_parser_float.cpp
+-	@$(CXX) -c $(FLAGS) -o $(OBJ_DIR)/parameter_parser_float.o parameter_parser_float.cpp
+-	@$(CXX) -c $(FLAGS) -o $(OBJ_DIR)/mq_train_float.o mq_train_float.cpp -I$(FANN)/include
++	$(CC)  $(CFLAGS)   $(CPPFLAGS) -c -o $(OBJ_DIR)/floatfann.o $(FANN)/floatfann.c -I$(FANN)/include
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c -o $(OBJ_DIR)/sam_parser_float.o sam_parser_float.cpp
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c -o $(OBJ_DIR)/parameter_parser_float.o parameter_parser_float.cpp
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c -o $(OBJ_DIR)/mq_train_float.o mq_train_float.cpp -I$(FANN)/include
+ 	@echo "  * linking ......"
+-	@$(CXX) $(FLAGS) $(OBJ_DIR)/*.o -o $(PROGRAM)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) $(OBJ_DIR)/*.o -o $(PROGRAM)
+ 
+ .PHONY: all
+ 
diff --git a/sci-biology/mosaik/files/mosaik-2.2.30-remove-platform-code.patch b/sci-biology/mosaik/files/mosaik-2.2.30-remove-platform-code.patch
new file mode 100644
index 000000000000..8573573ec125
--- /dev/null
+++ b/sci-biology/mosaik/files/mosaik-2.2.30-remove-platform-code.patch
@@ -0,0 +1,10 @@
+- Remove macro for enabling large file support, this is better handled at an
+  ebuild level, where the LFS flags can be handled for multiple architectures
+- Remove static flag, which is contrary to Gentoo policy
+
+--- a/includes/linux.inc
++++ b/includes/linux.inc
+@@ -1,2 +1,2 @@
+ # define our processor specific flags
+-export PLATFORM_FLAGS = -D_FILE_OFFSET_BITS=64 -static
++export PLATFORM_FLAGS =