| 1 |
commit: b57cefc0475955dc9dce44855af6a5795a78a001 |
| 2 |
Author: David Seifert <soap <AT> gentoo <DOT> org> |
| 3 |
AuthorDate: Sun Sep 4 12:59:47 2016 +0000 |
| 4 |
Commit: David Seifert <soap <AT> gentoo <DOT> org> |
| 5 |
CommitDate: Sun Sep 4 13:00:11 2016 +0000 |
| 6 |
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b57cefc0 |
| 7 |
|
| 8 |
sci-biology/mosaik: Version bump to 2.2.30 |
| 9 |
|
| 10 |
* EAPI=6 |
| 11 |
* Make build system verbose |
| 12 |
* Honour CPPFLAGS and LDFLAGS |
| 13 |
* Handle LFS properly |
| 14 |
* Fix -Werror=format-security errors |
| 15 |
|
| 16 |
Package-Manager: portage-2.3.0 |
| 17 |
|
| 18 |
sci-biology/mosaik/Manifest | 1 + |
| 19 |
.../files/mosaik-2.2.30-Wformat-security.patch | 84 ++++++++ |
| 20 |
.../files/mosaik-2.2.30-fix-build-system.patch | 226 +++++++++++++++++++++ |
| 21 |
.../files/mosaik-2.2.30-remove-platform-code.patch | 10 + |
| 22 |
sci-biology/mosaik/mosaik-2.2.30.ebuild | 53 +++++ |
| 23 |
5 files changed, 374 insertions(+) |
| 24 |
|
| 25 |
diff --git a/sci-biology/mosaik/Manifest b/sci-biology/mosaik/Manifest |
| 26 |
index 77f5aa8..de9954a 100644 |
| 27 |
--- a/sci-biology/mosaik/Manifest |
| 28 |
+++ b/sci-biology/mosaik/Manifest |
| 29 |
@@ -1,2 +1,3 @@ |
| 30 |
DIST Mosaik-1.0.1367-source.tar.bz2 8700231 SHA256 2a6ee1d25af835028b71f2518c6a00e929e64e7be6305183dfe0e242a015c750 SHA512 2100cd3b182a77be9a7411dce61ee51cb28b5e8e64282ec26e74d86c1e41d3254f7f62bd69f2ee4ad4d60c535e00e604b5f84f748f5c43ad4b0ac939cf8ed81a WHIRLPOOL cf25de6062201956068f02c339216d11fc1b473d68d7b4e9aed12d6f53ac5485995082a386b972d9545672346fac08f607bae34ac839bc8edf461b84e7430456 |
| 31 |
DIST Mosaik-1.0.1388-source.tar.bz2 8730164 SHA256 d6a8effa49adac617a388e2132aaf1a6b0679c783574d7df2cbd952a5f96e60c SHA512 cb6c4035cf9a6433b25800d841b74add3c88f06a87ac0261ffbba7be0528bcb02460fbbd0095656e60ca44c28ea249fe702bb0a4262d2ba64574a7e54a05a2bb WHIRLPOOL 5bf926898ab0f40f21858e511c366586d82450f4ef9af14e4add2e7e889be27a543afa23006de3bb2f49d2a43a81d32473958946a5cc08da0a26feee41c7a3e0 |
| 32 |
+DIST mosaik-2.2.30.tar.gz 4387062 SHA256 685dcc4cde1b56d19be37bfb238ae4cddeb25dced6da7b3880e68973957e940e SHA512 1acf534e6defc927fc22937a7bae6786e85ab7aa234b4209169f1267f1a9bd68415b441c6aed2e7cd667f694a562017ebc9457251958f77386259ffce9812b10 WHIRLPOOL 493291cc94cc5f95f5f1f62c3208f1c8dbb8cb0efcf6a21cca3e3963228f02ab0e59f11e00d8a9724a99733ffd290bc979262c0e553a1ee55c1adc9c392c3813 |
| 33 |
|
| 34 |
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 |
| 35 |
new file mode 100644 |
| 36 |
index 00000000..9f72718 |
| 37 |
--- /dev/null |
| 38 |
+++ b/sci-biology/mosaik/files/mosaik-2.2.30-Wformat-security.patch |
| 39 |
@@ -0,0 +1,84 @@ |
| 40 |
+- Fix incorrect printf format specifier (-Wformat) |
| 41 |
+* fann.c: In function ‘fann_print_connections’: |
| 42 |
+* fann.c:889:11: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long int’ [-Wformat=] |
| 43 |
+* printf("L %3d / N %4d %s\n", layer_it - ann->first_layer, |
| 44 |
+ |
| 45 |
+- Fix erroneous memset call |
| 46 |
+* md5.c: In function ‘MD5Final’: |
| 47 |
+* 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] |
| 48 |
+* memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */ |
| 49 |
+ |
| 50 |
+--- a/fann-2.1.0/fann.c |
| 51 |
++++ b/fann-2.1.0/fann.c |
| 52 |
+@@ -886,7 +886,7 @@ |
| 53 |
+ neurons[ann->connections[i] - ann->first_layer->first_neuron] = (char)('A' + value); |
| 54 |
+ } |
| 55 |
+ } |
| 56 |
+- printf("L %3d / N %4d %s\n", layer_it - ann->first_layer, |
| 57 |
++ printf("L %3ld / N %4ld %s\n", layer_it - ann->first_layer, |
| 58 |
+ neuron_it - ann->first_layer->first_neuron, neurons); |
| 59 |
+ } |
| 60 |
+ } |
| 61 |
+@@ -987,12 +987,12 @@ |
| 62 |
+ { |
| 63 |
+ if(ann->network_type == FANN_NETTYPE_SHORTCUT) |
| 64 |
+ { |
| 65 |
+- printf(" Hidden layer :%4d neurons, 0 bias\n", |
| 66 |
++ printf(" Hidden layer :%4ld neurons, 0 bias\n", |
| 67 |
+ layer_it->last_neuron - layer_it->first_neuron); |
| 68 |
+ } |
| 69 |
+ else |
| 70 |
+ { |
| 71 |
+- printf(" Hidden layer :%4d neurons, 1 bias\n", |
| 72 |
++ printf(" Hidden layer :%4ld neurons, 1 bias\n", |
| 73 |
+ layer_it->last_neuron - layer_it->first_neuron - 1); |
| 74 |
+ } |
| 75 |
+ } |
| 76 |
+--- a/fann-2.1.0/fann_io.c |
| 77 |
++++ b/fann-2.1.0/fann_io.c |
| 78 |
+@@ -174,7 +174,7 @@ |
| 79 |
+ #endif |
| 80 |
+ |
| 81 |
+ /* Save network parameters */ |
| 82 |
+- fprintf(conf, "num_layers=%u\n", ann->last_layer - ann->first_layer); |
| 83 |
++ fprintf(conf, "num_layers=%ld\n", ann->last_layer - ann->first_layer); |
| 84 |
+ fprintf(conf, "learning_rate=%f\n", ann->learning_rate); |
| 85 |
+ fprintf(conf, "connection_rate=%f\n", ann->connection_rate); |
| 86 |
+ fprintf(conf, "network_type=%u\n", ann->network_type); |
| 87 |
+@@ -236,7 +236,7 @@ |
| 88 |
+ for(layer_it = ann->first_layer; layer_it != ann->last_layer; layer_it++) |
| 89 |
+ { |
| 90 |
+ /* the number of neurons in the layers (in the last layer, there is always one too many neurons, because of an unused bias) */ |
| 91 |
+- fprintf(conf, "%u ", layer_it->last_neuron - layer_it->first_neuron); |
| 92 |
++ fprintf(conf, "%ld ", layer_it->last_neuron - layer_it->first_neuron); |
| 93 |
+ } |
| 94 |
+ fprintf(conf, "\n"); |
| 95 |
+ |
| 96 |
+@@ -316,14 +316,14 @@ |
| 97 |
+ if(save_as_fixed) |
| 98 |
+ { |
| 99 |
+ /* save the connection "(source weight) " */ |
| 100 |
+- fprintf(conf, "(%u, %d) ", |
| 101 |
++ fprintf(conf, "(%ld, %d) ", |
| 102 |
+ connected_neurons[i] - first_neuron, |
| 103 |
+ (int) floor((weights[i] * fixed_multiplier) + 0.5)); |
| 104 |
+ } |
| 105 |
+ else |
| 106 |
+ { |
| 107 |
+ /* save the connection "(source weight) " */ |
| 108 |
+- fprintf(conf, "(%u, " FANNPRINTF ") ", connected_neurons[i] - first_neuron, weights[i]); |
| 109 |
++ fprintf(conf, "(%ld, " FANNPRINTF ") ", connected_neurons[i] - first_neuron, weights[i]); |
| 110 |
+ } |
| 111 |
+ #else |
| 112 |
+ /* save the connection "(source weight) " */ |
| 113 |
+--- a/CommonSource/Utilities/md5.c |
| 114 |
++++ b/CommonSource/Utilities/md5.c |
| 115 |
+@@ -149,7 +149,7 @@ |
| 116 |
+ MD5Transform(ctx->buf, (uint32 *) ctx->in); |
| 117 |
+ byteReverse((unsigned char *) ctx->buf, 4); |
| 118 |
+ memcpy(digest, ctx->buf, 16); |
| 119 |
+- memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */ |
| 120 |
++ memset(ctx, 0, sizeof(*ctx)); /* In case it's sensitive */ |
| 121 |
+ } |
| 122 |
+ |
| 123 |
+ |
| 124 |
|
| 125 |
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 |
| 126 |
new file mode 100644 |
| 127 |
index 00000000..00a9bec |
| 128 |
--- /dev/null |
| 129 |
+++ b/sci-biology/mosaik/files/mosaik-2.2.30-fix-build-system.patch |
| 130 |
@@ -0,0 +1,226 @@ |
| 131 |
+- Make build system verbose by default, as required by Gentoo policy |
| 132 |
+ See also: https://bugs.gentoo.org/show_bug.cgi?id=429308 |
| 133 |
+- Remove CFLAGS and CXXFLAGS defaults |
| 134 |
+- Fix order of flags and honour CPPFLAGS for LFS support |
| 135 |
+ and LDFLAGS for --as-needed, respectively |
| 136 |
+ |
| 137 |
+--- a/CommonSource/DataStructures/Makefile |
| 138 |
++++ b/CommonSource/DataStructures/Makefile |
| 139 |
+@@ -22,7 +22,7 @@ |
| 140 |
+ |
| 141 |
+ $(BUILT_OBJECTS): $(SOURCES) |
| 142 |
+ @echo " * compiling" $(*F).cpp |
| 143 |
+- @$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) |
| 144 |
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 145 |
+ |
| 146 |
+ clean: |
| 147 |
+ @echo "Cleaning up." |
| 148 |
+--- a/CommonSource/ExternalReadFormats/Makefile |
| 149 |
++++ b/CommonSource/ExternalReadFormats/Makefile |
| 150 |
+@@ -22,7 +22,7 @@ |
| 151 |
+ |
| 152 |
+ $(BUILT_OBJECTS): $(SOURCES) |
| 153 |
+ @echo " * compiling" $(*F).cpp |
| 154 |
+- @$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) |
| 155 |
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 156 |
+ |
| 157 |
+ clean: |
| 158 |
+ @echo "Cleaning up." |
| 159 |
+--- a/CommonSource/MosaikReadFormat/Makefile |
| 160 |
++++ b/CommonSource/MosaikReadFormat/Makefile |
| 161 |
+@@ -22,7 +22,7 @@ |
| 162 |
+ |
| 163 |
+ $(BUILT_OBJECTS): $(SOURCES) |
| 164 |
+ @echo " * compiling" $(*F).cpp |
| 165 |
+- @$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) |
| 166 |
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 167 |
+ |
| 168 |
+ clean: |
| 169 |
+ @echo "Cleaning up." |
| 170 |
+--- a/CommonSource/PairwiseAlignment/Makefile |
| 171 |
++++ b/CommonSource/PairwiseAlignment/Makefile |
| 172 |
+@@ -26,11 +26,11 @@ |
| 173 |
+ |
| 174 |
+ $(BUILT_OBJECTS): $(SOURCES) |
| 175 |
+ @echo " * compiling" $(*F).cpp |
| 176 |
+- @$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) |
| 177 |
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 178 |
+ |
| 179 |
+ $(CBUILT_OBJECTS): $(CSOURCES) |
| 180 |
+ @echo " * compiling" $(*F).c |
| 181 |
+- @$(CC) -c -o $@ $(*F).c -O3 $(PLATFORM_FLAGS) $(INCLUDES) |
| 182 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).c |
| 183 |
+ |
| 184 |
+ clean: |
| 185 |
+ @echo "Cleaning up." |
| 186 |
+--- a/CommonSource/Utilities/Makefile |
| 187 |
++++ b/CommonSource/Utilities/Makefile |
| 188 |
+@@ -48,11 +48,11 @@ |
| 189 |
+ |
| 190 |
+ $(BUILT_OBJECTS): $(SOURCES) |
| 191 |
+ @echo " * compiling" $(*F).cpp |
| 192 |
+- @$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) |
| 193 |
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 194 |
+ |
| 195 |
+ $(CBUILT_OBJECTS): $(CSOURCES) |
| 196 |
+ @echo " * compiling" $(*F).c |
| 197 |
+- @$(CC) -c -o $@ $(*F).c -O3 -w -DSQLITE_OMIT_LOAD_EXTENSION $(PLATFORM_FLAGS) $(INCLUDES) |
| 198 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) -DSQLITE_OMIT_LOAD_EXTENSION $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).c |
| 199 |
+ |
| 200 |
+ clean: |
| 201 |
+ @echo "Cleaning up." |
| 202 |
+--- a/fann-2.1.0/Makefile |
| 203 |
++++ b/fann-2.1.0/Makefile |
| 204 |
+@@ -12,7 +12,7 @@ |
| 205 |
+ |
| 206 |
+ $(CBUILT_OBJECTS): $(CSOURCES) |
| 207 |
+ @echo " * compiling" $(*F).c |
| 208 |
+- @$(CC) -c -o $@ $(*F).c -O3 $(PLATFORM_FLAGS) -I$(INCLUDES) |
| 209 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) -I$(INCLUDES) -c -o $@ $(*F).c |
| 210 |
+ |
| 211 |
+ clean: |
| 212 |
+ @echo "Cleaning up." |
| 213 |
+--- a/Makefile |
| 214 |
++++ b/Makefile |
| 215 |
+@@ -4,8 +4,8 @@ |
| 216 |
+ # ========================== |
| 217 |
+ |
| 218 |
+ # define our object and binary directories |
| 219 |
+-export OBJ_DIR = ../obj |
| 220 |
+-export BIN_DIR = ../bin |
| 221 |
++export OBJ_DIR = ./obj |
| 222 |
++export BIN_DIR = ./bin |
| 223 |
+ |
| 224 |
+ # define our common source directories |
| 225 |
+ export ASSEMBLY_DIR = CommonSource/AssemblyFormats |
| 226 |
+@@ -16,20 +16,6 @@ |
| 227 |
+ export PAIRWISE_DIR = CommonSource/PairwiseAlignment |
| 228 |
+ export UTILITIES_DIR = CommonSource/Utilities |
| 229 |
+ |
| 230 |
+-# define some default flags |
| 231 |
+-FLAGS = -Wall -Wno-char-subscripts -ansi -O3 |
| 232 |
+-#FLAGS = -Wall -Wno-char-subscripts -ansi -g -D VERBOSE_DEBUG #gdb debugging |
| 233 |
+-#FLAGS = -Wall -Wno-char-subscripts -ansi -O3 -D VERBOSE_DEBUG #enables verbose debugging |
| 234 |
+-CFLAGS = |
| 235 |
+-CXXFLAGS = |
| 236 |
+-#CXXFLAGS = -ansi -pedantic -Wextra -Weffc++ |
| 237 |
+-CFLAGS += $(FLAGS) |
| 238 |
+-CXXFLAGS += $(FLAGS) |
| 239 |
+-export CFLAGS |
| 240 |
+-export CXXFLAGS |
| 241 |
+-#export LDFLAGS = -Wl |
| 242 |
+-export CXX ?= g++ |
| 243 |
+- |
| 244 |
+ # define our platform |
| 245 |
+ export BLD_PLATFORM ?= linux |
| 246 |
+ include includes/$(BLD_PLATFORM).inc |
| 247 |
+--- a/MosaikAligner/Makefile |
| 248 |
++++ b/MosaikAligner/Makefile |
| 249 |
+@@ -68,11 +68,11 @@ |
| 250 |
+ |
| 251 |
+ $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) |
| 252 |
+ @echo " * linking $(PROGRAM)" |
| 253 |
+- @$(CXX) $(LDFLAGS) $(CXXFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS) |
| 254 |
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS) |
| 255 |
+ |
| 256 |
+ $(BUILT_OBJECTS): $(SOURCES) |
| 257 |
+ @echo " * compiling" $(*F).cpp |
| 258 |
+- @$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) |
| 259 |
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 260 |
+ |
| 261 |
+ $(EXT_OBJECTS): |
| 262 |
+ @$(MAKE) --no-print-directory -C $(TD)$(DATA_STRUCT_DIR) |
| 263 |
+--- a/MosaikBuild/Makefile |
| 264 |
++++ b/MosaikBuild/Makefile |
| 265 |
+@@ -26,11 +26,11 @@ |
| 266 |
+ |
| 267 |
+ $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) |
| 268 |
+ @echo " * linking $(PROGRAM)" |
| 269 |
+- @$(CXX) $(LDFLAGS) $(CXXFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS) |
| 270 |
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS) |
| 271 |
+ |
| 272 |
+ $(BUILT_OBJECTS): $(SOURCES) |
| 273 |
+ @echo " * compiling" $(*F).cpp |
| 274 |
+- @$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) |
| 275 |
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 276 |
+ |
| 277 |
+ $(EXT_OBJECTS): |
| 278 |
+ @$(MAKE) --no-print-directory -C $(TD)$(DATA_STRUCT_DIR) |
| 279 |
+--- a/MosaikJump/Makefile |
| 280 |
++++ b/MosaikJump/Makefile |
| 281 |
+@@ -26,11 +26,11 @@ |
| 282 |
+ |
| 283 |
+ $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) |
| 284 |
+ @echo " * linking $(PROGRAM)" |
| 285 |
+- @$(CXX) $(LDFLAGS) $(CXXFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS) |
| 286 |
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS) |
| 287 |
+ |
| 288 |
+ $(BUILT_OBJECTS): $(SOURCES) |
| 289 |
+ @echo " * compiling" $(*F).cpp |
| 290 |
+- @$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) |
| 291 |
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 292 |
+ |
| 293 |
+ $(EXT_OBJECTS): |
| 294 |
+ @$(MAKE) --no-print-directory -C $(TD)$(MOSAIKREAD_DIR) |
| 295 |
+--- a/MosaikText/Makefile |
| 296 |
++++ b/MosaikText/Makefile |
| 297 |
+@@ -26,11 +26,11 @@ |
| 298 |
+ |
| 299 |
+ $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) |
| 300 |
+ @echo " * linking $(PROGRAM)" |
| 301 |
+- @$(CXX) $(LDFLAGS) $(CXXFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS) |
| 302 |
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS) |
| 303 |
+ |
| 304 |
+ $(BUILT_OBJECTS): $(SOURCES) |
| 305 |
+ @echo " * compiling" $(*F).cpp |
| 306 |
+- @$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) |
| 307 |
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 308 |
+ |
| 309 |
+ $(EXT_OBJECTS): |
| 310 |
+ @$(MAKE) --no-print-directory -C $(TD)$(MOSAIKREAD_DIR) |
| 311 |
+--- a/networkFile/retrainCode/attachXC/Makefile |
| 312 |
++++ b/networkFile/retrainCode/attachXC/Makefile |
| 313 |
+@@ -3,12 +3,11 @@ |
| 314 |
+ # (c) 2012 Wan-Ping Lee |
| 315 |
+ # ========================== |
| 316 |
+ |
| 317 |
+-FLAGS = -Wall -O3 |
| 318 |
+ |
| 319 |
+ |
| 320 |
+ all: xc_pe.cpp xc_se.cpp |
| 321 |
+- @$(CXX) $(FLAGS) xc_pe.cpp -o xc_pe |
| 322 |
+- @$(CXX) $(FLAGS) xc_se.cpp -o xc_se |
| 323 |
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) xc_pe.cpp -o xc_pe |
| 324 |
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) xc_se.cpp -o xc_se |
| 325 |
+ |
| 326 |
+ .PHONY: all |
| 327 |
+ |
| 328 |
+--- a/networkFile/retrainCode/trainNetwork/Makefile |
| 329 |
++++ b/networkFile/retrainCode/trainNetwork/Makefile |
| 330 |
+@@ -5,8 +5,6 @@ |
| 331 |
+ |
| 332 |
+ OBJ_DIR = ./obj |
| 333 |
+ |
| 334 |
+-FLAGS = -Wall -O3 |
| 335 |
+-CFLAGS = -O3 |
| 336 |
+ FANN=../../../fann-2.1.0 |
| 337 |
+ |
| 338 |
+ SOURCES = sam_parser_float.cpp parameter_parser_float.cpp mq_train_float.cpp |
| 339 |
+@@ -15,12 +13,12 @@ |
| 340 |
+ all: $(FANN)/floatfann.c $(SOURCES) |
| 341 |
+ @test -d $(OBJ_DIR) || mkdir $(OBJ_DIR) |
| 342 |
+ @echo " * compiling ......" |
| 343 |
+- @$(CC) $(CFLAGS) -c -o $(OBJ_DIR)/floatfann.o $(FANN)/floatfann.c -I$(FANN)/include |
| 344 |
+- @$(CXX) -c $(FLAGS) -o $(OBJ_DIR)/sam_parser_float.o sam_parser_float.cpp |
| 345 |
+- @$(CXX) -c $(FLAGS) -o $(OBJ_DIR)/parameter_parser_float.o parameter_parser_float.cpp |
| 346 |
+- @$(CXX) -c $(FLAGS) -o $(OBJ_DIR)/mq_train_float.o mq_train_float.cpp -I$(FANN)/include |
| 347 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $(OBJ_DIR)/floatfann.o $(FANN)/floatfann.c -I$(FANN)/include |
| 348 |
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) -c -o $(OBJ_DIR)/sam_parser_float.o sam_parser_float.cpp |
| 349 |
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) -c -o $(OBJ_DIR)/parameter_parser_float.o parameter_parser_float.cpp |
| 350 |
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) -c -o $(OBJ_DIR)/mq_train_float.o mq_train_float.cpp -I$(FANN)/include |
| 351 |
+ @echo " * linking ......" |
| 352 |
+- @$(CXX) $(FLAGS) $(OBJ_DIR)/*.o -o $(PROGRAM) |
| 353 |
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) $(OBJ_DIR)/*.o -o $(PROGRAM) |
| 354 |
+ |
| 355 |
+ .PHONY: all |
| 356 |
+ |
| 357 |
|
| 358 |
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 |
| 359 |
new file mode 100644 |
| 360 |
index 00000000..8573573 |
| 361 |
--- /dev/null |
| 362 |
+++ b/sci-biology/mosaik/files/mosaik-2.2.30-remove-platform-code.patch |
| 363 |
@@ -0,0 +1,10 @@ |
| 364 |
+- Remove macro for enabling large file support, this is better handled at an |
| 365 |
+ ebuild level, where the LFS flags can be handled for multiple architectures |
| 366 |
+- Remove static flag, which is contrary to Gentoo policy |
| 367 |
+ |
| 368 |
+--- a/includes/linux.inc |
| 369 |
++++ b/includes/linux.inc |
| 370 |
+@@ -1,2 +1,2 @@ |
| 371 |
+ # define our processor specific flags |
| 372 |
+-export PLATFORM_FLAGS = -D_FILE_OFFSET_BITS=64 -static |
| 373 |
++export PLATFORM_FLAGS = |
| 374 |
|
| 375 |
diff --git a/sci-biology/mosaik/mosaik-2.2.30.ebuild b/sci-biology/mosaik/mosaik-2.2.30.ebuild |
| 376 |
new file mode 100644 |
| 377 |
index 00000000..ab1d891 |
| 378 |
--- /dev/null |
| 379 |
+++ b/sci-biology/mosaik/mosaik-2.2.30.ebuild |
| 380 |
@@ -0,0 +1,53 @@ |
| 381 |
+# Copyright 1999-2016 Gentoo Foundation |
| 382 |
+# Distributed under the terms of the GNU General Public License v2 |
| 383 |
+# $Id$ |
| 384 |
+ |
| 385 |
+EAPI=6 |
| 386 |
+ |
| 387 |
+inherit flag-o-matic toolchain-funcs vcs-snapshot |
| 388 |
+ |
| 389 |
+DESCRIPTION="A reference-guided aligner for next-generation sequencing technologies" |
| 390 |
+HOMEPAGE="https://github.com/wanpinglee/MOSAIK" |
| 391 |
+SRC_URI="https://github.com/wanpinglee/MOSAIK/archive/5c25216d3522d6a33e53875cd76a6d65001e4e67.tar.gz -> ${P}.tar.gz" |
| 392 |
+ |
| 393 |
+LICENSE="GPL-2" |
| 394 |
+SLOT="0" |
| 395 |
+IUSE="" |
| 396 |
+KEYWORDS="~amd64 ~x86" |
| 397 |
+ |
| 398 |
+DEPEND="" |
| 399 |
+RDEPEND="" |
| 400 |
+ |
| 401 |
+S="${WORKDIR}/${P}/src" |
| 402 |
+ |
| 403 |
+PATCHES=( |
| 404 |
+ "${FILESDIR}/${P}-remove-platform-code.patch" |
| 405 |
+ "${FILESDIR}/${P}-fix-build-system.patch" |
| 406 |
+ "${FILESDIR}/${P}-Wformat-security.patch" |
| 407 |
+) |
| 408 |
+ |
| 409 |
+src_configure() { |
| 410 |
+ # readd default warning flags from build system |
| 411 |
+ append-flags -Wall -Wno-char-subscripts |
| 412 |
+ append-lfs-flags |
| 413 |
+ export BLD_PLATFORM=linux |
| 414 |
+} |
| 415 |
+ |
| 416 |
+src_compile() { |
| 417 |
+ emake \ |
| 418 |
+ CC=$(tc-getCC) \ |
| 419 |
+ CXX=$(tc-getCXX) \ |
| 420 |
+ CFLAGS="${CFLAGS}" \ |
| 421 |
+ CXXFLAGS="${CXXFLAGS}" \ |
| 422 |
+ CPPFLAGS="${CPPFLAGS}" \ |
| 423 |
+ LDFLAGS="${LDFLAGS}" |
| 424 |
+} |
| 425 |
+ |
| 426 |
+src_install() { |
| 427 |
+ dobin bin/Mosaik* |
| 428 |
+ |
| 429 |
+ dodoc ../README |
| 430 |
+ |
| 431 |
+ insinto /usr/share/${PN}/examples |
| 432 |
+ doins -r ../demo/. |
| 433 |
+} |
Archives