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xarthisius 10/10/05 08:27:06 |
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Added: mothur-1.13.0-overflows.patch |
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mothur-1.13.0-makefile.patch |
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Log: |
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Fix buffer overflows and building with --as-needed wrt bug 339753. Thanks to Diego for the report. Correct dependencies. Drop old. |
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(Portage version: 2.2_rc88/cvs/Linux x86_64) |
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Revision Changes Path |
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1.1 sci-biology/mothur/files/mothur-1.13.0-overflows.patch |
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mothur/files/mothur-1.13.0-overflows.patch?rev=1.1&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mothur/files/mothur-1.13.0-overflows.patch?rev=1.1&content-type=text/plain |
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|
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Index: mothur-1.13.0-overflows.patch |
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=================================================================== |
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Fix buffer overflows |
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|
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http://www.mothur.org/forum/viewtopic.php?f=4&t=591 |
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|
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--- Mothur.source/filterseqscommand.cpp |
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+++ Mothur.source/filterseqscommand.cpp |
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@@ -305,8 +305,8 @@ |
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|
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//wait on chidren |
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for(int i = 1; i < processors; i++) { |
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- char buf[4]; |
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- MPI_Recv(buf, 4, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status); |
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+ char buf[5]; |
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+ MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status); |
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} |
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|
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}else { //you are a child process |
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@@ -326,11 +326,11 @@ |
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if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); return 0; } |
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- char buf[4]; |
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+ char buf[5]; |
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strcpy(buf, "done"); |
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|
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//tell parent you are done. |
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- MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD); |
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+ MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD); |
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} |
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|
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MPI_File_close(&outMPI); |
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--- Mothur.source/distancecommand.cpp |
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+++ Mothur.source/distancecommand.cpp |
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@@ -271,8 +271,8 @@ |
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for(int i = 1; i < processors; i++) { |
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if (m->control_pressed) { MPI_File_close(&outMPI); delete distCalculator; return 0; } |
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|
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- char buf[4]; |
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- MPI_Recv(buf, 4, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status); |
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+ char buf[5]; |
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+ MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status); |
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} |
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}else { //you are a child process |
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//do your part |
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@@ -280,10 +280,10 @@ |
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|
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if (m->control_pressed) { MPI_File_close(&outMPI); delete distCalculator; return 0; } |
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|
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- char buf[4]; |
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+ char buf[5]; |
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strcpy(buf, "done"); |
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//tell parent you are done. |
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- MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD); |
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+ MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD); |
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} |
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|
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MPI_File_close(&outMPI); |
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--- Mothur.source/chimeracheckcommand.cpp |
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+++ Mothur.source/chimeracheckcommand.cpp |
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@@ -269,8 +269,8 @@ |
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|
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//wait on chidren |
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for(int j = 1; j < processors; j++) { |
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- char buf[4]; |
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- MPI_Recv(buf, 4, MPI_CHAR, j, tag, MPI_COMM_WORLD, &status); |
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+ char buf[5]; |
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+ MPI_Recv(buf, 5, MPI_CHAR, j, tag, MPI_COMM_WORLD, &status); |
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} |
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}else{ //you are a child process |
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MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status); |
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@@ -288,9 +288,9 @@ |
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if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; } |
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|
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//tell parent you are done. |
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- char buf[4]; |
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+ char buf[5]; |
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strcpy(buf, "done"); |
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- MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD); |
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+ MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD); |
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} |
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|
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//close files |
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|
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|
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1.1 sci-biology/mothur/files/mothur-1.13.0-makefile.patch |
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mothur/files/mothur-1.13.0-makefile.patch?rev=1.1&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mothur/files/mothur-1.13.0-makefile.patch?rev=1.1&content-type=text/plain |
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Index: mothur-1.13.0-makefile.patch |
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=================================================================== |
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Fix build with --as-needed, respect CXX, CXXFLAGS |
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|
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http://www.mothur.org/forum/viewtopic.php?f=4&t=590 |
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http://bugs.gentoo.org/show_bug.cgi?id=339753 |
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|
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--- makefile |
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+++ makefile |
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@@ -11,7 +11,7 @@ |
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|
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# Optimize to level 3: |
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|
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-CXXFLAGS += -O3 |
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+#CXXFLAGS += -O3 |
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|
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MOTHUR_FILES = "\"Enter_your_default_path_here\"" |
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|
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@@ -49,7 +49,7 @@ |
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|
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ifeq ($(strip $(USEREADLINE)),yes) |
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CXXFLAGS += -DUSE_READLINE |
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- LDFLAGS += \ |
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+ LIBS = \ |
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-lreadline\ |
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-lncurses |
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endif |
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@@ -57,7 +57,7 @@ |
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USEMPI ?= no |
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|
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ifeq ($(strip $(USEMPI)),yes) |
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- CXX = mpic++ |
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+# CXX = mpic++ |
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CXXFLAGS += -DUSE_MPI |
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endif |
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@@ -74,7 +74,7 @@ |
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OBJECTS=$(patsubst %.cpp,%.o,$(wildcard *.cpp)) |
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mothur : $(OBJECTS) |
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- $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) |
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+ $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS) |
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|
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install : mothur |
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cp mothur ../Release/mothur |
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