Commit 41e5874d authored by Tomasz Buchert's avatar Tomasz Buchert
Browse files

New upstream version 1.40.2

parent ab8478c5

Makefile

+20 −6
Original line number Diff line number Diff line
@@ -15,27 +15,33 @@ 
# BOOST_INCLUDE_DIR - location of boost include files

# MOTHUR_FILES - default location for mothur to look for input files at runtime. Most often used for reference files.



PREFIX := ${CURDIR} 



64BIT_VERSION ?= yes

OPTIMIZE ?= yes

USEREADLINE ?= yes

USEBOOST ?= yes

LOGFILE_NAME ?= yes

BOOST_LIBRARY_DIR="\"Enter_your_boost_library_path_here\""

BOOST_INCLUDE_DIR="\"Enter_your_boost_include_path_here\""

MOTHUR_FILES="\"Enter_your_default_path_here\""

RELEASE_DATE = "\"3/20/2017\""

VERSION = "\"1.39.5\""

VERSION = "\"1.40.2\""



ifeq  ($(strip $(64BIT_VERSION)),yes)

    CXXFLAGS += -DBIT_VERSION

endif



# Fastest

# Set a static logfile name

ifeq  ($(strip $(LOGFILE_NAME)),yes)

    LOGFILE_NAME="\"silent\""

endif



ifeq  ($(strip $(OPTIMIZE)),yes)

    CXXFLAGS += -O3

endif



CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION} -std=c++0x

LDFLAGS += -std=c++0x

CXXFLAGS += -std=c++11 -DVERSION=${VERSION}

LDFLAGS += -std=c++11 -pthread



ifeq  ($(strip $(MOTHUR_FILES)),"\"Enter_your_default_path_here\"")

else
@@ -89,7 +95,15 @@ mothur : $(OBJECTS) uchime 
uchime:

	cd source/uchime_src && ./mk && mv uchime ../../ && cd ..



install : mothur

install : mothur uchime

#if [ "${CURDIR}" = "$(PREFIX)" ]; then \

#		echo 'done'; \

#	else \

#		mkdir -p $(PREFIX); \

#		for file in mothur uchime; do \

#			cp -f $$file $(PREFIX) ; \

#		done \

#	fi





%.o : %.c %.h

Makefile-Windows

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+80 −0
Original line number Diff line number Diff line 
###################################################

#

# Makefile for mothur

#

###################################################



#

# Macros

#

# 64BIT_VERSION - set to no if you are using a 32bit arch.

# OPTIMIZE - yes will increase speed of executable.

# USEREADLINE - link with readline libraries.  Must have readline installed. Windows set to no.

# USEBOOST - link with boost libraries. Must install boost. Allows the make.contigs command to read .gz files.

# BOOST_LIBRARY_DIR - location of boost libraries

# BOOST_INCLUDE_DIR - location of boost include files

# MOTHUR_FILES - default location for mothur to look for input files at runtime. Most often used for reference files.



64BIT_VERSION ?= yes

USEREADLINE ?= no

USEBOOST ?= no

RELEASE_DATE = "\"09/01/2017\""

VERSION = "\"1.40.0\""



# Optimize to level 3:

		CXXFLAGS += -O3



#CPP_11

	CXXFLAGS += -std=c++11



ifeq  ($(strip $(64BIT_VERSION)),yes)

		#if you using cygwin to build Windows the following line

		CXX = x86_64-w64-mingw32-g++

		CC = x86_64-w64-mingw32-g++

		TARGET_ARCH += -m64 -static

		CXXFLAGS += -DBIT_VERSION

endif



CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION}



# INCLUDE directories for mothur

		VPATH=source/calculators:source/chimera:source/classifier:source/clearcut:source/commands:source/communitytype:source/datastructures:source/metastats:source/randomforest:source/read:source/svm

		skipUchime := source/uchime_src/

		subdirs :=  $(sort $(dir $(filter-out  $(skipUchime), $(wildcard source/*/))))

		subDirIncludes = $(patsubst %, -I %, $(subdirs))

		subDirLinking =  $(patsubst %, -L%, $(subdirs))

		CXXFLAGS += -I. $(subDirIncludes)

		LDFLAGS += $(subDirLinking)



#

# Get the list of all .cpp files, rename to .o files

#

		OBJECTS=$(patsubst %.cpp,%.o,$(wildcard $(addsuffix *.cpp,$(subdirs))))

		OBJECTS+=$(patsubst %.c,%.o,$(wildcard $(addsuffix *.c,$(subdirs))))

		OBJECTS+=$(patsubst %.cpp,%.o,$(wildcard *.cpp))

		OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))



mothur : $(OBJECTS) uchime

		$(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)

		strip mothur





uchime:

		cd source/uchime_src && ./mk && mv uchime ../../ && cd ..





install : mothur





%.o : %.c %.h

		$(COMPILE.c) $(OUTPUT_OPTION) $<

%.o : %.cpp %.h

		$(COMPILE.cpp) $(OUTPUT_OPTION) $<

%.o : %.cpp %.hpp

		$(COMPILE.cpp) $(OUTPUT_OPTION) $<







clean :

		@rm -f $(OBJECTS)

		@rm -f uchime

Mothur.xcodeproj/project.pbxproj

+561 −225

File changed.

Preview size limit exceeded, changes collapsed.

TestMothur/custom/gtest-port.h

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+69 −0
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// Copyright 2015, Google Inc.

// All rights reserved.

//

// Redistribution and use in source and binary forms, with or without

// modification, are permitted provided that the following conditions are

// met:

//

//     * Redistributions of source code must retain the above copyright

// notice, this list of conditions and the following disclaimer.

//     * Redistributions in binary form must reproduce the above

// copyright notice, this list of conditions and the following disclaimer

// in the documentation and/or other materials provided with the

// distribution.

//     * Neither the name of Google Inc. nor the names of its

// contributors may be used to endorse or promote products derived from

// this software without specific prior written permission.

//

// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS

// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT

// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR

// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT

// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,

// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT

// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,

// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY

// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT

// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE

// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

//

// Injection point for custom user configurations.

// The following macros can be defined:

//

//   Flag related macros:

//     GTEST_FLAG(flag_name)

//     GTEST_USE_OWN_FLAGFILE_FLAG_  - Define to 0 when the system provides its

//                                     own flagfile flag parsing.

//     GTEST_DECLARE_bool_(name)

//     GTEST_DECLARE_int32_(name)

//     GTEST_DECLARE_string_(name)

//     GTEST_DEFINE_bool_(name, default_val, doc)

//     GTEST_DEFINE_int32_(name, default_val, doc)

//     GTEST_DEFINE_string_(name, default_val, doc)

//

//   Test filtering:

//     GTEST_TEST_FILTER_ENV_VAR_ - The name of an environment variable that

//                                  will be used if --GTEST_FLAG(test_filter)

//                                  is not provided.

//

//   Logging:

//     GTEST_LOG_(severity)

//     GTEST_CHECK_(condition)

//     Functions LogToStderr() and FlushInfoLog() have to be provided too.

//

//   Threading:

//     GTEST_HAS_NOTIFICATION_ - Enabled if Notification is already provided.

//     GTEST_HAS_MUTEX_AND_THREAD_LOCAL_ - Enabled if Mutex and ThreadLocal are

//                                         already provided.

//     Must also provide GTEST_DECLARE_STATIC_MUTEX_(mutex) and

//     GTEST_DEFINE_STATIC_MUTEX_(mutex)

//

//     GTEST_EXCLUSIVE_LOCK_REQUIRED_(locks)

//     GTEST_LOCK_EXCLUDED_(locks)

//

// ** Custom implementation starts here **



#ifndef GTEST_INCLUDE_GTEST_INTERNAL_CUSTOM_GTEST_PORT_H_

#define GTEST_INCLUDE_GTEST_INTERNAL_CUSTOM_GTEST_PORT_H_



#endif  // GTEST_INCLUDE_GTEST_INTERNAL_CUSTOM_GTEST_PORT_H_

TestMothur/custom/gtest-printers.h

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+42 −0
Original line number Diff line number Diff line 
// Copyright 2015, Google Inc.

// All rights reserved.

//

// Redistribution and use in source and binary forms, with or without

// modification, are permitted provided that the following conditions are

// met:

//

//     * Redistributions of source code must retain the above copyright

// notice, this list of conditions and the following disclaimer.

//     * Redistributions in binary form must reproduce the above

// copyright notice, this list of conditions and the following disclaimer

// in the documentation and/or other materials provided with the

// distribution.

//     * Neither the name of Google Inc. nor the names of its

// contributors may be used to endorse or promote products derived from

// this software without specific prior written permission.

//

// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS

// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT

// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR

// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT

// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,

// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT

// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,

// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY

// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT

// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE

// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

//

// This file provides an injection point for custom printers in a local

// installation of gTest.

// It will be included from gtest-printers.h and the overrides in this file

// will be visible to everyone.

// See documentation at gtest-printers.h for details on how to define a

// custom printer.

//

// ** Custom implementation starts here **



#ifndef GTEST_INCLUDE_GTEST_INTERNAL_CUSTOM_GTEST_PRINTERS_H_

#define GTEST_INCLUDE_GTEST_INTERNAL_CUSTOM_GTEST_PRINTERS_H_



#endif  // GTEST_INCLUDE_GTEST_INTERNAL_CUSTOM_GTEST_PRINTERS_H_