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Last change on this file was 19440, checked in by westram, 21 months ago
full update from 'trunk' into 'ali' fixes for debian11 version adds: log:trunk@19416:19424,19426:19439
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 87.4 KB

Rev	Line
[5223]	1	# =============================================================== #
	2	# #
	3	# File : Makefile #
	4	# #
	5	# Institute of Microbiology (Technical University Munich) #
	6	# http://www.arb-home.de/ #
	7	# #
	8	# =============================================================== #
[2]	9
[5223]	10	# -----------------------------------------------------
	11	# The ARB Makefile is aware of the following defines:
[1107]	12	#
[10968]	13	# CC C compiler (should be defined by OS)
	14	# CXX C++ compiler (should be defined by OS)
	15	#
	16	# DEVELOPER=name special compilation (values: ANY,RELEASE,your name)
[5223]	17	# OPENGL=0/1 whether OPENGL is available
[1107]	18	#
[5223]	19	# -----------------------------------------------------
[14944]	20	# Paths for several libraries may be set from config.makefile by using:
	21	#
	22	# export XLIBS=$(shell pkg-config --libs xpm xerces-c)
[15655]	23	# export XINCLUDES=$(shell pkg-config --cflags x11)
[14944]	24	# export XAW_LIBS=$(shell pkg-config --libs xaw7)
	25	# export XML_INCLUDES=$(shell pkg-config --cflags xerces-c)
	26	#
[15655]	27	# You make have to explicitely point pkg-config to the *.pc files needed.
[17618]	28	# For example, Xquartz X11 libraries on macOS can be located by adding
[15655]	29	# the following line before those given above:
	30	#
	31	# export PKG_CONFIG_PATH=/usr/X11/lib/pkgconfig
	32	#
[17618]	33	# If you introduce a new variable that is handled as described above,
	34	# please add to section .@InjectedEnvironment
	35	#
[14944]	36	# -----------------------------------------------------
[5223]	37	# ARB Makefile and ARB source code are aware of the following defines:
	38	#
[6342]	39	# $(MACH) name of the machine (LINUX or DARWIN; see config.makefile)
[5223]	40	# DEBUG compiles the DEBUG sections
	41	# DEBUG_GRAPHICS all X-graphics are flushed immediately (for debugging)
	42	# ARB_64=0/1 1=>compile 64 bit version
[6451]	43	# UNIT_TESTS=0/1 1=>compile in unit tests and call them after build
[6712]	44	# COVERAGE=0/1/2 compile in gcov support (useful together with UNIT_TESTS=1)
	45	# 0=no, 1+2=compile in, 1=show
[11460]	46	# STABS=0/1 force stabs format? (0 = "use default format")
[13077]	47	# SANITIZE=0/#/all use Sanitizer? (defaults to 0,
	48	# 1=AddressSanitizer+LeakSanitizer,
	49	# 2=UndefinedBehaviorSanitizer,
	50	# combine bit-values to activate multiple Sanitizers,
	51	# specify 'all' to activate all)
[18426]	52	# IGNORE_LEAKS=1 does not abort when leaks are detected (while using SANITIZE=1/all)
[13019]	53	# SHOWTODO=0/1 activate TODO-warnings? (defaults to 0, except for ralf)
[5223]	54	#
	55	# -----------------------------------------------------
	56	# The ARB source code is aware of the following defines:
	57	#
[6141]	58	# NDEBUG doesn't compile the DEBUG sections
[5133]	59	# DEVEL_$(DEVELOPER) developer-dependent flag (enables you to have private sections in code)
[1336]	60	# DEVELOPER='ANY' (default setting) will be ignored
	61	# configurable in config.makefile
[1107]	62	#
[5223]	63	# -----------------------------------------------------
[19245]	64
	65	ifndef ARB_ORG_MAKEFLAGS
	66	ARB_ORG_MAKEFLAGS=$(MAKEFLAGS)
	67	else
	68	ifeq ($(ARB_ORG_MAKEFLAGS),)
	69	ARB_ORG_MAKEFLAGS=$(MAKEFLAGS)
	70	endif
	71	endif
	72
[13923]	73	# Read configuration
[5223]	74	include config.makefile
[17424]	75	CONFIG_MAKEFILE_FOUND=$(strip $(wildcard config.makefile))
[5223]	76
[19074]	77	# strip spaces from values defined in config.makefile
	78	# (otherwise they easily have spaces appended)
	79	ifdef DEVELOPER
	80	DEVELOPER := $(strip $(DEVELOPER))
	81	endif
	82	ifdef OPENGL
	83	OPENGL := $(strip $(OPENGL))
	84	endif
	85	ifdef ISINA
	86	ISINA := $(strip $(ISINA))
	87	endif
	88	ifdef DEBUG
	89	DEBUG := $(strip $(DEBUG))
	90	endif
	91	ifdef UNIT_TESTS
	92	UNIT_TESTS := $(strip $(UNIT_TESTS))
	93	endif
	94	ifdef COVERAGE
	95	COVERAGE := $(strip $(COVERAGE))
	96	endif
	97	ifdef SHOWTODO
	98	SHOWTODO := $(strip $(SHOWTODO))
	99	endif
	100	ifdef STABS
	101	STABS := $(strip $(STABS))
	102	endif
	103	ifdef TRACESYM
	104	TRACESYM := $(strip $(TRACESYM))
	105	endif
	106	ifdef DEBUG_GRAPHICS
	107	DEBUG_GRAPHICS := $(strip $(DEBUG_GRAPHICS))
	108	endif
	109
	110	# set defaults for (or strip) variables commented out in config.makefile:
[19076]	111	ifdef SANITIZE
	112	SANITIZE := $(strip $(SANITIZE))
	113	else
	114	SANITIZE:=0
	115	endif
	116	ifdef IGNORE_LEAKS
	117	IGNORE_LEAKS := $(strip $(IGNORE_LEAKS))
	118	else
	119	IGNORE_LEAKS:=0
	120	endif
[11804]	121	ifndef DARWIN
[15496]	122	DARWIN:=0
[19074]	123	else
	124	DARWIN := $(strip $(DARWIN))
[11804]	125	endif
	126	ifndef LINUX
[15496]	127	LINUX:=0
[19074]	128	else
	129	LINUX := $(strip $(LINUX))
[11804]	130	endif
	131	ifndef DEBIAN
[15496]	132	DEBIAN:=0
[19074]	133	else
	134	DEBIAN := $(strip $(DEBIAN))
[11804]	135	endif
	136	ifndef ARB_64
[15496]	137	ARB_64=1#default to 64bit
[19074]	138	else
	139	ARB_64 := $(strip $(ARB_64))
[11804]	140	endif
	141
[17618]	142	# Variables allowed for injection [InjectedEnvironment]
	143	# (alternatively initialize them with '?=', e.g. done for XLIBS and XINCLUDES)
	144	# In both cases add them to SOURCE_TOOLS/export2sub
	145	ifndef XML_INCLUDES
	146	XML_INCLUDES=
	147	endif
	148	ifndef XAW_LIBS
	149	XAW_LIBS=
	150	endif
[17424]	151
[17618]	152
[17424]	153	ifneq ($(CONFIG_MAKEFILE_FOUND),)
	154	ifneq ($(DARWIN)$(LINUX),10)
	155	ifneq ($(DARWIN)$(LINUX),01)
	156	$(error exactly one of DARWIN=1 or LINUX=1 has to be defined (got:$(DARWIN)$(LINUX)))
	157	endif
[17375]	158	endif
	159	endif
	160
[10970]	161	# compiler settings:
[12299]	162	ifneq ($(CC),use__A_CC__instead_of__CC)
[15496]	163	A_CC:=$(CC)# compile C
	164	A_CXX:=$(CXX)# compile C++
[12299]	165
[10978]	166	# uncomment to ensure no submakefile uses CC and CXX directly
[15496]	167	override CC:=use__A_CC__instead_of__CC
	168	override CXX:=use__A_CXX__instead_of__CXX
[12299]	169	endif
	170
[12309]	171	export CC CXX A_CC A_CXX
	172
[12985]	173	# unconditionally prepend $(ARBHOME)/lib to LD_LIBRARY_PATH if not found
	174	ifeq ($(findstring $(ARBHOME)/lib,$(LD_LIBRARY_PATH)),)
[15496]	175	LD_LIBRARY_PATH:=${ARBHOME}/lib:$(LD_LIBRARY_PATH)
[5829]	176	endif
	177
[14792]	178	# store LD_LIBRARY_PATH to circumvent SIP restrictions:
	179	ARBBUILD_LIBRARY_PATH:=$(LD_LIBRARY_PATH)
	180
[2]	181	FORCEMASK = umask 002
[6711]	182	NODIR=--no-print-directory
[2]	183
[9750]	184	SED:=$(ARBHOME)/SH/arb_sed
	185	READLINK:=$(ARBHOME)/SH/arb_readlink
	186
[4034]	187	# ---------------------- compiler version detection
	188
[10993]	189	# supported gcc versions:
	190	ALLOWED_gcc_VERSIONS=\
[19060]	191	4.4.3 4.4.5 4.4.6 4.4.7 \
	192	4.5.2 \
	193	4.6.1 4.6.2 4.6.3 4.6.4 \
	194	4.7.1 4.7.2 4.7.3 4.7.4 \
	195	4.8.0 4.8.1 4.8.2 4.8.3 4.8.4 4.8.5 \
	196	4.9.0 4.9.1 4.9.2 4.9.3 4.9.4 \
	197	5.1.0 5.2.0 5.3.0 5.4.0 5.5.0 \
	198	6.1.0 6.2.0 6.3.0 6.4.0 6.5.0 \
	199	7.1.0 7.2.0 7.3.0 7.4.0 7.5.0 \
	200	8.1.0 8.2.0 8.3.0 8.4.0 8.5.0 \
	201	9.1.0 9.2.0 9.3.0 9.4.0 9.5.0 \
[19440]	202	10.1.0 10.2.0 10.3.0 10.4.0 10.5.0 \
[5556]	203
[17904]	204	# Note: starting with version 5, arb silently accepts any subversion number
	205	# above zero. See SOURCE_TOOLS/arb_compiler_version.pl@acceptSubVersions
	206	#
	207	# This may cause problems when manually checking for compiler versions in code
	208	# (GCC_VERSION_CODE is not affected, GCC_PATCHLEVEL_CODE may cause problems!)
[10993]	209	# ----------------------
[3227]	210
[12309]	211	COMPILER_INFO:=$(shell SOURCE_TOOLS/arb_compiler_version.pl $(A_CXX))
	212	COMPILER_NAME:=$(word 1,$(COMPILER_INFO))
	213	COMPILER_VERSION:=$(word 2,$(COMPILER_INFO))
[10993]	214
	215	USE_CLANG:=0
	216	ifneq ($(COMPILER_NAME),gcc)
	217	ifeq ($(COMPILER_NAME),clang)
	218	USE_CLANG:=1
	219	else
[16582]	220	ifeq ($(COMPILER_VERSION),4.6.4)
	221	# gcc version 4.6.4 segfaults when dumping symbols for detection (silently accept as gcc)
	222	COMPILER_NAME:=gcc
	223	else
	224	$(error failed to detect COMPILER_NAME (got '$(COMPILER_NAME)', expected 'clang' or 'gcc'))
	225	endif
[10993]	226	endif
	227	endif
	228
	229	ifeq ($(USE_CLANG),1)
[14790]	230	# accept all clang versions:
[15496]	231	ALLOWED_COMPILER_VERSIONS=$(COMPILER_VERSION)
[10993]	232	else
[15496]	233	ALLOWED_COMPILER_VERSIONS=$(ALLOWED_gcc_VERSIONS)
[10993]	234	endif
	235
	236	COMPILER_VERSION_ALLOWED=$(strip $(subst ___,,$(foreach version,$(ALLOWED_COMPILER_VERSIONS),$(findstring ___$(version)___,___$(COMPILER_VERSION)___))))
	237
[13923]	238	#---------------------- split gcc version
[5188]	239
[10993]	240	SPLITTED_VERSION:=$(subst ., ,$(COMPILER_VERSION))
[7343]	241
	242	USE_GCC_MAJOR:=$(word 1,$(SPLITTED_VERSION))
	243	USE_GCC_MINOR:=$(word 2,$(SPLITTED_VERSION))
	244	USE_GCC_PATCHLEVEL:=$(word 3,$(SPLITTED_VERSION))
	245
	246	USE_GCC_452_OR_HIGHER:=
[12513]	247	USE_GCC_46_OR_HIGHER:=
[8817]	248	USE_GCC_47_OR_HIGHER:=
[9516]	249	USE_GCC_48_OR_HIGHER:=
[13019]	250	USE_GCC_49_OR_HIGHER:=
[13761]	251	USE_GCC_50_OR_HIGHER:=
[15488]	252	USE_GCC_60_OR_HIGHER:=
[15869]	253	USE_GCC_70_OR_HIGHER:=
[16683]	254	USE_GCC_80_OR_HIGHER:=
[17877]	255	USE_GCC_90_OR_HIGHER:=
[8817]	256
[14790]	257	ifeq ($(USE_CLANG),0)
	258	ifeq ($(USE_GCC_MAJOR),4)
	259	ifeq ($(USE_GCC_MINOR),5)
	260	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),23456789)','')
	261	USE_GCC_452_OR_HIGHER:=yes
	262	endif
	263	else
	264	ifneq ('$(findstring $(USE_GCC_MINOR),6789)','')
	265	USE_GCC_452_OR_HIGHER:=yes
	266	USE_GCC_46_OR_HIGHER:=yes
	267	ifneq ($(USE_GCC_MINOR),6)
	268	USE_GCC_47_OR_HIGHER:=yes
	269	ifneq ($(USE_GCC_MINOR),7)
	270	USE_GCC_48_OR_HIGHER:=yes
	271	ifneq ($(USE_GCC_MINOR),8)
	272	USE_GCC_49_OR_HIGHER:=yes
	273	endif
	274	endif
[9516]	275	endif
[8817]	276	endif
[7930]	277	endif
[14790]	278	else
[15488]	279	# gcc 5.x or higher
[14790]	280	USE_GCC_452_OR_HIGHER:=yes
	281	USE_GCC_46_OR_HIGHER:=yes
	282	USE_GCC_47_OR_HIGHER:=yes
	283	USE_GCC_48_OR_HIGHER:=yes
	284	USE_GCC_49_OR_HIGHER:=yes
	285	USE_GCC_50_OR_HIGHER:=yes
[15488]	286	ifneq ($(USE_GCC_MAJOR),5)
	287	# gcc 6.x or higher
	288	USE_GCC_60_OR_HIGHER:=yes
[15869]	289	ifneq ($(USE_GCC_MAJOR),6)
	290	# gcc 7.x or higher
	291	USE_GCC_70_OR_HIGHER:=yes
[16683]	292	ifneq ($(USE_GCC_MAJOR),7)
	293	# gcc 8.x or higher
	294	USE_GCC_80_OR_HIGHER:=yes
[17877]	295	ifneq ($(USE_GCC_MAJOR),8)
	296	# gcc 9.x or higher
	297	USE_GCC_90_OR_HIGHER:=yes
	298	endif
[16683]	299	endif
[15869]	300	endif
[15488]	301	endif
[7343]	302	endif
	303	endif
	304
[5877]	305	#---------------------- define special directories for non standard builds
	306
[11804]	307	ifeq ($(DARWIN),1)
[15496]	308	OSX_FW:=/System/Library/Frameworks
	309	OSX_FW_OPENGL:=$(OSX_FW)/OpenGL.framework/Versions/A/Libraries
	310	OSX_FW_GLUT:=$(OSX_FW)/GLUT.framework/Versions/A/Libraries
	311	OSX_FW_IMAGEIO:=$(OSX_FW)/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources
[5877]	312	endif
	313
[17342]	314	#---------------------- SSE vectorization
	315	# for details about vectorization checks see SOURCE_TOOLS/vectorize.README
	316
[17877]	317	DISABLE_VECTORIZE_CHECK:=0# set to 1 to completely disable vectorization checks
[17342]	318	TRACE_MISSED_VECTORIZATIONS:=0# set to 1 to activate detailed output about failed vectorizations
	319	# (does also show details about successful vectorized loops, which are not optimal)
[17877]	320	VECTORIZATION_CHECK_CANDIDATES:=0# set to 1 to show vectorizations that may be checked
	321	# (for yet unchecked files)
	322	# Note: TRACE_MISSED_VECTORIZATIONS and VECTORIZATION_CHECK_CANDIDATES cannot be used together!
[17342]	323
[18842]	324	#---------------------- Support for OPENMP
	325
	326	USE_OPENMP:=1
	327	ifeq ($(DARWIN),1)
	328	USE_OPENMP:=0
	329	endif
	330
[5223]	331	#----------------------
[4034]	332
[11804]	333	ifeq ($(DARWIN),1)
[15496]	334	LINK_STATIC=1# link static
[5877]	335	else
[15496]	336	LINK_STATIC=0# link dynamically
	337	# LINK_STATIC=1# link static (testing only)
[5877]	338	endif
[5829]	339
[5223]	340	shared_cflags :=# flags for shared lib compilation
[11815]	341	clflags :=# linker flags (when passed through gcc)
[5887]	342	extended_warnings :=# warning flags for C and C++-compiler
	343	extended_cpp_warnings :=# warning flags for C++-compiler only
[5188]	344
[5223]	345	ifeq ($(DEBUG),0)
[15496]	346	dflags := -DNDEBUG# defines
	347	ifeq ($(USE_CLANG),1)
	348	cflags := -O3# compiler flags (C and C++)
	349	else
	350	clflags += -Wl,-O2# passthrough linker flags
[18729]	351	# ------- standard optimization:
[15496]	352	cflags := -O3# compiler flags (C and C++)
	353	# ------- test changed optimization (DISABLE_VECTORIZE_CHECK for -O2 or lower):
	354	# cflags := -O2# do not commit uncommented!
	355	# DISABLE_VECTORIZE_CHECK:=1
	356	endif
[4034]	357	endif
	358
[11815]	359	ifeq ($(DEBIAN),1)
[15496]	360	clflags += -Wl,-rpath=/usr/lib/arb/lib -Wl,-z,relro
[11815]	361	endif
	362
[5223]	363	ifeq ($(DEBUG),1)
[15496]	364	dflags := -DDEBUG
[8608]	365
[15496]	366	gdb_common := -g -g3 -ggdb -ggdb3
[8608]	367
[18959]	368	DBGOPTI:=-O0
[19033]	369	ifneq ('$(SANITIZE)','0')
	370	# sanitizer report several bogus buffer-overflows when arb is build with -O0 (e.g. with gcc 7.5.0)
	371	DBGOPTI:=-O1
	372	endif
[12478]	373
[16383]	374	ifeq ($(STABS),1)
[18959]	375	$(error STABS no longer supported)
[15496]	376	endif
[11460]	377
[18959]	378	cflags := $(DBGOPTI) $(gdb_common)
	379	# cflags := -O2 $(gdb_common) # use this for callgrind (force inlining)
[11460]	380
[15496]	381	ifeq ($(DARWIN),0)
	382	clflags += -Wl,-g
[14358]	383	# Note:
	384	# Previously '-Wl,-noinhibit-exec' was added to 'clflags' here,
	385	# to fix some issues with launchpad binutils (see [12972]).
	386	# But that change also caused 'undefined symbols' NOT to be reported as errors
	387	# at link time, producing executables that fail at runtime :/
[15496]	388	endif
[14358]	389
[13133]	390	ifeq ($(DEBUG_GRAPHICS),1)
[15496]	391	dflags += -DDEBUG_GRAPHICS
[13133]	392	endif
	393
	394	endif # DEBUG only
	395
[17342]	396	# ------------------------------ POST_COMPILE - control how much you get spammed
	397	# (please do not change default in SVN)
[15496]	398	POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl
[16628]	399
[17342]	400	# POST_COMPILE += --original # dont modify compiler output
	401	# POST_COMPILE += --hide-Noncopyable-advices
	402	# POST_COMPILE += --show-useless-Weff++
	403	# POST_COMPILE += --no-warnings
	404	# POST_COMPILE += --only-first-error
	405	# POST_COMPILE += --no-warnings --only-first-error
[5133]	406
[16683]	407	# always pass used compiler version to postcompile:
	408	POST_COMPILE += --compiler=$(COMPILER_VERSION)
	409
[17342]	410	# ------------------------------
	411
[7343]	412	# Enable extra warnings
[15496]	413	extended_warnings :=
	414	extended_cpp_warnings :=
[7346]	415
[15496]	416	# C and C++
[18337]	417	extended_warnings += -Wwrite-strings -Wunused -Wno-aggregate-return
[7346]	418
[18337]	419	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
	420	# disable shadow warnings for gcc 4.8 (and lower)
	421	# (does e.g. warn if a method-name is used as parameter in another method - even for derived classes. unusable!)
	422	extended_warnings += -Wshadow
	423	endif
	424
[15496]	425	# C++ only
	426	extended_cpp_warnings += -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute
[16683]	427	extended_cpp_warnings += -Wctor-dtor-privacy
	428	# extended_cpp_warnings += -Wfloat-equal
[7346]	429
[16683]	430	extended_cpp_warnings += -Wmissing-noreturn
	431	# extended_cpp_warnings += -Wold-style-cast# (warns about 28405 old-style casts)
	432	extended_cpp_warnings += -Winit-self
	433	extended_cpp_warnings += -Wstrict-aliasing
	434	extended_cpp_warnings += -Wextra
[7346]	435
[16683]	436	# ------- above only warning-options already available in gcc 4.4.3
	437
[13077]	438	# -Weffc++ broken in 4.7.x series
	439	# gcc 4.7.3 crashes on GenomeImport.cxx when -Weffc++ is active
	440	# (bug reported https://gcc.gnu.org/bugzilla/show_bug.cgi?id=56923; apparently wont be fixed for 4.7-series)
	441	# gcc 4.7.4 crashes on DBwriter.cxx when -Weffc++ is active
[16683]	442	WEFFC_BROKEN:=0
	443	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
	444	ifneq ('$(USE_GCC_48_OR_HIGHER)','yes')
[15496]	445	WEFFC_BROKEN:=1
[13077]	446	endif
[15496]	447	endif
	448	ifeq ('$(WEFFC_BROKEN)','0')
[16683]	449	extended_cpp_warnings += -Weffc++
[15496]	450	endif
	451
[16683]	452	# turn off -Wmaybe-uninitialized in debug mode (gets activated with -Wextra). too many bogus warnings
[15496]	453	ifeq ($(DEBUG),1)
	454	ifeq ($(USE_CLANG),0)
	455	extended_cpp_warnings += -Wno-maybe-uninitialized
[10674]	456	endif
[15496]	457	endif
[16683]	458
[17877]	459	SUGGEST_FINAL:=
	460
[15496]	461	ifeq ('$(USE_GCC_452_OR_HIGHER)','yes')
	462	extended_cpp_warnings += -Wlogical-op# gcc 4.5.2
	463	endif
	464	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
[16763]	465	extended_cpp_warnings += -Wzero-as-null-pointer-constant# gcc 4.7
[15496]	466	endif
	467	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
	468	extended_cpp_warnings += -Wunused-local-typedefs# available since gcc 4.7 (but fails for each STATIC_ASSERT, so enable only for Cxx11)
	469	endif
[17277]	470	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
	471	extended_cpp_warnings += -Wswitch-bool
	472	extended_cpp_warnings += -Wlogical-not-parentheses
	473	extended_cpp_warnings += -Wsizeof-array-argument
	474	extended_cpp_warnings += -Wbool-compare
[5133]	475
[17877]	476	SUGGEST_FINAL:=yes
[17277]	477	endif
	478	ifeq ('$(USE_GCC_60_OR_HIGHER)','yes')
	479	extended_cpp_warnings += -Wduplicated-cond
	480	endif
	481	ifeq ('$(USE_GCC_80_OR_HIGHER)','yes')
	482	extended_cpp_warnings += -Wmultistatement-macros
	483	endif
[15513]	484
[18385]	485	# switch off final suggestions for 8.3.0 and 8.4.0:
[17877]	486	ifeq ('$(COMPILER_VERSION)','8.3.0')
	487	SUGGEST_FINAL:=no
	488	endif
[18385]	489	ifeq ('$(COMPILER_VERSION)','8.4.0')
	490	SUGGEST_FINAL:=no
[17877]	491	endif
	492
	493	ifeq ($(DEVELOPER),RELEASE)
	494	# switch off final suggestions in RELEASE:
	495	SUGGEST_FINAL:=no
	496	endif
	497	# suggest final:
	498	ifeq ('$(SUGGEST_FINAL)','yes')
	499	extended_cpp_warnings += -Wsuggest-final-types
	500	extended_cpp_warnings += -Wsuggest-final-methods
	501	dflags += -DSUGGESTS_FINAL
	502	endif
	503
[10999]	504	#---------------------- turn off clang bogus warnings
[4034]	505
[10999]	506	ifeq ($(USE_CLANG),1)
[11005]	507	# -Wmismatched-tags warns about struct/class mismatch in forward declarations (which is explicitely allowed)
	508	# -Wchar-subscripts reports too many bogus warnings for "array['x']" (when 'x' is known to be in range [0..128])
	509	# -Wunused-private-field report too many false positives (currently ~ 2 of 3)
[11012]	510	# -Wstring-plus-int warns about common ARB coding practice
	511	# -Wgnu-static-float-init warns about accepted GNU extension
[15579]	512	extended_cpp_warnings += -Wno-mismatched-tags -Wno-char-subscripts -Wno-unused-private-field -Wno-string-plus-int
	513	ifeq ('$(COMPILER_VERSION)','4.2.1')
	514	# jenkins build (doesn't know switch -Wno-gnu-static-float-init)
	515	extended_cpp_warnings += -Wno-gnu
	516	else
	517	extended_cpp_warnings += -Wno-gnu-static-float-init
	518	endif
[10999]	519	endif
	520
	521	#---------------------- developer
	522
[5223]	523	ifneq ($(DEVELOPER),ANY) # ANY=default setting (skip all developer specific code)
[15496]	524	dflags += -DDEVEL_$(DEVELOPER)# activate developer/release specific code
[2869]	525	endif
[7337]	526
[13019]	527	#---------------------- activate TODO warnings?
	528
[7337]	529	ifndef SHOWTODO
	530	ifeq ($(DEVELOPER),RALF)
[15496]	531	SHOWTODO:=1
[7337]	532	else
[15496]	533	SHOWTODO:=0
[7337]	534	endif
[5223]	535	endif
[7337]	536	ifeq ($(SHOWTODO),1)
[15496]	537	dflags += -DWARN_TODO# activate "TODO" warnings
[7337]	538	endif
[2869]	539
[16880]	540	#---------------------- activate threads?
	541	# only useful if compiler is able to compile Cxx11 or better
	542
	543	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
	544	# see also ./TEMPLATES/cxxforward.h@USE_Cxx11
	545	cflags += -pthread
	546	clflags += -pthread
	547	endif
	548
[13077]	549	#---------------------- activate Sanitizers?
[13019]	550
[13077]	551	ASAN_OPTIONS:=handle_segv=0:color=0
[18426]	552	ifeq ($(IGNORE_LEAKS),1)
	553	ASAN_OPTIONS+=:detect_leaks=0 # disable leak-detection
	554	else
	555	ASAN_OPTIONS+=:detect_leaks=1 # detect leaks (normal setting)
	556	endif
[13077]	557	ASAN_OPTIONS+=:check_initialization_order=1
[13799]	558	# ASAN_OPTIONS+=:abort_on_error=1
[13077]	559
	560	# suppressions: SOURCE_TOOLS/arb.leaksan.supp
	561	LSAN_OPTIONS:=max_leaks=3:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp
	562
[17703]	563	UBSAN_OPTIONS:=print_stacktrace=1
[13077]	564
	565	SANITIZE_ADDRESS:=0
	566	SANITIZE_UNDEFINED:=0
	567
	568	ifneq ($(SANITIZE),0)
	569	ifeq ($(SANITIZE),all)
	570	SANITIZE:=3
	571	endif
	572
	573	ifeq ($(SANITIZE),1)
	574	SANITIZE_ADDRESS:=1
	575	else
	576	ifeq ($(SANITIZE),2)
	577	SANITIZE_UNDEFINED:=1
	578	else
	579	ifeq ($(SANITIZE),3)
	580	SANITIZE_ADDRESS:=1
	581	SANITIZE_UNDEFINED:=1
	582	else
	583	$(error Unknown value '$(SANITIZE)' specified for SANITIZE in config.makefile)
	584	endif
	585	endif
	586	endif
	587	endif
	588
	589	ifeq ($(SANITIZE_ADDRESS),1)
	590	ifneq ('$(USE_GCC_48_OR_HIGHER)','yes')
	591	$(info AddressSanitizer not usable with gcc $(COMPILER_VERSION) - disabled)
	592	SANITIZE_ADDRESS:=0
	593	else
	594	ifneq ('$(USE_GCC_49_OR_HIGHER)','yes')
[18119]	595	$(info LeakSanitizer does not work with gcc $(COMPILER_VERSION) - disabled)
	596	# need to disable AddressSanitizer (otherwise build fails; only affects gcc 4.8.x series)
[18118]	597	SANITIZE_ADDRESS:=0
[13077]	598	endif
	599	endif
	600	endif
	601
	602	ifeq ($(SANITIZE_UNDEFINED),1)
	603	ifneq ('$(USE_GCC_49_OR_HIGHER)','yes')
	604	$(info UndefinedBehaviorSanitizer not usable with gcc $(COMPILER_VERSION) - disabled)
	605	SANITIZE_UNDEFINED:=0
	606	endif
	607	endif
	608
[13774]	609	SANITIZE_ANY:=0
	610	ifeq ($(SANITIZE_ADDRESS),1)
	611	SANITIZE_ANY:=1
	612	endif
	613	ifeq ($(SANITIZE_UNDEFINED),1)
	614	SANITIZE_ANY:=1
	615	endif
	616
[16683]	617	# vectorization fails if sanitizer active where it normally succeeds -> disable check
[14813]	618	ifeq ($(SANITIZE_ANY),1)
[18117]	619	$(info disabling vectorize checks. would fail with sanitized code)
[14813]	620	DISABLE_VECTORIZE_CHECK:=1
[18117]	621	else
	622	$(info no sanitizer enabled. reset: SANITIZE=0)
	623	SANITIZE:=0
[14813]	624	endif
	625
[16683]	626	# deactivate some bogus warnings occurring when sanitizing NDEBUG version
	627	# (do not disable for future gcc-version >= 8.x -> test again when available)
	628	ifeq ($(SANITIZE_ANY),1)
	629	ifeq ($(DEBUG),0)
	630	ifneq ('$(USE_GCC_80_OR_HIGHER)','yes')
	631	extended_cpp_warnings += -Wno-format-overflow
	632	extended_cpp_warnings += -Wno-maybe-uninitialized
	633	endif
	634	endif
	635	endif
	636
[5223]	637	#---------------------- 32 or 64 bit
[2]	638
[6732]	639	cross_cflags:=
	640	cross_lflags:=
[11818]	641	cross_clflags:=
[6732]	642
[5223]	643	ifeq ($(ARB_64),1)
[17738]	644	dflags += -DARB_64
[15496]	645	shared_cflags += -fPIC
[17738]	646	CROSS_LIB:=# empty => autodetect below
	647	ifeq ($(DARWIN),1)
	648	cross_cflags += -arch x86_64
	649	cross_lflags += -arch x86_64
	650	cross_clflags += -arch x86_64
[15496]	651	endif
[2]	652	else
[17738]	653	CROSS_LIB:=/lib
[2]	654	endif
	655
[11818]	656	cflags += $(cross_cflags)
	657	clflags += $(cross_clflags)
[6732]	658
[5223]	659	ifeq ('$(CROSS_LIB)','')
	660	# autodetect libdir
[15496]	661	ifeq ($(ARB_64),1)
	662	CROSS_LIB:=$(shell (test -d /lib64 && echo lib64) \|\| echo lib)
	663	else
	664	CROSS_LIB:=$(shell (test -d /lib32 && echo lib32) \|\| echo lib)
	665	endif
[5223]	666	endif
[655]	667
[6451]	668	#---------------------- unit tests
	669
	670	ifndef UNIT_TESTS
[15496]	671	UNIT_TESTS=0#default is "no tests"
[6451]	672	endif
	673	ifeq ($(UNIT_TESTS),1)
[15496]	674	dflags += -DUNIT_TESTS
	675	UNIT_TESTER_LIB=UNIT_TESTER/UNIT_TESTER.a
[6451]	676	else
[15496]	677	UNIT_TESTER_LIB=
[6451]	678	endif
	679
[6526]	680	#---------------------- use gcov
	681
	682	ifndef COVERAGE
[15496]	683	COVERAGE=0#default is "no"
[6526]	684	endif
[6712]	685	ifneq ($(COVERAGE),0)
[16223]	686	GCOV_FLAGS=--coverage
[18634]	687	$(info disabling vectorize checks. would fail with COVERAGE on)
	688	DISABLE_VECTORIZE_CHECK:=1
[6526]	689	else
[16223]	690	GCOV_FLAGS=
[6526]	691	endif
	692
[16223]	693	cflags += $(GCOV_FLAGS)
	694	clflags += $(GCOV_FLAGS)
	695	cross_lflags += $(GCOV_FLAGS)
	696
[5223]	697	#---------------------- other flags
[655]	698
[5223]	699	dflags += -D$(MACH) # define machine
[655]	700
[11804]	701	ifeq ($(DARWIN),1)
[15496]	702	shared_cflags += -fno-common
[5877]	703	else
[15496]	704	dflags += $(shell getconf LFS_CFLAGS)
[655]	705	endif
	706
[5223]	707	cflags += -pipe
[17618]	708	cflags += -fmessage-length=0# dont wrap compiler output
[7802]	709	cflags += -fshow-column# show columns
[5708]	710	cflags += -funit-at-a-time
[5897]	711	cflags += -fPIC
[7621]	712	cflags += -fno-common# link all global data into one namespace
[7347]	713	cflags += -fstrict-aliasing# gcc 3.4
[17342]	714
	715
[9516]	716	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
	717	cflags += -fno-diagnostics-show-caret#gcc 4.8 (4.7.?)
	718	endif
[8616]	719	#cflags += -save-temps# uncomment to see preprocessor output
[7347]	720
[13077]	721	#---------------------- various sanitizers
[15447]	722	# There are some disabled tests in CORE/arb_misc.cxx@sanitizers
	723	# which trigger sanitizer reports.
[13077]	724
[15447]	725	ifeq ($(SANITIZE_ANY),1)
	726	cflags += -ggdb3 -fno-omit-frame-pointer
	727	endif
[13077]	728
[19245]	729	SANI_CFLAGS:=
	730	SANI_CLFLAGS:=
	731
[13077]	732	# activate AddressSanitizer+LeakSanitizer?
	733	ifeq ($(SANITIZE_ADDRESS),1)
[19245]	734	SANI_CFLAGS += -fsanitize=address
	735	SANI_CLFLAGS += -fsanitize=address
[15447]	736	dflags += -DLEAKS_SANITIZED
[13077]	737	endif
	738
	739	# activate UndefinedBehaviorSanitizer?
	740	ifeq ($(SANITIZE_UNDEFINED),1)
[19245]	741	SANI_CFLAGS += -fsanitize=undefined
	742	SANI_CLFLAGS += -fsanitize=undefined
[15447]	743	dflags += -DUNDEF_SANITIZED
	744	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
	745	# abort on runtime errors
[19245]	746	SANI_CFLAGS += -fno-sanitize-recover=all
[15447]	747	endif
[19245]	748
	749	cflags += $(SANI_CFLAGS)
	750	clflags += $(SANI_CLFLAGS)
	751
[15447]	752	#
[13785]	753	# Note: alignment-sanitizer is deactivated for ARBDB and PROBE!
[13077]	754	ifeq ('$(DEBUG)','1')
[13082]	755	ifeq ($(USE_GCC_MAJOR),4)
	756	ifeq ($(USE_GCC_MINOR),9)
	757	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),01)','')
	758	# workaround https://gcc.gnu.org/bugzilla/show_bug.cgi?id=63531 for 4.9.0 + 4.9.1
[13120]	759	# (problem is fixed in 4.9.2 release)
[13082]	760	extended_cpp_warnings:=$(subst -Weffc++,,$(extended_cpp_warnings))
	761	endif
	762	endif
	763	endif
[13019]	764	endif
	765	endif
	766
[5223]	767	#---------------------- X11 location
[2350]	768
[11804]	769	ifeq ($(DARWIN),1)
[15496]	770	XHOME:=$(PREFIX)
[8656]	771	else
[11815]	772	ifeq ($(DEBIAN),1)
[15496]	773	XHOME:=$(PREFIX)
[11815]	774	else
[15496]	775	XHOME:=/usr/X11R6
[11815]	776	endif
[5877]	777	endif
	778
[14934]	779	XINCLUDES ?= -I$(XHOME)/include
	780	XLIBS ?= -L$(XHOME)/$(CROSS_LIB)
[11804]	781	ifeq ($(DARWIN),1)
[15496]	782	XINCLUDES += -I$(OSX_FW)/GLUT.framework/Headers -I$(OSX_FW)/OpenGL.framework/Headers -I$(OSX_SDK)/usr/include/krb5
[8656]	783
[15496]	784	XLIBS += -lXm -lpng -lz -lXt -lX11 -lXext -lXp -lXmu -lXi
	785	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGL.dylib:$(OSX_FW_OPENGL)/libGL.dylib
	786	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGLU.dylib:$(OSX_FW_OPENGL)/libGLU.dylib
[344]	787	else
[15496]	788	XLIBS += -lXm -lXpm -lXt -lXext -lX11
[1491]	789	endif
	790
[5223]	791	#---------------------- open GL
[3635]	792
[13923]	793	ifeq ($(OPENGL),1)
[15496]	794	cflags += -DARB_OPENGL # activate OPENGL code
	795	GL := gl # this is the name of the OPENGL base target
	796	GL_LIB_SYS := -lGL -lGLU
	797	GL_LIB_ARB := -L$(ARBHOME)/GL/glAW -lglAW
[5877]	798
[15496]	799	ifeq ($(DARWIN),1)
	800	GL_LIB_SYS += -lpthread
	801	endif
[5877]	802
[15496]	803	GL_PNGLIBS_ARB := -L$(ARBHOME)/GL/glpng -lglpng_arb
	804	GL_PNGLIBS_SYS := -lpng
[5877]	805
[15496]	806	GLEWLIB := -lGLEW -lGLw
[18655]	807	GLUTLIB := -lglut
[5877]	808
[15496]	809	GL_LIBS_SYS := $(GL_LIB_SYS) $(GL_PNGLIBS_SYS) $(GLEWLIB) $(GLUTLIB)
	810	GL_LIBS_ARB := $(GL_LIB_ARB) $(GL_PNGLIBS_ARB)
[5877]	811
[15496]	812	RNA3D_LIB := RNA3D/RNA3D.a
[5881]	813	else
[18426]	814	GL_LIBS_SYS:=# no opengl -> no libs
[15496]	815	GL_LIBS_ARB:=# no opengl -> no libs
[17738]	816	GL:=# dont build ARB openGL libs
[5881]	817
[15496]	818	RNA3D_LIB :=
[5223]	819	endif
	820
[9578]	821	RNA3D_LIB_4_DEPENDS := RNA3D/RNA3D.a
[6863]	822
[6451]	823	GL_LIBS:=$(GL_LIBS_ARB) $(GL_LIBS_SYS)
	824
[19245]	825	#---------------------- sina:
	826
	827	ifndef ISINA
	828	# build sina delivered with arb?
	829	ifeq ($(LINUX),1)
	830	ifeq ('$(USE_GCC_70_OR_HIGHER)','yes')
	831	ISINA := 1# default to 'yes' for linux with gcc>=7
	832	endif
	833	endif
	834	ifndef ISINA
	835	ISINA := 0# 'no' otherwise
	836	endif
	837	endif
	838
[5877]	839	#---------------------- tiff lib:
	840
[8656]	841	TIFFLIBS := -ltiff
[3635]	842
[13923]	843	#---------------------- XML lib:
	844
	845	XMLLIBS := -lxerces-c
	846
[11664]	847	#---------------------- glib:
	848
[11668]	849	ARB_NEEDED_GLIB=glib-2.0
[11664]	850
[11668]	851	ARB_GLIB_INCLUDE:=$(strip $(shell pkg-config --cflags $(ARB_NEEDED_GLIB)))
	852	ARB_GLIB_LIBS:=$(strip $(shell pkg-config --libs $(ARB_NEEDED_GLIB)))
	853
[18982]	854	#---------------------- sunrpc lib:
	855	# Note: sunrpc has been removed from glibc
	856	# (e.g. in SuSE Leap 15.3 and Fedora 28)
	857	# see https://fedoraproject.org/wiki/Changes/SunRPCRemoval
	858	#
	859	HAVE_LIBTIRPC=$(strip $(shell pkg-config --exists libtirpc && echo libtirpc))
	860	ifeq ($(HAVE_LIBTIRPC),)
	861	ARB_RPC_INCLUDE:=
	862	ARB_RPC_LIBS:=
	863	else
	864	ARB_RPC_INCLUDE:=$(strip $(shell pkg-config --cflags $(HAVE_LIBTIRPC)))
	865	ARB_RPC_LIBS:=$(strip $(shell pkg-config --libs $(HAVE_LIBTIRPC)))
	866	endif
	867
[5223]	868	#---------------------- basic libs:
	869
[18982]	870	ARB_CORE_LIBS:=$(ARB_GLIB_LIBS) $(ARB_RPC_LIBS)
[18981]	871
[5877]	872	SYSLIBS:=
[11804]	873	ifeq ($(DARWIN),1)
[15496]	874	SYSLIBS += -lstdc++
[5877]	875	else
[18981]	876	SYSLIBS += -lm $(ARB_CORE_LIBS)
[5223]	877	endif
	878
[8675]	879	#---------------------- system dependent commands
	880
[11804]	881	ifeq ($(DARWIN),1)
[15496]	882	TIME:=gtime
[8675]	883	else
[15496]	884	TIME:=/usr/bin/time
[8675]	885	endif
	886
[13443]	887	#---------------------- SSE vectorizer
[16628]	888	# for details see SOURCE_TOOLS/vectorize.README
[13443]	889
	890	ifeq ($(DEBUG),0)
	891	ifeq ($(USE_GCC_49_OR_HIGHER),yes)
[14813]	892	ifeq ($(DISABLE_VECTORIZE_CHECK),0)
[15496]	893	cflags += -fopt-info-vec
[18014]	894	cflags += -fopt-info-vec-missed
[17342]	895	ifeq ($(TRACE_MISSED_VECTORIZATIONS),1)
	896	# Shows reasons for unsuccessful vectorization:
	897	cflags += -ftree-vectorizer-verbose=10
	898	POST_COMPILE += --dump-loop-optimization
[17877]	899	ifeq ($(VECTORIZATION_CHECK_CANDIDATES),1)
	900	$(error TRACE_MISSED_VECTORIZATIONS and VECTORIZATION_CHECK_CANDIDATES may not be used together!)
	901	endif
[17342]	902	endif
[17877]	903	ifeq ($(VECTORIZATION_CHECK_CANDIDATES),1)
	904	POST_COMPILE += --loop-optimization-candi
	905	endif
[16683]	906	POST_COMPILE += --check-loop-optimization
[13774]	907	endif
[13788]	908	else
	909	ifeq ($(USE_GCC_48_OR_HIGHER),yes)
	910	# no automatic vectorization-check for gcc<4.9.0
	911	# -> uncomment the next 2 lines and grep the spam it will produce for 'vectorized.*loops'
[15496]	912	# cflags += -fopt-info -fopt-info-vec-missed
	913	# POST_COMPILE += --original
[13788]	914	endif
[13443]	915	endif
	916	endif
	917
[13775]	918	#---------------------- stop early on broken flags/compiler combination
	919
	920	ifeq ($(DEBUG),0)
	921	ifeq ($(SANITIZE_ANY),1)
	922	ifeq ('$(COMPILER_VERSION)','4.9.1')
	923	$(error compiling DEBUG=0 + SANITIZE!=0 crashes with gcc $(COMPILER_VERSION) (gcc 4.9.2 works))
	924	endif
	925	endif
	926	endif
	927
[18321]	928	#---------------------- include symbols?
[14357]	929
[18321]	930	ifeq ($(TRACESYM),1)
	931	ifeq ($(USE_CLANG),0)
	932	cflags += -rdynamic
	933	clflags += -rdynamic -Wl,--export-dynamic
	934	endif
	935	endif
	936
	937	#---------------------- warn about duplicate variable definitions
	938
	939	ifeq ($(DARWIN),1)
	940	clflags += -Wl,-warn_commons
	941	else
[18320]	942	clflags += -Wl,--warn-common
[18321]	943	endif
[18320]	944
[18321]	945	#---------------------- differences between linking executables and shared libs:
	946
[14357]	947	# executables:
	948	ifeq ($(DARWIN),1)
[15496]	949	blflags:=$(clflags)
[14357]	950	else
[15496]	951	blflags:=$(clflags) -Wl,--no-undefined
[14357]	952	endif
	953
	954	# shared libraries
	955	llflags:=$(clflags)
	956
	957	# dont use clflags below
	958	clflags:=
	959
[8675]	960	# -------------------------------------------------------------------------
[15496]	961	# Don't put any machine/version/etc conditionals below!
	962	# (instead define variables above)
[5223]	963	# -------------------------------------------------------------------------
[2]	964
[11827]	965	cflags += -W -Wall $(dflags) $(extended_warnings)
[10956]	966	cxxflags := $(extended_cpp_warnings)
[2]	967
[11815]	968	# add CFLAGS + CPPFLAGS from environment for DEBIAN build
	969	ifeq ($(DEBIAN),1)
[15496]	970	cflags := $(CFLAGS) $(cflags)
	971	cxxflags += $(CPPFLAGS)
[11815]	972	endif
	973
[15529]	974	ifeq ('$(USE_CLANG)','1')
	975	# none of the following standards works with clang3.3 (under linux) => dont use standard (as done before r15516)
	976	# cxxflags += -std=gnu++11
	977	# cxxflags += -std=gnu++0x
[9516]	978	else
[15529]	979	ifeq ('$(USE_GCC_60_OR_HIGHER)','yes')
	980	cxxflags += -std=gnu++14# see also TEMPLATES/cxxforward.h@USE_Cxx14
	981	else
	982	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
	983	cxxflags += -std=gnu++11# see also TEMPLATES/cxxforward.h@USE_Cxx11
	984	else
	985	# gcc versions between 4.3 (lowest supported) and <4.7
	986	cxxflags += -std=gnu++0x
	987	endif
[8817]	988	endif
[6114]	989	endif
	990
[17625]	991	LINK_STATIC_LIB := $(AR) -csq# link static lib
[14357]	992	LINK_EXECUTABLE := $(A_CXX) $(blflags) -o# link executable (c++)
[2389]	993
[5829]	994	ifeq ($(LINK_STATIC),1)
[15496]	995	SHARED_LIB_SUFFIX = a# static lib suffix
	996	LINK_SHARED_LIB := $(LINK_STATIC_LIB)
[5829]	997	else
[15496]	998	SHARED_LIB_SUFFIX = so# shared lib suffix
[16223]	999	LINK_SHARED_LIB := $(A_CXX) $(llflags) -shared -o# link shared lib
[5829]	1000	endif
	1001
[13741]	1002	ifeq ($(DARWIN),1)
[15496]	1003	lflags4perl:=
[13741]	1004	else
[15496]	1005	lflags4perl:=$(cross_lflags) -shared
[13741]	1006	endif
[13740]	1007
[10969]	1008	# delete variables unused below
[14357]	1009	blflags:=
	1010	llflags:=
[10969]	1011
[5223]	1012	# other used tools
[5829]	1013	MAKEDEPEND_PLAIN = makedepend
	1014	MAKEDEPEND = $(FORCEMASK);$(MAKEDEPEND_PLAIN)
	1015
[18919]	1016	SEPNODATE:=--------------------------------------------------------------------------------
[7819]	1017	SEP=[`date +%M:%S.%N`] ------------------------------------------------
	1018	# to analyse timings run
	1019	# make -j9 clean; make -j9 all \| grep '^\[' \| sort
	1020	# make -j9 "TIMED_TARGET=perl" clean_timed_target \| grep '^\[' \| sort
[2389]	1021
[16223]	1022	# ------------------------------------------------------------ DYNLIBDEFS
	1023	# various dynamic library definitions for linking executables:
	1024	#
	1025	# SYSLIBS: system libraries needed by database lib
	1026	# ARBDB_LIB: database lib
	1027	# DBSYS_LIBS: executable using database (but no GUI)
	1028	# GUI_LIBS: executable using database and GUI (arb gui uses database)
	1029	#
	1030	# Note: definitions exported to sub-makefiles are described in SOURCE_TOOLS/parent_make.txt
	1031
[10962]	1032	CORE_LIB=-lCORE
	1033	ARBDB_LIB=-lARBDB $(CORE_LIB)
[16223]	1034	DBSYS_LIBS = $(ARBDB_LIB) $(SYSLIBS)
[10962]	1035
	1036	GUI_LIBS_PREFIX:=
[11804]	1037	ifeq ($(DARWIN),1)
[15496]	1038	# this seem to be added at wrong place, since opengl is only needed to link EDIT4
	1039	GUI_LIBS_PREFIX:=-framework GLUT -framework OpenGL
[10962]	1040	endif
	1041
[16223]	1042	GUI_LIBS=$(GUI_LIBS_PREFIX) $(DBSYS_LIBS) -lAWT -lWINDOW $(XLIBS)
[10965]	1043
[10962]	1044	LIBPATH = -L$(ARBHOME)/lib
	1045
	1046	DEST_LIB = lib
	1047	DEST_BIN = bin
	1048
[18982]	1049	CC_INCLUDES := -I. -I$(ARBHOME)/INCLUDE $(XINCLUDES) $(ARB_GLIB_INCLUDE) $(ARB_RPC_INCLUDE)
[10976]	1050	CXX_INCLUDES := $(CC_INCLUDES)
[10962]	1051	MAKEDEPENDFLAGS := -- -DARB_OPENGL -DUNIT_TESTS -D__cplusplus -I. -Y$(ARBHOME)/INCLUDE
	1052
	1053	# ---------------------------------------
	1054	# wrap main()
	1055
	1056	use_ARB_main=$(ARBHOME)/SOURCE_TOOLS/arb_main_cpp.o
	1057	use_ARB_main_C=$(ARBHOME)/SOURCE_TOOLS/arb_main_c.o
	1058
[13923]	1059	# -----------------------------------------
[17366]	1060	# unique build-id
	1061	# - different for different calls of make
	1062	# - constant in recursive calls
	1063
[17618]	1064	ifndef ARBBID
[17366]	1065	ARBBID:=$(shell SOURCE_TOOLS/uniqueID.sh)
	1066	endif
	1067
	1068	# -----------------------------------------
[13923]	1069	# export variables to submakefiles
[10962]	1070
	1071	include SOURCE_TOOLS/export2sub
	1072
[13923]	1073	# do not define (exported) variables below this point
[10962]	1074
[13923]	1075	# -------------------------
	1076	# Main arb targets:
	1077	# -------------------------
[2]	1078
[1076]	1079	first_target:
	1080	$(MAKE) checks
[18919]	1081	@echo $(SEPNODATE)
[643]	1082	@echo 'Main targets:'
	1083	@echo ''
	1084	@echo ' all - Compile ARB + TOOLs + and copy shared libs + link foreign software'
	1085	@echo ' (That is most likely the target you want)'
	1086	@echo ''
[4692]	1087	@echo ' clean - remove generated files ("SUBDIR/SUBDIR.clean" to clean only SUBDIR)'
[4632]	1088	@echo ' rebuild - clean + all'
[14205]	1089	@echo ' cleanlinked - remove all binaries'
	1090	@echo ' relink - cleanlinked + all (=relink all from objects)'
[643]	1091	@echo ''
[18920]	1092	@echo 'Targets for automated builds:'
[18917]	1093	@echo ''
[18925]	1094	@echo ' ALL, REBUILD, TARFILE + TARFILE_QUICK '
	1095	@echo ' - same as all, rebuild, tarfile + tarfile_quick'
	1096	@echo ' - if errors occur, they are extracted and listed at tail of output'
[643]	1097	@echo ''
[18920]	1098	@echo $(SEPNODATE)
	1099	@echo ''
[643]	1100	@echo 'Development targets:'
	1101	@echo ''
[18919]	1102	@echo ' depends - create or update dependencies ("SUBDIR/SUBDIR.depends" to update only SUBDIR)'
	1103	@echo ' proto - create or update prototypes ("SUBDIR/SUBDIR.proto" to update only SUBDIR)'
	1104	@echo ' tags - create tags for xemacs'
	1105	@echo ' show - show available shortcuts (AKA subtargets)'
	1106	@echo ' up - shortcut for depends+proto+tags'
[6558]	1107	ifeq ($(UNIT_TESTS),1)
[16425]	1108	@echo ' ut - only run tests'
	1109	@echo ' "UNIT=..." oneunit - build one unit and run tests (see also UNIT_TESTER/Makefile.setup.local)'
[6558]	1110	endif
[15094]	1111	ifneq ($(SANITIZE),0)
[18919]	1112	@echo ' sanitize - all + run arb_ntree with sanitizer (test.arb + execute _logged)'
[15094]	1113	endif
[18919]	1114	@echo ' modified - rebuild files modified in svn checkout (does touch)'
	1115	@echo ' touch - touch files modified in svn checkout'
[643]	1116	@echo ''
[18919]	1117	@echo 'Some often used sub targets:'
	1118	@echo ''
	1119	@echo ' arb - Just compile ARB (but none of the integrated tools)'
	1120	@echo ' menus - create lib/gde/arb.menu from GDEHELP/ARB_GDEmenus.source'
	1121	@echo ' perl - Compile the PERL XSUBS into lib/ARB.so and create links in lib to perl'
	1122	@echo ' binlink - Create all links in the bin directory'
	1123	@echo ''
[6141]	1124	@echo 'Internal maintenance:'
[643]	1125	@echo ''
[18919]	1126	@echo ' relinfo - show help on release targets'
	1127	@echo ' tarfile - make rebuild and create arb version tarfile ("tarfile_quick" to skip rebuild)'
	1128	@echo ' save - save all basic ARB sources into arbsrc_DATE ("savetest" to check filelist)'
	1129	@echo ' patch - save svn diff to patchfile'
	1130	@echo ' source_doc - create doxygen documentation'
	1131	@echo ' relocated - rebuild partly (use when you have relocated ARBHOME)'
	1132	@echo ' check_res - check resource usage'
	1133	@echo ' dep_graph - Build dependency graphs'
	1134	@echo ' clean_cov - Clean coverage results'
[643]	1135	@echo ''
[18919]	1136	@echo ' clean_opengl_changed - clean after changing OPENGL setting in config.Makefile'
	1137	@echo ' clean_checked_vect - clean units containing vectorization checks'
	1138	@echo ' cleanRelinkable - similar to cleanlinked (but skips raxml8 to avoid rebuild)'
[15737]	1139	@echo ''
[18919]	1140	@echo ' post_commit_check - Checks whether'
	1141	@echo ' * main make targets work,'
	1142	@echo ' * dependencies and prototypes are up to date,'
	1143	@echo ' * SVN-controlled files remain unaffected by called targets and'
	1144	@echo ' * all generated files are ignored.'
	1145	@echo ' (has to be called in a clean SVN checkout)'
	1146	@echo $(SEPNODATE)
[743]	1147	@echo ''
[2]	1148
[11669]	1149	relinfo:
	1150	@echo ''
[18919]	1151	@echo $(SEPNODATE)
[11669]	1152	@echo 'Release targets:'
	1153	@echo ''
	1154	@echo ' inc_candi - increase RC candidate-number (only possible in "rc" branch, not needed for RC1)'
	1155	@echo ' inc_patch - increase release patchlevel (only possible in "stable" branch)'
	1156	@echo ' inc_minor - increase minor version number (only possible in "trunk")'
	1157	@echo ' inc_major - increase MAJOR version number (only possible in "trunk")'
	1158	@echo ''
[11674]	1159	@echo ' show_version - show version tag'
	1160	@echo ''
[18919]	1161	@echo $(SEPNODATE)
[11669]	1162	@echo ''
[1459]	1163
	1164	# auto-generate config.makefile:
	1165
	1166	config.makefile : config.makefile.template
	1167	@echo --------------------------------------------------------------------------------
[17424]	1168	ifeq ($(CONFIG_MAKEFILE_FOUND),)
[1459]	1169	@cp $< $@
[5708]	1170	@echo '$(ARBHOME)/$@:1: has been generated.'
[1459]	1171	@echo 'Please edit $@ to configure your system!'
[6162]	1172	@echo --------------------------------------------------------------------------------
	1173	@false
[1459]	1174	else
[5708]	1175	@echo '$(ARBHOME)/$<:1: is more recent than'
	1176	@echo '$(ARBHOME)/$@:1:'
[1459]	1177	@ls -al config.makefile*
[6162]	1178	@echo --------------------------------------------------------------------------------
	1179	@echo "Updating $@ (if this fails, check manually)"
	1180	SOURCE_TOOLS/update_config_makefile.pl
	1181	@echo "Sucessfully updated $@"
	1182	@echo --------------------------------------------------------------------------------
	1183	@ls -al config.makefile*
	1184	@echo --------------------------------------------------------------------------------
	1185	@echo "Diff to your old config.makefile:"
	1186	@echo --------------------------------------------------------------------------------
[6164]	1187	-diff $@.bak $@
[6162]	1188	@echo --------------------------------------------------------------------------------
[1459]	1189	endif
	1190
[1076]	1191	# check if everything is configured correctly
[2]	1192
[1076]	1193	check_DEVELOPER:
	1194	ifndef DEVELOPER
[2988]	1195	@echo 'config.makefile:1: DEVELOPER not defined'
[1076]	1196	@false
	1197	endif
	1198
	1199	check_DEBUG:
[643]	1200	ifndef dflags
[2988]	1201	@echo 'config.makefile:1: DEBUG has to be defined. Valid values are 0 and 1'
[643]	1202	@false
	1203	endif
[2]	1204
[5133]	1205	check_ARB_64:
	1206	ifndef ARB_64
	1207	@echo 'config.makefile:1: ARB_64 has to be defined. Valid values are 0 and 1'
	1208	@false
	1209	endif
	1210
[1238]	1211	# ---------------------------------------- check gcc version
	1212
[13044]	1213	COMPILER_BROKEN:=0
	1214
[16582]	1215	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.6.4')
	1216	COMPILER_BROKEN:=1
	1217	endif
[13923]	1218	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.8.0')
[13044]	1219	COMPILER_BROKEN:=1
	1220	endif
	1221
[3311]	1222	check_same_GCC_VERSION:
[10993]	1223	$(ARBHOME)/SOURCE_TOOLS/check_same_compiler_version.pl $(COMPILER_NAME) $(COMPILER_VERSION_ALLOWED)
[3311]	1224
[1238]	1225	check_GCC_VERSION:
[10993]	1226	@echo 'Compiler version check:'
[14590]	1227	# see .@ALLOWED_gcc_VERSIONS
[10993]	1228	ifeq ('$(COMPILER_VERSION_ALLOWED)', '')
	1229	@echo " - Your compiler is '$(COMPILER_NAME)' version '$(COMPILER_VERSION)'"
	1230	@echo ' This version is not in the list of supported $(COMPILER_NAME)-versions:'
	1231	@$(foreach version,$(ALLOWED_COMPILER_VERSIONS),echo ' * $(version)';)
[3227]	1232	@echo ' - You may either ..'
[10993]	1233	@echo ' - add your version to ALLOWED_$(COMPILER_NAME)_VERSIONS in the Makefile and try it out or'
[3790]	1234	@echo ' - switch to one of the allowed versions (see arb_README_gcc.txt for installing'
	1235	@echo ' a different version of gcc)'
[13044]	1236	$(error Unsupported compiler '$(COMPILER_NAME)' version '$(COMPILER_VERSION)')
[1238]	1237	else
[15529]	1238	ifeq ($(COMPILER_BROKEN),1)
[16582]	1239	$(error compilation refused for $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)'. Refer to http://bugs.arb-home.de/wiki/GccVersionInfo for details.)
[15529]	1240	else
[10993]	1241	@echo " - Supported $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)' detected - fine!"
[1238]	1242	@echo ''
[15529]	1243	ifeq ($(USE_CLANG),1)
	1244	@echo "Dump clang version:"
	1245	$(A_CXX) -v
	1246	endif
[3311]	1247	$(MAKE) check_same_GCC_VERSION
[15529]	1248	endif
[1238]	1249	endif
	1250
[1459]	1251	#---------------------- check ARBHOME
	1252
	1253	# use arb_INSTALL.txt to determine whether ARBHOME points to correct directory
	1254	ARB_INSTALL_FOUND=$(wildcard $(ARBHOME)/arb_INSTALL.txt)
	1255
	1256	check_ARBHOME:
	1257	ifeq ($(strip $(ARB_INSTALL_FOUND)),)
	1258	@echo ------------------------------------------------------------
	1259	@echo "ARBHOME is set to '$(ARBHOME)'"
	1260	@echo "The environment variable ARBHOME has to point to the top arb source directory."
	1261	@echo "If you use bash enter:"
	1262	@echo " export ARBHOME='`pwd`'"
	1263	@echo ------------------------------------------------------------
	1264	@false
	1265	endif
	1266
	1267	ARB_PATH_SET=$(findstring $(ARBHOME)/bin,$(PATH))
	1268
	1269	check_PATH: check_ARBHOME
	1270	ifeq ($(strip $(ARB_PATH_SET)),)
	1271	@echo ------------------------------------------------------------
	1272	@echo "The environment variable PATH has to contain $(ARBHOME)/bin"
	1273	@echo "If you use bash enter:"
	1274	@echo ' export PATH=$$ARBHOME/bin:$$PATH'
	1275	@echo ------------------------------------------------------------
	1276	@false
	1277	endif
	1278
[5829]	1279	check_TOOLS:
	1280	@util/arb_check_build_env.pl \
[10955]	1281	"$(A_CC)" \
	1282	"$(A_CXX)" \
[5829]	1283	"$(LINK_SHARED_LIB)" \
[1459]	1284
[19043]	1285	have_makedepend:
	1286	@util/arb_check_build_env.pl --check-only "$(MAKEDEPEND_PLAIN)"
	1287
[5829]	1288	check_ENVIRONMENT : check_PATH check_TOOLS
[12312]	1289	@echo "-------------------- Environment [start]"
	1290	@echo "ARBHOME='$(ARBHOME)'"
	1291	@echo "PATH='$(PATH)'"
	1292	@echo "LD_LIBRARY_PATH='$(LD_LIBRARY_PATH)'"
	1293	@echo "-------------------- Environment [end]"
[5829]	1294
[5387]	1295	check_tabs: check_setup
	1296	ifeq ($(DEBUG),1)
	1297	@SOURCE_TOOLS/tabBrake.pl
	1298	endif
	1299
	1300	force_tab_check:
[8614]	1301	@touch -t 198001010000 SOURCE_TOOLS/stamp.tabBrake
[5829]	1302	@$(MAKE) check_tabs
[5387]	1303
	1304
[1459]	1305	# ---------------------
	1306
[13923]	1307	check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION
[1076]	1308	@echo Your setup seems to be ok.
[2]	1309
[5387]	1310	checks: check_setup check_tabs
[7623]	1311	@rm -f SOURCE_TOOLS/postcompile.sav
[2]	1312
[5387]	1313
[1459]	1314	# end test section ------------------------------
	1315
[7801]	1316	# ---------------------------------------
[7819]	1317	# List of standard top level directories
	1318	#
	1319	# sub-makefiles have to define the targets
	1320	# - 'depends' and
	1321	# - 'clean'
	1322	#
[18426]	1323	# when adding new libraries/subdirs here, also add a dependency vs 'links' or 'links_non_perl' in .@DD_links_non_perl
[5629]	1324
[18426]	1325	TL_ARCHIVES = \
[7819]	1326	AISC/AISC.a \
[5565]	1327	ARB_GDE/ARB_GDE.a \
	1328	AWTC/AWTC.a \
	1329	AWTI/AWTI.a \
	1330	CONSENSUS_TREE/CONSENSUS_TREE.a \
	1331	CONVERTALN/CONVERTALN.a \
	1332	DBSERVER/DBSERVER.a \
	1333	DIST/DIST.a \
	1334	EDIT4/EDIT4.a \
	1335	EISPACK/EISPACK.a \
	1336	GENOM/GENOM.a \
	1337	GENOM_IMPORT/GENOM_IMPORT.a \
	1338	ISLAND_HOPPING/ISLAND_HOPPING.a \
	1339	MERGE/MERGE.a \
	1340	MULTI_PROBE/MULTI_PROBE.a \
	1341	NALIGNER/NALIGNER.a \
	1342	NAMES/NAMES.a \
	1343	NAMES_COM/server.a \
	1344	NTREE/NTREE.a \
	1345	PARSIMONY/PARSIMONY.a \
	1346	PHYLO/PHYLO.a \
	1347	PRIMER_DESIGN/PRIMER_DESIGN.a \
[17738]	1348	PROBE/PROBE.a \
[866]	1349	PROBE_COM/server.a \
[2]	1350	PROBE_DESIGN/PROBE_DESIGN.a \
[18426]	1351	$(RNA3D_LIB) \
[7895]	1352	RNACMA/RNACMA.a \
[866]	1353	SECEDIT/SECEDIT.a \
[3494]	1354	SEQ_QUALITY/SEQ_QUALITY.a \
[866]	1355	SERVERCNTRL/SERVERCNTRL.a \
	1356	STAT/STAT.a \
	1357	TREEGEN/TREEGEN.a \
	1358	WETC/WETC.a \
	1359	XML/XML.a \
[2]	1360
[18426]	1361	TL_SHARED_ARCHIVES = \
	1362	ARBDB/libARBDB.so \
	1363	CORE/libCORE.so \
	1364	AWT/libAWT.so \
	1365	WINDOW/libWINDOW.so \
	1366
	1367	TL_ARCHIV_COLLECTIONS = \
	1368	SL/SL.archColl \
	1369
	1370	TL_TOOLS_COLLECTIONS = \
	1371	AISC_MKPTPS/AISC_MKPTPS.toolColl \
	1372	TOOLS/TOOLS.toolColl \
	1373	PERLTOOLS/PERLTOOLS.toolColl \
	1374	PROBE_SET/PROBE_SET.toolColl \
	1375	READSEQ/READSEQ.toolColl \
	1376
	1377	RECURSIVE_SUBS = \
	1378	GDE/GDE.sub \
	1379	UNIT_TESTER/UNIT_TESTER.sub \
	1380
	1381	SUBDIRS = \
	1382	$(RECURSIVE_SUBS) \
	1383	$(TL_ARCHIVES:.a=.sub) \
	1384	$(TL_SHARED_ARCHIVES:.so=.sub) \
	1385	$(TL_ARCHIV_COLLECTIONS:.archColl=.sub) \
	1386	$(TL_TOOLS_COLLECTIONS:.toolColl=.sub) \
	1387
	1388	# sub directories inside TL_ARCHIV_COLLECTIONS
	1389	CL_ARCH_DIRS = $(foreach coll,$(TL_ARCHIV_COLLECTIONS),$(shell find $(dir $(coll)) -maxdepth 1 -mindepth 1 -type d))
	1390
	1391	# archives inside CL_ARCH_DIRS:
	1392	CL_ARCHIVES = $(foreach adir,$(CL_ARCH_DIRS),$(dir $(adir))$(notdir $(adir))/$(notdir $(adir)).a)
	1393
[13923]	1394	# -----------------------
	1395	# library packets
[6280]	1396
[13923]	1397	ARCHS_CLIENT_PROBE = PROBE_COM/client.a
	1398	ARCHS_CLIENT_NAMES = NAMES_COM/client.a
[11060]	1399
[7819]	1400	ARCHS_MAKEBIN = AISC_MKPTPS/AISC_MKPTPS.a AISC/AISC.a
[2]	1401
[200]	1402	# communication libs need aisc and aisc_mkpts:
[2]	1403
[7819]	1404	AISC/AISC.dummy: proto_tools
[7621]	1405
[7819]	1406	comtools: AISC/AISC.dummy
[7621]	1407
[6280]	1408	ARCHS_SEQUENCE = \
	1409	SL/SEQUENCE/SEQUENCE.a \
	1410	SL/ALIVIEW/ALIVIEW.a \
	1411	SL/PRONUC/PRONUC.a \
	1412
	1413	ARCHS_TREE = \
[14038]	1414	SL/ARB_TREE/ARB_TREE.a \
	1415	SL/FILTER/FILTER.a \
[6280]	1416	$(ARCHS_SEQUENCE) \
	1417
[6318]	1418	# parsimony tree (used by NTREE, PARSIMONY, STAT(->EDIT4), DIST(obsolete!))
[6280]	1419	ARCHS_AP_TREE = \
[14038]	1420	SL/AP_TREE/AP_TREE.a \
[6280]	1421	$(ARCHS_TREE) \
	1422
[7819]	1423	# --------------------------------------------------------------------------------
	1424	# dependencies for linking shared libs
	1425
	1426	link_core: core
	1427	link_db: db link_core
	1428	link_aw: aw link_db
	1429	link_awt: awt link_aw
	1430
[2]	1431	#***************************************************************************************
[13923]	1432	# Individual_Programs_Section
[2]	1433	#***************************************************************************************
	1434
[10962]	1435	arbmainwrapper:
	1436	$(MAKE) -C SOURCE_TOOLS -r mainwrapper
	1437
	1438
[2]	1439	#********************************* arb_ntree ************************************
	1440	NTREE = bin/arb_ntree
[591]	1441	ARCHS_NTREE = \
[6427]	1442	NTREE/NTREE.a \
[591]	1443	ARB_GDE/ARB_GDE.a \
[15966]	1444	SL/GROUP_SEARCH/GROUP_SEARCH.a \
[18311]	1445	SL/SAICALC/SAICALC.a \
[14038]	1446	SL/DB_UI/DB_UI.a \
[591]	1447	AWTC/AWTC.a \
	1448	AWTI/AWTI.a \
[8587]	1449	CONSENSUS_TREE/CONSENSUS_TREE.a \
[14038]	1450	GENOM_IMPORT/GENOM_IMPORT.a \
[591]	1451	GENOM/GENOM.a \
	1452	MERGE/MERGE.a \
	1453	MULTI_PROBE/MULTI_PROBE.a \
	1454	PRIMER_DESIGN/PRIMER_DESIGN.a \
	1455	PROBE_DESIGN/PROBE_DESIGN.a \
[3821]	1456	SEQ_QUALITY/SEQ_QUALITY.a \
[591]	1457	SERVERCNTRL/SERVERCNTRL.a \
[12754]	1458	SL/ALILINK/ALILINK.a \
[3821]	1459	SL/AW_NAME/AW_NAME.a \
[14425]	1460	SL/CONSENSUS/CONSENSUS.a \
[3821]	1461	SL/DB_SCANNER/DB_SCANNER.a \
[7801]	1462	SL/DB_QUERY/DB_QUERY.a \
[15852]	1463	SL/QUERY/QUERY.a \
[6550]	1464	SL/SEQIO/SEQIO.a \
[14038]	1465	STAT/STAT.a \
[6280]	1466	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
[5805]	1467	SL/HELIX/HELIX.a \
	1468	SL/REGEXPR/REGEXPR.a \
[7801]	1469	SL/REFENTRIES/REFENTRIES.a \
	1470	SL/NDS/NDS.a \
[15054]	1471	SL/ITEM_SHADER/ITEM_SHADER.a \
[7801]	1472	SL/ITEMS/ITEMS.a \
[9633]	1473	SL/INSDEL/INSDEL.a \
[8250]	1474	SL/LOCATION/LOCATION.a \
[10083]	1475	SL/MACROS/MACROS.a \
[16904]	1476	SL/PVP/PVP.a \
[6280]	1477	SL/TRANSLATE/TRANSLATE.a \
	1478	SL/TREEDISP/TREEDISP.a \
[8557]	1479	SL/TREE_ADMIN/TREE_ADMIN.a \
[6023]	1480	SL/TREE_READ/TREE_READ.a \
	1481	SL/TREE_WRITE/TREE_WRITE.a \
[18092]	1482	SL/XFERGUI/XFERGUI.a \
[18088]	1483	SL/XFERSET/XFERSET.a \
[591]	1484	XML/XML.a \
[15691]	1485	$(ARCHS_AP_TREE) \
[2]	1486
[17618]	1487	ARCHS_NTREE_ALL = $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(XMLLIBS)
	1488
[7819]	1489	$(NTREE): $(ARCHS_NTREE:.a=.dummy) link_awt
[17618]	1490	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NTREE_ALL) \|\| ( \
[7819]	1491	echo "$(SEP) Link $@"; \
[17618]	1492	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE_ALL)" ; \
	1493	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE_ALL) && \
[7819]	1494	echo "$(SEP) Link $@ [done]"; \
[2744]	1495	)
[591]	1496
[2]	1497	#********************************* arb_edit4 ************************************
	1498	EDIT4 = bin/arb_edit4
[3477]	1499
[5223]	1500	ARCHS_EDIT4 := \
[6427]	1501	EDIT4/EDIT4.a \
[6280]	1502	ARB_GDE/ARB_GDE.a \
[14038]	1503	SL/FAST_ALIGNER/FAST_ALIGNER.a \
[989]	1504	AWTC/AWTC.a \
[6280]	1505	ISLAND_HOPPING/ISLAND_HOPPING.a \
[989]	1506	SECEDIT/SECEDIT.a \
	1507	SERVERCNTRL/SERVERCNTRL.a \
[3494]	1508	SL/AW_HELIX/AW_HELIX.a \
[3821]	1509	SL/AW_NAME/AW_NAME.a \
[14425]	1510	SL/CONSENSUS/CONSENSUS.a \
[7801]	1511	SL/ITEMS/ITEMS.a \
[14038]	1512	STAT/STAT.a \
[6280]	1513	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
	1514	SL/HELIX/HELIX.a \
	1515	SL/TRANSLATE/TRANSLATE.a \
[10083]	1516	SL/MACROS/MACROS.a \
[10494]	1517	SL/NDS/NDS.a \
[14038]	1518	$(ARCHS_AP_TREE) \
[989]	1519	XML/XML.a \
	1520
[5223]	1521	ifeq ($(OPENGL),1)
	1522	ARCHS_EDIT4 += RNA3D/RNA3D.a
[3477]	1523	endif
[7819]	1524
[17618]	1525	ARCHS_EDIT4_ALL = $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4)
	1526
[5877]	1527	LIBS_EDIT4 := $(GL_LIBS)
[3462]	1528
[13923]	1529	$(EDIT4): $(ARCHS_EDIT4:.a=.dummy) link_awt
[17618]	1530	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_EDIT4_ALL) \|\| ( \
[7819]	1531	echo "$(SEP) Link $@"; \
[17618]	1532	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4_ALL)" ; \
	1533	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4_ALL) && \
[7819]	1534	echo "$(SEP) Link $@ [done]"; \
[3462]	1535	)
	1536
[7895]	1537	#********************************* arb_rnacma ************************************
	1538	RNACMA = bin/arb_rnacma
	1539	ARCHS_RNACMA = \
	1540	RNACMA/RNACMA.a \
	1541
[17618]	1542	ARCHS_RNACMA_ALL = $(ARCHS_RNACMA) $(DBSYS_LIBS)
	1543
[8240]	1544	$(RNACMA) : $(ARCHS_RNACMA:.a=.dummy) link_db
[17618]	1545	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_RNACMA_ALL) \|\| ( \
[7895]	1546	echo "$(SEP) Link $@"; \
[18426]	1547	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_RNACMA_ALL)"; \
	1548	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_RNACMA_ALL) && \
[7895]	1549	echo "$(SEP) Link $@ [done]"; \
	1550	)
	1551
[2]	1552	#********************************* arb_wetc ************************************
	1553	WETC = bin/arb_wetc
[989]	1554	ARCHS_WETC = \
	1555	WETC/WETC.a \
[3494]	1556	SL/HELIX/HELIX.a \
[6280]	1557	SL/FILTER/FILTER.a \
[989]	1558	XML/XML.a \
	1559
[17618]	1560	ARCHS_WETC_ALL = $(ARCHS_WETC) $(GUI_LIBS)
	1561
[7819]	1562	$(WETC): $(ARCHS_WETC:.a=.dummy) link_awt
[17618]	1563	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_WETC_ALL) \|\| ( \
[7819]	1564	echo "$(SEP) Link $@"; \
[17618]	1565	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC_ALL)" ; \
	1566	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC_ALL) && \
[7819]	1567	echo "$(SEP) Link $@ [done]"; \
[2744]	1568	)
[2]	1569
	1570	#********************************* arb_dist ************************************
	1571	DIST = bin/arb_dist
[989]	1572	ARCHS_DIST = \
[14038]	1573	DIST/DIST.a \
[6280]	1574	CONSENSUS_TREE/CONSENSUS_TREE.a \
	1575	EISPACK/EISPACK.a \
[989]	1576	SERVERCNTRL/SERVERCNTRL.a \
[6280]	1577	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
[3494]	1578	SL/HELIX/HELIX.a \
[6280]	1579	SL/MATRIX/MATRIX.a \
[10083]	1580	SL/MACROS/MACROS.a \
[7801]	1581	SL/NDS/NDS.a \
	1582	SL/ITEMS/ITEMS.a \
[6280]	1583	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.a \
[989]	1584	XML/XML.a \
[14038]	1585	$(ARCHS_AP_TREE) \
[989]	1586
[17618]	1587	ARCHS_DIST_ALL = $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS)
	1588
[7819]	1589	$(DIST): $(ARCHS_DIST:.a=.dummy) link_awt
[17618]	1590	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_DIST_ALL) \|\| ( \
[7819]	1591	echo "$(SEP) Link $@"; \
[17618]	1592	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST_ALL)" ; \
	1593	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST_ALL) && \
[7819]	1594	echo "$(SEP) Link $@ [done]"; \
[2744]	1595	)
[2]	1596
	1597	#********************************* arb_pars ************************************
[866]	1598	PARSIMONY = bin/arb_pars
[989]	1599	ARCHS_PARSIMONY = \
[6280]	1600	PARSIMONY/PARSIMONY.a \
[3821]	1601	SERVERCNTRL/SERVERCNTRL.a \
[6280]	1602	SL/AW_NAME/AW_NAME.a \
	1603	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
[3494]	1604	SL/HELIX/HELIX.a \
[10083]	1605	SL/MACROS/MACROS.a \
[7801]	1606	SL/NDS/NDS.a \
	1607	SL/ITEMS/ITEMS.a \
[6280]	1608	SL/TRANSLATE/TRANSLATE.a \
	1609	SL/TREEDISP/TREEDISP.a \
[989]	1610	XML/XML.a \
[14038]	1611	$(ARCHS_AP_TREE) \
[989]	1612
[17618]	1613	ARCHS_PARSIMONY_ALL = $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS)
	1614
[7819]	1615	$(PARSIMONY): $(ARCHS_PARSIMONY:.a=.dummy) link_awt
[17618]	1616	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_PARSIMONY_ALL) \|\| ( \
[7819]	1617	echo "$(SEP) Link $@"; \
[17618]	1618	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY_ALL)" ; \
	1619	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY_ALL) && \
[7819]	1620	echo "$(SEP) Link $@ [done]"; \
[2744]	1621	)
[2]	1622
[7046]	1623	#********************************* arb_convert_aln ************************************
	1624	CONVERT_ALN = bin/arb_convert_aln
	1625	ARCHS_CONVERT_ALN = \
	1626	CONVERTALN/CONVERTALN.a \
	1627
[17618]	1628	ARCHS_CONVERT_ALN_ALL = $(ARCHS_CONVERT_ALN) $(DBSYS_LIBS)
	1629
[8240]	1630	$(CONVERT_ALN) : $(ARCHS_CONVERT_ALN:.a=.dummy) link_db
[17618]	1631	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_CONVERT_ALN_ALL) \|\| ( \
[7819]	1632	echo "$(SEP) Link $@"; \
[17618]	1633	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN_ALL)"; \
	1634	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN_ALL) && \
[7819]	1635	echo "$(SEP) Link $@ [done]"; \
[7046]	1636	)
	1637
[866]	1638	#********************************* arb_treegen ************************************
[8240]	1639
[866]	1640	TREEGEN = bin/arb_treegen
[989]	1641	ARCHS_TREEGEN = \
	1642	TREEGEN/TREEGEN.a \
	1643
[17618]	1644	ARCHS_TREEGEN_ALL = $(ARCHS_TREEGEN)
	1645
[1617]	1646	$(TREEGEN) : $(ARCHS_TREEGEN:.a=.dummy)
[17618]	1647	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main_C) $(ARCHS_TREEGEN_ALL) \|\| ( \
[7819]	1648	echo "$(SEP) Link $@"; \
[17618]	1649	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN_ALL)" ; \
	1650	$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN_ALL) && \
[7819]	1651	echo "$(SEP) Link $@ [done]"; \
[2744]	1652	)
[2]	1653
	1654	#********************************* arb_naligner ************************************
	1655	NALIGNER = bin/arb_naligner
[989]	1656	ARCHS_NALIGNER = \
	1657	NALIGNER/NALIGNER.a \
	1658	SERVERCNTRL/SERVERCNTRL.a \
[3494]	1659	SL/HELIX/HELIX.a \
[989]	1660
[17618]	1661	ARCHS_NALIGNER_ALL = $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(DBSYS_LIBS)
	1662
[7819]	1663	$(NALIGNER): $(ARCHS_NALIGNER:.a=.dummy) link_db
[17618]	1664	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NALIGNER_ALL) \|\| ( \
[7819]	1665	echo "$(SEP) Link $@"; \
[17618]	1666	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER_ALL)" ; \
	1667	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER_ALL) && \
[7819]	1668	echo "$(SEP) Link $@ [done]"; \
[2744]	1669	)
[2]	1670
	1671	#********************************* arb_phylo ************************************
	1672	PHYLO = bin/arb_phylo
[989]	1673	ARCHS_PHYLO = \
	1674	PHYLO/PHYLO.a \
[3494]	1675	SL/HELIX/HELIX.a \
[6280]	1676	SL/FILTER/FILTER.a \
[10083]	1677	SL/MACROS/MACROS.a \
[989]	1678	XML/XML.a \
	1679
[17618]	1680	ARCHS_PHYLO_ALL = $(ARCHS_PHYLO) $(GUI_LIBS)
	1681
[7819]	1682	$(PHYLO): $(ARCHS_PHYLO:.a=.dummy) link_awt
[17618]	1683	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_PHYLO_ALL) \|\| ( \
[7819]	1684	echo "$(SEP) Link $@"; \
[17618]	1685	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO_ALL)" ; \
	1686	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO_ALL) && \
[7819]	1687	echo "$(SEP) Link $@ [done]"; \
[2744]	1688	)
[2]	1689
	1690	#***************************************************************************************
	1691	# SERVER SECTION
	1692	#***************************************************************************************
	1693
	1694	#********************************* arb_db_server ************************************
	1695	DBSERVER = bin/arb_db_server
[989]	1696	ARCHS_DBSERVER = \
	1697	DBSERVER/DBSERVER.a \
	1698	SERVERCNTRL/SERVERCNTRL.a \
	1699
[17618]	1700	ARCHS_DBSERVER_ALL = $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS)
	1701
[7819]	1702	$(DBSERVER): $(ARCHS_DBSERVER:.a=.dummy) link_db
[17618]	1703	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_DBSERVER_ALL) \|\| ( \
[7819]	1704	echo "$(SEP) Link $@"; \
[17618]	1705	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER_ALL)" ; \
	1706	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER_ALL) && \
[7819]	1707	echo "$(SEP) Link $@ [done]"; \
[2744]	1708	)
[2]	1709
	1710	#********************************* arb_pt_server ************************************
	1711	PROBE = bin/arb_pt_server
[17738]	1712
	1713	ARCHS_PROBE_DEPEND = \
	1714	PROBE/PROBE.a \
[14038]	1715	SL/PTCLEAN/PTCLEAN.a \
[5565]	1716	SERVERCNTRL/SERVERCNTRL.a \
	1717	SL/HELIX/HELIX.a \
	1718
[17738]	1719	ARCHS_PROBE_ALL = $(ARCHS_PROBE_DEPEND) $(ARCHS_CLIENT_PROBE) $(ARBDB_LIB) $(SYSLIBS)
[989]	1720
[13923]	1721	$(PROBE): $(ARCHS_PROBE_DEPEND:.a=.dummy) link_db
[17618]	1722	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) config.makefile $(ARCHS_PROBE_ALL) \|\| ( \
[7819]	1723	echo "$(SEP) Link $@"; \
[17618]	1724	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_ALL)" ; \
	1725	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_ALL) && \
[7819]	1726	echo "$(SEP) Link $@ [done]"; \
[2744]	1727	)
[2]	1728
	1729	#********************************* arb_name_server ************************************
	1730	NAMES = bin/arb_name_server
[989]	1731	ARCHS_NAMES = \
	1732	NAMES/NAMES.a \
	1733	SERVERCNTRL/SERVERCNTRL.a \
	1734
[17618]	1735	ARCHS_NAMES_ALL = $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS)
	1736
[7819]	1737	$(NAMES): $(ARCHS_NAMES:.a=.dummy) link_db
[17618]	1738	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NAMES_ALL) \|\| ( \
[7819]	1739	echo "$(SEP) Link $@"; \
[17618]	1740	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES_ALL)" ; \
	1741	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES_ALL) && \
[7819]	1742	echo "$(SEP) Link $@ [done]"; \
[2744]	1743	)
[2]	1744
[989]	1745	#********************************* SHARED LIBRARIES SECTION ************************************
[2]	1746
[8567]	1747	prepare_libdir: addlibs
[989]	1748
[6038]	1749	addlibs:
	1750	(perl $(ARBHOME)/SOURCE_TOOLS/provide_libs.pl \
	1751	"arbhome=$(ARBHOME)" \
	1752	"opengl=$(OPENGL)" \
	1753	"link_static=$(LINK_STATIC)" \
	1754	)
	1755
[2]	1756	#***************************************************************************************
[6141]	1757	# Recursive calls to sub-makefiles
[2]	1758	#***************************************************************************************
[1617]	1759
[19043]	1760	%.depends: have_makedepend
[1617]	1761	@cp -p $(@D)/Makefile $(@D)/Makefile.old # save old Makefile
	1762	@$(MAKE) -C $(@D) -r \
[4632]	1763	"AUTODEPENDS=1" \
[5872]	1764	"MAIN=nothing" \
[6474]	1765	"cflags=noCflagsHere_use_MAKEDEPENDFLAGS" \
[10956]	1766	"cxxflags=noCxxflagsHere_use_MAKEDEPENDFLAGS" \
[9577]	1767	depends
[1617]	1768	@grep "^# DO NOT DELETE" $(@D)/Makefile >/dev/null
	1769	@cat $(@D)/Makefile \
[9574]	1770	\| SOURCE_TOOLS/fix_depends.pl "(from main)" \
[1617]	1771	>$(@D)/Makefile.2
	1772	@mv $(@D)/Makefile.old $(@D)/Makefile # restore old Makefile
	1773	@$(ARBHOME)/SOURCE_TOOLS/mv_if_diff $(@D)/Makefile.2 $(@D)/Makefile # update Makefile if changed
[2]	1774
[4600]	1775	%.proto:
[13077]	1776	@($(MAKE) -C $(@D) \
[4632]	1777	"AUTODEPENDS=0" \
[5872]	1778	"MAIN=nothing" \
	1779	"cflags=noCflags" \
[10956]	1780	"cxxflags=noCxxflags" \
[13077]	1781	proto 2>&1 ) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
[4600]	1782
[4632]	1783	%.clean:
	1784	@$(MAKE) -C $(@D) \
	1785	"AUTODEPENDS=0" \
[5872]	1786	"MAIN=nothing" \
	1787	"cflags=noCflags" \
[10956]	1788	"cxxflags=noCxxflags" \
[4632]	1789	clean
	1790
[8574]	1791
[18426]	1792	# stop wrong targets:
[8574]	1793	target_is_missing_lib_prefix:
	1794	@echo "Error: Denied to build shared library target with missing 'lib'-prefix"
	1795	false
	1796
	1797	ARBDB/ARBDB.dummy: target_is_missing_lib_prefix
	1798	CORE/CORE.dummy: target_is_missing_lib_prefix
	1799	AWT/AWT.dummy: target_is_missing_lib_prefix
	1800	WINDOW/WINDOW.dummy: target_is_missing_lib_prefix
	1801
[4632]	1802	# rule to generate main target (normally a library):
[11656]	1803	# @@@ check effect of setting LANG=C below
[2]	1804	%.dummy:
[7802]	1805	@( export ID=$$$$; LANG=C; \
[5165]	1806	(( \
[7819]	1807	echo "$(SEP) Make $(@D)"; \
[5143]	1808	$(MAKE) -C $(@D) -r \
[4632]	1809	"AUTODEPENDS=1" \
[10956]	1810	"MAIN=$(@F:.dummy=.a)" \
	1811	"cflags=$(cflags) -DIN_ARB_$(subst /,_,$(@D))" \
	1812	&& \
[7819]	1813	echo "$(SEP) Make $(@D) [done]"; \
[5165]	1814	) >$(@D).$$ID.log 2>&1 && (cat $(@D).$$ID.log;rm $(@D).$$ID.log)) \|\| (cat $(@D).$$ID.log;rm $(@D).$$ID.log;false))
[2]	1815
[2223]	1816	# Additional dependencies for subtargets:
	1817
	1818	PROBE_COM/PROBE_COM.dummy : comtools
	1819	NAMES_COM/NAMES_COM.dummy : comtools
	1820
[7819]	1821	com: PROBE_COM/PROBE_COM.dummy NAMES_COM/NAMES_COM.dummy
[2223]	1822
[18426]	1823	# stop wrong more targets:
[7819]	1824	PROBE_COM/server.dummy:
	1825	@echo Unwanted request to make target $<
	1826	false
	1827
	1828	PROBE_COM/client.dummy:
	1829	@echo Unwanted request to make target $<
	1830	false
	1831
[13923]	1832	NAMES_COM/server.dummy:
[7819]	1833	@echo Unwanted request to make target $<
	1834	false
	1835
	1836	NAMES_COM/client.dummy:
	1837	@echo Unwanted request to make target $<
	1838	false
	1839
	1840
	1841	ARBDB/libARBDB.dummy: links
	1842	CORE/libCORE.dummy: links
	1843
[8588]	1844	PERLTOOLS/PERLTOOLS.dummy: core db
[7819]	1845
[9580]	1846	# all subdirs perl not depends on go here (ADD_links_non_perl)
[7819]	1847	AWT/libAWT.dummy: links_non_perl
	1848	AWTI/AWTI.dummy: links_non_perl
	1849	CONSENSUS_TREE/CONSENSUS_TREE.dummy: links_non_perl
[8297]	1850	CONVERTALN/CONVERTALN.dummy: links_non_perl
[7819]	1851	DBSERVER/DBSERVER.dummy: links_non_perl
	1852	DIST/DIST.dummy: links_non_perl
[14055]	1853	EDIT4/EDIT4.dummy: links_non_perl com
[7819]	1854	EISPACK/EISPACK.dummy: links_non_perl
	1855	GDE/GDE.dummy: links_non_perl
	1856	GENOM/GENOM.dummy: links_non_perl
[8297]	1857	GENOM_IMPORT/GENOM_IMPORT.dummy: links_non_perl
[7819]	1858	ISLAND_HOPPING/ISLAND_HOPPING.dummy: links_non_perl
[8297]	1859	MERGE/MERGE.dummy: links_non_perl
[14055]	1860	NTREE/NTREE.dummy: links_non_perl
[7819]	1861	PARSIMONY/PARSIMONY.dummy: links_non_perl
	1862	PHYLO/PHYLO.dummy: links_non_perl
	1863	PRIMER_DESIGN/PRIMER_DESIGN.dummy: links_non_perl
	1864	PROBE_SET/PROBE_SET.dummy: links_non_perl link_db
	1865	READSEQ/READSEQ.dummy: links_non_perl
[8670]	1866	RNACMA/RNACMA.dummy: links_non_perl header_libs
[7819]	1867	SECEDIT/SECEDIT.dummy: links_non_perl
[8297]	1868	SEQ_QUALITY/SEQ_QUALITY.dummy: links_non_perl
	1869	SERVERCNTRL/SERVERCNTRL.dummy: links_non_perl com
[12754]	1870	SL/ALILINK/ALILINK.dummy: links_non_perl
[7819]	1871	SL/ALIVIEW/ALIVIEW.dummy: links_non_perl
	1872	SL/AP_TREE/AP_TREE.dummy: links_non_perl
	1873	SL/ARB_TREE/ARB_TREE.dummy: links_non_perl
	1874	SL/AW_HELIX/AW_HELIX.dummy: links_non_perl
[14425]	1875	SL/CONSENSUS/CONSENSUS.dummy: links_non_perl
[8297]	1876	SL/DB_QUERY/DB_QUERY.dummy: links_non_perl
	1877	SL/DB_SCANNER/DB_SCANNER.dummy: links_non_perl
	1878	SL/DB_UI/DB_UI.dummy: links_non_perl
[7819]	1879	SL/FAST_ALIGNER/FAST_ALIGNER.dummy: links_non_perl
	1880	SL/FILTER/FILTER.dummy: links_non_perl
[16119]	1881	SL/FILTSEQEXP/FILTSEQEXP.dummy: links_non_perl
	1882	SL/GROUP_SEARCH/GROUP_SEARCH.dummy: links_non_perl
[7819]	1883	SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy: links_non_perl
[18959]	1884	SL/HEADERTESTS/HEADERTESTS.dummy: links_non_perl
[7819]	1885	SL/HELIX/HELIX.dummy: links_non_perl
[9633]	1886	SL/INSDEL/INSDEL.dummy: links_non_perl
[16119]	1887	SL/ITEM_SHADER/ITEM_SHADER.dummy: links_non_perl
[7819]	1888	SL/ITEMS/ITEMS.dummy: links_non_perl
[8297]	1889	SL/LOCATION/LOCATION.dummy: links_non_perl
[10083]	1890	SL/MACROS/MACROS.dummy: links_non_perl
[7819]	1891	SL/MATRIX/MATRIX.dummy: links_non_perl
	1892	SL/NDS/NDS.dummy: links_non_perl
	1893	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.dummy: links_non_perl
	1894	SL/PRONUC/PRONUC.dummy: links_non_perl
[8097]	1895	SL/PTCLEAN/PTCLEAN.dummy: links_non_perl link_db
[16904]	1896	SL/PVP/PVP.dummy: links_non_perl
[15852]	1897	SL/QUERY/QUERY.dummy: links_non_perl link_db
[8297]	1898	SL/REFENTRIES/REFENTRIES.dummy: links_non_perl
	1899	SL/REGEXPR/REGEXPR.dummy: links_non_perl
[18311]	1900	SL/SAICALC/SAICALC.dummy: links_non_perl
[8297]	1901	SL/SEQIO/SEQIO.dummy: links_non_perl
[7819]	1902	SL/SEQUENCE/SEQUENCE.dummy: links_non_perl
	1903	SL/TRANSLATE/TRANSLATE.dummy: links_non_perl
[8557]	1904	SL/TREE_ADMIN/TREE_ADMIN.dummy: links_non_perl
[7819]	1905	SL/TREE_READ/TREE_READ.dummy: links_non_perl
	1906	SL/TREE_WRITE/TREE_WRITE.dummy: links_non_perl
	1907	SL/TREEDISP/TREEDISP.dummy: links_non_perl
[18092]	1908	SL/XFERGUI/XFERGUI.dummy: links_non_perl
[18088]	1909	SL/XFERSET/XFERSET.dummy: links_non_perl
[7819]	1910	STAT/STAT.dummy: links_non_perl
	1911	TREEGEN/TREEGEN.dummy: links_non_perl
[8297]	1912	WETC/WETC.dummy: links_non_perl
[7819]	1913	WINDOW/libWINDOW.dummy: links_non_perl
	1914	XML/XML.dummy: links_non_perl
	1915
	1916	ifeq ($(OPENGL),1)
	1917	GL/glAW/glAW.dummy: links_non_perl
	1918	GL/glpng/glpng.dummy: links_non_perl
	1919	GL/GL.dummy: GL/glAW/glAW.dummy GL/glpng/glpng.dummy
	1920	RNA3D/RNA3D.dummy: links_non_perl gl
	1921	endif
	1922
	1923	UNIT_TESTER/UNIT_TESTER.dummy: link_db \
[7409]	1924	SERVERCNTRL/SERVERCNTRL.dummy \
[7819]	1925
[13765]	1926	# see also TOOLS/Makefile@TOOLSLIBDEPENDS
[7819]	1927	TOOLS/TOOLS.dummy : links_non_perl link_db \
[13765]	1928	CONSENSUS_TREE/CONSENSUS_TREE.dummy \
[7819]	1929	SERVERCNTRL/SERVERCNTRL.dummy \
[13765]	1930	SL/FILTER/FILTER.dummy \
[16119]	1931	SL/FILTSEQEXP/FILTSEQEXP.dummy \
[13765]	1932	SL/INSDEL/INSDEL.dummy \
	1933	SL/REGEXPR/REGEXPR.dummy \
	1934	SL/SEQIO/SEQIO.dummy \
	1935	SL/TREE_READ/TREE_READ.dummy \
[7409]	1936	SL/TREE_WRITE/TREE_WRITE.dummy \
	1937	XML/XML.dummy \
[5143]	1938
[7819]	1939	AWTC/AWTC.dummy : com
[7409]	1940
[7819]	1941	NAMES/NAMES.dummy : com
	1942	SL/AW_NAME/AW_NAME.dummy : com
[5143]	1943
[7819]	1944	PROBE/PROBE.dummy : com
	1945	MULTI_PROBE/MULTI_PROBE.dummy : com
	1946	PROBE_DESIGN/PROBE_DESIGN.dummy : com
	1947	NALIGNER/NALIGNER.dummy : com
[5143]	1948
[18875]	1949	ARB_GDE/ARB_GDE.dummy : proto_tools menus
[5143]	1950
[11533]	1951	compile_compatibility: SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.dummy
	1952
[2]	1953	#***************************************************************************************
	1954	# Short aliases to make targets
	1955	#***************************************************************************************
	1956
[1076]	1957	show:
	1958	@echo $(SEP)
	1959	@echo 'Aliases for often needed targets:'
	1960	@echo ''
	1961	@echo ' executables:'
	1962	@echo ''
	1963	@echo ' nt arb_ntree'
	1964	@echo ' e4 arb_edit4 (includes secedit)'
	1965	@echo ' di arb_dist'
	1966	@echo ' ph arb_phylo'
	1967	@echo ' pa arb_parsimony'
	1968	@echo ' tg arb_treegen'
	1969	@echo ' ds arb_dbserver'
[1938]	1970	@echo ' pt arb_pt_server'
[1076]	1971	@echo ' na arb_name_server'
	1972	@echo ''
	1973	@echo ' libraries:'
	1974	@echo ''
	1975	@echo ' com communication libraries'
[6318]	1976	@echo ' db ARB database'
[1076]	1977	@echo ' aw GUI lib'
	1978	@echo ' awt GUI toolkit'
	1979	@echo ' awtc general purpose library'
	1980	@echo ' awti import/export library'
	1981	@echo ' mp multi probe library'
	1982	@echo ' ge genome library'
	1983	@echo ' pd probe design lib'
	1984	@echo ' prd primer design lib'
	1985	@echo ''
	1986	@echo ' other targets:'
	1987	@echo ''
	1988	@echo ' help recompile help files'
	1989	@echo ' tools make small tools used by arb'
	1990	@echo ''
	1991	@echo ' foreign targets:'
	1992	@echo ''
	1993	@echo ' gde GDE'
	1994	@echo ' agde ARB_GDE'
	1995	@echo ''
	1996	@echo 'for other targets inspect $(ARBHOME)/Makefile'
	1997	@echo ''
	1998	@echo $(SEP)
	1999
[2520]	2000	source_doc:
[6864]	2001	@echo "Remove some links (doxygen crashes otherwise):"
	2002	find . $ -name "AISC" -o -name "C" -o -name "GDEHELP" $ -type l -exec rm {} \;
[11492]	2003	doxygen 2>&1 1>/dev/null
[6864]	2004	$(MAKE) forcelinks
[1138]	2005
[7633]	2006	dep_graph:
	2007	@echo "Building some dependency graphs"
	2008	SOURCE_TOOLS/dependency_graphs.pl
	2009
[5166]	2010	help: HELP_SOURCE/HELP_SOURCE.dummy
[369]	2011
[10842]	2012	HELP_SOURCE/HELP_SOURCE.dummy: link_core xml menus
[5143]	2013
	2014	db: ARBDB/libARBDB.dummy
[7183]	2015	core: CORE/libCORE.dummy
[6407]	2016	aw: WINDOW/libWINDOW.dummy
[2]	2017	awt: AWT/libAWT.dummy
[33]	2018	awtc: AWTC/AWTC.dummy
[68]	2019	awti: AWTI/AWTI.dummy
[2]	2020
	2021	mp: MULTI_PROBE/MULTI_PROBE.dummy
[5143]	2022	mg: MERGE/MERGE.dummy
[26]	2023	ge: GENOM/GENOM.dummy
[113]	2024	prd: PRIMER_DESIGN/PRIMER_DESIGN.dummy
[2]	2025
[3447]	2026	nt: menus $(NTREE)
[2]	2027
[866]	2028	nal: $(NALIGNER)
[2]	2029
[3447]	2030	di: $(DIST)
	2031	ph: $(PHYLO)
	2032	pa: $(PARSIMONY)
	2033	tg: $(TREEGEN)
[3429]	2034
[7819]	2035	ifeq ($(OPENGL),1)
[4844]	2036	3d: RNA3D/RNA3D.dummy
[3447]	2037	gl: GL/GL.dummy
[7819]	2038	else
	2039	noopengl:
	2040	@echo "invalid target for OPENGL=0"
	2041	3d: noopengl
	2042	gl: noopengl
	2043	endif
[2]	2044
[7819]	2045	SL/SL.dummy: com
	2046
[3447]	2047	ds: $(DBSERVER)
	2048	pt: $(PROBE)
[5143]	2049	pst: PROBE_SET/PROBE_SET.dummy
[3447]	2050	pd: PROBE_DESIGN/PROBE_DESIGN.dummy
	2051	na: $(NAMES)
[5660]	2052	sq: SEQ_QUALITY/SEQ_QUALITY.dummy
[7899]	2053	cma: $(RNACMA)
[2]	2054
[5704]	2055	sec: SECEDIT/SECEDIT.dummy
[2]	2056
[7819]	2057	e4: $(EDIT4) readseq menus
	2058
[3447]	2059	gi: GENOM_IMPORT/GENOM_IMPORT.dummy
[5884]	2060	wetc: $(WETC)
[2]	2061
[151]	2062	xml: XML/XML.dummy
[6393]	2063	stat: STAT/STAT.dummy $(NTREE) $(EDIT4)
[6691]	2064	fa: SL/FAST_ALIGNER/FAST_ALIGNER.dummy
[151]	2065
[2]	2066	#********************************************************************************
	2067
[13443]	2068	up_by_remake: depends proto vectorize_checks
[4559]	2069
[8706]	2070	up: up_by_remake tags valgrind_update
[7890]	2071
[4559]	2072	#********************************************************************************
	2073
[7178]	2074	touch:
[5952]	2075	SOURCE_TOOLS/touch_modified.pl
[7178]	2076
	2077	modified: touch
[5952]	2078	$(MAKE) all
	2079
	2080	#********************************************************************************
	2081
[7819]	2082	libdepends:
[9578]	2083	$(MAKE) -C "SOURCE_TOOLS" \
	2084	"RNA3D_LIB=$(RNA3D_LIB_4_DEPENDS)" \
	2085	libdepends
[7819]	2086
	2087	#********************************************************************************
	2088
[9577]	2089	# create generated headers:
	2090	genheaders: TEMPLATES/TEMPLATES.dummy
	2091
	2092	clrdotdepends:
[14799]	2093	rm PROBE_COM/.depends \|\| true
	2094	rm NAMES_COM/.depends \|\| true
	2095	rm PERL2ARB/.depends \|\| true
[9577]	2096
[19043]	2097	comdepends: comtools clrdotdepends have_makedepend
[9577]	2098	@echo "$(SEP) Partially build com interface"
[10153]	2099	$(MAKE) PROBE_COM/PROBE_COM.depends NAMES_COM/NAMES_COM.depends
	2100	$(MAKE) PROBE_COM/server.depends NAMES_COM/server.depends
[9577]	2101
[19043]	2102	depends: genheaders comdepends vectorize_checks have_makedepend
[9577]	2103	@echo "$(SEP) Updating other dependencies"
[18426]	2104	$(MAKE) $(subst NAMES_COM/server.depends,,$(subst PROBE_COM/server.depends,,$(SUBDIRS:.sub=.depends))) \
[11533]	2105	HELP_SOURCE/HELP_SOURCE.depends \
	2106	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.depends \
	2107
[9577]	2108	$(MAKE) libdepends
[200]	2109
[5714]	2110	depend: depends
	2111
[10153]	2112	# ------------------------------------------------------------
	2113	# dependency generation tests for AISC code
	2114	#(all should work w/o creating wrong dependencies;
	2115	# neither in XXX_COM/Makefile nor in code using AISC interface)
	2116	dependstest1: silent_clean
	2117	$(MAKE) depends
	2118	dependstest2: silent_clean
	2119	$(MAKE) com
	2120	dependstest3: silent_clean
	2121	$(MAKE) aw
	2122	dependstest4: silent_clean
	2123	$(MAKE) pt
	2124	dependstest5: silent_clean
	2125	$(MAKE) na
	2126	dependstest6: silent_clean
	2127	$(MAKE) nt
	2128	dependstest7: silent_clean
	2129	$(MAKE) all
	2130	# ------------------------------------------------------------
	2131
[13443]	2132	vectorize_checks:
	2133	$(MAKE) -C SOURCE_TOOLS -r vectorize_checks
	2134
[16628]	2135	clean_checked_vect: lib/lib.clean
	2136	SOURCE_TOOLS/clean_checked_vectorizations.sh
	2137
[13443]	2138	# ------------------------------------------------------------
	2139
[7819]	2140	AISC_MKPTPS/AISC_MKPTPS.dummy: links
[5143]	2141
[7819]	2142	proto_tools: AISC_MKPTPS/AISC_MKPTPS.dummy
	2143
[5843]	2144	proto: proto_tools
[5845]	2145	@echo $(SEP) Updating prototypes
	2146	$(MAKE) \
	2147	ARBDB/ARBDB.proto \
[8818]	2148	AISC_COM/AISC_COM.proto \
[5845]	2149	ARB_GDE/ARB_GDE.proto \
[7339]	2150	CORE/CORE.proto \
[5845]	2151	CONVERTALN/CONVERTALN.proto \
	2152	NTREE/NTREE.proto \
[9797]	2153	MERGE/MERGE.proto \
[17738]	2154	PROBE/PROBE.proto \
[5845]	2155	SERVERCNTRL/SERVERCNTRL.proto \
[6280]	2156	SL/SL.proto \
[4600]	2157
[200]	2158	#********************************************************************************
	2159
[7819]	2160	valgrind_update: links
[5845]	2161	@echo $(SEP) Updating for valgrind
	2162	$(MAKE) -C SOURCE_TOOLS valgrind_update
[4844]	2163
	2164	#********************************************************************************
	2165
[2586]	2166	TAGFILE=TAGS
[17367]	2167	UTAGS=TAGS.$(ARBBID)
	2168	TAGFILE_TMP=$(UTAGS).tmp
[2586]	2169
[17367]	2170	TAG_SOURCE_HEADERS=$(UTAGS).headers.tmp
	2171	TAG_SOURCE_CODE=$(UTAGS).codefiles.tmp
[7819]	2172	TAG_SOURCE_LISTS=$(TAG_SOURCE_HEADERS) $(TAG_SOURCE_CODE)
[200]	2173
[15513]	2174	ETAGS_IGNORE_LIST=SOURCE_TOOLS/etags_ignore.lst
	2175
	2176	ETAGS=ctags -e -I @$(ETAGS_IGNORE_LIST) --sort=no --if0=no --extra=q
[7819]	2177	ETAGS_TYPES=--C-kinds=cgnsut --C++-kinds=cgnsut
	2178	ETAGS_FUN =--C-kinds=fm --C++-kinds=fm
	2179	ETAGS_REST =--C-kinds=dev --C++-kinds=dev
[200]	2180
[10573]	2181	FILTER_TAGS_SOURCES= \
	2182	$(SED) -e 's/^.\///g' \| \
[15483]	2183	grep -vi '^HEADERLIBS\\|^GDE/\\|/GEN[CH]/'
[10573]	2184
[7819]	2185	$(TAG_SOURCE_HEADERS): links
[17696]	2186	@find . $ -name '.hxx' -o -name ".h" $ -type f \| $(FILTER_TAGS_SOURCES) > $@
[2]	2187
[7819]	2188	$(TAG_SOURCE_CODE): links
[17696]	2189	@find . $ -name '.cxx' -o -name ".c" $ -type f \| $(FILTER_TAGS_SOURCES) > $@
[7819]	2190
[17367]	2191	$(UTAGS).1.tmp: $(TAG_SOURCE_HEADERS)
[17696]	2192	@$(ETAGS) -f $@ $(ETAGS_TYPES) -L $<
[17367]	2193	$(UTAGS).2.tmp: $(TAG_SOURCE_HEADERS)
[17696]	2194	@$(ETAGS) -f $@ $(ETAGS_FUN) -L $<
[17367]	2195	$(UTAGS).3.tmp: $(TAG_SOURCE_HEADERS)
[17696]	2196	@$(ETAGS) -f $@ $(ETAGS_REST) -L $<
[17367]	2197	$(UTAGS).4.tmp: $(TAG_SOURCE_CODE)
[17696]	2198	@$(ETAGS) -f $@ $(ETAGS_TYPES) -L $<
[17367]	2199	$(UTAGS).5.tmp: $(TAG_SOURCE_CODE)
[17696]	2200	@$(ETAGS) -f $@ $(ETAGS_FUN) -L $<
[17367]	2201	$(UTAGS).6.tmp: $(TAG_SOURCE_CODE)
[17696]	2202	@$(ETAGS) -f $@ $(ETAGS_REST) -L $<
[15513]	2203
[17367]	2204	TAGS_ALL_PARTS=$(UTAGS).1.tmp $(UTAGS).2.tmp $(UTAGS).3.tmp $(UTAGS).4.tmp $(UTAGS).5.tmp $(UTAGS).6.tmp
[15513]	2205
	2206	$(TAGFILE_TMP) : $(TAGS_ALL_PARTS)
[17696]	2207	@cat $(TAGS_ALL_PARTS) > $@
	2208	@rm $(TAGS_ALL_PARTS) $(TAG_SOURCE_LISTS)
[15513]	2209
[17727]	2210	cleanOldTags:
	2211	@find $(ARBHOME) -name 'TAGS.*.tmp' -ctime +2 -exec rm {} \;
	2212
	2213	tags: $(TAGFILE_TMP) cleanOldTags
[17696]	2214	@mv_if_diff $(TAGFILE_TMP) $(TAGFILE)
[7819]	2215
[200]	2216	#********************************************************************************
	2217
[8614]	2218	LINKSTAMP=SOURCE_TOOLS/stamp.generate_all_links
[2]	2219
[8246]	2220	links: checks $(LINKSTAMP) arbmainwrapper
[8439]	2221	links_no_checks: $(LINKSTAMP) arbmainwrapper
[6359]	2222
[6864]	2223	forcelinks:
[6872]	2224	-rm $(LINKSTAMP)
[6864]	2225	$(MAKE) links
	2226
[14055]	2227	$(LINKSTAMP): SOURCE_TOOLS/generate_all_links.sh genheaders
[7769]	2228	+SOURCE_TOOLS/generate_all_links.sh
[6359]	2229	touch $(LINKSTAMP)
[12]	2230
[7409]	2231	clean_links:
	2232	# avoid to delete linked pts, nas or arb_tcp.dat:
[6378]	2233	find . -path './lib' -prune -o -type l -exec rm {} \;
[10842]	2234	# removed obsolete file - refuses to disappear due to 'prune' above
	2235	@rm -f lib/help/GDEHELP
[7409]	2236	@rm -f $(LINKSTAMP) lib/inputMasks/format.readme
	2237
	2238	redo_links: clean_links
[8439]	2239	$(MAKE) links_no_checks
[6359]	2240
[7894]	2241	#********************************************************************************
	2242
[8670]	2243	header_libs:
[16266]	2244	@(( \
	2245	echo "$(SEP) Make HEADERLIBS"; \
	2246	$(MAKE) -C HEADERLIBS all && \
	2247	echo "$(SEP) Make HEADERLIBS [done]"; \
	2248	) > HEADERLIBS.log 2>&1 && (cat HEADERLIBS.log;rm HEADERLIBS.log)) \|\| (cat HEADERLIBS.log;rm HEADERLIBS.log;false)
[7894]	2249
	2250	#********************************************************************************
	2251
[2]	2252	gde: GDE/GDE.dummy
[2223]	2253	GDE: gde
[31]	2254	agde: ARB_GDE/ARB_GDE.dummy
[7409]	2255	tools: TOOLS/TOOLS.dummy
[7046]	2256	convert: $(CONVERT_ALN)
[2]	2257	readseq: READSEQ/READSEQ.dummy
	2258
	2259	#***************************************************************************************
	2260	# Some user commands
	2261	#***************************************************************************************
	2262
[7819]	2263	menus: binlink links
[5179]	2264	@(( \
[7819]	2265	echo "$(SEP) Make GDEHELP"; \
[8807]	2266	$(MAKE) -C GDEHELP -r all && \
[7819]	2267	echo "$(SEP) Make GDEHELP [done]"; \
[5179]	2268	) > GDEHELP.log 2>&1 && (cat GDEHELP.log;rm GDEHELP.log)) \|\| (cat GDEHELP.log;rm GDEHELP.log;false)
[2]	2269
[2303]	2270	ifeq ($(DEBUG),1)
	2271	BIN_TARGET=develall
	2272	else
	2273	BIN_TARGET=all
	2274	endif
	2275
	2276
[2]	2277	binlink:
[2303]	2278	$(MAKE) -C bin $(BIN_TARGET)
[2]	2279
[16127]	2280	check_bin_dep: binlink
	2281	SOURCE_TOOLS/check_bin_dependencies.pl
	2282
[18168]	2283	fig_cure:
	2284	SOURCE_TOOLS/sortfig.pl doit
	2285
[4218]	2286	preplib:
[5223]	2287	(cd lib;$(MAKE) all)
[369]	2288
[7819]	2289	# --------------------------------------------------------------------------------
	2290	# This section is quite tricky:
	2291	#
	2292	# make 'perl' is a BIG target, so when it has to be made, it has to be started
	2293	# as early as possible to reduce overall compile time. Since 'make' does not
[17738]	2294	# provide any priorities, i force it to build all 'perl'-prerequisites early, by
	2295	# adding artificial dependencies to these prerequisites
[7819]	2296	#
	2297	# That behavior is likely to be system-dependent.
	2298	# My goal was only to make it work on my current development system,
	2299	# where this saves about 20% of overall build time.
	2300
	2301	ifeq ($(WITHPERL),1)
	2302	links_non_perl: PERLTOOLS/PERLTOOLS.dummy
	2303	perltools: links_non_perl
	2304	perl: realperl
	2305	else
	2306	links_non_perl: links
[18907]	2307	perl: links
[7819]	2308	$(MAKE) "WITHPERL=1" perl
	2309	endif
	2310
[4632]	2311	# ---------------------------------------- perl
[2]	2312
[7819]	2313	realperl: perltools
[8320]	2314	(( \
[7819]	2315	echo "$(SEP) Make PERL2ARB" ; \
[8675]	2316	$(TIME) $(MAKE) -C PERL2ARB -r -f Makefile.main \
[7819]	2317	"AUTODEPENDS=1" \
	2318	"dflags=$(dflags)" \
[13739]	2319	"cflags4perl=$(cflags) $(cxxflags) $(dflags)" \
[13740]	2320	"lflags4perl=$(lflags4perl)" \
[10993]	2321	"COMPILER_VERSION=$(COMPILER_VERSION)" \
[7819]	2322	all && \
[17738]	2323	$(MAKE) -C PERL_SCRIPTS/test test && \
[7819]	2324	echo "$(SEP) Make PERL2ARB [done]" ; \
	2325	) > PERL2ARB.log 2>&1 && (cat PERL2ARB.log;rm PERL2ARB.log)) \|\| (cat PERL2ARB.log;rm PERL2ARB.log;false)
[2]	2326
[4632]	2327	perl_clean:
	2328	@$(MAKE) -C PERL2ARB -r -f Makefile.main \
	2329	"AUTODEPENDS=0" \
	2330	clean
[2142]	2331
[7409]	2332	PERL2ARB/PERL2ARB.clean:
	2333	$(MAKE) perl_clean
[12695]	2334	$(MAKE) -C PERL_SCRIPTS/test clean
[7409]	2335
[8848]	2336	# ---------------------------------------- bindings to script languages
[7409]	2337
[8848]	2338	bindings: lib/libCORE.so lib/libARBDB.so
	2339	$(MAKE) -C BINDINGS all ARBDEPENDS="$(^:%=../%)" DFLAGS="$(dflags)"
	2340
	2341	bindings_clean:
	2342	$(MAKE) -C BINDINGS clean
	2343
[14141]	2344	# ---------------------------------------- check resources
[5887]	2345
[6122]	2346	check_res:
[14141]	2347	$(ARBHOME)/SOURCE_TOOLS/check_resources.pl
[5887]	2348
[4632]	2349	# ---------------------------------------- cleaning
	2350
[2]	2351	rmbak:
[16437]	2352	@echo "[cleanup backup/core files]"
[7409]	2353	@find . \( -name '*%' \
	2354	-o -name '*.bak' \
	2355	-o -name '*~' \) \
[10439]	2356	-o $ -name 'core' -a \! -type d $ \
[16437]	2357	-exec rm -v {} \; \|\| \
	2358	echo "Warning: target 'rmbak' reported problems when removing misc. backup files (ignored)"
	2359	@echo "[cleanup done]"
[2]	2360
[7409]	2361	bin_reinit:
	2362	$(MAKE) bin/bin.clean
[7769]	2363	$(MAKE) -C "bin" all
[2]	2364
[7409]	2365	clean_directories:
[7673]	2366	-rm -rf \
[7409]	2367	$(ARBHOME)/PROBE_SET/bin \
	2368	$(ARBHOME)/INCLUDE \
	2369
[2907]	2370	libclean:
[7769]	2371	-find $(ARBHOME) -type f $ -name '*.a' ! -type l $ -exec rm -f {} \;
[18140]	2372	-find $(ARBHOME) -type f $ -name 'lib*.so' ! -type l $ -exec rm -f {} \;
[2907]	2373
[5672]	2374	objclean:
[7769]	2375	-find $(ARBHOME) -type f $ -name '*.o' ! -type l $ -exec rm -f {} \;
[5672]	2376
[7769]	2377	# bin.clean and HELP_SOURCE.clean interfere
	2378	clean3:
	2379	$(MAKE) bin/bin.clean
	2380	$(MAKE) HELP_SOURCE/HELP_SOURCE.clean
	2381
[18120]	2382
	2383	# delete all binaries (similar to 'cleanlinked')
	2384	cleanRelinkable: libclean UNIT_TESTER/UNIT_TESTER.clean
	2385	$(MAKE) -C bin cleanbinariesRelinkable
[18140]	2386	$(MAKE) -C PROBE_SET cleanLinked
[18120]	2387
	2388
[18426]	2389	clean2: $(SUBDIRS:.sub=.clean) \
[7769]	2390	clean3 \
[7409]	2391	rmbak \
	2392	libclean \
	2393	objclean \
	2394	lib/lib.clean \
[4632]	2395	GDEHELP/GDEHELP.clean \
[7895]	2396	HEADERLIBS/HEADERLIBS.clean \
[4632]	2397	SOURCE_TOOLS/SOURCE_TOOLS.clean \
[11533]	2398	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.clean \
[6460]	2399	UNIT_TESTER/UNIT_TESTER.clean \
[7409]	2400	TEMPLATES/TEMPLATES.clean \
	2401	perl_clean \
	2402	clean_directories \
[2]	2403
[10993]	2404	rm -f .last_gcc .last_compiler config.makefile.bak
[7409]	2405
[4923]	2406	# links are needed for cleanup
[9777]	2407	clean: redo_links motif_xpm_hack_clean
[4923]	2408	$(MAKE) clean2
[7810]	2409	$(MAKE) clean_cov_all clean_links
[4923]	2410
[10153]	2411	silent_clean:
	2412	$(MAKE) clean >/dev/null
	2413
[5672]	2414	# 'relocated' is about 50% faster than 'rebuild'
[5833]	2415	reloc_clean: links
[5663]	2416	@echo "---------------------------------------- Relocation cleanup"
[5672]	2417	$(MAKE) \
	2418	perl_clean \
	2419	GDEHELP/GDEHELP.clean \
	2420	HELP_SOURCE/genhelp/genhelp.clean \
[7431]	2421	bin/bin.clean \
[5672]	2422	libclean \
	2423	objclean
[5833]	2424
	2425	relocated: links
	2426	$(MAKE) reloc_clean
[5672]	2427	@echo "---------------------------------------- and remake"
[7409]	2428	$(MAKE) build
[5663]	2429
[4632]	2430	# -----------------------------------
[12400]	2431	# some stress tests
	2432	# (helpful to reveal race conditions with -j)
[2]	2433
[7409]	2434	rebuild4ever: rebuild
	2435	$(MAKE) rebuild4ever
	2436
	2437	build4ever: build
	2438	$(MAKE) build4ever
	2439
	2440	clean4ever: clean
	2441	$(MAKE) clean4ever
	2442
	2443	test4ever: ut
	2444	$(MAKE) test4ever
	2445
[13923]	2446	perl4ever: clean
[7409]	2447	$(MAKE) links
	2448	$(MAKE) perl
	2449	$(MAKE) perl4ever
	2450
[12400]	2451	help4ever: clean
	2452	$(MAKE) help
	2453	$(MAKE) help4ever
[7409]	2454
	2455	# -----------------------------------
	2456
[14205]	2457	cleanlinked: bin/bin.clean libclean
[2907]	2458
[14205]	2459	relink: cleanlinked
	2460	$(MAKE) all
	2461
[18924]	2462	# --------------------------------------------------------------------------------
	2463	# source related targets
[4632]	2464
[18923]	2465	CLOC=cloc
	2466	CLOCFLAGS=--no3 --quiet --progress-rate=0
	2467	CLOCARB=--exclude-dir=GDE .
	2468	CLOCEXT=GDE
	2469	CLOCCODE=--force-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.code.def
	2470	CLOCREST=--force-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.rest.def
	2471	CLOCFILT=tail --lines=+4
	2472
	2473	cloc:
	2474	@echo 'Arb code:'
	2475	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCARB) \| $(CLOCFILT)
	2476	@echo 'Arb rest:'
	2477	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCARB) \| $(CLOCFILT)
	2478	@echo 'External code:'
	2479	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCEXT) \| $(CLOCFILT)
	2480	@echo 'External rest:'
	2481	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCEXT) \| $(CLOCFILT)
	2482
	2483
[18924]	2484	# patch generation
[6718]	2485	patch:
[18912]	2486	SOURCE_TOOLS/arb_create_patch.sh arbPatch --svn
[6718]	2487
[18924]	2488	# source tarball generation
	2489	save: sourcetarfile
	2490
	2491	sourcetarfile: rmbak
	2492	util/arb_save
	2493
[6718]	2494	# test early whether save will work
[7184]	2495	savetest:
[5257]	2496	@util/arb_srclst.pl >/dev/null
	2497
[7184]	2498	testsave: savetest
	2499
[4844]	2500	save2: rmbak
[5477]	2501	util/arb_save ignore
[4844]	2502
[5947]	2503	save_test: rmbak
	2504	@echo "Testing source list.."
	2505	@util/arb_srclst.pl > /dev/null
	2506
[8606]	2507	save_test_no_error:
	2508	@-$(MAKE) save_test
	2509
[18924]	2510	# --------------------------------------------------------------------------------
	2511	# version management
	2512
[11669]	2513	inc_candi:
	2514	touch SOURCE_TOOLS/inc_candi.stamp
	2515	$(MAKE) do_version_update
	2516
	2517	inc_patch:
	2518	touch SOURCE_TOOLS/inc_patch.stamp
	2519	$(MAKE) do_version_update
	2520
	2521	inc_minor:
[5477]	2522	touch SOURCE_TOOLS/inc_minor.stamp
[11669]	2523	$(MAKE) do_version_update
[5477]	2524
[11669]	2525	inc_major:
[5477]	2526	touch SOURCE_TOOLS/inc_major.stamp
[11669]	2527	$(MAKE) do_version_update
[5477]	2528
[13923]	2529	do_version_update:
[11669]	2530	@echo Incrementing version information
[15805]	2531	$(MAKE) savetest
[9577]	2532	$(MAKE) genheaders # auto upgrades version early
[3346]	2533
[11674]	2534	show_version:
	2535	$(MAKE) genheaders # updates version info
	2536	@echo "$(SEP) ARB version info"
	2537	@grep ARB_VERSION TEMPLATES/arb_build.h
	2538	@echo "$(SEP)"
	2539
[1878]	2540	# --------------------------------------------------------------------------------
[15737]	2541	# special cleanups
[1878]	2542
[15737]	2543	clean_opengl_changed: RNA3D/RNA3D.clean EDIT4/EDIT4.clean WINDOW/WINDOW.clean GL/GL.clean
	2544
	2545	# --------------------------------------------------------------------------------
	2546
[10137]	2547	arbapplications: nt pa e4 wetc pt na nal di ph ds wetc cma
[2]	2548
[18426]	2549	arb_external: convert tools gde readseq tg pst
[3635]	2550
[7819]	2551	arb_no_perl: arbapplications help arb_external
[866]	2552
[9777]	2553	arb: motif_xpm_hack
[7819]	2554	$(MAKE) "WITHPERL=1" perl arb_no_perl
[866]	2555
[9777]	2556	motif_xpm_hack:
	2557	$(MAKE) -r -C "lib/motifHack" all
	2558
	2559	motif_xpm_hack_clean:
	2560	$(MAKE) -r -C "lib/motifHack" clean
	2561
[7819]	2562	# --------------------------------------------------------------------------------
	2563	# special targets for SOURCE_TOOLS/remake_after_change.pl
[866]	2564
[7819]	2565	rac_arb_dist: di
	2566	rac_arb_edit4: e4
	2567	rac_arb_ntree: nt
	2568	rac_arb_pars: pa
	2569	rac_arb_phylo: ph
	2570	rac_arb_wetc: wetc
	2571	rac_arb_naligner: nal
	2572	rac_arb_pt_server: pt
	2573	rac_arb_db_server: ds
	2574	rac_arb_name_server: na
	2575	rac_arb_convert_aln: convert
	2576	rac_arb_treegen: tg
[7895]	2577	rac_arb_rnacma: cma
[10951]	2578	rac_arb_help2xml: help
[10948]	2579
	2580	rac_arb_a2ps: tools
	2581	rac_arb_consensus_tree: tools
	2582	rac_arb_dnarates: tools
	2583	rac_arb_export_rates: tools
	2584	rac_arb_export_tree: tools
	2585	rac_arb_gene_probe: tools
	2586	rac_arb_message: tools
	2587	rac_arb_primer: tools
[10943]	2588	rac_arb_probe: tools
[10948]	2589	rac_arb_read_tree: tools
[866]	2590
[6451]	2591	# --------------------------------------------------------------------------------
[13923]	2592	# unit testing
[6546]	2593	# @@@ work in progress
	2594	#
	2595	# goal is to automatically test all libraries/executables using TESTED_UNITS_AUTO
[18426]	2596	# currently not all test executables link w/o error.
	2597	# therefor units are organized in three sets:
[6546]	2598	#
[18426]	2599	# TESTED_UNITS = testable and contain tests
	2600	# UNTESTED_UNITS = testable, but no tests written yet
	2601	# UNTESTABLE_UNITS = not testable
[6451]	2602
[18426]	2603	# always define OPENGL units manually:
	2604	OPENGL_TESTS :=
	2605	ifeq ($(OPENGL),1)
	2606	OPENGL_TESTS += \
	2607	$(subst .a,.test,$(RNA3D_LIB)) \
	2608	GL/glAW/libglAW.test \
	2609	GL/glpng/libglpng_arb.test \
[6863]	2610
[18426]	2611	endif
[6451]	2612
[18426]	2613	UNITS_NOT_AUTODETECTED = \
	2614	HELP_SOURCE/HELP_SOURCE.tooltests
	2615
	2616	TESTED_UNITS_AUTO = \
	2617	$(OPENGL_TESTS) \
	2618	$(TL_ARCHIVES:.a=.test) \
	2619	$(TL_SHARED_ARCHIVES:.so=.test) \
	2620	$(CL_ARCHIVES:.a=.test) \
	2621	$(TL_TOOLS_COLLECTIONS:.toolColl=.tooltests) \
	2622	$(UNITS_NOT_AUTODETECTED) \
	2623
	2624	UNTESTED_UNITS = \
	2625	$(OPENGL_TESTS) \
[7801]	2626	EISPACK/EISPACK.test \
[8250]	2627	GENOM/GENOM.test \
[6451]	2628	ISLAND_HOPPING/ISLAND_HOPPING.test \
[7801]	2629	NALIGNER/NALIGNER.test \
	2630	NAMES/NAMES.test \
	2631	PHYLO/PHYLO.test \
	2632	PRIMER_DESIGN/PRIMER_DESIGN.test \
[18426]	2633	READSEQ/READSEQ.tooltests \
[7801]	2634	SECEDIT/SECEDIT.test \
	2635	SEQ_QUALITY/SEQ_QUALITY.test \
	2636	SERVERCNTRL/SERVERCNTRL.test \
[6451]	2637	SL/ALIVIEW/ALIVIEW.test \
	2638	SL/AP_TREE/AP_TREE.test \
	2639	SL/ARB_TREE/ARB_TREE.test \
	2640	SL/AW_HELIX/AW_HELIX.test \
	2641	SL/AW_NAME/AW_NAME.test \
	2642	SL/DB_SCANNER/DB_SCANNER.test \
[18426]	2643	SL/DB_UI/DB_UI.test \
[6451]	2644	SL/GUI_ALIVIEW/GUI_ALIVIEW.test \
	2645	SL/HELIX/HELIX.test \
[15852]	2646	SL/QUERY/QUERY.test \
[7801]	2647	SL/REFENTRIES/REFENTRIES.test \
[6451]	2648	SL/SEQUENCE/SEQUENCE.test \
[8557]	2649	SL/TREE_ADMIN/TREE_ADMIN.test \
[6451]	2650	SL/TREE_WRITE/TREE_WRITE.test \
[18140]	2651	SL/XFERGUI/XFERGUI.test \
[6451]	2652	STAT/STAT.test \
[7801]	2653	TREEGEN/TREEGEN.test \
[6451]	2654	WETC/WETC.test \
[7801]	2655	XML/XML.test \
[6451]	2656
[6865]	2657	# untestable units
[6451]	2658
[18426]	2659	UNTESTABLE_UNITS = \
	2660	AISC/AISC.test \
	2661	NAMES_COM/server.test \
	2662	PROBE_COM/server.test \
[6451]	2663
[18426]	2664	# --------------------
	2665	# put all units containing tests into the following 4 sections (see also TESTED_UNITS below)
[6865]	2666
[16564]	2667	# recent development
[7819]	2668	UNITS_TESTED_FIRST = \
[18634]	2669	SL/MATRIX/MATRIX.test \
[16564]	2670	AWTI/AWTI.test \
[16119]	2671	SL/FILTSEQEXP/FILTSEQEXP.test \
[15966]	2672	SL/GROUP_SEARCH/GROUP_SEARCH.test \
[18426]	2673	SL/PVP/PVP.test \
	2674	SL/SAICALC/SAICALC.test \
	2675	SL/TRANSLATE/TRANSLATE.test \
	2676	SL/XFERSET/XFERSET.test \
[13625]	2677
[16564]	2678	# start units with long duration early
[15579]	2679	UNITS_RUNNING_LONG = \
	2680	ARBDB/libARBDB.test \
	2681	AWTC/AWTC.test \
[18426]	2682	TOOLS/TOOLS.tooltests \
[15579]	2683
[16564]	2684	# plain test-libaries that are not linked anywhere
	2685	TEST_SANDBOXES = \
	2686	SL/CB/CB.test \
[18959]	2687	SL/HEADERTESTS/HEADERTESTS.test \
[16564]	2688
[13625]	2689	UNITS_TESTED = \
[18426]	2690	AISC_MKPTPS/AISC_MKPTPS.tooltests \
[10380]	2691	ARB_GDE/ARB_GDE.test \
[15579]	2692	AWT/libAWT.test \
[8460]	2693	CONSENSUS_TREE/CONSENSUS_TREE.test \
[15579]	2694	CONVERTALN/CONVERTALN.test \
	2695	CORE/libCORE.test \
[8101]	2696	DBSERVER/DBSERVER.test \
[15579]	2697	DIST/DIST.test \
	2698	EDIT4/EDIT4.test \
	2699	GENOM_IMPORT/GENOM_IMPORT.test \
[18426]	2700	HELP_SOURCE/HELP_SOURCE.tooltests \
[6865]	2701	MERGE/MERGE.test \
[15579]	2702	MULTI_PROBE/MULTI_PROBE.test \
	2703	NTREE/NTREE.test \
	2704	PARSIMONY/PARSIMONY.test \
[18426]	2705	PERLTOOLS/PERLTOOLS.tooltests \
[15579]	2706	PROBE/PROBE.test \
[19339]	2707	PROBE_DESIGN/PROBE_DESIGN.test \
[18426]	2708	PROBE_SET/PROBE_SET.tooltests \
	2709	RNACMA/RNACMA.test \
[15579]	2710	SL/ALILINK/ALILINK.test \
	2711	SL/CONSENSUS/CONSENSUS.test \
	2712	SL/DB_QUERY/DB_QUERY.test \
[6688]	2713	SL/FAST_ALIGNER/FAST_ALIGNER.test \
[15579]	2714	SL/FILTER/FILTER.test \
	2715	SL/INSDEL/INSDEL.test \
	2716	SL/ITEM_SHADER/ITEM_SHADER.test \
	2717	SL/ITEMS/ITEMS.test \
[18426]	2718	SL/LOCATION/LOCATION.test \
[15579]	2719	SL/MACROS/MACROS.test \
	2720	SL/NDS/NDS.test \
	2721	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.test \
[6865]	2722	SL/PRONUC/PRONUC.test \
[15579]	2723	SL/PTCLEAN/PTCLEAN.test \
	2724	SL/REGEXPR/REGEXPR.test \
	2725	SL/SEQIO/SEQIO.test \
	2726	SL/TREE_READ/TREE_READ.test \
	2727	SL/TREEDISP/TREEDISP.test \
[8574]	2728	WINDOW/libWINDOW.test \
[6451]	2729
[15579]	2730	TESTED_UNITS = \
	2731	$(UNITS_TESTED_FIRST) \
[16564]	2732	$(UNITS_RUNNING_LONG) \
[10205]	2733	$(TEST_SANDBOXES) \
[6546]	2734	$(UNITS_TESTED) \
[6451]	2735
[18426]	2736	# ----------------------------------------
[8249]	2737
[18426]	2738	ifeq ($(DEVELOPER),RALF)
	2739
	2740	DEFINED_TEST_UNITS = \
	2741	$(TESTED_UNITS) \
	2742	$(UNTESTED_UNITS) \
	2743	$(UNTESTABLE_UNITS) \
	2744
	2745	list_undefined_units:
	2746	@UNIT_TESTER/list_undefined_units.pl $(DEFINED_TEST_UNITS) -- $(TESTED_UNITS_AUTO)
	2747
	2748	else
	2749
	2750	list_undefined_units:
	2751
	2752	endif
	2753
[6743]	2754	# ----------------------------------------
	2755
	2756	TEST_LOG_DIR = UNIT_TESTER/logs
[6863]	2757	TEST_RUN_SUITE=$(MAKE) $(NODIR) -C UNIT_TESTER -f Makefile.suite -r
[18322]	2758	# -> UNIT_TESTER/Makefile.suite
[7802]	2759	TEST_MAKE_FLAGS=
	2760	TEST_POST_CLEAN=
	2761	ifeq ($(COVERAGE),1)
[7810]	2762	TEST_POST_CLEAN=$(MAKE) clean_cov
[7802]	2763	TEST_MAKE_FLAGS+=-j1
	2764	endif
[6743]	2765
[7802]	2766
[10205]	2767	%.test:
[6743]	2768	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
	2769	( \
[18361]	2770	echo "take[1]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
[6451]	2771	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
	2772	"UNITDIR=$(@D)" \
	2773	"UNITLIBNAME=$(@F:.test=)" \
[6526]	2774	"COVERAGE=$(COVERAGE)" \
[7819]	2775	"ARB_PID=$(ARB_PID)_$(@F)" \
[7802]	2776	runtest; \
[18361]	2777	echo "take[1]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"; \
[7802]	2778	$(TEST_POST_CLEAN) \
[11190]	2779	) >$(TEST_LOG_DIR)/$(@F).log 2>&1; \
	2780	UNIT_TESTER/log_result.pl $(TEST_LOG_DIR)/$(@F).log )
[6451]	2781
[18426]	2782	%.notest:
	2783	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
	2784	( \
	2785	echo "take[4]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
	2786	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
	2787	"UNITDIR=$(@D)" \
	2788	"UNITLIBNAME=$(@F:.notest=)" \
	2789	"COVERAGE=0" \
	2790	"ARB_PID=$(ARB_PID)_$(@F)" \
	2791	check_no_test; \
	2792	echo "take[4]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'" \
	2793	) >$(TEST_LOG_DIR)/$(@F).log 2>&1 )
[7808]	2794
[18426]	2795
	2796	# tool test aliases (used to test one or multiple executable(s) in a single subdir):
	2797	%.tooltests:
	2798	$(error please define an explicit tooltest alias for $@)
	2799
	2800	AISC_MKPTPS/AISC_MKPTPS.tooltests : AISC_MKPTPS/mkptypes.test
	2801	@echo "aliasing $@ -> $^"
	2802	PERLTOOLS/PERLTOOLS.tooltests : PERLTOOLS/arb_proto_2_xsub.test
	2803	@echo "aliasing $@ -> $^"
	2804	PROBE_SET/PROBE_SET.tooltests : PROBE_SET/fb_test.test
	2805	@echo "aliasing $@ -> $^"
	2806	HELP_SOURCE/HELP_SOURCE.tooltests : HELP_SOURCE/arb_help2xml.test
	2807	@echo "aliasing $@ -> $^"
	2808	TOOLS/TOOLS.tooltests : TOOLS/arb_consensus_tree.test TOOLS/arb_probe.test TOOLS/arb_test.test
	2809	@echo "aliasing $@ -> $^"
	2810
	2811	# aliases for tools w/o tests:
	2812	READSEQ/READSEQ.tooltests:
	2813	@echo "Note: no tests for $@"
	2814
	2815
[10205]	2816	test_base: $(UNIT_TESTER_LIB:.a=.dummy) $(subst .test,.dummy,$(TEST_SANDBOXES))
[6451]	2817
[7810]	2818	clean_cov:
[6529]	2819	find . $ -name ".gcda" -o -name ".gcov" -o -name "*.cov" $ -exec rm {} \;
[6526]	2820
[7810]	2821	clean_cov_all: clean_cov
[6526]	2822	find . $ -name "*.gcno" $ -exec rm {} \;
	2823
[10677]	2824	cleanup_faked_arbpids:
[14799]	2825	@rm ~/.arb_tmp/tmp/arb_pids_${USER}_${ARB_PID}_* \|\| true
[10677]	2826
	2827	cleanup_faked_arbpids_and_fail: cleanup_faked_arbpids
[10676]	2828	@false
	2829
[18426]	2830	NOTESTS_IN_UNTESTED = $(subst .test,.notest,$(UNTESTED_UNITS))
[17701]	2831
[7819]	2832	run_tests_faked_arbpid:
[7769]	2833	+@$(TEST_RUN_SUITE) init
[18361]	2834	@echo "take[2]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
[18426]	2835	@$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(TESTED_UNITS) $(NOTESTS_IN_UNTESTED) \|\| $(MAKE) cleanup_faked_arbpids_and_fail
[18361]	2836	@echo "take[2]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
[10676]	2837	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
[8606]	2838	@$(MAKE) clean_cov >/dev/null
[10677]	2839	@$(MAKE) cleanup_faked_arbpids
[6451]	2840
[17665]	2841	# @@@ instead of only running UNIT, this should as well run all tests this unit depends on? according to 'needs_libs'
	2842	# @@@ 'run_tests_faked_arbpid' does not work for UNIT=ARBDB/libARBDB or UNIT=PARS/PARS -> could be solved via extra suffix, e.g. ARBDB/libARBDB.unit
	2843
	2844	run_onetest_faked_arbpid:
	2845	+@$(TEST_RUN_SUITE) init
[18361]	2846	@echo "take[3]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
[17665]	2847	test -n "$(UNIT)" \|\| (echo "Error: UNIT has to be defined for target 'run_onetest_faked_arbpid'!"; false)
	2848	$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(UNIT).test \|\| $(MAKE) cleanup_faked_arbpids_and_fail
[18361]	2849	@echo "take[3]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
[17665]	2850	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
	2851	@$(MAKE) clean_cov >/dev/null
	2852	@$(MAKE) cleanup_faked_arbpids
	2853
[17701]	2854	run_tests: test_base clean_cov
[18426]	2855	$(MAKE) "ARB_PID=UT_$$$$" run_tests_faked_arbpid list_undefined_units
[17701]	2856
	2857	run_oneunitstests: test_base
	2858	$(MAKE) "ARB_PID=UT_$$$$" run_onetest_faked_arbpid
	2859
	2860
[7046]	2861	ut:
	2862	ifeq ($(UNIT_TESTS),1)
[7819]	2863	@echo $(MAKE) run_tests
	2864	@$(MAKE) run_tests
[7046]	2865	else
	2866	@echo "Not compiled with unit tests"
	2867	endif
[6558]	2868
[7046]	2869
[6863]	2870	aut:
[7769]	2871	+@$(TEST_RUN_SUITE) unskip
[6863]	2872	$(MAKE) ut
	2873
[6451]	2874	# --------------------------------------------------------------------------------
	2875
[6708]	2876	TIMELOG=$(ARBHOME)/arb_time.log
[17618]	2877	TIMEARGS=--append --output=$(TIMELOG) --format=" * %E(%S+%U) %P [%C]"
[8675]	2878	TIMECMD=$(TIME) $(TIMEARGS)
[6708]	2879
[7819]	2880	time_one:
	2881	ifeq ($(ONE_TIMED_TARGET),)
	2882	@echo "Error: You have to pass ONE_TIMED_TARGET to $@"
	2883	false
	2884	else
	2885	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET)"
	2886	@$(TIMECMD) $(MAKE) $(ONE_TIMED_TARGET)
	2887	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET) [done]"
	2888	endif
[7409]	2889
[7819]	2890	timed_target:
	2891	ifeq ($(TIMED_TARGET),)
	2892	@echo "Error: You have to pass TIMED_TARGET to $@"
	2893	false
	2894	else
	2895	@echo "Build time:" > $(TIMELOG)
	2896	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
	2897	@cat $(TIMELOG)
	2898	@rm $(TIMELOG)
	2899	endif
	2900
	2901	timed_target_tested:
	2902	ifeq ($(TIMED_TARGET),)
	2903	@echo "Error: You have to pass TIMED_TARGET to $@"
	2904	false
	2905	else
	2906	@echo "Build time:" > $(TIMELOG)
	2907	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
	2908	$(MAKE) "ONE_TIMED_TARGET=ut" time_one
	2909	@cat $(TIMELOG)
	2910	@rm $(TIMELOG)
	2911	endif
	2912
	2913	clean_timed_target:
	2914	ifeq ($(TIMED_TARGET),)
	2915	@echo "Error: You have to pass TIMED_TARGET to $@"
	2916	false
	2917	else
	2918	@echo "Build time:" > $(TIMELOG)
	2919	$(MAKE) "ONE_TIMED_TARGET=clean" time_one
	2920	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
	2921	@cat $(TIMELOG)
	2922	@rm $(TIMELOG)
	2923	endif
	2924
	2925	# --------------------------------------------------------------------------------
	2926
[10345]	2927	CHECKOUT_MODIFIED=0# set to 1 to temporarily skip test for modifications (do not check in if set to 1)
	2928
[10344]	2929	check_svn_does_not_contain_generated:
[13923]	2930	ifeq ($(CHECKOUT_MODIFIED),0)
[10344]	2931	@echo "Testing that build does not modify files in SVN"
[10354]	2932	@test 0 = `svn status \| wc -l` \|\| ( \
[10344]	2933	echo "The checkout is not/no longer clean:"; \
	2934	svn status; \
	2935	echo "- if this fails instantly, your checkout is not clean"; \
	2936	echo "- if this fails after other targets, these targets modify checked in data"; \
	2937	echo " (a common cause may be that depends are not up to date)"; \
	2938	false)
[10345]	2939	else
	2940	grep -Hn 'CHECKOUT_MODIFIED' Makefile
	2941	endif
[10344]	2942
	2943	check_svn_ignores_generated:
[10354]	2944	@test 0 = `svn status \| grep '^\?' \| wc -l` \|\| ( \
[10344]	2945	echo "There are svn-unignored files:"; \
	2946	svn status \| grep '^\?'; \
	2947	echo "(all generated files should be svn-ignored)"; \
	2948	false)
	2949
	2950	check_svn_state: check_svn_does_not_contain_generated
	2951	$(MAKE) check_svn_ignores_generated
	2952	$(MAKE) savetest
	2953
	2954	things_that_always_should_work: depends proto
	2955
	2956	post_commit_check:
	2957	@echo "---------------------------------------- [Initial]"
	2958	$(MAKE) check_svn_state
	2959
	2960	$(MAKE) clean
	2961	@echo "---------------------------------------- [After 'make clean']"
	2962	$(MAKE) check_svn_state
	2963
	2964	$(MAKE) things_that_always_should_work
	2965	@echo "---------------------------------------- [After 'make things_that_always_should_work']"
	2966	$(MAKE) check_svn_state
	2967
	2968	$(MAKE) all
	2969	@echo "---------------------------------------- [After 'make all']"
	2970	$(MAKE) check_svn_state
	2971
	2972	$(MAKE) things_that_always_should_work
	2973	@echo "---------------------------------------- [Final]"
	2974	$(MAKE) check_svn_state
	2975
	2976	# --------------------------------------------------------------------------------
[13745]	2977	# sanitize arb_ntree; also works for clients (arb_edit4, ...) started from there.
[10344]	2978
[13745]	2979	sanitize: all
[13747]	2980	( \
	2981	export "LSAN_OPTIONS=max_leaks=30:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp"; \
	2982	echo "sake[1]: Entering directory \`$(ARBHOME)'"; \
	2983	$(ARBHOME)/bin/arb_ntree --execute _logged ~/data/test.arb 2>&1 ; \
	2984	echo "sake[1]: Leaving directory \`$(ARBHOME)'" \
	2985	) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
[13745]	2986
	2987	# --------------------------------------------------------------------------------
[16425]	2988	# build and test one unit:
[13745]	2989
[17701]	2990	build_oneunit:
[16425]	2991	$(MAKE) "WITHPERL=1" $(UNIT).dummy
	2992
	2993	oneunit:
	2994	ifndef UNIT
	2995	@echo "Please define UNIT, e.g. using"
	2996	@echo " make \"UNIT=ARBDB/libARBDB\" oneunit"
	2997	@echo " make \"UNIT=SL/TREEDISP/TREEDISP\" oneunit"
	2998	@echo "(Note: 1st is a shared library, 2nd isn't)"
	2999	false
	3000	else
	3001	@echo "Build time" > $(TIMELOG)
[17701]	3002	@echo "$(SEP) $(MAKE) build_oneunit"
	3003	@$(TIMECMD) $(MAKE) build_oneunit
[16425]	3004	ifeq ($(UNIT_TESTS),1)
[17665]	3005	@echo "$(SEP) $(MAKE) run_oneunitstests"
	3006	@$(TIMECMD) $(MAKE) run_oneunitstests
[16425]	3007	endif
	3008	@cat $(TIMELOG)
	3009	@rm $(TIMELOG)
	3010	endif
	3011
	3012	# --------------------------------------------------------------------------------
[18924]	3013	# Main targets:
[16425]	3014
[18924]	3015	tarfile: rebuild
	3016	$(MAKE) prepare_libdir
	3017	util/arb_compress
	3018
	3019	tarfile_quick: all
	3020	$(MAKE) prepare_libdir
	3021	util/arb_compress
	3022
	3023	# -----------------------------------
	3024
[7819]	3025	build: arb
[18168]	3026	$(MAKE) check_bin_dep preplib compile_compatibility fig_cure
[6708]	3027
[18917]	3028	all:
[6717]	3029	@echo "Build time" > $(TIMELOG)
[16653]	3030	# $(MAKE) clean_checked_vect # uncomment to rebuild sources where expected vectorization gets tested
[17665]	3031	@echo "$(SEP) $(MAKE) all"
[6717]	3032	@$(TIMECMD) $(MAKE) build
[5143]	3033	@echo $(SEP)
	3034	@echo "made 'all' with success."
	3035	@echo "to start arb enter 'arb'"
[18920]	3036	ifeq ($(UNIT_TESTS),1)
[17665]	3037	@echo "$(SEP) $(MAKE) run_tests"
[7819]	3038	@$(TIMECMD) $(MAKE) run_tests
[18920]	3039	endif
[17665]	3040	@echo "$(SEP) $(MAKE) all [done]"
[18920]	3041	ifeq ($(DEBUG),1)
[8606]	3042	@$(MAKE) save_test_no_error >/dev/null # just show hints
[18920]	3043	endif
[6708]	3044	@cat $(TIMELOG)
	3045	@rm $(TIMELOG)
[7819]	3046
[18924]	3047	rebuild: clean
	3048	$(MAKE) all
	3049
[18916]	3050	# --------------------------------------------------------------------------------
[18920]	3051	# special targets showing obvious error at bottom
	3052	# (intended to be used from automated builds)
[18916]	3053
	3054	BUILD_LOG=build.log
	3055	SHELL=bash
[18920]	3056	REDIRECT_KEEP_EXITCODE = tee $(BUILD_LOG) ; exit "$${PIPESTATUS[0]}"
	3057	EXTRACT_ERROR_SUMMARY = (./SOURCE_TOOLS/short_error_summary.pl $(BUILD_LOG); false)
[18916]	3058
[18920]	3059	ALL:
	3060	@(($(MAKE) all 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
[18916]	3061
[18920]	3062	REBUILD:
	3063	@(($(MAKE) rebuild 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
	3064
[18925]	3065	TARFILE:
	3066	@(($(MAKE) tarfile 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
	3067
	3068	TARFILE_QUICK:
	3069	@(($(MAKE) tarfile_quick 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
	3070

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