Context Navigation

← Previous Revision
Next Revision →
Normal
Revision Log

source: trunk/Makefile

Visit:

Last change on this file was 19446, checked in by westram, 20 months ago
introduce `onlyC_flags` flags used for C compilation only. similar to `cxxflags` (references added). pass down onlyC_flags into AxML, CLUSTAL, CLUSTALW, FASTDNAML, FASTTREE, GL, MrBAYES, PHYLIP, PHYML*, RAxML, SINA(unused), SOURCE_TOOLS, SUPPORT, TOOLS, TREEGEN + TREEPUZZLE. set flags to `-Werror-implicit-function-declaration` error is only effective in a small part of these modules. TODO need to activate warnings → will activate the error as well.
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 87.6 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:=$(ARBHOME)/SH/arb_readlink
	186
[4034]	187	# ---------------------- compiler version detection
	188
[10993]	189	# supported gcc versions:
	190	ALLOWED_gcc_VERSIONS=\
[19060]	191	4.4.3 4.4.5 4.4.6 4.4.7 \
	192	4.5.2 \
	193	4.6.1 4.6.2 4.6.3 4.6.4 \
	194	4.7.1 4.7.2 4.7.3 4.7.4 \
	195	4.8.0 4.8.1 4.8.2 4.8.3 4.8.4 4.8.5 \
	196	4.9.0 4.9.1 4.9.2 4.9.3 4.9.4 \
	197	5.1.0 5.2.0 5.3.0 5.4.0 5.5.0 \
	198	6.1.0 6.2.0 6.3.0 6.4.0 6.5.0 \
	199	7.1.0 7.2.0 7.3.0 7.4.0 7.5.0 \
	200	8.1.0 8.2.0 8.3.0 8.4.0 8.5.0 \
	201	9.1.0 9.2.0 9.3.0 9.4.0 9.5.0 \
[19435]	202	10.1.0 10.2.0 10.3.0 10.4.0 10.5.0 \
[5556]	203
[17904]	204	# Note: starting with version 5, arb silently accepts any subversion number
	205	# above zero. See SOURCE_TOOLS/arb_compiler_version.pl@acceptSubVersions
	206	#
	207	# This may cause problems when manually checking for compiler versions in code
	208	# (GCC_VERSION_CODE is not affected, GCC_PATCHLEVEL_CODE may cause problems!)
[10993]	209	# ----------------------
[3227]	210
[12309]	211	COMPILER_INFO:=$(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
[19446]	341	onlyC_flags :=# flags only suitable for C (not C++; see cxxflags).
[11815]	342	clflags :=# linker flags (when passed through gcc)
[5887]	343	extended_warnings :=# warning flags for C and C++-compiler
	344	extended_cpp_warnings :=# warning flags for C++-compiler only
[5188]	345
[5223]	346	ifeq ($(DEBUG),0)
[15496]	347	dflags := -DNDEBUG# defines
	348	ifeq ($(USE_CLANG),1)
	349	cflags := -O3# compiler flags (C and C++)
	350	else
	351	clflags += -Wl,-O2# passthrough linker flags
[18729]	352	# ------- standard optimization:
[15496]	353	cflags := -O3# compiler flags (C and C++)
	354	# ------- test changed optimization (DISABLE_VECTORIZE_CHECK for -O2 or lower):
	355	# cflags := -O2# do not commit uncommented!
	356	# DISABLE_VECTORIZE_CHECK:=1
	357	endif
[4034]	358	endif
	359
[11815]	360	ifeq ($(DEBIAN),1)
[15496]	361	clflags += -Wl,-rpath=/usr/lib/arb/lib -Wl,-z,relro
[11815]	362	endif
	363
[5223]	364	ifeq ($(DEBUG),1)
[15496]	365	dflags := -DDEBUG
[8608]	366
[15496]	367	gdb_common := -g -g3 -ggdb -ggdb3
[8608]	368
[18959]	369	DBGOPTI:=-O0
[19033]	370	ifneq ('$(SANITIZE)','0')
	371	# sanitizer report several bogus buffer-overflows when arb is build with -O0 (e.g. with gcc 7.5.0)
	372	DBGOPTI:=-O1
	373	endif
[12478]	374
[16383]	375	ifeq ($(STABS),1)
[18959]	376	$(error STABS no longer supported)
[15496]	377	endif
[11460]	378
[18959]	379	cflags := $(DBGOPTI) $(gdb_common)
	380	# cflags := -O2 $(gdb_common) # use this for callgrind (force inlining)
[11460]	381
[15496]	382	ifeq ($(DARWIN),0)
	383	clflags += -Wl,-g
[14358]	384	# Note:
	385	# Previously '-Wl,-noinhibit-exec' was added to 'clflags' here,
	386	# to fix some issues with launchpad binutils (see [12972]).
	387	# But that change also caused 'undefined symbols' NOT to be reported as errors
	388	# at link time, producing executables that fail at runtime :/
[15496]	389	endif
[14358]	390
[13133]	391	ifeq ($(DEBUG_GRAPHICS),1)
[15496]	392	dflags += -DDEBUG_GRAPHICS
[13133]	393	endif
	394
	395	endif # DEBUG only
	396
[17342]	397	# ------------------------------ POST_COMPILE - control how much you get spammed
	398	# (please do not change default in SVN)
[15496]	399	POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl
[16628]	400
[17342]	401	# POST_COMPILE += --original # dont modify compiler output
	402	# POST_COMPILE += --hide-Noncopyable-advices
	403	# POST_COMPILE += --show-useless-Weff++
	404	# POST_COMPILE += --no-warnings
	405	# POST_COMPILE += --only-first-error
	406	# POST_COMPILE += --no-warnings --only-first-error
[5133]	407
[16683]	408	# always pass used compiler version to postcompile:
	409	POST_COMPILE += --compiler=$(COMPILER_VERSION)
	410
[17342]	411	# ------------------------------
	412
[7343]	413	# Enable extra warnings
[15496]	414	extended_warnings :=
	415	extended_cpp_warnings :=
[7346]	416
[15496]	417	# C and C++
[18337]	418	extended_warnings += -Wwrite-strings -Wunused -Wno-aggregate-return
[7346]	419
[18337]	420	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
	421	# disable shadow warnings for gcc 4.8 (and lower)
	422	# (does e.g. warn if a method-name is used as parameter in another method - even for derived classes. unusable!)
	423	extended_warnings += -Wshadow
	424	endif
	425
[15496]	426	# C++ only
	427	extended_cpp_warnings += -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute
[16683]	428	extended_cpp_warnings += -Wctor-dtor-privacy
	429	# extended_cpp_warnings += -Wfloat-equal
[7346]	430
[16683]	431	extended_cpp_warnings += -Wmissing-noreturn
	432	# extended_cpp_warnings += -Wold-style-cast# (warns about 28405 old-style casts)
	433	extended_cpp_warnings += -Winit-self
	434	extended_cpp_warnings += -Wstrict-aliasing
	435	extended_cpp_warnings += -Wextra
[7346]	436
[16683]	437	# ------- above only warning-options already available in gcc 4.4.3
	438
[13077]	439	# -Weffc++ broken in 4.7.x series
	440	# gcc 4.7.3 crashes on GenomeImport.cxx when -Weffc++ is active
	441	# (bug reported https://gcc.gnu.org/bugzilla/show_bug.cgi?id=56923; apparently wont be fixed for 4.7-series)
	442	# gcc 4.7.4 crashes on DBwriter.cxx when -Weffc++ is active
[16683]	443	WEFFC_BROKEN:=0
	444	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
	445	ifneq ('$(USE_GCC_48_OR_HIGHER)','yes')
[15496]	446	WEFFC_BROKEN:=1
[13077]	447	endif
[15496]	448	endif
	449	ifeq ('$(WEFFC_BROKEN)','0')
[16683]	450	extended_cpp_warnings += -Weffc++
[15496]	451	endif
	452
[16683]	453	# turn off -Wmaybe-uninitialized in debug mode (gets activated with -Wextra). too many bogus warnings
[15496]	454	ifeq ($(DEBUG),1)
	455	ifeq ($(USE_CLANG),0)
	456	extended_cpp_warnings += -Wno-maybe-uninitialized
[10674]	457	endif
[15496]	458	endif
[16683]	459
[17877]	460	SUGGEST_FINAL:=
	461
[15496]	462	ifeq ('$(USE_GCC_452_OR_HIGHER)','yes')
	463	extended_cpp_warnings += -Wlogical-op# gcc 4.5.2
	464	endif
	465	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
[16763]	466	extended_cpp_warnings += -Wzero-as-null-pointer-constant# gcc 4.7
[15496]	467	endif
	468	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
	469	extended_cpp_warnings += -Wunused-local-typedefs# available since gcc 4.7 (but fails for each STATIC_ASSERT, so enable only for Cxx11)
	470	endif
[17277]	471	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
	472	extended_cpp_warnings += -Wswitch-bool
	473	extended_cpp_warnings += -Wlogical-not-parentheses
	474	extended_cpp_warnings += -Wsizeof-array-argument
	475	extended_cpp_warnings += -Wbool-compare
[5133]	476
[17877]	477	SUGGEST_FINAL:=yes
[17277]	478	endif
	479	ifeq ('$(USE_GCC_60_OR_HIGHER)','yes')
	480	extended_cpp_warnings += -Wduplicated-cond
	481	endif
	482	ifeq ('$(USE_GCC_80_OR_HIGHER)','yes')
	483	extended_cpp_warnings += -Wmultistatement-macros
	484	endif
[15513]	485
[18385]	486	# switch off final suggestions for 8.3.0 and 8.4.0:
[17877]	487	ifeq ('$(COMPILER_VERSION)','8.3.0')
	488	SUGGEST_FINAL:=no
	489	endif
[18385]	490	ifeq ('$(COMPILER_VERSION)','8.4.0')
	491	SUGGEST_FINAL:=no
[17877]	492	endif
	493
	494	ifeq ($(DEVELOPER),RELEASE)
	495	# switch off final suggestions in RELEASE:
	496	SUGGEST_FINAL:=no
	497	endif
	498	# suggest final:
	499	ifeq ('$(SUGGEST_FINAL)','yes')
	500	extended_cpp_warnings += -Wsuggest-final-types
	501	extended_cpp_warnings += -Wsuggest-final-methods
	502	dflags += -DSUGGESTS_FINAL
	503	endif
	504
[10999]	505	#---------------------- turn off clang bogus warnings
[4034]	506
[10999]	507	ifeq ($(USE_CLANG),1)
[11005]	508	# -Wmismatched-tags warns about struct/class mismatch in forward declarations (which is explicitely allowed)
	509	# -Wchar-subscripts reports too many bogus warnings for "array['x']" (when 'x' is known to be in range [0..128])
	510	# -Wunused-private-field report too many false positives (currently ~ 2 of 3)
[11012]	511	# -Wstring-plus-int warns about common ARB coding practice
	512	# -Wgnu-static-float-init warns about accepted GNU extension
[15579]	513	extended_cpp_warnings += -Wno-mismatched-tags -Wno-char-subscripts -Wno-unused-private-field -Wno-string-plus-int
	514	ifeq ('$(COMPILER_VERSION)','4.2.1')
	515	# jenkins build (doesn't know switch -Wno-gnu-static-float-init)
	516	extended_cpp_warnings += -Wno-gnu
	517	else
	518	extended_cpp_warnings += -Wno-gnu-static-float-init
	519	endif
[10999]	520	endif
	521
	522	#---------------------- developer
	523
[5223]	524	ifneq ($(DEVELOPER),ANY) # ANY=default setting (skip all developer specific code)
[15496]	525	dflags += -DDEVEL_$(DEVELOPER)# activate developer/release specific code
[2869]	526	endif
[7337]	527
[13019]	528	#---------------------- activate TODO warnings?
	529
[7337]	530	ifndef SHOWTODO
	531	ifeq ($(DEVELOPER),RALF)
[15496]	532	SHOWTODO:=1
[7337]	533	else
[15496]	534	SHOWTODO:=0
[7337]	535	endif
[5223]	536	endif
[7337]	537	ifeq ($(SHOWTODO),1)
[15496]	538	dflags += -DWARN_TODO# activate "TODO" warnings
[7337]	539	endif
[2869]	540
[16880]	541	#---------------------- activate threads?
	542	# only useful if compiler is able to compile Cxx11 or better
	543
	544	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
	545	# see also ./TEMPLATES/cxxforward.h@USE_Cxx11
	546	cflags += -pthread
	547	clflags += -pthread
	548	endif
	549
[13077]	550	#---------------------- activate Sanitizers?
[13019]	551
[13077]	552	ASAN_OPTIONS:=handle_segv=0:color=0
[18426]	553	ifeq ($(IGNORE_LEAKS),1)
	554	ASAN_OPTIONS+=:detect_leaks=0 # disable leak-detection
	555	else
	556	ASAN_OPTIONS+=:detect_leaks=1 # detect leaks (normal setting)
	557	endif
[13077]	558	ASAN_OPTIONS+=:check_initialization_order=1
[13799]	559	# ASAN_OPTIONS+=:abort_on_error=1
[13077]	560
	561	# suppressions: SOURCE_TOOLS/arb.leaksan.supp
	562	LSAN_OPTIONS:=max_leaks=3:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp
	563
[17703]	564	UBSAN_OPTIONS:=print_stacktrace=1
[13077]	565
	566	SANITIZE_ADDRESS:=0
	567	SANITIZE_UNDEFINED:=0
	568
	569	ifneq ($(SANITIZE),0)
	570	ifeq ($(SANITIZE),all)
	571	SANITIZE:=3
	572	endif
	573
	574	ifeq ($(SANITIZE),1)
	575	SANITIZE_ADDRESS:=1
	576	else
	577	ifeq ($(SANITIZE),2)
	578	SANITIZE_UNDEFINED:=1
	579	else
	580	ifeq ($(SANITIZE),3)
	581	SANITIZE_ADDRESS:=1
	582	SANITIZE_UNDEFINED:=1
	583	else
	584	$(error Unknown value '$(SANITIZE)' specified for SANITIZE in config.makefile)
	585	endif
	586	endif
	587	endif
	588	endif
	589
	590	ifeq ($(SANITIZE_ADDRESS),1)
	591	ifneq ('$(USE_GCC_48_OR_HIGHER)','yes')
	592	$(info AddressSanitizer not usable with gcc $(COMPILER_VERSION) - disabled)
	593	SANITIZE_ADDRESS:=0
	594	else
	595	ifneq ('$(USE_GCC_49_OR_HIGHER)','yes')
[18119]	596	$(info LeakSanitizer does not work with gcc $(COMPILER_VERSION) - disabled)
	597	# need to disable AddressSanitizer (otherwise build fails; only affects gcc 4.8.x series)
[18118]	598	SANITIZE_ADDRESS:=0
[13077]	599	endif
	600	endif
	601	endif
	602
	603	ifeq ($(SANITIZE_UNDEFINED),1)
	604	ifneq ('$(USE_GCC_49_OR_HIGHER)','yes')
	605	$(info UndefinedBehaviorSanitizer not usable with gcc $(COMPILER_VERSION) - disabled)
	606	SANITIZE_UNDEFINED:=0
	607	endif
	608	endif
	609
[13774]	610	SANITIZE_ANY:=0
	611	ifeq ($(SANITIZE_ADDRESS),1)
	612	SANITIZE_ANY:=1
	613	endif
	614	ifeq ($(SANITIZE_UNDEFINED),1)
	615	SANITIZE_ANY:=1
	616	endif
	617
[16683]	618	# vectorization fails if sanitizer active where it normally succeeds -> disable check
[14813]	619	ifeq ($(SANITIZE_ANY),1)
[18117]	620	$(info disabling vectorize checks. would fail with sanitized code)
[14813]	621	DISABLE_VECTORIZE_CHECK:=1
[18117]	622	else
	623	$(info no sanitizer enabled. reset: SANITIZE=0)
	624	SANITIZE:=0
[14813]	625	endif
	626
[16683]	627	# deactivate some bogus warnings occurring when sanitizing NDEBUG version
	628	# (do not disable for future gcc-version >= 8.x -> test again when available)
	629	ifeq ($(SANITIZE_ANY),1)
	630	ifeq ($(DEBUG),0)
	631	ifneq ('$(USE_GCC_80_OR_HIGHER)','yes')
	632	extended_cpp_warnings += -Wno-format-overflow
	633	extended_cpp_warnings += -Wno-maybe-uninitialized
	634	endif
	635	endif
	636	endif
	637
[5223]	638	#---------------------- 32 or 64 bit
[2]	639
[6732]	640	cross_cflags:=
	641	cross_lflags:=
[11818]	642	cross_clflags:=
[6732]	643
[5223]	644	ifeq ($(ARB_64),1)
[17738]	645	dflags += -DARB_64
[15496]	646	shared_cflags += -fPIC
[17738]	647	CROSS_LIB:=# empty => autodetect below
	648	ifeq ($(DARWIN),1)
	649	cross_cflags += -arch x86_64
	650	cross_lflags += -arch x86_64
	651	cross_clflags += -arch x86_64
[15496]	652	endif
[2]	653	else
[17738]	654	CROSS_LIB:=/lib
[2]	655	endif
	656
[11818]	657	cflags += $(cross_cflags)
	658	clflags += $(cross_clflags)
[6732]	659
[5223]	660	ifeq ('$(CROSS_LIB)','')
	661	# autodetect libdir
[15496]	662	ifeq ($(ARB_64),1)
	663	CROSS_LIB:=$(shell (test -d /lib64 && echo lib64) \|\| echo lib)
	664	else
	665	CROSS_LIB:=$(shell (test -d /lib32 && echo lib32) \|\| echo lib)
	666	endif
[5223]	667	endif
[655]	668
[6451]	669	#---------------------- unit tests
	670
	671	ifndef UNIT_TESTS
[15496]	672	UNIT_TESTS=0#default is "no tests"
[6451]	673	endif
	674	ifeq ($(UNIT_TESTS),1)
[15496]	675	dflags += -DUNIT_TESTS
	676	UNIT_TESTER_LIB=UNIT_TESTER/UNIT_TESTER.a
[6451]	677	else
[15496]	678	UNIT_TESTER_LIB=
[6451]	679	endif
	680
[6526]	681	#---------------------- use gcov
	682
	683	ifndef COVERAGE
[15496]	684	COVERAGE=0#default is "no"
[6526]	685	endif
[6712]	686	ifneq ($(COVERAGE),0)
[16223]	687	GCOV_FLAGS=--coverage
[18634]	688	$(info disabling vectorize checks. would fail with COVERAGE on)
	689	DISABLE_VECTORIZE_CHECK:=1
[6526]	690	else
[16223]	691	GCOV_FLAGS=
[6526]	692	endif
	693
[16223]	694	cflags += $(GCOV_FLAGS)
	695	clflags += $(GCOV_FLAGS)
	696	cross_lflags += $(GCOV_FLAGS)
	697
[5223]	698	#---------------------- other flags
[655]	699
[5223]	700	dflags += -D$(MACH) # define machine
[655]	701
[11804]	702	ifeq ($(DARWIN),1)
[15496]	703	shared_cflags += -fno-common
[5877]	704	else
[15496]	705	dflags += $(shell getconf LFS_CFLAGS)
[655]	706	endif
	707
[5223]	708	cflags += -pipe
[17618]	709	cflags += -fmessage-length=0# dont wrap compiler output
[7802]	710	cflags += -fshow-column# show columns
[5708]	711	cflags += -funit-at-a-time
[5897]	712	cflags += -fPIC
[7621]	713	cflags += -fno-common# link all global data into one namespace
[7347]	714	cflags += -fstrict-aliasing# gcc 3.4
[17342]	715
[19446]	716	onlyC_flags += -Werror-implicit-function-declaration
[17342]	717
[9516]	718	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
	719	cflags += -fno-diagnostics-show-caret#gcc 4.8 (4.7.?)
	720	endif
[8616]	721	#cflags += -save-temps# uncomment to see preprocessor output
[7347]	722
[13077]	723	#---------------------- various sanitizers
[15447]	724	# There are some disabled tests in CORE/arb_misc.cxx@sanitizers
	725	# which trigger sanitizer reports.
[13077]	726
[15447]	727	ifeq ($(SANITIZE_ANY),1)
	728	cflags += -ggdb3 -fno-omit-frame-pointer
	729	endif
[13077]	730
[19245]	731	SANI_CFLAGS:=
	732	SANI_CLFLAGS:=
	733
[13077]	734	# activate AddressSanitizer+LeakSanitizer?
	735	ifeq ($(SANITIZE_ADDRESS),1)
[19245]	736	SANI_CFLAGS += -fsanitize=address
	737	SANI_CLFLAGS += -fsanitize=address
[15447]	738	dflags += -DLEAKS_SANITIZED
[13077]	739	endif
	740
	741	# activate UndefinedBehaviorSanitizer?
	742	ifeq ($(SANITIZE_UNDEFINED),1)
[19245]	743	SANI_CFLAGS += -fsanitize=undefined
	744	SANI_CLFLAGS += -fsanitize=undefined
[15447]	745	dflags += -DUNDEF_SANITIZED
	746	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
	747	# abort on runtime errors
[19245]	748	SANI_CFLAGS += -fno-sanitize-recover=all
[15447]	749	endif
[19245]	750
	751	cflags += $(SANI_CFLAGS)
	752	clflags += $(SANI_CLFLAGS)
	753
[15447]	754	#
[13785]	755	# Note: alignment-sanitizer is deactivated for ARBDB and PROBE!
[13077]	756	ifeq ('$(DEBUG)','1')
[13082]	757	ifeq ($(USE_GCC_MAJOR),4)
	758	ifeq ($(USE_GCC_MINOR),9)
	759	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),01)','')
	760	# workaround https://gcc.gnu.org/bugzilla/show_bug.cgi?id=63531 for 4.9.0 + 4.9.1
[13120]	761	# (problem is fixed in 4.9.2 release)
[13082]	762	extended_cpp_warnings:=$(subst -Weffc++,,$(extended_cpp_warnings))
	763	endif
	764	endif
	765	endif
[13019]	766	endif
	767	endif
	768
[5223]	769	#---------------------- X11 location
[2350]	770
[11804]	771	ifeq ($(DARWIN),1)
[15496]	772	XHOME:=$(PREFIX)
[8656]	773	else
[11815]	774	ifeq ($(DEBIAN),1)
[15496]	775	XHOME:=$(PREFIX)
[11815]	776	else
[15496]	777	XHOME:=/usr/X11R6
[11815]	778	endif
[5877]	779	endif
	780
[14934]	781	XINCLUDES ?= -I$(XHOME)/include
	782	XLIBS ?= -L$(XHOME)/$(CROSS_LIB)
[11804]	783	ifeq ($(DARWIN),1)
[15496]	784	XINCLUDES += -I$(OSX_FW)/GLUT.framework/Headers -I$(OSX_FW)/OpenGL.framework/Headers -I$(OSX_SDK)/usr/include/krb5
[8656]	785
[15496]	786	XLIBS += -lXm -lpng -lz -lXt -lX11 -lXext -lXp -lXmu -lXi
	787	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGL.dylib:$(OSX_FW_OPENGL)/libGL.dylib
	788	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGLU.dylib:$(OSX_FW_OPENGL)/libGLU.dylib
[344]	789	else
[15496]	790	XLIBS += -lXm -lXpm -lXt -lXext -lX11
[1491]	791	endif
	792
[5223]	793	#---------------------- open GL
[3635]	794
[13923]	795	ifeq ($(OPENGL),1)
[15496]	796	cflags += -DARB_OPENGL # activate OPENGL code
	797	GL := gl # this is the name of the OPENGL base target
	798	GL_LIB_SYS := -lGL -lGLU
	799	GL_LIB_ARB := -L$(ARBHOME)/GL/glAW -lglAW
[5877]	800
[15496]	801	ifeq ($(DARWIN),1)
	802	GL_LIB_SYS += -lpthread
	803	endif
[5877]	804
[15496]	805	GL_PNGLIBS_ARB := -L$(ARBHOME)/GL/glpng -lglpng_arb
	806	GL_PNGLIBS_SYS := -lpng
[5877]	807
[15496]	808	GLEWLIB := -lGLEW -lGLw
[18655]	809	GLUTLIB := -lglut
[5877]	810
[15496]	811	GL_LIBS_SYS := $(GL_LIB_SYS) $(GL_PNGLIBS_SYS) $(GLEWLIB) $(GLUTLIB)
	812	GL_LIBS_ARB := $(GL_LIB_ARB) $(GL_PNGLIBS_ARB)
[5877]	813
[15496]	814	RNA3D_LIB := RNA3D/RNA3D.a
[5881]	815	else
[18426]	816	GL_LIBS_SYS:=# no opengl -> no libs
[15496]	817	GL_LIBS_ARB:=# no opengl -> no libs
[17738]	818	GL:=# dont build ARB openGL libs
[5881]	819
[15496]	820	RNA3D_LIB :=
[5223]	821	endif
	822
[9578]	823	RNA3D_LIB_4_DEPENDS := RNA3D/RNA3D.a
[6863]	824
[6451]	825	GL_LIBS:=$(GL_LIBS_ARB) $(GL_LIBS_SYS)
	826
[19245]	827	#---------------------- sina:
	828
	829	ifndef ISINA
	830	# build sina delivered with arb?
	831	ifeq ($(LINUX),1)
	832	ifeq ('$(USE_GCC_70_OR_HIGHER)','yes')
	833	ISINA := 1# default to 'yes' for linux with gcc>=7
	834	endif
	835	endif
	836	ifndef ISINA
	837	ISINA := 0# 'no' otherwise
	838	endif
	839	endif
	840
[5877]	841	#---------------------- tiff lib:
	842
[8656]	843	TIFFLIBS := -ltiff
[3635]	844
[13923]	845	#---------------------- XML lib:
	846
	847	XMLLIBS := -lxerces-c
	848
[11664]	849	#---------------------- glib:
	850
[11668]	851	ARB_NEEDED_GLIB=glib-2.0
[11664]	852
[11668]	853	ARB_GLIB_INCLUDE:=$(strip $(shell pkg-config --cflags $(ARB_NEEDED_GLIB)))
	854	ARB_GLIB_LIBS:=$(strip $(shell pkg-config --libs $(ARB_NEEDED_GLIB)))
	855
[18982]	856	#---------------------- sunrpc lib:
	857	# Note: sunrpc has been removed from glibc
	858	# (e.g. in SuSE Leap 15.3 and Fedora 28)
	859	# see https://fedoraproject.org/wiki/Changes/SunRPCRemoval
	860	#
	861	HAVE_LIBTIRPC=$(strip $(shell pkg-config --exists libtirpc && echo libtirpc))
	862	ifeq ($(HAVE_LIBTIRPC),)
	863	ARB_RPC_INCLUDE:=
	864	ARB_RPC_LIBS:=
	865	else
	866	ARB_RPC_INCLUDE:=$(strip $(shell pkg-config --cflags $(HAVE_LIBTIRPC)))
	867	ARB_RPC_LIBS:=$(strip $(shell pkg-config --libs $(HAVE_LIBTIRPC)))
	868	endif
	869
[5223]	870	#---------------------- basic libs:
	871
[18982]	872	ARB_CORE_LIBS:=$(ARB_GLIB_LIBS) $(ARB_RPC_LIBS)
[18981]	873
[5877]	874	SYSLIBS:=
[11804]	875	ifeq ($(DARWIN),1)
[15496]	876	SYSLIBS += -lstdc++
[5877]	877	else
[18981]	878	SYSLIBS += -lm $(ARB_CORE_LIBS)
[5223]	879	endif
	880
[8675]	881	#---------------------- system dependent commands
	882
[11804]	883	ifeq ($(DARWIN),1)
[15496]	884	TIME:=gtime
[8675]	885	else
[15496]	886	TIME:=/usr/bin/time
[8675]	887	endif
	888
[13443]	889	#---------------------- SSE vectorizer
[16628]	890	# for details see SOURCE_TOOLS/vectorize.README
[13443]	891
	892	ifeq ($(DEBUG),0)
	893	ifeq ($(USE_GCC_49_OR_HIGHER),yes)
[14813]	894	ifeq ($(DISABLE_VECTORIZE_CHECK),0)
[15496]	895	cflags += -fopt-info-vec
[18014]	896	cflags += -fopt-info-vec-missed
[17342]	897	ifeq ($(TRACE_MISSED_VECTORIZATIONS),1)
	898	# Shows reasons for unsuccessful vectorization:
	899	cflags += -ftree-vectorizer-verbose=10
	900	POST_COMPILE += --dump-loop-optimization
[17877]	901	ifeq ($(VECTORIZATION_CHECK_CANDIDATES),1)
	902	$(error TRACE_MISSED_VECTORIZATIONS and VECTORIZATION_CHECK_CANDIDATES may not be used together!)
	903	endif
[17342]	904	endif
[17877]	905	ifeq ($(VECTORIZATION_CHECK_CANDIDATES),1)
	906	POST_COMPILE += --loop-optimization-candi
	907	endif
[16683]	908	POST_COMPILE += --check-loop-optimization
[13774]	909	endif
[13788]	910	else
	911	ifeq ($(USE_GCC_48_OR_HIGHER),yes)
	912	# no automatic vectorization-check for gcc<4.9.0
	913	# -> uncomment the next 2 lines and grep the spam it will produce for 'vectorized.*loops'
[15496]	914	# cflags += -fopt-info -fopt-info-vec-missed
	915	# POST_COMPILE += --original
[13788]	916	endif
[13443]	917	endif
	918	endif
	919
[13775]	920	#---------------------- stop early on broken flags/compiler combination
	921
	922	ifeq ($(DEBUG),0)
	923	ifeq ($(SANITIZE_ANY),1)
	924	ifeq ('$(COMPILER_VERSION)','4.9.1')
	925	$(error compiling DEBUG=0 + SANITIZE!=0 crashes with gcc $(COMPILER_VERSION) (gcc 4.9.2 works))
	926	endif
	927	endif
	928	endif
	929
[18321]	930	#---------------------- include symbols?
[14357]	931
[18321]	932	ifeq ($(TRACESYM),1)
	933	ifeq ($(USE_CLANG),0)
	934	cflags += -rdynamic
	935	clflags += -rdynamic -Wl,--export-dynamic
	936	endif
	937	endif
	938
	939	#---------------------- warn about duplicate variable definitions
	940
	941	ifeq ($(DARWIN),1)
	942	clflags += -Wl,-warn_commons
	943	else
[18320]	944	clflags += -Wl,--warn-common
[18321]	945	endif
[18320]	946
[18321]	947	#---------------------- differences between linking executables and shared libs:
	948
[14357]	949	# executables:
	950	ifeq ($(DARWIN),1)
[15496]	951	blflags:=$(clflags)
[14357]	952	else
[15496]	953	blflags:=$(clflags) -Wl,--no-undefined
[14357]	954	endif
	955
	956	# shared libraries
	957	llflags:=$(clflags)
	958
	959	# dont use clflags below
	960	clflags:=
	961
[8675]	962	# -------------------------------------------------------------------------
[15496]	963	# Don't put any machine/version/etc conditionals below!
	964	# (instead define variables above)
[5223]	965	# -------------------------------------------------------------------------
[2]	966
[11827]	967	cflags += -W -Wall $(dflags) $(extended_warnings)
[19446]	968	cxxflags := $(extended_cpp_warnings)# flags only suitable for C++ (not C; see onlyC_flags).
[2]	969
[11815]	970	# add CFLAGS + CPPFLAGS from environment for DEBIAN build
	971	ifeq ($(DEBIAN),1)
[15496]	972	cflags := $(CFLAGS) $(cflags)
	973	cxxflags += $(CPPFLAGS)
[11815]	974	endif
	975
[15529]	976	ifeq ('$(USE_CLANG)','1')
	977	# none of the following standards works with clang3.3 (under linux) => dont use standard (as done before r15516)
	978	# cxxflags += -std=gnu++11
	979	# cxxflags += -std=gnu++0x
[9516]	980	else
[15529]	981	ifeq ('$(USE_GCC_60_OR_HIGHER)','yes')
	982	cxxflags += -std=gnu++14# see also TEMPLATES/cxxforward.h@USE_Cxx14
	983	else
	984	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
	985	cxxflags += -std=gnu++11# see also TEMPLATES/cxxforward.h@USE_Cxx11
	986	else
	987	# gcc versions between 4.3 (lowest supported) and <4.7
	988	cxxflags += -std=gnu++0x
	989	endif
[8817]	990	endif
[6114]	991	endif
	992
[17625]	993	LINK_STATIC_LIB := $(AR) -csq# link static lib
[14357]	994	LINK_EXECUTABLE := $(A_CXX) $(blflags) -o# link executable (c++)
[2389]	995
[5829]	996	ifeq ($(LINK_STATIC),1)
[15496]	997	SHARED_LIB_SUFFIX = a# static lib suffix
	998	LINK_SHARED_LIB := $(LINK_STATIC_LIB)
[5829]	999	else
[15496]	1000	SHARED_LIB_SUFFIX = so# shared lib suffix
[16223]	1001	LINK_SHARED_LIB := $(A_CXX) $(llflags) -shared -o# link shared lib
[5829]	1002	endif
	1003
[13741]	1004	ifeq ($(DARWIN),1)
[15496]	1005	lflags4perl:=
[13741]	1006	else
[15496]	1007	lflags4perl:=$(cross_lflags) -shared
[13741]	1008	endif
[13740]	1009
[10969]	1010	# delete variables unused below
[14357]	1011	blflags:=
	1012	llflags:=
[10969]	1013
[5223]	1014	# other used tools
[5829]	1015	MAKEDEPEND_PLAIN = makedepend
	1016	MAKEDEPEND = $(FORCEMASK);$(MAKEDEPEND_PLAIN)
	1017
[18919]	1018	SEPNODATE:=--------------------------------------------------------------------------------
[7819]	1019	SEP=[`date +%M:%S.%N`] ------------------------------------------------
	1020	# to analyse timings run
	1021	# make -j9 clean; make -j9 all \| grep '^\[' \| sort
	1022	# make -j9 "TIMED_TARGET=perl" clean_timed_target \| grep '^\[' \| sort
[2389]	1023
[16223]	1024	# ------------------------------------------------------------ DYNLIBDEFS
	1025	# various dynamic library definitions for linking executables:
	1026	#
	1027	# SYSLIBS: system libraries needed by database lib
	1028	# ARBDB_LIB: database lib
	1029	# DBSYS_LIBS: executable using database (but no GUI)
	1030	# GUI_LIBS: executable using database and GUI (arb gui uses database)
	1031	#
	1032	# Note: definitions exported to sub-makefiles are described in SOURCE_TOOLS/parent_make.txt
	1033
[10962]	1034	CORE_LIB=-lCORE
	1035	ARBDB_LIB=-lARBDB $(CORE_LIB)
[16223]	1036	DBSYS_LIBS = $(ARBDB_LIB) $(SYSLIBS)
[10962]	1037
	1038	GUI_LIBS_PREFIX:=
[11804]	1039	ifeq ($(DARWIN),1)
[15496]	1040	# this seem to be added at wrong place, since opengl is only needed to link EDIT4
	1041	GUI_LIBS_PREFIX:=-framework GLUT -framework OpenGL
[10962]	1042	endif
	1043
[16223]	1044	GUI_LIBS=$(GUI_LIBS_PREFIX) $(DBSYS_LIBS) -lAWT -lWINDOW $(XLIBS)
[10965]	1045
[10962]	1046	LIBPATH = -L$(ARBHOME)/lib
	1047
	1048	DEST_LIB = lib
	1049	DEST_BIN = bin
	1050
[18982]	1051	CC_INCLUDES := -I. -I$(ARBHOME)/INCLUDE $(XINCLUDES) $(ARB_GLIB_INCLUDE) $(ARB_RPC_INCLUDE)
[10976]	1052	CXX_INCLUDES := $(CC_INCLUDES)
[10962]	1053	MAKEDEPENDFLAGS := -- -DARB_OPENGL -DUNIT_TESTS -D__cplusplus -I. -Y$(ARBHOME)/INCLUDE
	1054
	1055	# ---------------------------------------
	1056	# wrap main()
	1057
	1058	use_ARB_main=$(ARBHOME)/SOURCE_TOOLS/arb_main_cpp.o
	1059	use_ARB_main_C=$(ARBHOME)/SOURCE_TOOLS/arb_main_c.o
	1060
[13923]	1061	# -----------------------------------------
[17366]	1062	# unique build-id
	1063	# - different for different calls of make
	1064	# - constant in recursive calls
	1065
[17618]	1066	ifndef ARBBID
[17366]	1067	ARBBID:=$(shell SOURCE_TOOLS/uniqueID.sh)
	1068	endif
	1069
	1070	# -----------------------------------------
[13923]	1071	# export variables to submakefiles
[10962]	1072
	1073	include SOURCE_TOOLS/export2sub
	1074
[13923]	1075	# do not define (exported) variables below this point
[10962]	1076
[13923]	1077	# -------------------------
	1078	# Main arb targets:
	1079	# -------------------------
[2]	1080
[1076]	1081	first_target:
	1082	$(MAKE) checks
[18919]	1083	@echo $(SEPNODATE)
[643]	1084	@echo 'Main targets:'
	1085	@echo ''
	1086	@echo ' all - Compile ARB + TOOLs + and copy shared libs + link foreign software'
	1087	@echo ' (That is most likely the target you want)'
	1088	@echo ''
[4692]	1089	@echo ' clean - remove generated files ("SUBDIR/SUBDIR.clean" to clean only SUBDIR)'
[4632]	1090	@echo ' rebuild - clean + all'
[14205]	1091	@echo ' cleanlinked - remove all binaries'
	1092	@echo ' relink - cleanlinked + all (=relink all from objects)'
[643]	1093	@echo ''
[18920]	1094	@echo 'Targets for automated builds:'
[18917]	1095	@echo ''
[18925]	1096	@echo ' ALL, REBUILD, TARFILE + TARFILE_QUICK '
	1097	@echo ' - same as all, rebuild, tarfile + tarfile_quick'
	1098	@echo ' - if errors occur, they are extracted and listed at tail of output'
[643]	1099	@echo ''
[18920]	1100	@echo $(SEPNODATE)
	1101	@echo ''
[643]	1102	@echo 'Development targets:'
	1103	@echo ''
[18919]	1104	@echo ' depends - create or update dependencies ("SUBDIR/SUBDIR.depends" to update only SUBDIR)'
	1105	@echo ' proto - create or update prototypes ("SUBDIR/SUBDIR.proto" to update only SUBDIR)'
	1106	@echo ' tags - create tags for xemacs'
	1107	@echo ' show - show available shortcuts (AKA subtargets)'
	1108	@echo ' up - shortcut for depends+proto+tags'
[6558]	1109	ifeq ($(UNIT_TESTS),1)
[16425]	1110	@echo ' ut - only run tests'
	1111	@echo ' "UNIT=..." oneunit - build one unit and run tests (see also UNIT_TESTER/Makefile.setup.local)'
[6558]	1112	endif
[15094]	1113	ifneq ($(SANITIZE),0)
[18919]	1114	@echo ' sanitize - all + run arb_ntree with sanitizer (test.arb + execute _logged)'
[15094]	1115	endif
[18919]	1116	@echo ' modified - rebuild files modified in svn checkout (does touch)'
	1117	@echo ' touch - touch files modified in svn checkout'
[643]	1118	@echo ''
[18919]	1119	@echo 'Some often used sub targets:'
	1120	@echo ''
	1121	@echo ' arb - Just compile ARB (but none of the integrated tools)'
	1122	@echo ' menus - create lib/gde/arb.menu from GDEHELP/ARB_GDEmenus.source'
	1123	@echo ' perl - Compile the PERL XSUBS into lib/ARB.so and create links in lib to perl'
	1124	@echo ' binlink - Create all links in the bin directory'
	1125	@echo ''
[6141]	1126	@echo 'Internal maintenance:'
[643]	1127	@echo ''
[18919]	1128	@echo ' relinfo - show help on release targets'
	1129	@echo ' tarfile - make rebuild and create arb version tarfile ("tarfile_quick" to skip rebuild)'
	1130	@echo ' save - save all basic ARB sources into arbsrc_DATE ("savetest" to check filelist)'
	1131	@echo ' patch - save svn diff to patchfile'
	1132	@echo ' source_doc - create doxygen documentation'
	1133	@echo ' relocated - rebuild partly (use when you have relocated ARBHOME)'
	1134	@echo ' check_res - check resource usage'
	1135	@echo ' dep_graph - Build dependency graphs'
	1136	@echo ' clean_cov - Clean coverage results'
[643]	1137	@echo ''
[18919]	1138	@echo ' clean_opengl_changed - clean after changing OPENGL setting in config.Makefile'
	1139	@echo ' clean_checked_vect - clean units containing vectorization checks'
	1140	@echo ' cleanRelinkable - similar to cleanlinked (but skips raxml8 to avoid rebuild)'
[15737]	1141	@echo ''
[18919]	1142	@echo ' post_commit_check - Checks whether'
	1143	@echo ' * main make targets work,'
	1144	@echo ' * dependencies and prototypes are up to date,'
	1145	@echo ' * SVN-controlled files remain unaffected by called targets and'
	1146	@echo ' * all generated files are ignored.'
	1147	@echo ' (has to be called in a clean SVN checkout)'
	1148	@echo $(SEPNODATE)
[743]	1149	@echo ''
[2]	1150
[11669]	1151	relinfo:
	1152	@echo ''
[18919]	1153	@echo $(SEPNODATE)
[11669]	1154	@echo 'Release targets:'
	1155	@echo ''
	1156	@echo ' inc_candi - increase RC candidate-number (only possible in "rc" branch, not needed for RC1)'
	1157	@echo ' inc_patch - increase release patchlevel (only possible in "stable" branch)'
	1158	@echo ' inc_minor - increase minor version number (only possible in "trunk")'
	1159	@echo ' inc_major - increase MAJOR version number (only possible in "trunk")'
	1160	@echo ''
[11674]	1161	@echo ' show_version - show version tag'
	1162	@echo ''
[18919]	1163	@echo $(SEPNODATE)
[11669]	1164	@echo ''
[1459]	1165
	1166	# auto-generate config.makefile:
	1167
	1168	config.makefile : config.makefile.template
	1169	@echo --------------------------------------------------------------------------------
[17424]	1170	ifeq ($(CONFIG_MAKEFILE_FOUND),)
[1459]	1171	@cp $< $@
[5708]	1172	@echo '$(ARBHOME)/$@:1: has been generated.'
[1459]	1173	@echo 'Please edit $@ to configure your system!'
[6162]	1174	@echo --------------------------------------------------------------------------------
	1175	@false
[1459]	1176	else
[5708]	1177	@echo '$(ARBHOME)/$<:1: is more recent than'
	1178	@echo '$(ARBHOME)/$@:1:'
[1459]	1179	@ls -al config.makefile*
[6162]	1180	@echo --------------------------------------------------------------------------------
	1181	@echo "Updating $@ (if this fails, check manually)"
	1182	SOURCE_TOOLS/update_config_makefile.pl
	1183	@echo "Sucessfully updated $@"
	1184	@echo --------------------------------------------------------------------------------
	1185	@ls -al config.makefile*
	1186	@echo --------------------------------------------------------------------------------
	1187	@echo "Diff to your old config.makefile:"
	1188	@echo --------------------------------------------------------------------------------
[6164]	1189	-diff $@.bak $@
[6162]	1190	@echo --------------------------------------------------------------------------------
[1459]	1191	endif
	1192
[1076]	1193	# check if everything is configured correctly
[2]	1194
[1076]	1195	check_DEVELOPER:
	1196	ifndef DEVELOPER
[2988]	1197	@echo 'config.makefile:1: DEVELOPER not defined'
[1076]	1198	@false
	1199	endif
	1200
	1201	check_DEBUG:
[643]	1202	ifndef dflags
[2988]	1203	@echo 'config.makefile:1: DEBUG has to be defined. Valid values are 0 and 1'
[643]	1204	@false
	1205	endif
[2]	1206
[5133]	1207	check_ARB_64:
	1208	ifndef ARB_64
	1209	@echo 'config.makefile:1: ARB_64 has to be defined. Valid values are 0 and 1'
	1210	@false
	1211	endif
	1212
[1238]	1213	# ---------------------------------------- check gcc version
	1214
[13044]	1215	COMPILER_BROKEN:=0
	1216
[16582]	1217	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.6.4')
	1218	COMPILER_BROKEN:=1
	1219	endif
[13923]	1220	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.8.0')
[13044]	1221	COMPILER_BROKEN:=1
	1222	endif
	1223
[3311]	1224	check_same_GCC_VERSION:
[10993]	1225	$(ARBHOME)/SOURCE_TOOLS/check_same_compiler_version.pl $(COMPILER_NAME) $(COMPILER_VERSION_ALLOWED)
[3311]	1226
[1238]	1227	check_GCC_VERSION:
[10993]	1228	@echo 'Compiler version check:'
[14590]	1229	# see .@ALLOWED_gcc_VERSIONS
[10993]	1230	ifeq ('$(COMPILER_VERSION_ALLOWED)', '')
	1231	@echo " - Your compiler is '$(COMPILER_NAME)' version '$(COMPILER_VERSION)'"
	1232	@echo ' This version is not in the list of supported $(COMPILER_NAME)-versions:'
	1233	@$(foreach version,$(ALLOWED_COMPILER_VERSIONS),echo ' * $(version)';)
[3227]	1234	@echo ' - You may either ..'
[10993]	1235	@echo ' - add your version to ALLOWED_$(COMPILER_NAME)_VERSIONS in the Makefile and try it out or'
[3790]	1236	@echo ' - switch to one of the allowed versions (see arb_README_gcc.txt for installing'
	1237	@echo ' a different version of gcc)'
[13044]	1238	$(error Unsupported compiler '$(COMPILER_NAME)' version '$(COMPILER_VERSION)')
[1238]	1239	else
[15529]	1240	ifeq ($(COMPILER_BROKEN),1)
[16582]	1241	$(error compilation refused for $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)'. Refer to http://bugs.arb-home.de/wiki/GccVersionInfo for details.)
[15529]	1242	else
[10993]	1243	@echo " - Supported $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)' detected - fine!"
[1238]	1244	@echo ''
[15529]	1245	ifeq ($(USE_CLANG),1)
	1246	@echo "Dump clang version:"
	1247	$(A_CXX) -v
	1248	endif
[3311]	1249	$(MAKE) check_same_GCC_VERSION
[15529]	1250	endif
[1238]	1251	endif
	1252
[1459]	1253	#---------------------- check ARBHOME
	1254
	1255	# use arb_INSTALL.txt to determine whether ARBHOME points to correct directory
	1256	ARB_INSTALL_FOUND=$(wildcard $(ARBHOME)/arb_INSTALL.txt)
	1257
	1258	check_ARBHOME:
	1259	ifeq ($(strip $(ARB_INSTALL_FOUND)),)
	1260	@echo ------------------------------------------------------------
	1261	@echo "ARBHOME is set to '$(ARBHOME)'"
	1262	@echo "The environment variable ARBHOME has to point to the top arb source directory."
	1263	@echo "If you use bash enter:"
	1264	@echo " export ARBHOME='`pwd`'"
	1265	@echo ------------------------------------------------------------
	1266	@false
	1267	endif
	1268
	1269	ARB_PATH_SET=$(findstring $(ARBHOME)/bin,$(PATH))
	1270
	1271	check_PATH: check_ARBHOME
	1272	ifeq ($(strip $(ARB_PATH_SET)),)
	1273	@echo ------------------------------------------------------------
	1274	@echo "The environment variable PATH has to contain $(ARBHOME)/bin"
	1275	@echo "If you use bash enter:"
	1276	@echo ' export PATH=$$ARBHOME/bin:$$PATH'
	1277	@echo ------------------------------------------------------------
	1278	@false
	1279	endif
	1280
[5829]	1281	check_TOOLS:
	1282	@util/arb_check_build_env.pl \
[10955]	1283	"$(A_CC)" \
	1284	"$(A_CXX)" \
[5829]	1285	"$(LINK_SHARED_LIB)" \
[1459]	1286
[19043]	1287	have_makedepend:
	1288	@util/arb_check_build_env.pl --check-only "$(MAKEDEPEND_PLAIN)"
	1289
[5829]	1290	check_ENVIRONMENT : check_PATH check_TOOLS
[12312]	1291	@echo "-------------------- Environment [start]"
	1292	@echo "ARBHOME='$(ARBHOME)'"
	1293	@echo "PATH='$(PATH)'"
	1294	@echo "LD_LIBRARY_PATH='$(LD_LIBRARY_PATH)'"
	1295	@echo "-------------------- Environment [end]"
[5829]	1296
[5387]	1297	check_tabs: check_setup
	1298	ifeq ($(DEBUG),1)
	1299	@SOURCE_TOOLS/tabBrake.pl
	1300	endif
	1301
	1302	force_tab_check:
[8614]	1303	@touch -t 198001010000 SOURCE_TOOLS/stamp.tabBrake
[5829]	1304	@$(MAKE) check_tabs
[5387]	1305
	1306
[1459]	1307	# ---------------------
	1308
[13923]	1309	check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION
[1076]	1310	@echo Your setup seems to be ok.
[2]	1311
[5387]	1312	checks: check_setup check_tabs
[7623]	1313	@rm -f SOURCE_TOOLS/postcompile.sav
[2]	1314
[5387]	1315
[1459]	1316	# end test section ------------------------------
	1317
[7801]	1318	# ---------------------------------------
[7819]	1319	# List of standard top level directories
	1320	#
	1321	# sub-makefiles have to define the targets
	1322	# - 'depends' and
	1323	# - 'clean'
	1324	#
[18426]	1325	# when adding new libraries/subdirs here, also add a dependency vs 'links' or 'links_non_perl' in .@DD_links_non_perl
[5629]	1326
[18426]	1327	TL_ARCHIVES = \
[7819]	1328	AISC/AISC.a \
[5565]	1329	ARB_GDE/ARB_GDE.a \
	1330	AWTC/AWTC.a \
	1331	AWTI/AWTI.a \
	1332	CONSENSUS_TREE/CONSENSUS_TREE.a \
	1333	CONVERTALN/CONVERTALN.a \
	1334	DBSERVER/DBSERVER.a \
	1335	DIST/DIST.a \
	1336	EDIT4/EDIT4.a \
	1337	EISPACK/EISPACK.a \
	1338	GENOM/GENOM.a \
	1339	GENOM_IMPORT/GENOM_IMPORT.a \
	1340	ISLAND_HOPPING/ISLAND_HOPPING.a \
	1341	MERGE/MERGE.a \
	1342	MULTI_PROBE/MULTI_PROBE.a \
	1343	NALIGNER/NALIGNER.a \
	1344	NAMES/NAMES.a \
	1345	NAMES_COM/server.a \
	1346	NTREE/NTREE.a \
	1347	PARSIMONY/PARSIMONY.a \
	1348	PHYLO/PHYLO.a \
	1349	PRIMER_DESIGN/PRIMER_DESIGN.a \
[17738]	1350	PROBE/PROBE.a \
[866]	1351	PROBE_COM/server.a \
[2]	1352	PROBE_DESIGN/PROBE_DESIGN.a \
[18426]	1353	$(RNA3D_LIB) \
[7895]	1354	RNACMA/RNACMA.a \
[866]	1355	SECEDIT/SECEDIT.a \
[3494]	1356	SEQ_QUALITY/SEQ_QUALITY.a \
[866]	1357	SERVERCNTRL/SERVERCNTRL.a \
	1358	STAT/STAT.a \
	1359	TREEGEN/TREEGEN.a \
	1360	WETC/WETC.a \
	1361	XML/XML.a \
[2]	1362
[18426]	1363	TL_SHARED_ARCHIVES = \
	1364	ARBDB/libARBDB.so \
	1365	CORE/libCORE.so \
	1366	AWT/libAWT.so \
	1367	WINDOW/libWINDOW.so \
	1368
	1369	TL_ARCHIV_COLLECTIONS = \
	1370	SL/SL.archColl \
	1371
	1372	TL_TOOLS_COLLECTIONS = \
	1373	AISC_MKPTPS/AISC_MKPTPS.toolColl \
	1374	TOOLS/TOOLS.toolColl \
	1375	PERLTOOLS/PERLTOOLS.toolColl \
	1376	PROBE_SET/PROBE_SET.toolColl \
	1377	READSEQ/READSEQ.toolColl \
	1378
	1379	RECURSIVE_SUBS = \
	1380	GDE/GDE.sub \
	1381	UNIT_TESTER/UNIT_TESTER.sub \
	1382
	1383	SUBDIRS = \
	1384	$(RECURSIVE_SUBS) \
	1385	$(TL_ARCHIVES:.a=.sub) \
	1386	$(TL_SHARED_ARCHIVES:.so=.sub) \
	1387	$(TL_ARCHIV_COLLECTIONS:.archColl=.sub) \
	1388	$(TL_TOOLS_COLLECTIONS:.toolColl=.sub) \
	1389
	1390	# sub directories inside TL_ARCHIV_COLLECTIONS
	1391	CL_ARCH_DIRS = $(foreach coll,$(TL_ARCHIV_COLLECTIONS),$(shell find $(dir $(coll)) -maxdepth 1 -mindepth 1 -type d))
	1392
	1393	# archives inside CL_ARCH_DIRS:
	1394	CL_ARCHIVES = $(foreach adir,$(CL_ARCH_DIRS),$(dir $(adir))$(notdir $(adir))/$(notdir $(adir)).a)
	1395
[13923]	1396	# -----------------------
	1397	# library packets
[6280]	1398
[13923]	1399	ARCHS_CLIENT_PROBE = PROBE_COM/client.a
	1400	ARCHS_CLIENT_NAMES = NAMES_COM/client.a
[11060]	1401
[7819]	1402	ARCHS_MAKEBIN = AISC_MKPTPS/AISC_MKPTPS.a AISC/AISC.a
[2]	1403
[200]	1404	# communication libs need aisc and aisc_mkpts:
[2]	1405
[7819]	1406	AISC/AISC.dummy: proto_tools
[7621]	1407
[7819]	1408	comtools: AISC/AISC.dummy
[7621]	1409
[6280]	1410	ARCHS_SEQUENCE = \
	1411	SL/SEQUENCE/SEQUENCE.a \
	1412	SL/ALIVIEW/ALIVIEW.a \
	1413	SL/PRONUC/PRONUC.a \
	1414
	1415	ARCHS_TREE = \
[14038]	1416	SL/ARB_TREE/ARB_TREE.a \
	1417	SL/FILTER/FILTER.a \
[6280]	1418	$(ARCHS_SEQUENCE) \
	1419
[6318]	1420	# parsimony tree (used by NTREE, PARSIMONY, STAT(->EDIT4), DIST(obsolete!))
[6280]	1421	ARCHS_AP_TREE = \
[14038]	1422	SL/AP_TREE/AP_TREE.a \
[6280]	1423	$(ARCHS_TREE) \
	1424
[7819]	1425	# --------------------------------------------------------------------------------
	1426	# dependencies for linking shared libs
	1427
	1428	link_core: core
	1429	link_db: db link_core
	1430	link_aw: aw link_db
	1431	link_awt: awt link_aw
	1432
[2]	1433	#***************************************************************************************
[13923]	1434	# Individual_Programs_Section
[2]	1435	#***************************************************************************************
	1436
[10962]	1437	arbmainwrapper:
	1438	$(MAKE) -C SOURCE_TOOLS -r mainwrapper
	1439
	1440
[2]	1441	#********************************* arb_ntree ************************************
	1442	NTREE = bin/arb_ntree
[591]	1443	ARCHS_NTREE = \
[6427]	1444	NTREE/NTREE.a \
[591]	1445	ARB_GDE/ARB_GDE.a \
[15966]	1446	SL/GROUP_SEARCH/GROUP_SEARCH.a \
[18311]	1447	SL/SAICALC/SAICALC.a \
[14038]	1448	SL/DB_UI/DB_UI.a \
[591]	1449	AWTC/AWTC.a \
	1450	AWTI/AWTI.a \
[8587]	1451	CONSENSUS_TREE/CONSENSUS_TREE.a \
[14038]	1452	GENOM_IMPORT/GENOM_IMPORT.a \
[591]	1453	GENOM/GENOM.a \
	1454	MERGE/MERGE.a \
	1455	MULTI_PROBE/MULTI_PROBE.a \
	1456	PRIMER_DESIGN/PRIMER_DESIGN.a \
	1457	PROBE_DESIGN/PROBE_DESIGN.a \
[3821]	1458	SEQ_QUALITY/SEQ_QUALITY.a \
[591]	1459	SERVERCNTRL/SERVERCNTRL.a \
[12754]	1460	SL/ALILINK/ALILINK.a \
[3821]	1461	SL/AW_NAME/AW_NAME.a \
[14425]	1462	SL/CONSENSUS/CONSENSUS.a \
[3821]	1463	SL/DB_SCANNER/DB_SCANNER.a \
[7801]	1464	SL/DB_QUERY/DB_QUERY.a \
[15852]	1465	SL/QUERY/QUERY.a \
[6550]	1466	SL/SEQIO/SEQIO.a \
[14038]	1467	STAT/STAT.a \
[6280]	1468	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
[5805]	1469	SL/HELIX/HELIX.a \
	1470	SL/REGEXPR/REGEXPR.a \
[7801]	1471	SL/REFENTRIES/REFENTRIES.a \
	1472	SL/NDS/NDS.a \
[15054]	1473	SL/ITEM_SHADER/ITEM_SHADER.a \
[7801]	1474	SL/ITEMS/ITEMS.a \
[9633]	1475	SL/INSDEL/INSDEL.a \
[8250]	1476	SL/LOCATION/LOCATION.a \
[10083]	1477	SL/MACROS/MACROS.a \
[16904]	1478	SL/PVP/PVP.a \
[6280]	1479	SL/TRANSLATE/TRANSLATE.a \
	1480	SL/TREEDISP/TREEDISP.a \
[8557]	1481	SL/TREE_ADMIN/TREE_ADMIN.a \
[6023]	1482	SL/TREE_READ/TREE_READ.a \
	1483	SL/TREE_WRITE/TREE_WRITE.a \
[18092]	1484	SL/XFERGUI/XFERGUI.a \
[18088]	1485	SL/XFERSET/XFERSET.a \
[591]	1486	XML/XML.a \
[15691]	1487	$(ARCHS_AP_TREE) \
[2]	1488
[17618]	1489	ARCHS_NTREE_ALL = $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(XMLLIBS)
	1490
[7819]	1491	$(NTREE): $(ARCHS_NTREE:.a=.dummy) link_awt
[17618]	1492	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NTREE_ALL) \|\| ( \
[7819]	1493	echo "$(SEP) Link $@"; \
[17618]	1494	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE_ALL)" ; \
	1495	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE_ALL) && \
[7819]	1496	echo "$(SEP) Link $@ [done]"; \
[2744]	1497	)
[591]	1498
[2]	1499	#********************************* arb_edit4 ************************************
	1500	EDIT4 = bin/arb_edit4
[3477]	1501
[5223]	1502	ARCHS_EDIT4 := \
[6427]	1503	EDIT4/EDIT4.a \
[6280]	1504	ARB_GDE/ARB_GDE.a \
[14038]	1505	SL/FAST_ALIGNER/FAST_ALIGNER.a \
[989]	1506	AWTC/AWTC.a \
[6280]	1507	ISLAND_HOPPING/ISLAND_HOPPING.a \
[989]	1508	SECEDIT/SECEDIT.a \
	1509	SERVERCNTRL/SERVERCNTRL.a \
[3494]	1510	SL/AW_HELIX/AW_HELIX.a \
[3821]	1511	SL/AW_NAME/AW_NAME.a \
[14425]	1512	SL/CONSENSUS/CONSENSUS.a \
[7801]	1513	SL/ITEMS/ITEMS.a \
[14038]	1514	STAT/STAT.a \
[6280]	1515	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
	1516	SL/HELIX/HELIX.a \
	1517	SL/TRANSLATE/TRANSLATE.a \
[10083]	1518	SL/MACROS/MACROS.a \
[10494]	1519	SL/NDS/NDS.a \
[14038]	1520	$(ARCHS_AP_TREE) \
[989]	1521	XML/XML.a \
	1522
[5223]	1523	ifeq ($(OPENGL),1)
	1524	ARCHS_EDIT4 += RNA3D/RNA3D.a
[3477]	1525	endif
[7819]	1526
[17618]	1527	ARCHS_EDIT4_ALL = $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4)
	1528
[5877]	1529	LIBS_EDIT4 := $(GL_LIBS)
[3462]	1530
[13923]	1531	$(EDIT4): $(ARCHS_EDIT4:.a=.dummy) link_awt
[17618]	1532	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_EDIT4_ALL) \|\| ( \
[7819]	1533	echo "$(SEP) Link $@"; \
[17618]	1534	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4_ALL)" ; \
	1535	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4_ALL) && \
[7819]	1536	echo "$(SEP) Link $@ [done]"; \
[3462]	1537	)
	1538
[7895]	1539	#********************************* arb_rnacma ************************************
	1540	RNACMA = bin/arb_rnacma
	1541	ARCHS_RNACMA = \
	1542	RNACMA/RNACMA.a \
	1543
[17618]	1544	ARCHS_RNACMA_ALL = $(ARCHS_RNACMA) $(DBSYS_LIBS)
	1545
[8240]	1546	$(RNACMA) : $(ARCHS_RNACMA:.a=.dummy) link_db
[17618]	1547	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_RNACMA_ALL) \|\| ( \
[7895]	1548	echo "$(SEP) Link $@"; \
[18426]	1549	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_RNACMA_ALL)"; \
	1550	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_RNACMA_ALL) && \
[7895]	1551	echo "$(SEP) Link $@ [done]"; \
	1552	)
	1553
[2]	1554	#********************************* arb_wetc ************************************
	1555	WETC = bin/arb_wetc
[989]	1556	ARCHS_WETC = \
	1557	WETC/WETC.a \
[3494]	1558	SL/HELIX/HELIX.a \
[6280]	1559	SL/FILTER/FILTER.a \
[989]	1560	XML/XML.a \
	1561
[17618]	1562	ARCHS_WETC_ALL = $(ARCHS_WETC) $(GUI_LIBS)
	1563
[7819]	1564	$(WETC): $(ARCHS_WETC:.a=.dummy) link_awt
[17618]	1565	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_WETC_ALL) \|\| ( \
[7819]	1566	echo "$(SEP) Link $@"; \
[17618]	1567	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC_ALL)" ; \
	1568	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC_ALL) && \
[7819]	1569	echo "$(SEP) Link $@ [done]"; \
[2744]	1570	)
[2]	1571
	1572	#********************************* arb_dist ************************************
	1573	DIST = bin/arb_dist
[989]	1574	ARCHS_DIST = \
[14038]	1575	DIST/DIST.a \
[6280]	1576	CONSENSUS_TREE/CONSENSUS_TREE.a \
	1577	EISPACK/EISPACK.a \
[989]	1578	SERVERCNTRL/SERVERCNTRL.a \
[6280]	1579	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
[3494]	1580	SL/HELIX/HELIX.a \
[6280]	1581	SL/MATRIX/MATRIX.a \
[10083]	1582	SL/MACROS/MACROS.a \
[7801]	1583	SL/NDS/NDS.a \
	1584	SL/ITEMS/ITEMS.a \
[6280]	1585	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.a \
[989]	1586	XML/XML.a \
[14038]	1587	$(ARCHS_AP_TREE) \
[989]	1588
[17618]	1589	ARCHS_DIST_ALL = $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS)
	1590
[7819]	1591	$(DIST): $(ARCHS_DIST:.a=.dummy) link_awt
[17618]	1592	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_DIST_ALL) \|\| ( \
[7819]	1593	echo "$(SEP) Link $@"; \
[17618]	1594	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST_ALL)" ; \
	1595	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST_ALL) && \
[7819]	1596	echo "$(SEP) Link $@ [done]"; \
[2744]	1597	)
[2]	1598
	1599	#********************************* arb_pars ************************************
[866]	1600	PARSIMONY = bin/arb_pars
[989]	1601	ARCHS_PARSIMONY = \
[6280]	1602	PARSIMONY/PARSIMONY.a \
[3821]	1603	SERVERCNTRL/SERVERCNTRL.a \
[6280]	1604	SL/AW_NAME/AW_NAME.a \
	1605	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
[3494]	1606	SL/HELIX/HELIX.a \
[10083]	1607	SL/MACROS/MACROS.a \
[7801]	1608	SL/NDS/NDS.a \
	1609	SL/ITEMS/ITEMS.a \
[6280]	1610	SL/TRANSLATE/TRANSLATE.a \
	1611	SL/TREEDISP/TREEDISP.a \
[989]	1612	XML/XML.a \
[14038]	1613	$(ARCHS_AP_TREE) \
[989]	1614
[17618]	1615	ARCHS_PARSIMONY_ALL = $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS)
	1616
[7819]	1617	$(PARSIMONY): $(ARCHS_PARSIMONY:.a=.dummy) link_awt
[17618]	1618	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_PARSIMONY_ALL) \|\| ( \
[7819]	1619	echo "$(SEP) Link $@"; \
[17618]	1620	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY_ALL)" ; \
	1621	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY_ALL) && \
[7819]	1622	echo "$(SEP) Link $@ [done]"; \
[2744]	1623	)
[2]	1624
[7046]	1625	#********************************* arb_convert_aln ************************************
	1626	CONVERT_ALN = bin/arb_convert_aln
	1627	ARCHS_CONVERT_ALN = \
	1628	CONVERTALN/CONVERTALN.a \
	1629
[17618]	1630	ARCHS_CONVERT_ALN_ALL = $(ARCHS_CONVERT_ALN) $(DBSYS_LIBS)
	1631
[8240]	1632	$(CONVERT_ALN) : $(ARCHS_CONVERT_ALN:.a=.dummy) link_db
[17618]	1633	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_CONVERT_ALN_ALL) \|\| ( \
[7819]	1634	echo "$(SEP) Link $@"; \
[17618]	1635	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN_ALL)"; \
	1636	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN_ALL) && \
[7819]	1637	echo "$(SEP) Link $@ [done]"; \
[7046]	1638	)
	1639
[866]	1640	#********************************* arb_treegen ************************************
[8240]	1641
[866]	1642	TREEGEN = bin/arb_treegen
[989]	1643	ARCHS_TREEGEN = \
	1644	TREEGEN/TREEGEN.a \
	1645
[17618]	1646	ARCHS_TREEGEN_ALL = $(ARCHS_TREEGEN)
	1647
[1617]	1648	$(TREEGEN) : $(ARCHS_TREEGEN:.a=.dummy)
[17618]	1649	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main_C) $(ARCHS_TREEGEN_ALL) \|\| ( \
[7819]	1650	echo "$(SEP) Link $@"; \
[17618]	1651	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN_ALL)" ; \
	1652	$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN_ALL) && \
[7819]	1653	echo "$(SEP) Link $@ [done]"; \
[2744]	1654	)
[2]	1655
	1656	#********************************* arb_naligner ************************************
	1657	NALIGNER = bin/arb_naligner
[989]	1658	ARCHS_NALIGNER = \
	1659	NALIGNER/NALIGNER.a \
	1660	SERVERCNTRL/SERVERCNTRL.a \
[3494]	1661	SL/HELIX/HELIX.a \
[989]	1662
[17618]	1663	ARCHS_NALIGNER_ALL = $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(DBSYS_LIBS)
	1664
[7819]	1665	$(NALIGNER): $(ARCHS_NALIGNER:.a=.dummy) link_db
[17618]	1666	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NALIGNER_ALL) \|\| ( \
[7819]	1667	echo "$(SEP) Link $@"; \
[17618]	1668	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER_ALL)" ; \
	1669	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER_ALL) && \
[7819]	1670	echo "$(SEP) Link $@ [done]"; \
[2744]	1671	)
[2]	1672
	1673	#********************************* arb_phylo ************************************
	1674	PHYLO = bin/arb_phylo
[989]	1675	ARCHS_PHYLO = \
	1676	PHYLO/PHYLO.a \
[3494]	1677	SL/HELIX/HELIX.a \
[6280]	1678	SL/FILTER/FILTER.a \
[10083]	1679	SL/MACROS/MACROS.a \
[989]	1680	XML/XML.a \
	1681
[17618]	1682	ARCHS_PHYLO_ALL = $(ARCHS_PHYLO) $(GUI_LIBS)
	1683
[7819]	1684	$(PHYLO): $(ARCHS_PHYLO:.a=.dummy) link_awt
[17618]	1685	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_PHYLO_ALL) \|\| ( \
[7819]	1686	echo "$(SEP) Link $@"; \
[17618]	1687	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO_ALL)" ; \
	1688	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO_ALL) && \
[7819]	1689	echo "$(SEP) Link $@ [done]"; \
[2744]	1690	)
[2]	1691
	1692	#***************************************************************************************
	1693	# SERVER SECTION
	1694	#***************************************************************************************
	1695
	1696	#********************************* arb_db_server ************************************
	1697	DBSERVER = bin/arb_db_server
[989]	1698	ARCHS_DBSERVER = \
	1699	DBSERVER/DBSERVER.a \
	1700	SERVERCNTRL/SERVERCNTRL.a \
	1701
[17618]	1702	ARCHS_DBSERVER_ALL = $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS)
	1703
[7819]	1704	$(DBSERVER): $(ARCHS_DBSERVER:.a=.dummy) link_db
[17618]	1705	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_DBSERVER_ALL) \|\| ( \
[7819]	1706	echo "$(SEP) Link $@"; \
[17618]	1707	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER_ALL)" ; \
	1708	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER_ALL) && \
[7819]	1709	echo "$(SEP) Link $@ [done]"; \
[2744]	1710	)
[2]	1711
	1712	#********************************* arb_pt_server ************************************
	1713	PROBE = bin/arb_pt_server
[17738]	1714
	1715	ARCHS_PROBE_DEPEND = \
	1716	PROBE/PROBE.a \
[14038]	1717	SL/PTCLEAN/PTCLEAN.a \
[5565]	1718	SERVERCNTRL/SERVERCNTRL.a \
	1719	SL/HELIX/HELIX.a \
	1720
[17738]	1721	ARCHS_PROBE_ALL = $(ARCHS_PROBE_DEPEND) $(ARCHS_CLIENT_PROBE) $(ARBDB_LIB) $(SYSLIBS)
[989]	1722
[13923]	1723	$(PROBE): $(ARCHS_PROBE_DEPEND:.a=.dummy) link_db
[17618]	1724	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) config.makefile $(ARCHS_PROBE_ALL) \|\| ( \
[7819]	1725	echo "$(SEP) Link $@"; \
[17618]	1726	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_ALL)" ; \
	1727	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_ALL) && \
[7819]	1728	echo "$(SEP) Link $@ [done]"; \
[2744]	1729	)
[2]	1730
	1731	#********************************* arb_name_server ************************************
	1732	NAMES = bin/arb_name_server
[989]	1733	ARCHS_NAMES = \
	1734	NAMES/NAMES.a \
	1735	SERVERCNTRL/SERVERCNTRL.a \
	1736
[17618]	1737	ARCHS_NAMES_ALL = $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS)
	1738
[7819]	1739	$(NAMES): $(ARCHS_NAMES:.a=.dummy) link_db
[17618]	1740	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NAMES_ALL) \|\| ( \
[7819]	1741	echo "$(SEP) Link $@"; \
[17618]	1742	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES_ALL)" ; \
	1743	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES_ALL) && \
[7819]	1744	echo "$(SEP) Link $@ [done]"; \
[2744]	1745	)
[2]	1746
[989]	1747	#********************************* SHARED LIBRARIES SECTION ************************************
[2]	1748
[8567]	1749	prepare_libdir: addlibs
[989]	1750
[6038]	1751	addlibs:
	1752	(perl $(ARBHOME)/SOURCE_TOOLS/provide_libs.pl \
	1753	"arbhome=$(ARBHOME)" \
	1754	"opengl=$(OPENGL)" \
	1755	"link_static=$(LINK_STATIC)" \
	1756	)
	1757
[2]	1758	#***************************************************************************************
[6141]	1759	# Recursive calls to sub-makefiles
[2]	1760	#***************************************************************************************
[1617]	1761
[19043]	1762	%.depends: have_makedepend
[1617]	1763	@cp -p $(@D)/Makefile $(@D)/Makefile.old # save old Makefile
	1764	@$(MAKE) -C $(@D) -r \
[4632]	1765	"AUTODEPENDS=1" \
[5872]	1766	"MAIN=nothing" \
[6474]	1767	"cflags=noCflagsHere_use_MAKEDEPENDFLAGS" \
[10956]	1768	"cxxflags=noCxxflagsHere_use_MAKEDEPENDFLAGS" \
[9577]	1769	depends
[1617]	1770	@grep "^# DO NOT DELETE" $(@D)/Makefile >/dev/null
	1771	@cat $(@D)/Makefile \
[9574]	1772	\| SOURCE_TOOLS/fix_depends.pl "(from main)" \
[1617]	1773	>$(@D)/Makefile.2
	1774	@mv $(@D)/Makefile.old $(@D)/Makefile # restore old Makefile
	1775	@$(ARBHOME)/SOURCE_TOOLS/mv_if_diff $(@D)/Makefile.2 $(@D)/Makefile # update Makefile if changed
[2]	1776
[4600]	1777	%.proto:
[13077]	1778	@($(MAKE) -C $(@D) \
[4632]	1779	"AUTODEPENDS=0" \
[5872]	1780	"MAIN=nothing" \
	1781	"cflags=noCflags" \
[10956]	1782	"cxxflags=noCxxflags" \
[13077]	1783	proto 2>&1 ) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
[4600]	1784
[4632]	1785	%.clean:
	1786	@$(MAKE) -C $(@D) \
	1787	"AUTODEPENDS=0" \
[5872]	1788	"MAIN=nothing" \
	1789	"cflags=noCflags" \
[10956]	1790	"cxxflags=noCxxflags" \
[4632]	1791	clean
	1792
[8574]	1793
[18426]	1794	# stop wrong targets:
[8574]	1795	target_is_missing_lib_prefix:
	1796	@echo "Error: Denied to build shared library target with missing 'lib'-prefix"
	1797	false
	1798
	1799	ARBDB/ARBDB.dummy: target_is_missing_lib_prefix
	1800	CORE/CORE.dummy: target_is_missing_lib_prefix
	1801	AWT/AWT.dummy: target_is_missing_lib_prefix
	1802	WINDOW/WINDOW.dummy: target_is_missing_lib_prefix
	1803
[4632]	1804	# rule to generate main target (normally a library):
[11656]	1805	# @@@ check effect of setting LANG=C below
[2]	1806	%.dummy:
[7802]	1807	@( export ID=$$$$; LANG=C; \
[5165]	1808	(( \
[7819]	1809	echo "$(SEP) Make $(@D)"; \
[5143]	1810	$(MAKE) -C $(@D) -r \
[4632]	1811	"AUTODEPENDS=1" \
[10956]	1812	"MAIN=$(@F:.dummy=.a)" \
	1813	"cflags=$(cflags) -DIN_ARB_$(subst /,_,$(@D))" \
	1814	&& \
[7819]	1815	echo "$(SEP) Make $(@D) [done]"; \
[5165]	1816	) >$(@D).$$ID.log 2>&1 && (cat $(@D).$$ID.log;rm $(@D).$$ID.log)) \|\| (cat $(@D).$$ID.log;rm $(@D).$$ID.log;false))
[2]	1817
[2223]	1818	# Additional dependencies for subtargets:
	1819
	1820	PROBE_COM/PROBE_COM.dummy : comtools
	1821	NAMES_COM/NAMES_COM.dummy : comtools
	1822
[7819]	1823	com: PROBE_COM/PROBE_COM.dummy NAMES_COM/NAMES_COM.dummy
[2223]	1824
[18426]	1825	# stop wrong more targets:
[7819]	1826	PROBE_COM/server.dummy:
	1827	@echo Unwanted request to make target $<
	1828	false
	1829
	1830	PROBE_COM/client.dummy:
	1831	@echo Unwanted request to make target $<
	1832	false
	1833
[13923]	1834	NAMES_COM/server.dummy:
[7819]	1835	@echo Unwanted request to make target $<
	1836	false
	1837
	1838	NAMES_COM/client.dummy:
	1839	@echo Unwanted request to make target $<
	1840	false
	1841
	1842
	1843	ARBDB/libARBDB.dummy: links
	1844	CORE/libCORE.dummy: links
	1845
[8588]	1846	PERLTOOLS/PERLTOOLS.dummy: core db
[7819]	1847
[9580]	1848	# all subdirs perl not depends on go here (ADD_links_non_perl)
[7819]	1849	AWT/libAWT.dummy: links_non_perl
	1850	AWTI/AWTI.dummy: links_non_perl
	1851	CONSENSUS_TREE/CONSENSUS_TREE.dummy: links_non_perl
[8297]	1852	CONVERTALN/CONVERTALN.dummy: links_non_perl
[7819]	1853	DBSERVER/DBSERVER.dummy: links_non_perl
	1854	DIST/DIST.dummy: links_non_perl
[14055]	1855	EDIT4/EDIT4.dummy: links_non_perl com
[7819]	1856	EISPACK/EISPACK.dummy: links_non_perl
	1857	GDE/GDE.dummy: links_non_perl
	1858	GENOM/GENOM.dummy: links_non_perl
[8297]	1859	GENOM_IMPORT/GENOM_IMPORT.dummy: links_non_perl
[7819]	1860	ISLAND_HOPPING/ISLAND_HOPPING.dummy: links_non_perl
[8297]	1861	MERGE/MERGE.dummy: links_non_perl
[14055]	1862	NTREE/NTREE.dummy: links_non_perl
[7819]	1863	PARSIMONY/PARSIMONY.dummy: links_non_perl
	1864	PHYLO/PHYLO.dummy: links_non_perl
	1865	PRIMER_DESIGN/PRIMER_DESIGN.dummy: links_non_perl
	1866	PROBE_SET/PROBE_SET.dummy: links_non_perl link_db
	1867	READSEQ/READSEQ.dummy: links_non_perl
[8670]	1868	RNACMA/RNACMA.dummy: links_non_perl header_libs
[7819]	1869	SECEDIT/SECEDIT.dummy: links_non_perl
[8297]	1870	SEQ_QUALITY/SEQ_QUALITY.dummy: links_non_perl
	1871	SERVERCNTRL/SERVERCNTRL.dummy: links_non_perl com
[12754]	1872	SL/ALILINK/ALILINK.dummy: links_non_perl
[7819]	1873	SL/ALIVIEW/ALIVIEW.dummy: links_non_perl
	1874	SL/AP_TREE/AP_TREE.dummy: links_non_perl
	1875	SL/ARB_TREE/ARB_TREE.dummy: links_non_perl
	1876	SL/AW_HELIX/AW_HELIX.dummy: links_non_perl
[14425]	1877	SL/CONSENSUS/CONSENSUS.dummy: links_non_perl
[8297]	1878	SL/DB_QUERY/DB_QUERY.dummy: links_non_perl
	1879	SL/DB_SCANNER/DB_SCANNER.dummy: links_non_perl
	1880	SL/DB_UI/DB_UI.dummy: links_non_perl
[7819]	1881	SL/FAST_ALIGNER/FAST_ALIGNER.dummy: links_non_perl
	1882	SL/FILTER/FILTER.dummy: links_non_perl
[16119]	1883	SL/FILTSEQEXP/FILTSEQEXP.dummy: links_non_perl
	1884	SL/GROUP_SEARCH/GROUP_SEARCH.dummy: links_non_perl
[7819]	1885	SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy: links_non_perl
[18959]	1886	SL/HEADERTESTS/HEADERTESTS.dummy: links_non_perl
[7819]	1887	SL/HELIX/HELIX.dummy: links_non_perl
[9633]	1888	SL/INSDEL/INSDEL.dummy: links_non_perl
[16119]	1889	SL/ITEM_SHADER/ITEM_SHADER.dummy: links_non_perl
[7819]	1890	SL/ITEMS/ITEMS.dummy: links_non_perl
[8297]	1891	SL/LOCATION/LOCATION.dummy: links_non_perl
[10083]	1892	SL/MACROS/MACROS.dummy: links_non_perl
[7819]	1893	SL/MATRIX/MATRIX.dummy: links_non_perl
	1894	SL/NDS/NDS.dummy: links_non_perl
	1895	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.dummy: links_non_perl
	1896	SL/PRONUC/PRONUC.dummy: links_non_perl
[8097]	1897	SL/PTCLEAN/PTCLEAN.dummy: links_non_perl link_db
[16904]	1898	SL/PVP/PVP.dummy: links_non_perl
[15852]	1899	SL/QUERY/QUERY.dummy: links_non_perl link_db
[8297]	1900	SL/REFENTRIES/REFENTRIES.dummy: links_non_perl
	1901	SL/REGEXPR/REGEXPR.dummy: links_non_perl
[18311]	1902	SL/SAICALC/SAICALC.dummy: links_non_perl
[8297]	1903	SL/SEQIO/SEQIO.dummy: links_non_perl
[7819]	1904	SL/SEQUENCE/SEQUENCE.dummy: links_non_perl
	1905	SL/TRANSLATE/TRANSLATE.dummy: links_non_perl
[8557]	1906	SL/TREE_ADMIN/TREE_ADMIN.dummy: links_non_perl
[7819]	1907	SL/TREE_READ/TREE_READ.dummy: links_non_perl
	1908	SL/TREE_WRITE/TREE_WRITE.dummy: links_non_perl
	1909	SL/TREEDISP/TREEDISP.dummy: links_non_perl
[18092]	1910	SL/XFERGUI/XFERGUI.dummy: links_non_perl
[18088]	1911	SL/XFERSET/XFERSET.dummy: links_non_perl
[7819]	1912	STAT/STAT.dummy: links_non_perl
	1913	TREEGEN/TREEGEN.dummy: links_non_perl
[8297]	1914	WETC/WETC.dummy: links_non_perl
[7819]	1915	WINDOW/libWINDOW.dummy: links_non_perl
	1916	XML/XML.dummy: links_non_perl
	1917
	1918	ifeq ($(OPENGL),1)
	1919	GL/glAW/glAW.dummy: links_non_perl
	1920	GL/glpng/glpng.dummy: links_non_perl
	1921	GL/GL.dummy: GL/glAW/glAW.dummy GL/glpng/glpng.dummy
	1922	RNA3D/RNA3D.dummy: links_non_perl gl
	1923	endif
	1924
	1925	UNIT_TESTER/UNIT_TESTER.dummy: link_db \
[7409]	1926	SERVERCNTRL/SERVERCNTRL.dummy \
[7819]	1927
[13765]	1928	# see also TOOLS/Makefile@TOOLSLIBDEPENDS
[7819]	1929	TOOLS/TOOLS.dummy : links_non_perl link_db \
[13765]	1930	CONSENSUS_TREE/CONSENSUS_TREE.dummy \
[7819]	1931	SERVERCNTRL/SERVERCNTRL.dummy \
[13765]	1932	SL/FILTER/FILTER.dummy \
[16119]	1933	SL/FILTSEQEXP/FILTSEQEXP.dummy \
[13765]	1934	SL/INSDEL/INSDEL.dummy \
	1935	SL/REGEXPR/REGEXPR.dummy \
	1936	SL/SEQIO/SEQIO.dummy \
	1937	SL/TREE_READ/TREE_READ.dummy \
[7409]	1938	SL/TREE_WRITE/TREE_WRITE.dummy \
	1939	XML/XML.dummy \
[5143]	1940
[7819]	1941	AWTC/AWTC.dummy : com
[7409]	1942
[7819]	1943	NAMES/NAMES.dummy : com
	1944	SL/AW_NAME/AW_NAME.dummy : com
[5143]	1945
[7819]	1946	PROBE/PROBE.dummy : com
	1947	MULTI_PROBE/MULTI_PROBE.dummy : com
	1948	PROBE_DESIGN/PROBE_DESIGN.dummy : com
	1949	NALIGNER/NALIGNER.dummy : com
[5143]	1950
[18875]	1951	ARB_GDE/ARB_GDE.dummy : proto_tools menus
[5143]	1952
[11533]	1953	compile_compatibility: SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.dummy
	1954
[2]	1955	#***************************************************************************************
	1956	# Short aliases to make targets
	1957	#***************************************************************************************
	1958
[1076]	1959	show:
	1960	@echo $(SEP)
	1961	@echo 'Aliases for often needed targets:'
	1962	@echo ''
	1963	@echo ' executables:'
	1964	@echo ''
	1965	@echo ' nt arb_ntree'
	1966	@echo ' e4 arb_edit4 (includes secedit)'
	1967	@echo ' di arb_dist'
	1968	@echo ' ph arb_phylo'
	1969	@echo ' pa arb_parsimony'
	1970	@echo ' tg arb_treegen'
	1971	@echo ' ds arb_dbserver'
[1938]	1972	@echo ' pt arb_pt_server'
[1076]	1973	@echo ' na arb_name_server'
	1974	@echo ''
	1975	@echo ' libraries:'
	1976	@echo ''
	1977	@echo ' com communication libraries'
[6318]	1978	@echo ' db ARB database'
[1076]	1979	@echo ' aw GUI lib'
	1980	@echo ' awt GUI toolkit'
	1981	@echo ' awtc general purpose library'
	1982	@echo ' awti import/export library'
	1983	@echo ' mp multi probe library'
	1984	@echo ' ge genome library'
	1985	@echo ' pd probe design lib'
	1986	@echo ' prd primer design lib'
	1987	@echo ''
	1988	@echo ' other targets:'
	1989	@echo ''
	1990	@echo ' help recompile help files'
	1991	@echo ' tools make small tools used by arb'
	1992	@echo ''
	1993	@echo ' foreign targets:'
	1994	@echo ''
	1995	@echo ' gde GDE'
	1996	@echo ' agde ARB_GDE'
	1997	@echo ''
	1998	@echo 'for other targets inspect $(ARBHOME)/Makefile'
	1999	@echo ''
	2000	@echo $(SEP)
	2001
[2520]	2002	source_doc:
[6864]	2003	@echo "Remove some links (doxygen crashes otherwise):"
	2004	find . $ -name "AISC" -o -name "C" -o -name "GDEHELP" $ -type l -exec rm {} \;
[11492]	2005	doxygen 2>&1 1>/dev/null
[6864]	2006	$(MAKE) forcelinks
[1138]	2007
[7633]	2008	dep_graph:
	2009	@echo "Building some dependency graphs"
	2010	SOURCE_TOOLS/dependency_graphs.pl
	2011
[5166]	2012	help: HELP_SOURCE/HELP_SOURCE.dummy
[369]	2013
[10842]	2014	HELP_SOURCE/HELP_SOURCE.dummy: link_core xml menus
[5143]	2015
	2016	db: ARBDB/libARBDB.dummy
[7183]	2017	core: CORE/libCORE.dummy
[6407]	2018	aw: WINDOW/libWINDOW.dummy
[2]	2019	awt: AWT/libAWT.dummy
[33]	2020	awtc: AWTC/AWTC.dummy
[68]	2021	awti: AWTI/AWTI.dummy
[2]	2022
	2023	mp: MULTI_PROBE/MULTI_PROBE.dummy
[5143]	2024	mg: MERGE/MERGE.dummy
[26]	2025	ge: GENOM/GENOM.dummy
[113]	2026	prd: PRIMER_DESIGN/PRIMER_DESIGN.dummy
[2]	2027
[3447]	2028	nt: menus $(NTREE)
[2]	2029
[866]	2030	nal: $(NALIGNER)
[2]	2031
[3447]	2032	di: $(DIST)
	2033	ph: $(PHYLO)
	2034	pa: $(PARSIMONY)
	2035	tg: $(TREEGEN)
[3429]	2036
[7819]	2037	ifeq ($(OPENGL),1)
[4844]	2038	3d: RNA3D/RNA3D.dummy
[3447]	2039	gl: GL/GL.dummy
[7819]	2040	else
	2041	noopengl:
	2042	@echo "invalid target for OPENGL=0"
	2043	3d: noopengl
	2044	gl: noopengl
	2045	endif
[2]	2046
[7819]	2047	SL/SL.dummy: com
	2048
[3447]	2049	ds: $(DBSERVER)
	2050	pt: $(PROBE)
[5143]	2051	pst: PROBE_SET/PROBE_SET.dummy
[3447]	2052	pd: PROBE_DESIGN/PROBE_DESIGN.dummy
	2053	na: $(NAMES)
[5660]	2054	sq: SEQ_QUALITY/SEQ_QUALITY.dummy
[7899]	2055	cma: $(RNACMA)
[2]	2056
[5704]	2057	sec: SECEDIT/SECEDIT.dummy
[2]	2058
[7819]	2059	e4: $(EDIT4) readseq menus
	2060
[3447]	2061	gi: GENOM_IMPORT/GENOM_IMPORT.dummy
[5884]	2062	wetc: $(WETC)
[2]	2063
[151]	2064	xml: XML/XML.dummy
[6393]	2065	stat: STAT/STAT.dummy $(NTREE) $(EDIT4)
[6691]	2066	fa: SL/FAST_ALIGNER/FAST_ALIGNER.dummy
[151]	2067
[2]	2068	#********************************************************************************
	2069
[13443]	2070	up_by_remake: depends proto vectorize_checks
[4559]	2071
[8706]	2072	up: up_by_remake tags valgrind_update
[7890]	2073
[4559]	2074	#********************************************************************************
	2075
[7178]	2076	touch:
[5952]	2077	SOURCE_TOOLS/touch_modified.pl
[7178]	2078
	2079	modified: touch
[5952]	2080	$(MAKE) all
	2081
	2082	#********************************************************************************
	2083
[7819]	2084	libdepends:
[9578]	2085	$(MAKE) -C "SOURCE_TOOLS" \
	2086	"RNA3D_LIB=$(RNA3D_LIB_4_DEPENDS)" \
	2087	libdepends
[7819]	2088
	2089	#********************************************************************************
	2090
[9577]	2091	# create generated headers:
	2092	genheaders: TEMPLATES/TEMPLATES.dummy
	2093
	2094	clrdotdepends:
[14799]	2095	rm PROBE_COM/.depends \|\| true
	2096	rm NAMES_COM/.depends \|\| true
	2097	rm PERL2ARB/.depends \|\| true
[9577]	2098
[19043]	2099	comdepends: comtools clrdotdepends have_makedepend
[9577]	2100	@echo "$(SEP) Partially build com interface"
[10153]	2101	$(MAKE) PROBE_COM/PROBE_COM.depends NAMES_COM/NAMES_COM.depends
	2102	$(MAKE) PROBE_COM/server.depends NAMES_COM/server.depends
[9577]	2103
[19043]	2104	depends: genheaders comdepends vectorize_checks have_makedepend
[9577]	2105	@echo "$(SEP) Updating other dependencies"
[18426]	2106	$(MAKE) $(subst NAMES_COM/server.depends,,$(subst PROBE_COM/server.depends,,$(SUBDIRS:.sub=.depends))) \
[11533]	2107	HELP_SOURCE/HELP_SOURCE.depends \
	2108	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.depends \
	2109
[9577]	2110	$(MAKE) libdepends
[200]	2111
[5714]	2112	depend: depends
	2113
[10153]	2114	# ------------------------------------------------------------
	2115	# dependency generation tests for AISC code
	2116	#(all should work w/o creating wrong dependencies;
	2117	# neither in XXX_COM/Makefile nor in code using AISC interface)
	2118	dependstest1: silent_clean
	2119	$(MAKE) depends
	2120	dependstest2: silent_clean
	2121	$(MAKE) com
	2122	dependstest3: silent_clean
	2123	$(MAKE) aw
	2124	dependstest4: silent_clean
	2125	$(MAKE) pt
	2126	dependstest5: silent_clean
	2127	$(MAKE) na
	2128	dependstest6: silent_clean
	2129	$(MAKE) nt
	2130	dependstest7: silent_clean
	2131	$(MAKE) all
	2132	# ------------------------------------------------------------
	2133
[13443]	2134	vectorize_checks:
	2135	$(MAKE) -C SOURCE_TOOLS -r vectorize_checks
	2136
[16628]	2137	clean_checked_vect: lib/lib.clean
	2138	SOURCE_TOOLS/clean_checked_vectorizations.sh
	2139
[13443]	2140	# ------------------------------------------------------------
	2141
[7819]	2142	AISC_MKPTPS/AISC_MKPTPS.dummy: links
[5143]	2143
[7819]	2144	proto_tools: AISC_MKPTPS/AISC_MKPTPS.dummy
	2145
[5843]	2146	proto: proto_tools
[5845]	2147	@echo $(SEP) Updating prototypes
	2148	$(MAKE) \
	2149	ARBDB/ARBDB.proto \
[8818]	2150	AISC_COM/AISC_COM.proto \
[5845]	2151	ARB_GDE/ARB_GDE.proto \
[7339]	2152	CORE/CORE.proto \
[5845]	2153	CONVERTALN/CONVERTALN.proto \
	2154	NTREE/NTREE.proto \
[9797]	2155	MERGE/MERGE.proto \
[17738]	2156	PROBE/PROBE.proto \
[5845]	2157	SERVERCNTRL/SERVERCNTRL.proto \
[6280]	2158	SL/SL.proto \
[4600]	2159
[200]	2160	#********************************************************************************
	2161
[7819]	2162	valgrind_update: links
[5845]	2163	@echo $(SEP) Updating for valgrind
	2164	$(MAKE) -C SOURCE_TOOLS valgrind_update
[4844]	2165
	2166	#********************************************************************************
	2167
[2586]	2168	TAGFILE=TAGS
[17367]	2169	UTAGS=TAGS.$(ARBBID)
	2170	TAGFILE_TMP=$(UTAGS).tmp
[2586]	2171
[17367]	2172	TAG_SOURCE_HEADERS=$(UTAGS).headers.tmp
	2173	TAG_SOURCE_CODE=$(UTAGS).codefiles.tmp
[7819]	2174	TAG_SOURCE_LISTS=$(TAG_SOURCE_HEADERS) $(TAG_SOURCE_CODE)
[200]	2175
[15513]	2176	ETAGS_IGNORE_LIST=SOURCE_TOOLS/etags_ignore.lst
	2177
	2178	ETAGS=ctags -e -I @$(ETAGS_IGNORE_LIST) --sort=no --if0=no --extra=q
[7819]	2179	ETAGS_TYPES=--C-kinds=cgnsut --C++-kinds=cgnsut
	2180	ETAGS_FUN =--C-kinds=fm --C++-kinds=fm
	2181	ETAGS_REST =--C-kinds=dev --C++-kinds=dev
[200]	2182
[10573]	2183	FILTER_TAGS_SOURCES= \
	2184	$(SED) -e 's/^.\///g' \| \
[15483]	2185	grep -vi '^HEADERLIBS\\|^GDE/\\|/GEN[CH]/'
[10573]	2186
[7819]	2187	$(TAG_SOURCE_HEADERS): links
[17696]	2188	@find . $ -name '.hxx' -o -name ".h" $ -type f \| $(FILTER_TAGS_SOURCES) > $@
[2]	2189
[7819]	2190	$(TAG_SOURCE_CODE): links
[17696]	2191	@find . $ -name '.cxx' -o -name ".c" $ -type f \| $(FILTER_TAGS_SOURCES) > $@
[7819]	2192
[17367]	2193	$(UTAGS).1.tmp: $(TAG_SOURCE_HEADERS)
[17696]	2194	@$(ETAGS) -f $@ $(ETAGS_TYPES) -L $<
[17367]	2195	$(UTAGS).2.tmp: $(TAG_SOURCE_HEADERS)
[17696]	2196	@$(ETAGS) -f $@ $(ETAGS_FUN) -L $<
[17367]	2197	$(UTAGS).3.tmp: $(TAG_SOURCE_HEADERS)
[17696]	2198	@$(ETAGS) -f $@ $(ETAGS_REST) -L $<
[17367]	2199	$(UTAGS).4.tmp: $(TAG_SOURCE_CODE)
[17696]	2200	@$(ETAGS) -f $@ $(ETAGS_TYPES) -L $<
[17367]	2201	$(UTAGS).5.tmp: $(TAG_SOURCE_CODE)
[17696]	2202	@$(ETAGS) -f $@ $(ETAGS_FUN) -L $<
[17367]	2203	$(UTAGS).6.tmp: $(TAG_SOURCE_CODE)
[17696]	2204	@$(ETAGS) -f $@ $(ETAGS_REST) -L $<
[15513]	2205
[17367]	2206	TAGS_ALL_PARTS=$(UTAGS).1.tmp $(UTAGS).2.tmp $(UTAGS).3.tmp $(UTAGS).4.tmp $(UTAGS).5.tmp $(UTAGS).6.tmp
[15513]	2207
	2208	$(TAGFILE_TMP) : $(TAGS_ALL_PARTS)
[17696]	2209	@cat $(TAGS_ALL_PARTS) > $@
	2210	@rm $(TAGS_ALL_PARTS) $(TAG_SOURCE_LISTS)
[15513]	2211
[17727]	2212	cleanOldTags:
	2213	@find $(ARBHOME) -name 'TAGS.*.tmp' -ctime +2 -exec rm {} \;
	2214
	2215	tags: $(TAGFILE_TMP) cleanOldTags
[17696]	2216	@mv_if_diff $(TAGFILE_TMP) $(TAGFILE)
[7819]	2217
[200]	2218	#********************************************************************************
	2219
[8614]	2220	LINKSTAMP=SOURCE_TOOLS/stamp.generate_all_links
[2]	2221
[8246]	2222	links: checks $(LINKSTAMP) arbmainwrapper
[8439]	2223	links_no_checks: $(LINKSTAMP) arbmainwrapper
[6359]	2224
[6864]	2225	forcelinks:
[6872]	2226	-rm $(LINKSTAMP)
[6864]	2227	$(MAKE) links
	2228
[14055]	2229	$(LINKSTAMP): SOURCE_TOOLS/generate_all_links.sh genheaders
[7769]	2230	+SOURCE_TOOLS/generate_all_links.sh
[6359]	2231	touch $(LINKSTAMP)
[12]	2232
[7409]	2233	clean_links:
	2234	# avoid to delete linked pts, nas or arb_tcp.dat:
[6378]	2235	find . -path './lib' -prune -o -type l -exec rm {} \;
[10842]	2236	# removed obsolete file - refuses to disappear due to 'prune' above
	2237	@rm -f lib/help/GDEHELP
[7409]	2238	@rm -f $(LINKSTAMP) lib/inputMasks/format.readme
	2239
	2240	redo_links: clean_links
[8439]	2241	$(MAKE) links_no_checks
[6359]	2242
[7894]	2243	#********************************************************************************
	2244
[8670]	2245	header_libs:
[16266]	2246	@(( \
	2247	echo "$(SEP) Make HEADERLIBS"; \
	2248	$(MAKE) -C HEADERLIBS all && \
	2249	echo "$(SEP) Make HEADERLIBS [done]"; \
	2250	) > HEADERLIBS.log 2>&1 && (cat HEADERLIBS.log;rm HEADERLIBS.log)) \|\| (cat HEADERLIBS.log;rm HEADERLIBS.log;false)
[7894]	2251
	2252	#********************************************************************************
	2253
[2]	2254	gde: GDE/GDE.dummy
[2223]	2255	GDE: gde
[31]	2256	agde: ARB_GDE/ARB_GDE.dummy
[7409]	2257	tools: TOOLS/TOOLS.dummy
[7046]	2258	convert: $(CONVERT_ALN)
[2]	2259	readseq: READSEQ/READSEQ.dummy
	2260
	2261	#***************************************************************************************
	2262	# Some user commands
	2263	#***************************************************************************************
	2264
[7819]	2265	menus: binlink links
[5179]	2266	@(( \
[7819]	2267	echo "$(SEP) Make GDEHELP"; \
[8807]	2268	$(MAKE) -C GDEHELP -r all && \
[7819]	2269	echo "$(SEP) Make GDEHELP [done]"; \
[5179]	2270	) > GDEHELP.log 2>&1 && (cat GDEHELP.log;rm GDEHELP.log)) \|\| (cat GDEHELP.log;rm GDEHELP.log;false)
[2]	2271
[2303]	2272	ifeq ($(DEBUG),1)
	2273	BIN_TARGET=develall
	2274	else
	2275	BIN_TARGET=all
	2276	endif
	2277
	2278
[2]	2279	binlink:
[2303]	2280	$(MAKE) -C bin $(BIN_TARGET)
[2]	2281
[16127]	2282	check_bin_dep: binlink
	2283	SOURCE_TOOLS/check_bin_dependencies.pl
	2284
[18168]	2285	fig_cure:
	2286	SOURCE_TOOLS/sortfig.pl doit
	2287
[4218]	2288	preplib:
[5223]	2289	(cd lib;$(MAKE) all)
[369]	2290
[7819]	2291	# --------------------------------------------------------------------------------
	2292	# This section is quite tricky:
	2293	#
	2294	# make 'perl' is a BIG target, so when it has to be made, it has to be started
	2295	# as early as possible to reduce overall compile time. Since 'make' does not
[17738]	2296	# provide any priorities, i force it to build all 'perl'-prerequisites early, by
	2297	# adding artificial dependencies to these prerequisites
[7819]	2298	#
	2299	# That behavior is likely to be system-dependent.
	2300	# My goal was only to make it work on my current development system,
	2301	# where this saves about 20% of overall build time.
	2302
	2303	ifeq ($(WITHPERL),1)
	2304	links_non_perl: PERLTOOLS/PERLTOOLS.dummy
	2305	perltools: links_non_perl
	2306	perl: realperl
	2307	else
	2308	links_non_perl: links
[18907]	2309	perl: links
[7819]	2310	$(MAKE) "WITHPERL=1" perl
	2311	endif
	2312
[4632]	2313	# ---------------------------------------- perl
[2]	2314
[7819]	2315	realperl: perltools
[8320]	2316	(( \
[7819]	2317	echo "$(SEP) Make PERL2ARB" ; \
[8675]	2318	$(TIME) $(MAKE) -C PERL2ARB -r -f Makefile.main \
[7819]	2319	"AUTODEPENDS=1" \
	2320	"dflags=$(dflags)" \
[13739]	2321	"cflags4perl=$(cflags) $(cxxflags) $(dflags)" \
[13740]	2322	"lflags4perl=$(lflags4perl)" \
[10993]	2323	"COMPILER_VERSION=$(COMPILER_VERSION)" \
[7819]	2324	all && \
[17738]	2325	$(MAKE) -C PERL_SCRIPTS/test test && \
[7819]	2326	echo "$(SEP) Make PERL2ARB [done]" ; \
	2327	) > PERL2ARB.log 2>&1 && (cat PERL2ARB.log;rm PERL2ARB.log)) \|\| (cat PERL2ARB.log;rm PERL2ARB.log;false)
[2]	2328
[4632]	2329	perl_clean:
	2330	@$(MAKE) -C PERL2ARB -r -f Makefile.main \
	2331	"AUTODEPENDS=0" \
	2332	clean
[2142]	2333
[7409]	2334	PERL2ARB/PERL2ARB.clean:
	2335	$(MAKE) perl_clean
[12695]	2336	$(MAKE) -C PERL_SCRIPTS/test clean
[7409]	2337
[8848]	2338	# ---------------------------------------- bindings to script languages
[7409]	2339
[8848]	2340	bindings: lib/libCORE.so lib/libARBDB.so
	2341	$(MAKE) -C BINDINGS all ARBDEPENDS="$(^:%=../%)" DFLAGS="$(dflags)"
	2342
	2343	bindings_clean:
	2344	$(MAKE) -C BINDINGS clean
	2345
[14141]	2346	# ---------------------------------------- check resources
[5887]	2347
[6122]	2348	check_res:
[14141]	2349	$(ARBHOME)/SOURCE_TOOLS/check_resources.pl
[5887]	2350
[4632]	2351	# ---------------------------------------- cleaning
	2352
[2]	2353	rmbak:
[16437]	2354	@echo "[cleanup backup/core files]"
[7409]	2355	@find . \( -name '*%' \
	2356	-o -name '*.bak' \
	2357	-o -name '*~' \) \
[10439]	2358	-o $ -name 'core' -a \! -type d $ \
[16437]	2359	-exec rm -v {} \; \|\| \
	2360	echo "Warning: target 'rmbak' reported problems when removing misc. backup files (ignored)"
	2361	@echo "[cleanup done]"
[2]	2362
[7409]	2363	bin_reinit:
	2364	$(MAKE) bin/bin.clean
[7769]	2365	$(MAKE) -C "bin" all
[2]	2366
[7409]	2367	clean_directories:
[7673]	2368	-rm -rf \
[7409]	2369	$(ARBHOME)/PROBE_SET/bin \
	2370	$(ARBHOME)/INCLUDE \
	2371
[2907]	2372	libclean:
[7769]	2373	-find $(ARBHOME) -type f $ -name '*.a' ! -type l $ -exec rm -f {} \;
[18140]	2374	-find $(ARBHOME) -type f $ -name 'lib*.so' ! -type l $ -exec rm -f {} \;
[2907]	2375
[5672]	2376	objclean:
[7769]	2377	-find $(ARBHOME) -type f $ -name '*.o' ! -type l $ -exec rm -f {} \;
[5672]	2378
[7769]	2379	# bin.clean and HELP_SOURCE.clean interfere
	2380	clean3:
	2381	$(MAKE) bin/bin.clean
	2382	$(MAKE) HELP_SOURCE/HELP_SOURCE.clean
	2383
[18120]	2384
	2385	# delete all binaries (similar to 'cleanlinked')
	2386	cleanRelinkable: libclean UNIT_TESTER/UNIT_TESTER.clean
	2387	$(MAKE) -C bin cleanbinariesRelinkable
[18140]	2388	$(MAKE) -C PROBE_SET cleanLinked
[18120]	2389
	2390
[18426]	2391	clean2: $(SUBDIRS:.sub=.clean) \
[7769]	2392	clean3 \
[7409]	2393	rmbak \
	2394	libclean \
	2395	objclean \
	2396	lib/lib.clean \
[4632]	2397	GDEHELP/GDEHELP.clean \
[7895]	2398	HEADERLIBS/HEADERLIBS.clean \
[4632]	2399	SOURCE_TOOLS/SOURCE_TOOLS.clean \
[11533]	2400	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.clean \
[6460]	2401	UNIT_TESTER/UNIT_TESTER.clean \
[7409]	2402	TEMPLATES/TEMPLATES.clean \
	2403	perl_clean \
	2404	clean_directories \
[2]	2405
[10993]	2406	rm -f .last_gcc .last_compiler config.makefile.bak
[7409]	2407
[4923]	2408	# links are needed for cleanup
[9777]	2409	clean: redo_links motif_xpm_hack_clean
[4923]	2410	$(MAKE) clean2
[7810]	2411	$(MAKE) clean_cov_all clean_links
[4923]	2412
[10153]	2413	silent_clean:
	2414	$(MAKE) clean >/dev/null
	2415
[5672]	2416	# 'relocated' is about 50% faster than 'rebuild'
[5833]	2417	reloc_clean: links
[5663]	2418	@echo "---------------------------------------- Relocation cleanup"
[5672]	2419	$(MAKE) \
	2420	perl_clean \
	2421	GDEHELP/GDEHELP.clean \
	2422	HELP_SOURCE/genhelp/genhelp.clean \
[7431]	2423	bin/bin.clean \
[5672]	2424	libclean \
	2425	objclean
[5833]	2426
	2427	relocated: links
	2428	$(MAKE) reloc_clean
[5672]	2429	@echo "---------------------------------------- and remake"
[7409]	2430	$(MAKE) build
[5663]	2431
[4632]	2432	# -----------------------------------
[12400]	2433	# some stress tests
	2434	# (helpful to reveal race conditions with -j)
[2]	2435
[7409]	2436	rebuild4ever: rebuild
	2437	$(MAKE) rebuild4ever
	2438
	2439	build4ever: build
	2440	$(MAKE) build4ever
	2441
	2442	clean4ever: clean
	2443	$(MAKE) clean4ever
	2444
	2445	test4ever: ut
	2446	$(MAKE) test4ever
	2447
[13923]	2448	perl4ever: clean
[7409]	2449	$(MAKE) links
	2450	$(MAKE) perl
	2451	$(MAKE) perl4ever
	2452
[12400]	2453	help4ever: clean
	2454	$(MAKE) help
	2455	$(MAKE) help4ever
[7409]	2456
	2457	# -----------------------------------
	2458
[14205]	2459	cleanlinked: bin/bin.clean libclean
[2907]	2460
[14205]	2461	relink: cleanlinked
	2462	$(MAKE) all
	2463
[18924]	2464	# --------------------------------------------------------------------------------
	2465	# source related targets
[4632]	2466
[18923]	2467	CLOC=cloc
	2468	CLOCFLAGS=--no3 --quiet --progress-rate=0
	2469	CLOCARB=--exclude-dir=GDE .
	2470	CLOCEXT=GDE
	2471	CLOCCODE=--force-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.code.def
	2472	CLOCREST=--force-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.rest.def
	2473	CLOCFILT=tail --lines=+4
	2474
	2475	cloc:
	2476	@echo 'Arb code:'
	2477	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCARB) \| $(CLOCFILT)
	2478	@echo 'Arb rest:'
	2479	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCARB) \| $(CLOCFILT)
	2480	@echo 'External code:'
	2481	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCEXT) \| $(CLOCFILT)
	2482	@echo 'External rest:'
	2483	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCEXT) \| $(CLOCFILT)
	2484
	2485
[18924]	2486	# patch generation
[6718]	2487	patch:
[18912]	2488	SOURCE_TOOLS/arb_create_patch.sh arbPatch --svn
[6718]	2489
[18924]	2490	# source tarball generation
	2491	save: sourcetarfile
	2492
	2493	sourcetarfile: rmbak
	2494	util/arb_save
	2495
[6718]	2496	# test early whether save will work
[7184]	2497	savetest:
[5257]	2498	@util/arb_srclst.pl >/dev/null
	2499
[7184]	2500	testsave: savetest
	2501
[4844]	2502	save2: rmbak
[5477]	2503	util/arb_save ignore
[4844]	2504
[5947]	2505	save_test: rmbak
	2506	@echo "Testing source list.."
	2507	@util/arb_srclst.pl > /dev/null
	2508
[8606]	2509	save_test_no_error:
	2510	@-$(MAKE) save_test
	2511
[18924]	2512	# --------------------------------------------------------------------------------
	2513	# version management
	2514
[11669]	2515	inc_candi:
	2516	touch SOURCE_TOOLS/inc_candi.stamp
	2517	$(MAKE) do_version_update
	2518
	2519	inc_patch:
	2520	touch SOURCE_TOOLS/inc_patch.stamp
	2521	$(MAKE) do_version_update
	2522
	2523	inc_minor:
[5477]	2524	touch SOURCE_TOOLS/inc_minor.stamp
[11669]	2525	$(MAKE) do_version_update
[5477]	2526
[11669]	2527	inc_major:
[5477]	2528	touch SOURCE_TOOLS/inc_major.stamp
[11669]	2529	$(MAKE) do_version_update
[5477]	2530
[13923]	2531	do_version_update:
[11669]	2532	@echo Incrementing version information
[15805]	2533	$(MAKE) savetest
[9577]	2534	$(MAKE) genheaders # auto upgrades version early
[3346]	2535
[11674]	2536	show_version:
	2537	$(MAKE) genheaders # updates version info
	2538	@echo "$(SEP) ARB version info"
	2539	@grep ARB_VERSION TEMPLATES/arb_build.h
	2540	@echo "$(SEP)"
	2541
[1878]	2542	# --------------------------------------------------------------------------------
[15737]	2543	# special cleanups
[1878]	2544
[15737]	2545	clean_opengl_changed: RNA3D/RNA3D.clean EDIT4/EDIT4.clean WINDOW/WINDOW.clean GL/GL.clean
	2546
	2547	# --------------------------------------------------------------------------------
	2548
[10137]	2549	arbapplications: nt pa e4 wetc pt na nal di ph ds wetc cma
[2]	2550
[18426]	2551	arb_external: convert tools gde readseq tg pst
[3635]	2552
[7819]	2553	arb_no_perl: arbapplications help arb_external
[866]	2554
[9777]	2555	arb: motif_xpm_hack
[7819]	2556	$(MAKE) "WITHPERL=1" perl arb_no_perl
[866]	2557
[9777]	2558	motif_xpm_hack:
	2559	$(MAKE) -r -C "lib/motifHack" all
	2560
	2561	motif_xpm_hack_clean:
	2562	$(MAKE) -r -C "lib/motifHack" clean
	2563
[7819]	2564	# --------------------------------------------------------------------------------
	2565	# special targets for SOURCE_TOOLS/remake_after_change.pl
[866]	2566
[7819]	2567	rac_arb_dist: di
	2568	rac_arb_edit4: e4
	2569	rac_arb_ntree: nt
	2570	rac_arb_pars: pa
	2571	rac_arb_phylo: ph
	2572	rac_arb_wetc: wetc
	2573	rac_arb_naligner: nal
	2574	rac_arb_pt_server: pt
	2575	rac_arb_db_server: ds
	2576	rac_arb_name_server: na
	2577	rac_arb_convert_aln: convert
	2578	rac_arb_treegen: tg
[7895]	2579	rac_arb_rnacma: cma
[10951]	2580	rac_arb_help2xml: help
[10948]	2581
	2582	rac_arb_a2ps: tools
	2583	rac_arb_consensus_tree: tools
	2584	rac_arb_dnarates: tools
	2585	rac_arb_export_rates: tools
	2586	rac_arb_export_tree: tools
	2587	rac_arb_gene_probe: tools
	2588	rac_arb_message: tools
	2589	rac_arb_primer: tools
[10943]	2590	rac_arb_probe: tools
[10948]	2591	rac_arb_read_tree: tools
[866]	2592
[6451]	2593	# --------------------------------------------------------------------------------
[13923]	2594	# unit testing
[6546]	2595	# @@@ work in progress
	2596	#
	2597	# goal is to automatically test all libraries/executables using TESTED_UNITS_AUTO
[18426]	2598	# currently not all test executables link w/o error.
	2599	# therefor units are organized in three sets:
[6546]	2600	#
[18426]	2601	# TESTED_UNITS = testable and contain tests
	2602	# UNTESTED_UNITS = testable, but no tests written yet
	2603	# UNTESTABLE_UNITS = not testable
[6451]	2604
[18426]	2605	# always define OPENGL units manually:
	2606	OPENGL_TESTS :=
	2607	ifeq ($(OPENGL),1)
	2608	OPENGL_TESTS += \
	2609	$(subst .a,.test,$(RNA3D_LIB)) \
	2610	GL/glAW/libglAW.test \
	2611	GL/glpng/libglpng_arb.test \
[6863]	2612
[18426]	2613	endif
[6451]	2614
[18426]	2615	UNITS_NOT_AUTODETECTED = \
	2616	HELP_SOURCE/HELP_SOURCE.tooltests
	2617
	2618	TESTED_UNITS_AUTO = \
	2619	$(OPENGL_TESTS) \
	2620	$(TL_ARCHIVES:.a=.test) \
	2621	$(TL_SHARED_ARCHIVES:.so=.test) \
	2622	$(CL_ARCHIVES:.a=.test) \
	2623	$(TL_TOOLS_COLLECTIONS:.toolColl=.tooltests) \
	2624	$(UNITS_NOT_AUTODETECTED) \
	2625
	2626	UNTESTED_UNITS = \
	2627	$(OPENGL_TESTS) \
[7801]	2628	EISPACK/EISPACK.test \
[8250]	2629	GENOM/GENOM.test \
[6451]	2630	ISLAND_HOPPING/ISLAND_HOPPING.test \
[7801]	2631	NALIGNER/NALIGNER.test \
	2632	NAMES/NAMES.test \
	2633	PHYLO/PHYLO.test \
	2634	PRIMER_DESIGN/PRIMER_DESIGN.test \
[18426]	2635	READSEQ/READSEQ.tooltests \
[7801]	2636	SECEDIT/SECEDIT.test \
	2637	SEQ_QUALITY/SEQ_QUALITY.test \
	2638	SERVERCNTRL/SERVERCNTRL.test \
[6451]	2639	SL/ALIVIEW/ALIVIEW.test \
	2640	SL/AP_TREE/AP_TREE.test \
	2641	SL/ARB_TREE/ARB_TREE.test \
	2642	SL/AW_HELIX/AW_HELIX.test \
	2643	SL/AW_NAME/AW_NAME.test \
	2644	SL/DB_SCANNER/DB_SCANNER.test \
[18426]	2645	SL/DB_UI/DB_UI.test \
[6451]	2646	SL/GUI_ALIVIEW/GUI_ALIVIEW.test \
	2647	SL/HELIX/HELIX.test \
[15852]	2648	SL/QUERY/QUERY.test \
[7801]	2649	SL/REFENTRIES/REFENTRIES.test \
[6451]	2650	SL/SEQUENCE/SEQUENCE.test \
[8557]	2651	SL/TREE_ADMIN/TREE_ADMIN.test \
[6451]	2652	SL/TREE_WRITE/TREE_WRITE.test \
[18140]	2653	SL/XFERGUI/XFERGUI.test \
[6451]	2654	STAT/STAT.test \
[7801]	2655	TREEGEN/TREEGEN.test \
[6451]	2656	WETC/WETC.test \
[7801]	2657	XML/XML.test \
[6451]	2658
[6865]	2659	# untestable units
[6451]	2660
[18426]	2661	UNTESTABLE_UNITS = \
	2662	AISC/AISC.test \
	2663	NAMES_COM/server.test \
	2664	PROBE_COM/server.test \
[6451]	2665
[18426]	2666	# --------------------
	2667	# put all units containing tests into the following 4 sections (see also TESTED_UNITS below)
[6865]	2668
[16564]	2669	# recent development
[7819]	2670	UNITS_TESTED_FIRST = \
[18634]	2671	SL/MATRIX/MATRIX.test \
[16564]	2672	AWTI/AWTI.test \
[16119]	2673	SL/FILTSEQEXP/FILTSEQEXP.test \
[15966]	2674	SL/GROUP_SEARCH/GROUP_SEARCH.test \
[18426]	2675	SL/PVP/PVP.test \
	2676	SL/SAICALC/SAICALC.test \
	2677	SL/TRANSLATE/TRANSLATE.test \
	2678	SL/XFERSET/XFERSET.test \
[13625]	2679
[16564]	2680	# start units with long duration early
[15579]	2681	UNITS_RUNNING_LONG = \
	2682	ARBDB/libARBDB.test \
	2683	AWTC/AWTC.test \
[18426]	2684	TOOLS/TOOLS.tooltests \
[15579]	2685
[16564]	2686	# plain test-libaries that are not linked anywhere
	2687	TEST_SANDBOXES = \
	2688	SL/CB/CB.test \
[18959]	2689	SL/HEADERTESTS/HEADERTESTS.test \
[16564]	2690
[13625]	2691	UNITS_TESTED = \
[18426]	2692	AISC_MKPTPS/AISC_MKPTPS.tooltests \
[10380]	2693	ARB_GDE/ARB_GDE.test \
[15579]	2694	AWT/libAWT.test \
[8460]	2695	CONSENSUS_TREE/CONSENSUS_TREE.test \
[15579]	2696	CONVERTALN/CONVERTALN.test \
	2697	CORE/libCORE.test \
[8101]	2698	DBSERVER/DBSERVER.test \
[15579]	2699	DIST/DIST.test \
	2700	EDIT4/EDIT4.test \
	2701	GENOM_IMPORT/GENOM_IMPORT.test \
[18426]	2702	HELP_SOURCE/HELP_SOURCE.tooltests \
[6865]	2703	MERGE/MERGE.test \
[15579]	2704	MULTI_PROBE/MULTI_PROBE.test \
	2705	NTREE/NTREE.test \
	2706	PARSIMONY/PARSIMONY.test \
[18426]	2707	PERLTOOLS/PERLTOOLS.tooltests \
[15579]	2708	PROBE/PROBE.test \
[19339]	2709	PROBE_DESIGN/PROBE_DESIGN.test \
[18426]	2710	PROBE_SET/PROBE_SET.tooltests \
	2711	RNACMA/RNACMA.test \
[15579]	2712	SL/ALILINK/ALILINK.test \
	2713	SL/CONSENSUS/CONSENSUS.test \
	2714	SL/DB_QUERY/DB_QUERY.test \
[6688]	2715	SL/FAST_ALIGNER/FAST_ALIGNER.test \
[15579]	2716	SL/FILTER/FILTER.test \
	2717	SL/INSDEL/INSDEL.test \
	2718	SL/ITEM_SHADER/ITEM_SHADER.test \
	2719	SL/ITEMS/ITEMS.test \
[18426]	2720	SL/LOCATION/LOCATION.test \
[15579]	2721	SL/MACROS/MACROS.test \
	2722	SL/NDS/NDS.test \
	2723	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.test \
[6865]	2724	SL/PRONUC/PRONUC.test \
[15579]	2725	SL/PTCLEAN/PTCLEAN.test \
	2726	SL/REGEXPR/REGEXPR.test \
	2727	SL/SEQIO/SEQIO.test \
	2728	SL/TREE_READ/TREE_READ.test \
	2729	SL/TREEDISP/TREEDISP.test \
[8574]	2730	WINDOW/libWINDOW.test \
[6451]	2731
[15579]	2732	TESTED_UNITS = \
	2733	$(UNITS_TESTED_FIRST) \
[16564]	2734	$(UNITS_RUNNING_LONG) \
[10205]	2735	$(TEST_SANDBOXES) \
[6546]	2736	$(UNITS_TESTED) \
[6451]	2737
[18426]	2738	# ----------------------------------------
[8249]	2739
[18426]	2740	ifeq ($(DEVELOPER),RALF)
	2741
	2742	DEFINED_TEST_UNITS = \
	2743	$(TESTED_UNITS) \
	2744	$(UNTESTED_UNITS) \
	2745	$(UNTESTABLE_UNITS) \
	2746
	2747	list_undefined_units:
	2748	@UNIT_TESTER/list_undefined_units.pl $(DEFINED_TEST_UNITS) -- $(TESTED_UNITS_AUTO)
	2749
	2750	else
	2751
	2752	list_undefined_units:
	2753
	2754	endif
	2755
[6743]	2756	# ----------------------------------------
	2757
	2758	TEST_LOG_DIR = UNIT_TESTER/logs
[6863]	2759	TEST_RUN_SUITE=$(MAKE) $(NODIR) -C UNIT_TESTER -f Makefile.suite -r
[18322]	2760	# -> UNIT_TESTER/Makefile.suite
[7802]	2761	TEST_MAKE_FLAGS=
	2762	TEST_POST_CLEAN=
	2763	ifeq ($(COVERAGE),1)
[7810]	2764	TEST_POST_CLEAN=$(MAKE) clean_cov
[7802]	2765	TEST_MAKE_FLAGS+=-j1
	2766	endif
[6743]	2767
[7802]	2768
[10205]	2769	%.test:
[6743]	2770	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
	2771	( \
[18361]	2772	echo "take[1]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
[6451]	2773	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
	2774	"UNITDIR=$(@D)" \
	2775	"UNITLIBNAME=$(@F:.test=)" \
[6526]	2776	"COVERAGE=$(COVERAGE)" \
[7819]	2777	"ARB_PID=$(ARB_PID)_$(@F)" \
[7802]	2778	runtest; \
[18361]	2779	echo "take[1]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"; \
[7802]	2780	$(TEST_POST_CLEAN) \
[11190]	2781	) >$(TEST_LOG_DIR)/$(@F).log 2>&1; \
	2782	UNIT_TESTER/log_result.pl $(TEST_LOG_DIR)/$(@F).log )
[6451]	2783
[18426]	2784	%.notest:
	2785	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
	2786	( \
	2787	echo "take[4]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
	2788	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
	2789	"UNITDIR=$(@D)" \
	2790	"UNITLIBNAME=$(@F:.notest=)" \
	2791	"COVERAGE=0" \
	2792	"ARB_PID=$(ARB_PID)_$(@F)" \
	2793	check_no_test; \
	2794	echo "take[4]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'" \
	2795	) >$(TEST_LOG_DIR)/$(@F).log 2>&1 )
[7808]	2796
[18426]	2797
	2798	# tool test aliases (used to test one or multiple executable(s) in a single subdir):
	2799	%.tooltests:
	2800	$(error please define an explicit tooltest alias for $@)
	2801
	2802	AISC_MKPTPS/AISC_MKPTPS.tooltests : AISC_MKPTPS/mkptypes.test
	2803	@echo "aliasing $@ -> $^"
	2804	PERLTOOLS/PERLTOOLS.tooltests : PERLTOOLS/arb_proto_2_xsub.test
	2805	@echo "aliasing $@ -> $^"
	2806	PROBE_SET/PROBE_SET.tooltests : PROBE_SET/fb_test.test
	2807	@echo "aliasing $@ -> $^"
	2808	HELP_SOURCE/HELP_SOURCE.tooltests : HELP_SOURCE/arb_help2xml.test
	2809	@echo "aliasing $@ -> $^"
	2810	TOOLS/TOOLS.tooltests : TOOLS/arb_consensus_tree.test TOOLS/arb_probe.test TOOLS/arb_test.test
	2811	@echo "aliasing $@ -> $^"
	2812
	2813	# aliases for tools w/o tests:
	2814	READSEQ/READSEQ.tooltests:
	2815	@echo "Note: no tests for $@"
	2816
	2817
[10205]	2818	test_base: $(UNIT_TESTER_LIB:.a=.dummy) $(subst .test,.dummy,$(TEST_SANDBOXES))
[6451]	2819
[7810]	2820	clean_cov:
[6529]	2821	find . $ -name ".gcda" -o -name ".gcov" -o -name "*.cov" $ -exec rm {} \;
[6526]	2822
[7810]	2823	clean_cov_all: clean_cov
[6526]	2824	find . $ -name "*.gcno" $ -exec rm {} \;
	2825
[10677]	2826	cleanup_faked_arbpids:
[14799]	2827	@rm ~/.arb_tmp/tmp/arb_pids_${USER}_${ARB_PID}_* \|\| true
[10677]	2828
	2829	cleanup_faked_arbpids_and_fail: cleanup_faked_arbpids
[10676]	2830	@false
	2831
[18426]	2832	NOTESTS_IN_UNTESTED = $(subst .test,.notest,$(UNTESTED_UNITS))
[17701]	2833
[7819]	2834	run_tests_faked_arbpid:
[7769]	2835	+@$(TEST_RUN_SUITE) init
[18361]	2836	@echo "take[2]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
[18426]	2837	@$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(TESTED_UNITS) $(NOTESTS_IN_UNTESTED) \|\| $(MAKE) cleanup_faked_arbpids_and_fail
[18361]	2838	@echo "take[2]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
[10676]	2839	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
[8606]	2840	@$(MAKE) clean_cov >/dev/null
[10677]	2841	@$(MAKE) cleanup_faked_arbpids
[6451]	2842
[17665]	2843	# @@@ instead of only running UNIT, this should as well run all tests this unit depends on? according to 'needs_libs'
	2844	# @@@ '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
	2845
	2846	run_onetest_faked_arbpid:
	2847	+@$(TEST_RUN_SUITE) init
[18361]	2848	@echo "take[3]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
[17665]	2849	test -n "$(UNIT)" \|\| (echo "Error: UNIT has to be defined for target 'run_onetest_faked_arbpid'!"; false)
	2850	$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(UNIT).test \|\| $(MAKE) cleanup_faked_arbpids_and_fail
[18361]	2851	@echo "take[3]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
[17665]	2852	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
	2853	@$(MAKE) clean_cov >/dev/null
	2854	@$(MAKE) cleanup_faked_arbpids
	2855
[17701]	2856	run_tests: test_base clean_cov
[18426]	2857	$(MAKE) "ARB_PID=UT_$$$$" run_tests_faked_arbpid list_undefined_units
[17701]	2858
	2859	run_oneunitstests: test_base
	2860	$(MAKE) "ARB_PID=UT_$$$$" run_onetest_faked_arbpid
	2861
	2862
[7046]	2863	ut:
	2864	ifeq ($(UNIT_TESTS),1)
[7819]	2865	@echo $(MAKE) run_tests
	2866	@$(MAKE) run_tests
[7046]	2867	else
	2868	@echo "Not compiled with unit tests"
	2869	endif
[6558]	2870
[7046]	2871
[6863]	2872	aut:
[7769]	2873	+@$(TEST_RUN_SUITE) unskip
[6863]	2874	$(MAKE) ut
	2875
[6451]	2876	# --------------------------------------------------------------------------------
	2877
[6708]	2878	TIMELOG=$(ARBHOME)/arb_time.log
[17618]	2879	TIMEARGS=--append --output=$(TIMELOG) --format=" * %E(%S+%U) %P [%C]"
[8675]	2880	TIMECMD=$(TIME) $(TIMEARGS)
[6708]	2881
[7819]	2882	time_one:
	2883	ifeq ($(ONE_TIMED_TARGET),)
	2884	@echo "Error: You have to pass ONE_TIMED_TARGET to $@"
	2885	false
	2886	else
	2887	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET)"
	2888	@$(TIMECMD) $(MAKE) $(ONE_TIMED_TARGET)
	2889	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET) [done]"
	2890	endif
[7409]	2891
[7819]	2892	timed_target:
	2893	ifeq ($(TIMED_TARGET),)
	2894	@echo "Error: You have to pass TIMED_TARGET to $@"
	2895	false
	2896	else
	2897	@echo "Build time:" > $(TIMELOG)
	2898	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
	2899	@cat $(TIMELOG)
	2900	@rm $(TIMELOG)
	2901	endif
	2902
	2903	timed_target_tested:
	2904	ifeq ($(TIMED_TARGET),)
	2905	@echo "Error: You have to pass TIMED_TARGET to $@"
	2906	false
	2907	else
	2908	@echo "Build time:" > $(TIMELOG)
	2909	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
	2910	$(MAKE) "ONE_TIMED_TARGET=ut" time_one
	2911	@cat $(TIMELOG)
	2912	@rm $(TIMELOG)
	2913	endif
	2914
	2915	clean_timed_target:
	2916	ifeq ($(TIMED_TARGET),)
	2917	@echo "Error: You have to pass TIMED_TARGET to $@"
	2918	false
	2919	else
	2920	@echo "Build time:" > $(TIMELOG)
	2921	$(MAKE) "ONE_TIMED_TARGET=clean" time_one
	2922	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
	2923	@cat $(TIMELOG)
	2924	@rm $(TIMELOG)
	2925	endif
	2926
	2927	# --------------------------------------------------------------------------------
	2928
[10345]	2929	CHECKOUT_MODIFIED=0# set to 1 to temporarily skip test for modifications (do not check in if set to 1)
	2930
[10344]	2931	check_svn_does_not_contain_generated:
[13923]	2932	ifeq ($(CHECKOUT_MODIFIED),0)
[10344]	2933	@echo "Testing that build does not modify files in SVN"
[10354]	2934	@test 0 = `svn status \| wc -l` \|\| ( \
[10344]	2935	echo "The checkout is not/no longer clean:"; \
	2936	svn status; \
	2937	echo "- if this fails instantly, your checkout is not clean"; \
	2938	echo "- if this fails after other targets, these targets modify checked in data"; \
	2939	echo " (a common cause may be that depends are not up to date)"; \
	2940	false)
[10345]	2941	else
	2942	grep -Hn 'CHECKOUT_MODIFIED' Makefile
	2943	endif
[10344]	2944
	2945	check_svn_ignores_generated:
[10354]	2946	@test 0 = `svn status \| grep '^\?' \| wc -l` \|\| ( \
[10344]	2947	echo "There are svn-unignored files:"; \
	2948	svn status \| grep '^\?'; \
	2949	echo "(all generated files should be svn-ignored)"; \
	2950	false)
	2951
	2952	check_svn_state: check_svn_does_not_contain_generated
	2953	$(MAKE) check_svn_ignores_generated
	2954	$(MAKE) savetest
	2955
	2956	things_that_always_should_work: depends proto
	2957
	2958	post_commit_check:
	2959	@echo "---------------------------------------- [Initial]"
	2960	$(MAKE) check_svn_state
	2961
	2962	$(MAKE) clean
	2963	@echo "---------------------------------------- [After 'make clean']"
	2964	$(MAKE) check_svn_state
	2965
	2966	$(MAKE) things_that_always_should_work
	2967	@echo "---------------------------------------- [After 'make things_that_always_should_work']"
	2968	$(MAKE) check_svn_state
	2969
	2970	$(MAKE) all
	2971	@echo "---------------------------------------- [After 'make all']"
	2972	$(MAKE) check_svn_state
	2973
	2974	$(MAKE) things_that_always_should_work
	2975	@echo "---------------------------------------- [Final]"
	2976	$(MAKE) check_svn_state
	2977
	2978	# --------------------------------------------------------------------------------
[13745]	2979	# sanitize arb_ntree; also works for clients (arb_edit4, ...) started from there.
[10344]	2980
[13745]	2981	sanitize: all
[13747]	2982	( \
	2983	export "LSAN_OPTIONS=max_leaks=30:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp"; \
	2984	echo "sake[1]: Entering directory \`$(ARBHOME)'"; \
	2985	$(ARBHOME)/bin/arb_ntree --execute _logged ~/data/test.arb 2>&1 ; \
	2986	echo "sake[1]: Leaving directory \`$(ARBHOME)'" \
	2987	) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
[13745]	2988
	2989	# --------------------------------------------------------------------------------
[16425]	2990	# build and test one unit:
[13745]	2991
[17701]	2992	build_oneunit:
[16425]	2993	$(MAKE) "WITHPERL=1" $(UNIT).dummy
	2994
	2995	oneunit:
	2996	ifndef UNIT
	2997	@echo "Please define UNIT, e.g. using"
	2998	@echo " make \"UNIT=ARBDB/libARBDB\" oneunit"
	2999	@echo " make \"UNIT=SL/TREEDISP/TREEDISP\" oneunit"
	3000	@echo "(Note: 1st is a shared library, 2nd isn't)"
	3001	false
	3002	else
	3003	@echo "Build time" > $(TIMELOG)
[17701]	3004	@echo "$(SEP) $(MAKE) build_oneunit"
	3005	@$(TIMECMD) $(MAKE) build_oneunit
[16425]	3006	ifeq ($(UNIT_TESTS),1)
[17665]	3007	@echo "$(SEP) $(MAKE) run_oneunitstests"
	3008	@$(TIMECMD) $(MAKE) run_oneunitstests
[16425]	3009	endif
	3010	@cat $(TIMELOG)
	3011	@rm $(TIMELOG)
	3012	endif
	3013
	3014	# --------------------------------------------------------------------------------
[18924]	3015	# Main targets:
[16425]	3016
[18924]	3017	tarfile: rebuild
	3018	$(MAKE) prepare_libdir
	3019	util/arb_compress
	3020
	3021	tarfile_quick: all
	3022	$(MAKE) prepare_libdir
	3023	util/arb_compress
	3024
	3025	# -----------------------------------
	3026
[7819]	3027	build: arb
[18168]	3028	$(MAKE) check_bin_dep preplib compile_compatibility fig_cure
[6708]	3029
[18917]	3030	all:
[6717]	3031	@echo "Build time" > $(TIMELOG)
[16653]	3032	# $(MAKE) clean_checked_vect # uncomment to rebuild sources where expected vectorization gets tested
[17665]	3033	@echo "$(SEP) $(MAKE) all"
[6717]	3034	@$(TIMECMD) $(MAKE) build
[5143]	3035	@echo $(SEP)
	3036	@echo "made 'all' with success."
	3037	@echo "to start arb enter 'arb'"
[18920]	3038	ifeq ($(UNIT_TESTS),1)
[17665]	3039	@echo "$(SEP) $(MAKE) run_tests"
[7819]	3040	@$(TIMECMD) $(MAKE) run_tests
[18920]	3041	endif
[17665]	3042	@echo "$(SEP) $(MAKE) all [done]"
[18920]	3043	ifeq ($(DEBUG),1)
[8606]	3044	@$(MAKE) save_test_no_error >/dev/null # just show hints
[18920]	3045	endif
[6708]	3046	@cat $(TIMELOG)
	3047	@rm $(TIMELOG)
[7819]	3048
[18924]	3049	rebuild: clean
	3050	$(MAKE) all
	3051
[18916]	3052	# --------------------------------------------------------------------------------
[18920]	3053	# special targets showing obvious error at bottom
	3054	# (intended to be used from automated builds)
[18916]	3055
	3056	BUILD_LOG=build.log
	3057	SHELL=bash
[18920]	3058	REDIRECT_KEEP_EXITCODE = tee $(BUILD_LOG) ; exit "$${PIPESTATUS[0]}"
	3059	EXTRACT_ERROR_SUMMARY = (./SOURCE_TOOLS/short_error_summary.pl $(BUILD_LOG); false)
[18916]	3060
[18920]	3061	ALL:
	3062	@(($(MAKE) all 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
[18916]	3063
[18920]	3064	REBUILD:
	3065	@(($(MAKE) rebuild 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
	3066
[18925]	3067	TARFILE:
	3068	@(($(MAKE) tarfile 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
	3069
	3070	TARFILE_QUICK:
	3071	@(($(MAKE) tarfile_quick 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
	3072

Note: See TracBrowser for help on using the repository browser.

Context Navigation

source: trunk/Makefile

Download in other formats: