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Last change on this file was 19959, checked in by westram, 5 days ago
remove pre-`C++14` code.
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 86.9 KB

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1	# =============================================================== #
2	# #
3	# File : Makefile #
4	# #
5	# Institute of Microbiology (Technical University Munich) #
6	# http://www.arb-home.de/ #
7	# #
8	# =============================================================== #
9
10	# -----------------------------------------------------
11	# The ARB Makefile is aware of the following defines:
12	#
13	# [defined by make or env:]
14	#
15	# CC C compiler (cc)
16	# CXX C++ compiler (g++)
17	# AR Linker (ar)
18	#
19	# [defined by config.makefile:]
20	#
21	# DEVELOPER=name special compilation (values: ANY,RELEASE,your name)
22	# OPENGL=0/1 whether OPENGL is available
23	#
24	# -----------------------------------------------------
25	# Paths for several libraries may be set from config.makefile by using:
26	#
27	# export XLIBS=$(shell pkg-config --libs xpm xerces-c)
28	# export XINCLUDES=$(shell pkg-config --cflags x11)
29	# export XAW_LIBS=$(shell pkg-config --libs xaw7)
30	# export XML_INCLUDES=$(shell pkg-config --cflags xerces-c)
31	#
32	# You make have to explicitely point pkg-config to the *.pc files needed.
33	# For example, Xquartz X11 libraries on macOS can be located by adding
34	# the following line before those given above:
35	#
36	# export PKG_CONFIG_PATH=/usr/X11/lib/pkgconfig
37	#
38	# If you introduce a new variable that is handled as described above,
39	# please add to section .@InjectedEnvironment
40	#
41	# -----------------------------------------------------
42	# ARB Makefile and ARB source code are aware of the following defines:
43	#
44	# $(MACH) name of the machine (LINUX or DARWIN; see config.makefile)
45	# DEBUG compiles the DEBUG sections
46	# DEBUG_GRAPHICS all X-graphics are flushed immediately (for debugging)
47	# ARB_64=0/1 1=>compile 64 bit version
48	# UNIT_TESTS=0/1 1=>compile in unit tests and call them after build
49	# COVERAGE=0/1/2 compile in gcov support (useful together with UNIT_TESTS=1)
50	# 0=no, 1+2=compile in, 1=show
51	# STABS=0/1 force stabs format? (0 = "use default format")
52	# SANITIZE=0/#/all use Sanitizer? (defaults to 0,
53	# 1=AddressSanitizer+LeakSanitizer,
54	# 2=UndefinedBehaviorSanitizer,
55	# combine bit-values to activate multiple Sanitizers,
56	# specify 'all' to activate all)
57	# IGNORE_LEAKS=1 does not abort when leaks are detected (while using SANITIZE=1/all)
58	# SHOWTODO=0/1 activate TODO-warnings? (defaults to 0, except for ralf)
59	#
60	# -----------------------------------------------------
61	# The ARB source code is aware of the following defines:
62	#
63	# NDEBUG doesn't compile the DEBUG sections
64	# DEVEL_$(DEVELOPER) developer-dependent flag (enables you to have private sections in code)
65	# DEVELOPER='ANY' (default setting) will be ignored
66	# configurable in config.makefile
67	#
68	# -----------------------------------------------------
69
70	ifndef ARB_ORG_MAKEFLAGS
71	ARB_ORG_MAKEFLAGS=$(MAKEFLAGS)
72	else
73	ifeq ($(ARB_ORG_MAKEFLAGS),)
74	ARB_ORG_MAKEFLAGS=$(MAKEFLAGS)
75	endif
76	endif
77
78	# detect initial (i.e. non-recursive) call:
79	ifndef ARBBID
80	INITIAL_CALL:=yes
81	endif
82
83	# Read configuration
84	include config.makefile
85	CONFIG_MAKEFILE_FOUND=$(strip $(wildcard config.makefile))
86
87	# strip spaces from values defined in config.makefile
88	# (otherwise they easily have spaces appended)
89	ifdef DEVELOPER
90	DEVELOPER := $(strip $(DEVELOPER))
91	endif
92	ifdef OPENGL
93	OPENGL := $(strip $(OPENGL))
94	endif
95	ifdef DEBUG
96	DEBUG := $(strip $(DEBUG))
97	endif
98	ifdef UNIT_TESTS
99	UNIT_TESTS := $(strip $(UNIT_TESTS))
100	endif
101	ifdef COVERAGE
102	COVERAGE := $(strip $(COVERAGE))
103	endif
104	ifdef SHOWTODO
105	SHOWTODO := $(strip $(SHOWTODO))
106	endif
107	ifdef STABS
108	STABS := $(strip $(STABS))
109	endif
110	ifdef TRACESYM
111	TRACESYM := $(strip $(TRACESYM))
112	endif
113	ifdef DEBUG_GRAPHICS
114	DEBUG_GRAPHICS := $(strip $(DEBUG_GRAPHICS))
115	endif
116
117	# set defaults for (or strip) variables commented out in config.makefile:
118	SANITIZE ?= 0
119	SANITIZE := $(strip $(SANITIZE))
120
121	IGNORE_LEAKS ?= 0
122	IGNORE_LEAKS := $(strip $(IGNORE_LEAKS))
123
124	DARWIN ?= 0
125	DARWIN := $(strip $(DARWIN))
126
127	LINUX ?= 0
128	LINUX := $(strip $(LINUX))
129
130	DEBIAN ?= 0
131	DEBIAN := $(strip $(DEBIAN))
132
133	ARB_64 ?= 1 # default to 64bit
134	ARB_64 := $(strip $(ARB_64))
135
136	# Variables allowed for injection [InjectedEnvironment]
137	# (alternatively initialize them with '?=', e.g. done for XLIBS and XINCLUDES)
138	# In both cases add them to SOURCE_TOOLS/export2sub
139	ifndef XML_INCLUDES
140	XML_INCLUDES=
141	endif
142	ifndef XAW_LIBS
143	XAW_LIBS=
144	endif
145
146
147	ifneq ($(CONFIG_MAKEFILE_FOUND),)
148	ifneq ($(DARWIN)$(LINUX),10)
149	ifneq ($(DARWIN)$(LINUX),01)
150	$(error exactly one of DARWIN=1 or LINUX=1 has to be defined (got:$(DARWIN)$(LINUX)))
151	endif
152	endif
153	endif
154
155	# compiler settings:
156	ifneq ($(CC),use__A_CC__instead_of__CC)
157	A_CC:=$(CC)# compile C
158	A_CXX:=$(CXX)# compile C++
159
160	# uncomment to ensure no submakefile uses CC and CXX directly
161	override CC:=use__A_CC__instead_of__CC
162	override CXX:=use__A_CXX__instead_of__CXX
163	endif
164
165	# unconditionally prepend $(ARBHOME)/lib to LD_LIBRARY_PATH if not found
166	ifeq ($(findstring $(ARBHOME)/lib,$(LD_LIBRARY_PATH)),)
167	LD_LIBRARY_PATH:=${ARBHOME}/lib:$(LD_LIBRARY_PATH)
168	endif
169
170	# store LD_LIBRARY_PATH to circumvent SIP restrictions:
171	ARBBUILD_LIBRARY_PATH:=$(LD_LIBRARY_PATH)
172
173	FORCEMASK = umask 002
174	NODIR=--no-print-directory
175
176	SED:=$(ARBHOME)/SH/arb_sed
177	READLINK:=$(ARBHOME)/SH/arb_readlink
178
179	# ---------------------- compiler version detection
180
181	# supported gcc versions:
182	ALLOWED_gcc_VERSIONS=\
183	6.1.0 6.2.0 6.3.0 6.4.0 6.5.0 \
184	7.1.0 7.2.0 7.3.0 7.4.0 7.5.0 \
185	8.1.0 8.2.0 8.3.0 8.4.0 8.5.0 \
186	9.1.0 9.2.0 9.3.0 9.4.0 9.5.0 \
187	10.1.0 10.2.0 10.3.0 10.4.0 10.5.0 \
188	11.1.0 11.2.0 11.3.0 11.4.0 11.5.0 \
189	12.1.0 12.2.0 12.3.0 12.4.0 12.5.0 \
190	13.1.0 13.2.0 13.3.0 13.4.0 \
191	14.1.0 14.2.0 14.3.0 14.4.0 \
192	15.1.0 15.2.0 15.3.0 \
193	16.1.0 \
194
195	# Note: starting with version 5, arb silently accepts any subversion number
196	# above zero. See SOURCE_TOOLS/arb_compiler_version.pl@acceptSubVersions
197	#
198	# This may cause problems when manually checking for compiler versions in code
199	# (GCC_VERSION_CODE is not affected, GCC_PATCHLEVEL_CODE may cause problems!)
200	# ----------------------
201
202	COMPILER_INFO:=$(shell SOURCE_TOOLS/arb_compiler_version.pl $(A_CXX))
203	COMPILER_NAME:=$(word 1,$(COMPILER_INFO))
204	COMPILER_VERSION:=$(word 2,$(COMPILER_INFO))
205
206	USE_CLANG:=0
207	ifneq ($(COMPILER_NAME),gcc)
208	ifeq ($(COMPILER_NAME),clang)
209	USE_CLANG:=1
210	else
211	$(error failed to detect COMPILER_NAME (got '$(COMPILER_NAME)', expected 'clang' or 'gcc'))
212	endif
213	endif
214
215	ifeq ($(USE_CLANG),1)
216	# accept all clang versions:
217	ALLOWED_COMPILER_VERSIONS=$(COMPILER_VERSION)
218	else
219	ALLOWED_COMPILER_VERSIONS=$(ALLOWED_gcc_VERSIONS)
220	endif
221
222	COMPILER_VERSION_ALLOWED=$(strip $(subst ___,,$(foreach version,$(ALLOWED_COMPILER_VERSIONS),$(findstring ___$(version)___,___$(COMPILER_VERSION)___))))
223
224	#---------------------- force no root
225
226	YOU_ARE_ROOT := $(strip $(shell bash -c 'echo $$((EUID == 0))'))
227	ifeq ($(YOU_ARE_ROOT),1)
228	$(error Building arb as root user is not recommended)
229	# To install a custom-compiled arb system-wide, build target 'tarfile' as "normal" user.
230	# Afterwards, use arb_install.sh as root.
231	endif
232
233	#---------------------- split gcc version
234
235	SPLITTED_VERSION:=$(subst ., ,$(COMPILER_VERSION))
236
237	USE_GCC_MAJOR:=$(word 1,$(SPLITTED_VERSION))
238	USE_GCC_MINOR:=$(word 2,$(SPLITTED_VERSION))
239	USE_GCC_PATCHLEVEL:=$(word 3,$(SPLITTED_VERSION))
240
241	USE_GCC_70_OR_HIGHER:=
242	USE_GCC_80_OR_HIGHER:=
243	USE_GCC_90_OR_HIGHER:=
244	USE_GCC_100_OR_HIGHER:=
245	USE_GCC_110_OR_HIGHER:=
246	USE_GCC_120_OR_HIGHER:=
247	USE_GCC_130_OR_HIGHER:=
248	USE_GCC_140_OR_HIGHER:=
249	USE_GCC_150_OR_HIGHER:=
250
251	ifeq ($(USE_CLANG),0)
252	# minimum gcc version accepted is 6.1.0
253	ifneq ($(USE_GCC_MAJOR),6)
254	# gcc 7.x or higher
255	USE_GCC_70_OR_HIGHER:=yes
256	ifneq ($(USE_GCC_MAJOR),7)
257	# gcc 8.x or higher
258	USE_GCC_80_OR_HIGHER:=yes
259	ifneq ($(USE_GCC_MAJOR),8)
260	# gcc 9.x or higher
261	USE_GCC_90_OR_HIGHER:=yes
262	ifneq ($(USE_GCC_MAJOR),9)
263	# gcc 10.x or higher
264	USE_GCC_100_OR_HIGHER:=yes
265	ifneq ($(USE_GCC_MAJOR),10)
266	# gcc 11.x or higher
267	USE_GCC_110_OR_HIGHER:=yes
268	ifneq ($(USE_GCC_MAJOR),11)
269	# gcc 12.x or higher
270	USE_GCC_120_OR_HIGHER:=yes
271	ifneq ($(USE_GCC_MAJOR),12)
272	# gcc 13.x or higher
273	USE_GCC_130_OR_HIGHER:=yes
274	ifneq ($(USE_GCC_MAJOR),13)
275	# gcc 14.x or higher
276	USE_GCC_140_OR_HIGHER:=yes
277	ifneq ($(USE_GCC_MAJOR),14)
278	# gcc 15.x or higher
279	USE_GCC_150_OR_HIGHER:=yes
280	endif
281	endif
282	endif
283	endif
284	endif
285	endif
286	endif
287	endif
288	endif
289	endif
290
291	#---------------------- define special directories for non standard builds
292
293	ifeq ($(DARWIN),1)
294	OSX_FW:=/System/Library/Frameworks
295	OSX_FW_OPENGL:=$(OSX_FW)/OpenGL.framework/Versions/A/Libraries
296	OSX_FW_GLUT:=$(OSX_FW)/GLUT.framework/Versions/A/Libraries
297	OSX_FW_IMAGEIO:=$(OSX_FW)/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources
298	endif
299
300	#---------------------- SSE vectorization
301	# for details about vectorization checks see SOURCE_TOOLS/vectorize.README
302
303	DISABLE_VECTORIZE_CHECK:=0# # set to 1 to completely disable vectorization checks
304	TRACE_MISSED_VECTORIZATIONS:=0# # set to 1 to activate detailed output about failed vectorizations
305	# (does also show details about successful vectorized loops, which are not optimal)
306	VECTORIZATION_CHECK_CANDIDATES:=0# # set to 1 to show vectorizations that may be checked
307	# (for yet unchecked files)
308	# Note: TRACE_MISSED_VECTORIZATIONS and VECTORIZATION_CHECK_CANDIDATES cannot be used together!
309
310	#---------------------- Support for OPENMP
311
312	USE_OPENMP:=1
313	ifeq ($(USE_CLANG),1)
314	USE_OPENMP:=0
315	endif
316
317	#----------------------
318
319	ifeq ($(DARWIN),1)
320	LINK_STATIC=1# # link static
321	else
322	LINK_STATIC=0# # link dynamically
323	# LINK_STATIC=1# # link static (testing only)
324	endif
325
326	shared_cflags := # flags for shared lib compilation
327	onlyC_flags := # flags only suitable for C (not C++; see cxxflags).
328	clflags := # linker flags (when passed through gcc, i.e. used to link binaries and shared libraries)
329	extended_warnings := # warning flags for C and C++-compiler
330	extended_cpp_warnings := # warning flags for C++-compiler only
331
332	ifeq ($(DEBUG),0)
333	dflags := -DNDEBUG # defines
334	ifeq ($(USE_CLANG),1)
335	cflags := -O3 # compiler flags (C and C++)
336	DISABLE_VECTORIZE_CHECK:=1
337	else
338	clflags += -Wl,-O2 # passthrough linker flags
339	# ------- standard optimization:
340	cflags := -O3 # compiler flags (C and C++)
341	# ------- test changed optimization (DISABLE_VECTORIZE_CHECK for -O2 or lower):
342	# cflags := -O2 # do not commit uncommented!
343	# DISABLE_VECTORIZE_CHECK:=1
344	endif
345	endif
346
347	ifeq ($(DEBIAN),1)
348	clflags += -Wl,-rpath=/usr/lib/arb/lib -Wl,-z,relro
349	endif
350
351	ifeq ($(DEBUG),1)
352	dflags := -DDEBUG
353
354	# [AFAI understand cc doc, the previous setting used here (-g -g3 -ggdb -ggdb3) was same as (-ggdb3)]
355	# GDB_COMMON := -g
356	# GDB_COMMON := -g3
357	GDB_COMMON := -ggdb3
358	# GDB_COMMON := -gdwarf -g3
359
360	DBGOPTI:=-O0
361	ifneq ('$(SANITIZE)','0')
362	# sanitizer report several bogus buffer-overflows when arb is build with -O0 (e.g. with gcc 7.5.0)
363	DBGOPTI:=-O1
364	endif
365	# DBGOPTI:=-O2 # use this for callgrind (to force inlining)
366
367	ifeq ($(STABS),1)
368	$(error STABS no longer supported)
369	endif
370
371	cflags := $(DBGOPTI) $(GDB_COMMON)
372	clflags += $(DBGOPTI) $(GDB_COMMON)
373
374	# to debug link problems uncomment next line:
375	# clflags += -Wl,--verbose
376
377	ifeq ($(DEBUG_GRAPHICS),1)
378	dflags += -DDEBUG_GRAPHICS
379	endif
380
381	endif # DEBUG only
382
383	# ------------------------------ POST_COMPILE - control how much you get spammed
384	# (please do not change default in SVN)
385	POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl
386
387	# POST_COMPILE += --original # dont modify compiler output
388	# POST_COMPILE += --hide-Noncopyable-advices
389	# POST_COMPILE += --show-useless-Weff++
390	# POST_COMPILE += --no-warnings
391	# POST_COMPILE += --only-first-error
392	# POST_COMPILE += --no-warnings --only-first-error
393
394	# always pass used compiler version to postcompile:
395	POST_COMPILE += --compiler=$(COMPILER_VERSION)
396
397	# ------------------------------
398
399	# Enable extra warnings
400	extended_warnings :=
401	extended_cpp_warnings :=
402
403	# C and C++
404	extended_warnings += -Wwrite-strings -Wunused -Wno-aggregate-return
405	extended_warnings += -Wshadow
406
407	# C++ only
408	extended_cpp_warnings += -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute
409	extended_cpp_warnings += -Wctor-dtor-privacy
410	# extended_cpp_warnings += -Wfloat-equal
411
412	extended_cpp_warnings += -Wmissing-noreturn
413	# extended_cpp_warnings += -Wold-style-cast# (warns about 28405 old-style casts)
414	extended_cpp_warnings += -Winit-self
415	extended_cpp_warnings += -Wstrict-aliasing
416	extended_cpp_warnings += -Wextra
417	extended_cpp_warnings += -Weffc++
418
419	# turn off -Wmaybe-uninitialized in debug mode (gets activated with -Wextra). too many bogus warnings
420	ifeq ($(DEBUG),1)
421	ifeq ($(USE_CLANG),0)
422	extended_cpp_warnings += -Wno-maybe-uninitialized
423	endif
424	endif
425
426	ifeq ($(USE_CLANG),0)
427	extended_cpp_warnings += -Wlogical-op
428	extended_cpp_warnings += -Wzero-as-null-pointer-constant
429	extended_cpp_warnings += -Wbool-compare
430	extended_cpp_warnings += -Wduplicated-cond
431	endif
432
433	extended_cpp_warnings += -Wunused-local-typedefs
434	extended_cpp_warnings += -Wswitch-bool
435	extended_cpp_warnings += -Wlogical-not-parentheses
436	extended_cpp_warnings += -Wsizeof-array-argument
437
438	ifeq ('$(USE_GCC_80_OR_HIGHER)','yes')
439	extended_cpp_warnings += -Wmultistatement-macros
440	endif
441
442	# ------------------------------
443	# suggest final:
444	ifeq ($(USE_CLANG),1)
445	SUGGEST_FINAL:=no
446	else
447	SUGGEST_FINAL:=yes
448	endif
449	# switch off final suggestions for 8.3.0 and 8.4.0:
450	ifeq ('$(COMPILER_VERSION)','8.3.0')
451	SUGGEST_FINAL:=no
452	endif
453	ifeq ('$(COMPILER_VERSION)','8.4.0')
454	SUGGEST_FINAL:=no
455	endif
456	# switch off final suggestions in RELEASE:
457	ifeq ($(DEVELOPER),RELEASE)
458	SUGGEST_FINAL:=no
459	endif
460
461	ifeq ('$(SUGGEST_FINAL)','yes')
462	extended_cpp_warnings += -Wsuggest-final-types
463	extended_cpp_warnings += -Wsuggest-final-methods
464	dflags += -DSUGGESTS_FINAL
465	endif
466
467	# ------------------------------
468	# plain C builds may always use -std=c90 -std=c99 or -std=c11 (these are supported by all supported gcc versions)
469	ifeq ('$(USE_GCC_140_OR_HIGHER)','yes')
470	supportedCdialect := 23
471	else
472	ifeq ('$(USE_GCC_80_OR_HIGHER)','yes')
473	supportedCdialect := 17
474	else
475	supportedCdialect := 11
476	endif
477	endif
478
479	#---------------------- turn off clang bogus warnings
480
481	ifeq ($(USE_CLANG),1)
482	# -Wmismatched-tags warns about struct/class mismatch in forward declarations (which is explicitely allowed)
483	# -Wchar-subscripts reports too many bogus warnings for "array['x']" (when 'x' is known to be in range [0..128])
484	# -Wunused-private-field report too many false positives (currently ~ 2 of 3)
485	# -Wstring-plus-int warns about common ARB coding practice
486	# -Wgnu-static-float-init warns about accepted GNU extension
487	extended_cpp_warnings += -Wno-mismatched-tags -Wno-char-subscripts -Wno-unused-private-field -Wno-string-plus-int
488	ifeq ('$(COMPILER_VERSION)','4.2.1')
489	$(error clang build should use real clang version, not $(COMPILER_VERSION))
490	else
491	extended_cpp_warnings += -Wno-gnu-static-float-init
492	endif
493	endif
494
495	#---------------------- developer
496
497	ifneq ($(DEVELOPER),ANY) # ANY=default setting (skip all developer specific code)
498	dflags += -DDEVEL_$(DEVELOPER)# activate developer/release specific code
499	endif
500
501	#---------------------- activate TODO warnings?
502
503	ifndef SHOWTODO
504	ifeq ($(DEVELOPER),RALF)
505	SHOWTODO:=1
506	else
507	SHOWTODO:=0
508	endif
509	endif
510	ifeq ($(SHOWTODO),1)
511	dflags += -DWARN_TODO # activate "TODO" warnings
512	endif
513
514	#---------------------- be strict while building documentation?
515
516	STRICT_DOC:=0
517	ifeq ($(DEVELOPER),RALF)
518	STRICT_DOC:=1
519	endif
520
521	#---------------------- activate threads
522
523	cflags += -pthread
524	clflags += -pthread
525
526	#---------------------- activate Sanitizers?
527
528	ASAN_OPTIONS:=handle_segv=0:color=0
529	ifeq ($(IGNORE_LEAKS),1)
530	ASAN_OPTIONS+=:detect_leaks=0 # disable leak-detection
531	else
532	ASAN_OPTIONS+=:detect_leaks=1 # detect leaks (normal setting)
533	endif
534	ASAN_OPTIONS+=:check_initialization_order=1
535	# ASAN_OPTIONS+=:abort_on_error=1
536
537	# suppressions: SOURCE_TOOLS/arb.leaksan.supp
538	LSAN_OPTIONS:=max_leaks=3:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp
539
540	UBSAN_OPTIONS:=print_stacktrace=1
541
542	SANITIZE_ADDRESS:=0
543	SANITIZE_UNDEFINED:=0
544
545	ifneq ($(SANITIZE),0)
546	ifeq ($(SANITIZE),all)
547	SANITIZE:=3
548	endif
549
550	ifeq ($(SANITIZE),1)
551	SANITIZE_ADDRESS:=1
552	else
553	ifeq ($(SANITIZE),2)
554	SANITIZE_UNDEFINED:=1
555	else
556	ifeq ($(SANITIZE),3)
557	SANITIZE_ADDRESS:=1
558	SANITIZE_UNDEFINED:=1
559	else
560	$(error Unknown value '$(SANITIZE)' specified for SANITIZE in config.makefile)
561	endif
562	endif
563	endif
564	endif
565
566	SANITIZE_ANY:=0
567	ifeq ($(SANITIZE_ADDRESS),1)
568	SANITIZE_ANY:=1
569	endif
570	ifeq ($(SANITIZE_UNDEFINED),1)
571	SANITIZE_ANY:=1
572	endif
573
574	# vectorization fails if sanitizer active where it normally succeeds -> disable check
575	ifeq ($(SANITIZE_ANY),1)
576	$(info disabling vectorize checks. would fail with sanitized code)
577	DISABLE_VECTORIZE_CHECK:=1
578	else
579	$(info no sanitizer enabled. reset: SANITIZE=0)
580	SANITIZE:=0
581	endif
582
583	# deactivate some bogus warnings occurring when sanitizing NDEBUG version
584	# (do not disable for future gcc-version >= 8.x -> test again when available)
585	ifeq ($(SANITIZE_ANY),1)
586	ifeq ($(DEBUG),0)
587	ifneq ('$(USE_GCC_80_OR_HIGHER)','yes')
588	extended_cpp_warnings += -Wno-format-overflow
589	extended_cpp_warnings += -Wno-maybe-uninitialized
590	endif
591	endif
592	endif
593
594	#---------------------- 32 or 64 bit
595
596	cross_cflags:=
597	cross_lflags:=
598	cross_clflags:=
599
600	ifeq ($(ARB_64),1)
601	dflags += -DARB_64
602	shared_cflags += -fPIC
603	CROSS_LIB:= # empty => autodetect below
604	ifeq ($(DARWIN),1)
605	cross_cflags += -arch x86_64
606	cross_lflags += -arch x86_64
607	cross_clflags += -arch x86_64
608	endif
609	else
610	CROSS_LIB:=/lib
611	endif
612
613	cflags += $(cross_cflags)
614	clflags += $(cross_clflags)
615
616	ifeq ('$(CROSS_LIB)','')
617	# autodetect libdir
618	ifeq ($(ARB_64),1)
619	CROSS_LIB:=$(shell (test -d /lib64 && echo lib64) \|\| echo lib)
620	else
621	CROSS_LIB:=$(shell (test -d /lib32 && echo lib32) \|\| echo lib)
622	endif
623	endif
624
625	#---------------------- unit tests
626
627	ifndef UNIT_TESTS
628	UNIT_TESTS=0 #default is "no tests"
629	endif
630	ifeq ($(UNIT_TESTS),1)
631	dflags += -DUNIT_TESTS
632	UNIT_TESTER_LIB=UNIT_TESTER/UNIT_TESTER.a
633	else
634	UNIT_TESTER_LIB=
635	endif
636
637	#---------------------- use gcov
638
639	ifndef COVERAGE
640	COVERAGE=0# # default is "no"
641	endif
642	ifneq ($(COVERAGE),0)
643	GCOV_FLAGS=--coverage
644	$(info disabling vectorize checks. would fail with COVERAGE on)
645	DISABLE_VECTORIZE_CHECK:=1
646	else
647	GCOV_FLAGS=
648	endif
649
650	cflags += $(GCOV_FLAGS)
651	clflags += $(GCOV_FLAGS)
652	cross_lflags += $(GCOV_FLAGS)
653
654	#---------------------- disable vectorize checks atm
655
656	ifeq ('$(USE_GCC_110_OR_HIGHER)','yes')
657	ifdef INITIAL_CALL
658	$(warning Note: disabling vectorize checks. has to be fixed for gcc-11 and higher)
659	endif
660	DISABLE_VECTORIZE_CHECK:=1
661	endif
662
663	#---------------------- other flags
664
665	dflags += -D$(MACH) # define machine
666
667	ifeq ($(DARWIN),1)
668	shared_cflags += -fno-common
669	else
670	dflags += $(shell getconf LFS_CFLAGS)
671	endif
672
673	cflags += -pipe
674	cflags += -fmessage-length=0 # dont wrap compiler output
675	cflags += -fshow-column # show columns
676	cflags += -funit-at-a-time
677	cflags += -fPIC
678	cflags += -fno-common # link all global data into one namespace
679	cflags += -fstrict-aliasing
680
681	onlyC_flags += -Werror-implicit-function-declaration
682
683	ifeq ($(USE_CLANG),0)
684	cflags += -fno-diagnostics-show-caret
685	endif
686
687	#cflags += -save-temps# uncomment to see preprocessor output
688
689	#---------------------- various sanitizers
690	# There are some disabled tests in CORE/arb_misc.cxx@sanitizers
691	# which trigger sanitizer reports.
692
693	ifeq ($(SANITIZE_ANY),1)
694	cflags += -ggdb3 -fno-omit-frame-pointer
695	endif
696
697	SANI_CFLAGS:=
698	SANI_CLFLAGS:=
699
700	# activate AddressSanitizer+LeakSanitizer?
701	ifeq ($(SANITIZE_ADDRESS),1)
702	SANI_CFLAGS += -fsanitize=address
703	SANI_CLFLAGS += -fsanitize=address
704	dflags += -DLEAKS_SANITIZED
705	endif
706
707	# activate UndefinedBehaviorSanitizer?
708	ifeq ($(SANITIZE_UNDEFINED),1)
709	SANI_CFLAGS += -fsanitize=undefined
710	SANI_CLFLAGS += -fsanitize=undefined
711	dflags += -DUNDEF_SANITIZED
712
713	# abort on runtime errors
714	SANI_CFLAGS += -fno-sanitize-recover=all
715
716	cflags += $(SANI_CFLAGS)
717	clflags += $(SANI_CLFLAGS)
718
719	# Note: alignment-sanitizer is deactivated for ARBDB and PROBE (using -fno-sanitize=alignment)
720
721	endif
722
723	#---------------------- X11 location
724
725	ifeq ($(DARWIN),1)
726	XHOME:=$(PREFIX)
727	else
728	ifeq ($(DEBIAN),1)
729	XHOME:=$(PREFIX)
730	else
731	XHOME:=/usr/X11R6
732	endif
733	endif
734
735	XINCLUDES ?= -I$(XHOME)/include
736	XLIBS ?= -L$(XHOME)/$(CROSS_LIB)
737	ifeq ($(DARWIN),1)
738	XINCLUDES += -I$(OSX_FW)/GLUT.framework/Headers -I$(OSX_FW)/OpenGL.framework/Headers -I$(OSX_SDK)/usr/include/krb5
739
740	XLIBS += -lXm -lpng -lz -lXt -lX11 -lXext -lXp -lXmu -lXi
741	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGL.dylib:$(OSX_FW_OPENGL)/libGL.dylib
742	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGLU.dylib:$(OSX_FW_OPENGL)/libGLU.dylib
743	else
744	XLIBS += -lXm -lXpm -lXt -lXext -lX11
745	endif
746
747	#---------------------- open GL
748
749	ifeq ($(OPENGL),1)
750	cflags += -DARB_OPENGL # activate OPENGL code
751	GL := gl # this is the name of the OPENGL base target
752	GL_LIB_SYS := -lGL -lGLU
753	GL_LIB_ARB := -L$(ARBHOME)/GL/glAW -lglAW
754
755	ifeq ($(DARWIN),1)
756	GL_LIB_SYS += -lpthread
757	endif
758
759	GL_PNGLIBS_ARB := -L$(ARBHOME)/GL/glpng -lglpng_arb
760	GL_PNGLIBS_SYS := -lpng
761
762	GLEWLIB := -lGLEW -lGLw
763	GLUTLIB := -lglut
764
765	GL_LIBS_SYS := $(GL_LIB_SYS) $(GL_PNGLIBS_SYS) $(GLEWLIB) $(GLUTLIB)
766	GL_LIBS_ARB := $(GL_LIB_ARB) $(GL_PNGLIBS_ARB)
767
768	RNA3D_LIB := RNA3D/RNA3D.a
769	else
770	GL_LIBS_SYS:= # no opengl -> no libs
771	GL_LIBS_ARB:= # no opengl -> no libs
772	GL:= # dont build ARB openGL libs
773
774	RNA3D_LIB :=
775	endif
776
777	RNA3D_LIB_4_DEPENDS := RNA3D/RNA3D.a
778
779	GL_LIBS:=$(GL_LIBS_ARB) $(GL_LIBS_SYS)
780
781	#---------------------- sina:
782
783	# build sina delivered with arb?
784	ifndef ISINA
785	ifeq ($(LINUX),1)
786	ifeq ('$(USE_GCC_70_OR_HIGHER)','yes')
787	ISINA := 1 # default to 'yes' for linux with gcc>=7
788	endif
789	endif
790	ISINA ?= 0 # 'no' otherwise
791	endif
792	ISINA := $(strip $(ISINA))
793
794	#---------------------- tiff lib:
795
796	TIFFLIBS := -ltiff
797
798	#---------------------- XML lib:
799
800	XMLLIBS := -lxerces-c
801
802	#---------------------- glib:
803
804	ARB_NEEDED_GLIB=glib-2.0
805
806	ARB_GLIB_INCLUDE:=$(strip $(shell pkg-config --cflags $(ARB_NEEDED_GLIB)))
807	ARB_GLIB_LIBS:=$(strip $(shell pkg-config --libs $(ARB_NEEDED_GLIB)))
808
809	#---------------------- sunrpc lib:
810	# Note: sunrpc has been removed from glibc
811	# (e.g. in SuSE Leap 15.3 and Fedora 28)
812	# see https://fedoraproject.org/wiki/Changes/SunRPCRemoval
813	#
814	HAVE_LIBTIRPC=$(strip $(shell pkg-config --exists libtirpc && echo libtirpc))
815	ifeq ($(HAVE_LIBTIRPC),)
816	ARB_RPC_INCLUDE:=
817	ARB_RPC_LIBS:=
818	else
819	ARB_RPC_INCLUDE:=$(strip $(shell pkg-config --cflags $(HAVE_LIBTIRPC)))
820	ARB_RPC_LIBS:=$(strip $(shell pkg-config --libs $(HAVE_LIBTIRPC)))
821	endif
822
823	#---------------------- basic libs:
824
825	ARB_CORE_LIBS:=$(ARB_GLIB_LIBS) $(ARB_RPC_LIBS)
826
827	SYSLIBS:=
828	ifeq ($(DARWIN),1)
829	SYSLIBS += -lstdc++
830	else
831	SYSLIBS += -lm $(ARB_CORE_LIBS)
832	endif
833
834	#---------------------- system dependent commands
835
836	ifeq ($(DARWIN),1)
837	TIME:=gtime
838	else
839	TIME:=/usr/bin/time
840	endif
841
842	#---------------------- SSE vectorizer
843	# for details see SOURCE_TOOLS/vectorize.README
844
845	ifeq ($(DEBUG),0)
846	ifeq ($(DISABLE_VECTORIZE_CHECK),0)
847	cflags += -fopt-info-vec
848	cflags += -fopt-info-vec-missed
849	ifeq ($(TRACE_MISSED_VECTORIZATIONS),1)
850	# Shows reasons for unsuccessful vectorization:
851	cflags += -ftree-vectorizer-verbose=10
852	POST_COMPILE += --dump-loop-optimization
853	ifeq ($(VECTORIZATION_CHECK_CANDIDATES),1)
854	$(error TRACE_MISSED_VECTORIZATIONS and VECTORIZATION_CHECK_CANDIDATES may not be used together!)
855	endif
856	endif
857	ifeq ($(VECTORIZATION_CHECK_CANDIDATES),1)
858	POST_COMPILE += --loop-optimization-candi
859	endif
860	POST_COMPILE += --check-loop-optimization
861	endif
862	endif
863
864	#---------------------- include symbols?
865
866	ifeq ($(TRACESYM),1)
867	ifeq ($(USE_CLANG),0)
868	cflags += -rdynamic
869	clflags += -rdynamic -Wl,--export-dynamic
870	endif
871	endif
872
873	#---------------------- warn about duplicate variable definitions
874
875	ifeq ($(DARWIN),1)
876	clflags += -Wl,-warn_commons
877	else
878	clflags += -Wl,--warn-common
879	endif
880
881	#---------------------- differences between linking executables and shared libs:
882
883	# executables:
884	ifeq ($(DARWIN),1)
885	blflags:=$(clflags)
886	else
887	blflags:=$(clflags) -Wl,--no-undefined
888	endif
889
890	# shared libraries
891	llflags:=$(clflags)
892
893	# dont use clflags below
894	clflags:=
895
896	# -------------------------------------------------------------------------
897	# Don't put any machine/version/etc conditionals below!
898	# (instead define variables above)
899	# -------------------------------------------------------------------------
900
901	cflags += -W -Wall $(dflags) $(extended_warnings)
902	cxxflags := $(extended_cpp_warnings)# flags only suitable for C++ (not C; see onlyC_flags).
903
904	# add CFLAGS + CPPFLAGS from environment for DEBIAN build
905	ifeq ($(DEBIAN),1)
906	cflags := $(CFLAGS) $(cflags)
907	cxxflags += $(CPPFLAGS)
908	endif
909
910	ifeq ('$(USE_CLANG)','1')
911	# the following standards also work with clang 6.0.0 (under linux):
912	# cxxflags += -std=gnu++14
913	cxxflags += -std=gnu++17
914	else
915	# standard mostly supported by gcc version (according to https://gcc.gnu.org/projects/cxx-status.html)
916	# C++20 with gcc>=12
917	# C++23 with gcc>=15 (or 16 for reflection)
918
919	ifeq ('$(USE_GCC_110_OR_HIGHER)','yes')
920	# C++20 mostly supported by gcc>=11
921	cxxflags += -std=gnu++20 # see also TEMPLATES/cxxforward.h@USE_Cxx20
922	else
923	ifeq ('$(USE_GCC_80_OR_HIGHER)','yes')
924	# C++17 mostly supported by gcc>=8
925	cxxflags += -std=gnu++17 # see also TEMPLATES/cxxforward.h@USE_Cxx17
926	else
927	cxxflags += -std=gnu++14
928	endif # 80
929	endif # 110
930	endif # USE_CLANG
931
932	LINK_STATIC_LIB := $(AR) -csq # link static lib
933	LINK_EXECUTABLE := $(A_CXX) $(blflags) -o # link executable (c++)
934
935	ifeq ($(LINK_STATIC),1)
936	SHARED_LIB_SUFFIX = a# # static lib suffix
937	LINK_SHARED_LIB := $(LINK_STATIC_LIB)
938	else
939	SHARED_LIB_SUFFIX = so# # shared lib suffix
940	LINK_SHARED_LIB := $(A_CXX) $(llflags) -shared -o # link shared lib
941	endif
942
943	ifeq ($(DARWIN),1)
944	lflags4perl:=
945	else
946	lflags4perl:=$(cross_lflags) -shared
947	endif
948
949	# delete variables unused below
950	blflags:=
951	llflags:=
952
953	# other used tools
954	MAKEDEPEND_PLAIN = makedepend
955	MAKEDEPEND = $(FORCEMASK);$(MAKEDEPEND_PLAIN)
956
957	SEPNODATE:=--------------------------------------------------------------------------------
958	SEP=[`date +%M:%S.%N`] ------------------------------------------------
959	# to analyse timings run
960	# make -j9 clean; make -j9 all \| grep '^\[' \| sort
961	# make -j9 "TIMED_TARGET=perl" clean_timed_target \| grep '^\[' \| sort
962
963	# ------------------------------------------------------------ DYNLIBDEFS
964	# various dynamic library definitions for linking executables:
965	#
966	# SYSLIBS: system libraries needed by database lib
967	# ARBDB_LIB: database lib
968	# DBSYS_LIBS: executable using database (but no GUI)
969	# GUI_LIBS: executable using database and GUI (arb gui uses database)
970	#
971	# Note: definitions exported to sub-makefiles are described in SOURCE_TOOLS/parent_make.txt
972
973	CORE_LIB=-lCORE
974	ARBDB_LIB=-lARBDB $(CORE_LIB)
975	DBSYS_LIBS = $(ARBDB_LIB) $(SYSLIBS)
976
977	GUI_LIBS_PREFIX:=
978	ifeq ($(DARWIN),1)
979	# this seem to be added at wrong place, since opengl is only needed to link EDIT4
980	GUI_LIBS_PREFIX:=-framework GLUT -framework OpenGL
981	endif
982
983	GUI_LIBS=$(GUI_LIBS_PREFIX) $(DBSYS_LIBS) -lWINDOW $(XLIBS)
984
985	LIBPATH = -L$(ARBHOME)/lib
986
987	DEST_LIB = lib
988	DEST_BIN = bin
989
990	CC_INCLUDES := -I. -I$(ARBHOME)/INCLUDE $(XINCLUDES) $(ARB_GLIB_INCLUDE) $(ARB_RPC_INCLUDE)
991	CXX_INCLUDES := $(CC_INCLUDES)
992	MAKEDEPENDFLAGS := -- -DARB_OPENGL -DUNIT_TESTS -D__cplusplus -I. -Y$(ARBHOME)/INCLUDE
993
994	# ---------------------------------------
995	# wrap main()
996
997	use_ARB_main=$(ARBHOME)/SOURCE_TOOLS/arb_main_cpp.o
998	use_ARB_main_C=$(ARBHOME)/SOURCE_TOOLS/arb_main_c.o
999
1000	# -----------------------------------------
1001	# generate unique IDs:
1002	#
1003	# 1) ARBBID
1004	# - different for different calls of make
1005	# - constant in recursive calls (submake)
1006	#
1007	ifndef ARBBID
1008	ARBBID:=$(shell SOURCE_TOOLS/uniqueID.sh)
1009	endif
1010
1011	# 2) ARBCID
1012	# - identical for multiple calls of make with same gcc and config
1013	# - uses DEBUG, UNIT_TESTS, OPENGL, DEVELOPER, gcc-version
1014
1015	ifndef ARBCID
1016	# Main purpuse is to simply generate filenames based on current config,
1017	# in order to log data and later compare between different versions.
1018	#
1019	# Note: change free at will (i.e. don't rely on content)
1020	ARBCID := $(if $(filter 1,$(DEBUG)),_DEBUG,NDEBUG)
1021	ARBCID := $(ARBCID)$(if $(filter 1,$(UNIT_TESTS)),__TESTS,_NTESTS)
1022	ARBCID := $(ARBCID)$(if $(filter 1,$(OPENGL)),__OPENGL,_NOPENGL)
1023	# ARBCID := $(ARBCID)_$(DEVELOPER)
1024	ARBCID := $(ARBCID)_$(COMPILER_NAME)_$(COMPILER_VERSION)
1025	# $(error ARBCID = $(ARBCID))
1026
1027	endif
1028
1029	# -----------------------------------------
1030	# export variables to submakefiles
1031
1032	include SOURCE_TOOLS/export2sub
1033
1034	# do not define (exported) variables below this point
1035
1036	# -------------------------
1037	# Main arb targets:
1038	# -------------------------
1039
1040	first_target: showinfo
1041
1042	%.sync:
1043	@( export ID=$$$$; LANG=C; \
1044	(( $(MAKE) $(@F:.sync=.nosync)) >$(@F).$$ID.log 2>&1 && \
1045	(cat $(@F).$$ID.log;rm $(@F).$$ID.log)) \|\| (cat $(@F).$$ID.log;rm $(@F).$$ID.log;false))
1046
1047	# to avoid the output of (phony) targets gets interleaved,
1048	# append .nosync to their name and then add a rule like
1049	#
1050	# example: example.sync
1051
1052	showinfo: showinfo.sync checks
1053	showinfo.nosync:
1054	@echo 'Main targets:'
1055	@echo ''
1056	@echo ' all - Compile ARB + TOOLs + and copy shared libs + link foreign software'
1057	@echo ' (That is most likely the target you want)'
1058	@echo ''
1059	@echo ' clean - remove generated files ("SUBDIR/SUBDIR.clean" to clean only SUBDIR)'
1060	@echo ' rebuild - clean + all'
1061	@echo ' cleanlinked - remove all binaries'
1062	@echo ' relink - cleanlinked + all (=relink all from objects)'
1063	@echo ''
1064	@echo 'Targets for automated builds:'
1065	@echo ''
1066	@echo ' ALL, REBUILD, TARFILE + TARFILE_QUICK'
1067	@echo ' - same as all, rebuild, tarfile + tarfile_quick'
1068	@echo ' - if errors occur, they are extracted and listed at tail of output'
1069	@echo ''
1070	@echo $(SEPNODATE)
1071	@echo ''
1072	@echo 'Development targets:'
1073	@echo ''
1074	@echo ' depends - create or update dependencies ("SUBDIR/SUBDIR.depends" to update only SUBDIR)'
1075	@echo ' proto - create or update prototypes ("SUBDIR/SUBDIR.proto" to update only SUBDIR)'
1076	@echo ' tags - create tags for xemacs'
1077	@echo ' show - show available shortcuts (AKA subtargets)'
1078	@echo ' up - shortcut for depends+proto+tags'
1079	ifeq ($(UNIT_TESTS),1)
1080	@echo ' ut - only run tests'
1081	@echo ' "UNIT=..." oneunit - build one unit and run tests (see also UNIT_TESTER/Makefile.setup.local)'
1082	endif
1083	ifneq ($(SANITIZE),0)
1084	@echo ' sanitize - all + run arb_ntree with sanitizer (test.arb + execute _logged)'
1085	endif
1086	@echo ' modified - rebuild files modified in svn checkout (does touch)'
1087	@echo ' touch - touch files modified in svn checkout'
1088	@echo ''
1089	@echo 'Some often used sub targets:'
1090	@echo ''
1091	@echo ' arb - Just compile ARB (but none of the integrated tools)'
1092	@echo ' menus - create lib/gde/arb.menu from GDEHELP/ARB_GDEmenus.source'
1093	@echo ' perl - Compile the PERL XSUBS into lib/ARB.so and create links in lib to perl'
1094	@echo ' binlink - Create all links in the bin directory'
1095	@echo ''
1096	@echo 'Internal maintenance:'
1097	@echo ''
1098	@echo ' relinfo - show help on release targets'
1099	@echo ' tarfile - make rebuild and create arb version tarfile ("tarfile_quick" to skip rebuild)'
1100	@echo ' save - save all basic ARB sources into arbsrc_DATE ("savetest" to check filelist)'
1101	@echo ' patch - save svn diff to patchfile'
1102	@echo ' source_doc - create doxygen documentation'
1103	@echo ' relocated - rebuild partly (use when you have relocated ARBHOME)'
1104	@echo ' check_res - check resource usage'
1105	@echo ' dep_graph - Build dependency graphs'
1106	@echo ' clean_cov - Clean coverage results'
1107	@echo ''
1108	@echo ' clean_opengl_changed - clean after changing OPENGL setting in config.Makefile'
1109	@echo ' clean_checked_vect - clean units containing vectorization checks'
1110	@echo ' cleanRelinkable - similar to cleanlinked (but skips raxml8 to avoid rebuild)'
1111	@echo ''
1112	@echo ' post_commit_check - Checks whether'
1113	@echo ' * main make targets work,'
1114	@echo ' * dependencies and prototypes are up to date,'
1115	@echo ' * SVN-controlled files remain unaffected by called targets and'
1116	@echo ' * all generated files are ignored.'
1117	@echo ' (has to be called in a clean SVN checkout)'
1118	@echo $(SEPNODATE)
1119	@echo ''
1120
1121	relinfo: relinfo.sync
1122	relinfo.nosync:
1123	@echo ''
1124	@echo $(SEPNODATE)
1125	@echo 'Release targets:'
1126	@echo ''
1127	@echo ' inc_candi - increase RC candidate-number (only possible in "rc" branch, not needed for RC1)'
1128	@echo ' inc_patch - increase release patchlevel (only possible in "stable" branch)'
1129	@echo ' inc_minor - increase minor version number (only possible in "trunk")'
1130	@echo ' inc_major - increase MAJOR version number (only possible in "trunk")'
1131	@echo ''
1132	@echo ' show_version - show version tag'
1133	@echo ''
1134	@echo $(SEPNODATE)
1135	@echo ''
1136
1137	# auto-generate config.makefile:
1138
1139	config.makefile : config.makefile.template
1140	@echo --------------------------------------------------------------------------------
1141	ifeq ($(CONFIG_MAKEFILE_FOUND),)
1142	@cp $< $@
1143	@echo '$(ARBHOME)/$@:1: has been generated.'
1144	@echo 'Please edit $@ to configure your system!'
1145	@echo --------------------------------------------------------------------------------
1146	@false
1147	else
1148	@echo '$(ARBHOME)/$<:1: is more recent than'
1149	@echo '$(ARBHOME)/$@:1:'
1150	@ls -al config.makefile*
1151	@echo --------------------------------------------------------------------------------
1152	@echo "Updating $@ (if this fails, check manually)"
1153	SOURCE_TOOLS/update_config_makefile.pl
1154	@echo "Sucessfully updated $@"
1155	@echo --------------------------------------------------------------------------------
1156	@ls -al config.makefile*
1157	@echo --------------------------------------------------------------------------------
1158	@echo "Diff to your old config.makefile:"
1159	@echo --------------------------------------------------------------------------------
1160	-diff $@.bak $@
1161	@echo --------------------------------------------------------------------------------
1162	endif
1163
1164	# check if everything is configured correctly
1165
1166	check_DEVELOPER:
1167	ifndef DEVELOPER
1168	@echo 'config.makefile:1: DEVELOPER not defined'
1169	@false
1170	endif
1171
1172	check_DEBUG:
1173	ifndef dflags
1174	@echo 'config.makefile:1: DEBUG has to be defined. Valid values are 0 and 1'
1175	@false
1176	endif
1177
1178	check_ARB_64:
1179	ifndef ARB_64
1180	@echo 'config.makefile:1: ARB_64 has to be defined. Valid values are 0 and 1'
1181	@false
1182	endif
1183
1184	# ---------------------------------------- check gcc version
1185
1186	check_same_GCC_VERSION:
1187	$(ARBHOME)/SOURCE_TOOLS/check_same_compiler_version.pl $(COMPILER_NAME) $(COMPILER_VERSION_ALLOWED)
1188
1189	check_GCC_VERSION: check_GCC_VERSION.sync
1190	check_GCC_VERSION.nosync:
1191	@echo 'Compiler version check:'
1192	# see .@ALLOWED_gcc_VERSIONS
1193	ifeq ('$(COMPILER_VERSION_ALLOWED)', '')
1194	$(warning Unsupported compiler '$(COMPILER_NAME)' version '$(COMPILER_VERSION)')
1195	@echo " - Your compiler is '$(COMPILER_NAME)' version '$(COMPILER_VERSION)'"
1196	@echo ' This version is not in the list of supported $(COMPILER_NAME)-versions:'
1197	@$(foreach version,$(ALLOWED_COMPILER_VERSIONS),echo ' * $(version)';)
1198	@echo ' - You may either ..'
1199	@echo ' - add your version to ALLOWED_$(COMPILER_NAME)_VERSIONS in the Makefile and try it out or'
1200	@echo ' - switch to one of the allowed versions (see arb_README_gcc.txt for installing'
1201	@echo ' a different version of gcc)'
1202	@false
1203	else
1204	@echo " - Supported $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)' detected - fine!"
1205	@echo ''
1206	$(MAKE) check_same_GCC_VERSION
1207	endif
1208
1209
1210	#---------------------- check ARBHOME
1211
1212	# use arb_INSTALL.txt to determine whether ARBHOME points to correct directory
1213	ARB_INSTALL_FOUND=$(wildcard $(ARBHOME)/arb_INSTALL.txt)
1214
1215	check_ARBHOME : check_ARBHOME.sync
1216	check_ARBHOME.nosync:
1217	ifeq ($(strip $(ARB_INSTALL_FOUND)),)
1218	@echo ------------------------------------------------------------
1219	@echo "ARBHOME is set to '$(ARBHOME)'"
1220	@echo "The environment variable ARBHOME has to point to the top arb source directory."
1221	@echo "If you use bash enter:"
1222	@echo " export ARBHOME='`pwd`'"
1223	@echo ------------------------------------------------------------
1224	@false
1225	endif
1226
1227	ARB_PATH_SET=$(findstring $(ARBHOME)/bin,$(PATH))
1228
1229	check_PATH: check_PATH.sync
1230	check_PATH.nosync: check_ARBHOME
1231	ifeq ($(strip $(ARB_PATH_SET)),)
1232	@echo ------------------------------------------------------------
1233	@echo "The environment variable PATH has to contain $(ARBHOME)/bin"
1234	@echo "If you use bash enter:"
1235	@echo ' export PATH=$$ARBHOME/bin:$$PATH'
1236	@echo ------------------------------------------------------------
1237	@false
1238	endif
1239
1240	check_TOOLS: check_TOOLS.sync
1241	check_TOOLS.nosync:
1242	@util/arb_check_build_env.pl \
1243	"$(A_CC)" \
1244	"$(A_CXX)" \
1245	"$(LINK_SHARED_LIB)" \
1246
1247	have_makedepend:
1248	@util/arb_check_build_env.pl --check-only "$(MAKEDEPEND_PLAIN)"
1249
1250	check_ENVIRONMENT: check_ENVIRONMENT.sync
1251	check_ENVIRONMENT.nosync: check_PATH check_TOOLS
1252	@echo "-------------------- Environment [start]"
1253	@echo "ARBHOME='$(ARBHOME)'"
1254	@echo "PATH='$(PATH)'"
1255	@echo "LD_LIBRARY_PATH='$(LD_LIBRARY_PATH)'"
1256	@echo "-------------------- Environment [end]"
1257
1258	check_tabs: check_tabs.sync
1259	check_tabs.nosync: check_setup
1260	ifeq ($(DEBUG),1)
1261	@SOURCE_TOOLS/tabBrake.pl
1262	endif
1263
1264	force_tab_check:
1265	@touch -t 198001010000 SOURCE_TOOLS/stamp.tabBrake
1266	@$(MAKE) check_tabs
1267
1268
1269	# ---------------------
1270
1271	check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION
1272	@echo Your setup seems to be ok.
1273
1274	checks: check_setup check_tabs
1275	@rm -f SOURCE_TOOLS/postcompile.sav
1276
1277
1278	# end test section ------------------------------
1279
1280	# ---------------------------------------
1281	# List of standard top level directories
1282	#
1283	# sub-makefiles have to define the targets
1284	# - 'depends' and
1285	# - 'clean'
1286	#
1287	# when adding new libraries/subdirs here, also add a dependency vs 'links' or 'links_non_perl' in .@DD_links_non_perl
1288
1289	TL_ARCHIVES = \
1290	AISC/AISC.a \
1291	ARB_GDE/ARB_GDE.a \
1292	AWTC/AWTC.a \
1293	AWTI/AWTI.a \
1294	CONSENSUS_TREE/CONSENSUS_TREE.a \
1295	CONVERTALN/CONVERTALN.a \
1296	DBSERVER/DBSERVER.a \
1297	DIST/DIST.a \
1298	EDIT4/EDIT4.a \
1299	EISPACK/EISPACK.a \
1300	GENOM/GENOM.a \
1301	GENOM_IMPORT/GENOM_IMPORT.a \
1302	ISLAND_HOPPING/ISLAND_HOPPING.a \
1303	MERGE/MERGE.a \
1304	MULTI_PROBE/MULTI_PROBE.a \
1305	NAMES/NAMES.a \
1306	NAMES_COM/server.a \
1307	NTREE/NTREE.a \
1308	PARSIMONY/PARSIMONY.a \
1309	PHYLO/PHYLO.a \
1310	PRIMER_DESIGN/PRIMER_DESIGN.a \
1311	PROBE/PROBE.a \
1312	PROBE_COM/server.a \
1313	PROBE_DESIGN/PROBE_DESIGN.a \
1314	$(RNA3D_LIB) \
1315	RNACMA/RNACMA.a \
1316	SECEDIT/SECEDIT.a \
1317	SEQ_QUALITY/SEQ_QUALITY.a \
1318	SERVERCNTRL/SERVERCNTRL.a \
1319	STAT/STAT.a \
1320	TREEGEN/TREEGEN.a \
1321	WETC/WETC.a \
1322	XML/XML.a \
1323
1324	TL_SHARED_ARCHIVES = \
1325	ARBDB/libARBDB.so \
1326	CORE/libCORE.so \
1327	WINDOW/libWINDOW.so \
1328
1329	TL_ARCHIV_COLLECTIONS = \
1330	SL/SL.archColl \
1331
1332	TL_TOOLS_COLLECTIONS = \
1333	AISC_MKPTPS/AISC_MKPTPS.toolColl \
1334	TOOLS/TOOLS.toolColl \
1335	PERLTOOLS/PERLTOOLS.toolColl \
1336	PROBE_SET/PROBE_SET.toolColl \
1337	READSEQ/READSEQ.toolColl \
1338
1339	RECURSIVE_SUBS = \
1340	GDE/GDE.sub \
1341	UNIT_TESTER/UNIT_TESTER.sub \
1342
1343	SUBDIRS = \
1344	$(RECURSIVE_SUBS) \
1345	$(TL_ARCHIVES:.a=.sub) \
1346	$(TL_SHARED_ARCHIVES:.so=.sub) \
1347	$(TL_ARCHIV_COLLECTIONS:.archColl=.sub) \
1348	$(TL_TOOLS_COLLECTIONS:.toolColl=.sub) \
1349
1350	# sub directories inside TL_ARCHIV_COLLECTIONS
1351	CL_ARCH_DIRS = $(foreach coll,$(TL_ARCHIV_COLLECTIONS),$(shell find $(dir $(coll)) -maxdepth 1 -mindepth 1 -type d))
1352
1353	# archives inside CL_ARCH_DIRS:
1354	CL_ARCHIVES = $(foreach adir,$(CL_ARCH_DIRS),$(dir $(adir))$(notdir $(adir))/$(notdir $(adir)).a)
1355
1356	# -----------------------
1357	# library packets
1358
1359	ARCHS_CLIENT_PROBE = PROBE_COM/client.a
1360	ARCHS_CLIENT_NAMES = NAMES_COM/client.a
1361
1362	ARCHS_MAKEBIN = AISC_MKPTPS/AISC_MKPTPS.a AISC/AISC.a
1363
1364	# communication libs need aisc and aisc_mkpts:
1365
1366	AISC/AISC.dummy: proto_tools
1367
1368	comtools: AISC/AISC.dummy
1369
1370	ARCHS_SEQUENCE = \
1371	SL/SEQUENCE/SEQUENCE.a \
1372	SL/ALIVIEW/ALIVIEW.a \
1373	SL/PRONUC/PRONUC.a \
1374
1375	ARCHS_TREE = \
1376	SL/ARB_TREE/ARB_TREE.a \
1377	SL/FILTER/FILTER.a \
1378	$(ARCHS_SEQUENCE) \
1379
1380	# parsimony tree (used by NTREE, PARSIMONY, STAT(->EDIT4), DIST(obsolete!))
1381	ARCHS_AP_TREE = \
1382	SL/AP_TREE/AP_TREE.a \
1383	$(ARCHS_TREE) \
1384
1385	# --------------------------------------------------------------------------------
1386	# dependencies for linking shared libs
1387
1388	link_core: core
1389	link_db: db link_core
1390	link_aw: aw link_db
1391
1392	#***************************************************************************************
1393	# Individual_Programs_Section
1394	#***************************************************************************************
1395
1396	arbmainwrapper:
1397	$(MAKE) -C SOURCE_TOOLS -r mainwrapper
1398
1399
1400	#********************************* arb_ntree ************************************
1401	NTREE = bin/arb_ntree
1402	ARCHS_NTREE = \
1403	NTREE/NTREE.a \
1404	ARB_GDE/ARB_GDE.a \
1405	SL/SPECSEL/SPECSEL.a \
1406	SL/GROUP_SEARCH/GROUP_SEARCH.a \
1407	SL/SAICALC/SAICALC.a \
1408	SL/DB_UI/DB_UI.a \
1409	SL/ARB_SPEC/ARB_SPEC.a \
1410	SL/MASKS/MASKS.a \
1411	AWTC/AWTC.a \
1412	AWTI/AWTI.a \
1413	CONSENSUS_TREE/CONSENSUS_TREE.a \
1414	GENOM_IMPORT/GENOM_IMPORT.a \
1415	GENOM/GENOM.a \
1416	MERGE/MERGE.a \
1417	MULTI_PROBE/MULTI_PROBE.a \
1418	PRIMER_DESIGN/PRIMER_DESIGN.a \
1419	PROBE_DESIGN/PROBE_DESIGN.a \
1420	SEQ_QUALITY/SEQ_QUALITY.a \
1421	SERVERCNTRL/SERVERCNTRL.a \
1422	SL/ALILINK/ALILINK.a \
1423	SL/AW_NAME/AW_NAME.a \
1424	SL/APP/APP.a \
1425	SL/CONSENSUS/CONSENSUS.a \
1426	SL/CANVAS/CANVAS.a \
1427	SL/DB_SCANNER/DB_SCANNER.a \
1428	SL/DB_QUERY/DB_QUERY.a \
1429	SL/QUERY/QUERY.a \
1430	SL/SEQIO/SEQIO.a \
1431	STAT/STAT.a \
1432	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1433	SL/GUI_TK/GUI_TK.a \
1434	SL/HELIX/HELIX.a \
1435	SL/REGEXPR/REGEXPR.a \
1436	SL/REFENTRIES/REFENTRIES.a \
1437	SL/NDS/NDS.a \
1438	SL/ITEM_SHADER/ITEM_SHADER.a \
1439	SL/ITEMS/ITEMS.a \
1440	SL/INSDEL/INSDEL.a \
1441	SL/LOCATION/LOCATION.a \
1442	SL/MACROS/MACROS.a \
1443	SL/PVP/PVP.a \
1444	SL/TRANSLATE/TRANSLATE.a \
1445	SL/TREEDISP/TREEDISP.a \
1446	SL/TREE_ADMIN/TREE_ADMIN.a \
1447	SL/TREE_READ/TREE_READ.a \
1448	SL/TREE_WRITE/TREE_WRITE.a \
1449	SL/XFERGUI/XFERGUI.a \
1450	SL/XFERSET/XFERSET.a \
1451	XML/XML.a \
1452	$(ARCHS_AP_TREE) \
1453
1454	ARCHS_NTREE_ALL = $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(XMLLIBS)
1455
1456	$(NTREE): $(ARCHS_NTREE:.a=.dummy) link_aw
1457	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NTREE_ALL) \|\| ( \
1458	echo "$(SEP) Link $@"; \
1459	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE_ALL)" ; \
1460	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE_ALL) && \
1461	echo "$(SEP) Link $@ [done]"; \
1462	)
1463
1464	#********************************* arb_edit4 ************************************
1465	EDIT4 = bin/arb_edit4
1466
1467	ARCHS_EDIT4 := \
1468	EDIT4/EDIT4.a \
1469	ARB_GDE/ARB_GDE.a \
1470	SL/FAST_ALIGNER/FAST_ALIGNER.a \
1471	AWTC/AWTC.a \
1472	ISLAND_HOPPING/ISLAND_HOPPING.a \
1473	SECEDIT/SECEDIT.a \
1474	SERVERCNTRL/SERVERCNTRL.a \
1475	SL/APP/APP.a \
1476	SL/GUI_TK/GUI_TK.a \
1477	SL/ARB_SPEC/ARB_SPEC.a \
1478	SL/AW_HELIX/AW_HELIX.a \
1479	SL/AW_NAME/AW_NAME.a \
1480	SL/CONSENSUS/CONSENSUS.a \
1481	SL/CANVAS/CANVAS.a \
1482	SL/ITEMS/ITEMS.a \
1483	STAT/STAT.a \
1484	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1485	SL/HELIX/HELIX.a \
1486	SL/TRANSLATE/TRANSLATE.a \
1487	SL/MACROS/MACROS.a \
1488	SL/MAPKEY/MAPKEY.a \
1489	SL/NDS/NDS.a \
1490	$(ARCHS_AP_TREE) \
1491	XML/XML.a \
1492
1493	ifeq ($(OPENGL),1)
1494	ARCHS_EDIT4 += RNA3D/RNA3D.a
1495	endif
1496
1497	ARCHS_EDIT4_ALL = $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4)
1498
1499	LIBS_EDIT4 := $(GL_LIBS)
1500
1501	$(EDIT4): $(ARCHS_EDIT4:.a=.dummy) link_aw
1502	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_EDIT4_ALL) \|\| ( \
1503	echo "$(SEP) Link $@"; \
1504	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4_ALL)" ; \
1505	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4_ALL) && \
1506	echo "$(SEP) Link $@ [done]"; \
1507	)
1508
1509	#********************************* arb_rnacma ************************************
1510	RNACMA = bin/arb_rnacma
1511	ARCHS_RNACMA = \
1512	RNACMA/RNACMA.a \
1513
1514	ARCHS_RNACMA_ALL = $(ARCHS_RNACMA) $(DBSYS_LIBS)
1515
1516	$(RNACMA) : $(ARCHS_RNACMA:.a=.dummy) link_db
1517	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_RNACMA_ALL) \|\| ( \
1518	echo "$(SEP) Link $@"; \
1519	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_RNACMA_ALL)"; \
1520	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_RNACMA_ALL) && \
1521	echo "$(SEP) Link $@ [done]"; \
1522	)
1523
1524	#********************************* arb_wetc ************************************
1525	WETC = bin/arb_wetc
1526	ARCHS_WETC = \
1527	WETC/WETC.a \
1528	SL/APP/APP.a \
1529	SL/MACROS/MACROS.a \
1530	SL/GUI_TK/GUI_TK.a \
1531	SL/HELIX/HELIX.a \
1532	SL/FILTER/FILTER.a \
1533	XML/XML.a \
1534
1535	ARCHS_WETC_ALL = $(ARCHS_WETC) $(GUI_LIBS)
1536
1537	$(WETC): $(ARCHS_WETC:.a=.dummy) link_aw
1538	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_WETC_ALL) \|\| ( \
1539	echo "$(SEP) Link $@"; \
1540	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC_ALL)" ; \
1541	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC_ALL) && \
1542	echo "$(SEP) Link $@ [done]"; \
1543	)
1544
1545	#********************************* arb_dist ************************************
1546	DIST = bin/arb_dist
1547	ARCHS_DIST = \
1548	DIST/DIST.a \
1549	CONSENSUS_TREE/CONSENSUS_TREE.a \
1550	EISPACK/EISPACK.a \
1551	SERVERCNTRL/SERVERCNTRL.a \
1552	SL/APP/APP.a \
1553	SL/GUI_TK/GUI_TK.a \
1554	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1555	SL/HELIX/HELIX.a \
1556	SL/MATRIX/MATRIX.a \
1557	SL/MACROS/MACROS.a \
1558	SL/NDS/NDS.a \
1559	SL/ITEMS/ITEMS.a \
1560	SL/ARB_SPEC/ARB_SPEC.a \
1561	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.a \
1562	XML/XML.a \
1563	$(ARCHS_AP_TREE) \
1564
1565	ARCHS_DIST_ALL = $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS)
1566
1567	$(DIST): $(ARCHS_DIST:.a=.dummy) link_aw
1568	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_DIST_ALL) \|\| ( \
1569	echo "$(SEP) Link $@"; \
1570	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST_ALL)" ; \
1571	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST_ALL) && \
1572	echo "$(SEP) Link $@ [done]"; \
1573	)
1574
1575	#********************************* arb_pars ************************************
1576	PARSIMONY = bin/arb_pars
1577	ARCHS_PARSIMONY = \
1578	PARSIMONY/PARSIMONY.a \
1579	SERVERCNTRL/SERVERCNTRL.a \
1580	SL/APP/APP.a \
1581	SL/GUI_TK/GUI_TK.a \
1582	SL/AW_NAME/AW_NAME.a \
1583	SL/CANVAS/CANVAS.a \
1584	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1585	SL/HELIX/HELIX.a \
1586	SL/MACROS/MACROS.a \
1587	SL/NDS/NDS.a \
1588	SL/ITEMS/ITEMS.a \
1589	SL/TRANSLATE/TRANSLATE.a \
1590	SL/TREEDISP/TREEDISP.a \
1591	XML/XML.a \
1592	$(ARCHS_AP_TREE) \
1593
1594	ARCHS_PARSIMONY_ALL = $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS)
1595
1596	$(PARSIMONY): $(ARCHS_PARSIMONY:.a=.dummy) link_aw
1597	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_PARSIMONY_ALL) \|\| ( \
1598	echo "$(SEP) Link $@"; \
1599	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY_ALL)" ; \
1600	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY_ALL) && \
1601	echo "$(SEP) Link $@ [done]"; \
1602	)
1603
1604	#********************************* arb_convert_aln ************************************
1605	CONVERT_ALN = bin/arb_convert_aln
1606	ARCHS_CONVERT_ALN = \
1607	CONVERTALN/CONVERTALN.a \
1608
1609	ARCHS_CONVERT_ALN_ALL = $(ARCHS_CONVERT_ALN) $(DBSYS_LIBS)
1610
1611	$(CONVERT_ALN) : $(ARCHS_CONVERT_ALN:.a=.dummy) link_db
1612	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_CONVERT_ALN_ALL) \|\| ( \
1613	echo "$(SEP) Link $@"; \
1614	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN_ALL)"; \
1615	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN_ALL) && \
1616	echo "$(SEP) Link $@ [done]"; \
1617	)
1618
1619	#********************************* arb_treegen ************************************
1620
1621	TREEGEN = bin/arb_treegen
1622	ARCHS_TREEGEN = \
1623	TREEGEN/TREEGEN.a \
1624
1625	ARCHS_TREEGEN_ALL = $(ARCHS_TREEGEN)
1626
1627	$(TREEGEN) : $(ARCHS_TREEGEN:.a=.dummy)
1628	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main_C) $(ARCHS_TREEGEN_ALL) \|\| ( \
1629	echo "$(SEP) Link $@"; \
1630	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN_ALL)" ; \
1631	$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN_ALL) && \
1632	echo "$(SEP) Link $@ [done]"; \
1633	)
1634
1635	#********************************* arb_phylo ************************************
1636	PHYLO = bin/arb_phylo
1637	ARCHS_PHYLO = \
1638	PHYLO/PHYLO.a \
1639	SL/APP/APP.a \
1640	SL/GUI_TK/GUI_TK.a \
1641	SL/HELIX/HELIX.a \
1642	SL/FILTER/FILTER.a \
1643	SL/MACROS/MACROS.a \
1644	XML/XML.a \
1645
1646	ARCHS_PHYLO_ALL = $(ARCHS_PHYLO) $(GUI_LIBS)
1647
1648	$(PHYLO): $(ARCHS_PHYLO:.a=.dummy) link_aw
1649	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_PHYLO_ALL) \|\| ( \
1650	echo "$(SEP) Link $@"; \
1651	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO_ALL)" ; \
1652	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO_ALL) && \
1653	echo "$(SEP) Link $@ [done]"; \
1654	)
1655
1656	#***************************************************************************************
1657	# SERVER SECTION
1658	#***************************************************************************************
1659
1660	#********************************* arb_db_server ************************************
1661	DBSERVER = bin/arb_db_server
1662	ARCHS_DBSERVER = \
1663	DBSERVER/DBSERVER.a \
1664	SERVERCNTRL/SERVERCNTRL.a \
1665
1666	ARCHS_DBSERVER_ALL = $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS)
1667
1668	$(DBSERVER): $(ARCHS_DBSERVER:.a=.dummy) link_db
1669	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_DBSERVER_ALL) \|\| ( \
1670	echo "$(SEP) Link $@"; \
1671	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER_ALL)" ; \
1672	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER_ALL) && \
1673	echo "$(SEP) Link $@ [done]"; \
1674	)
1675
1676	#********************************* arb_pt_server ************************************
1677	PROBE = bin/arb_pt_server
1678
1679	ARCHS_PROBE_DEPEND = \
1680	PROBE/PROBE.a \
1681	SL/PTCLEAN/PTCLEAN.a \
1682	SERVERCNTRL/SERVERCNTRL.a \
1683	SL/HELIX/HELIX.a \
1684
1685	ARCHS_PROBE_ALL = $(ARCHS_PROBE_DEPEND) $(ARCHS_CLIENT_PROBE) $(ARBDB_LIB) $(SYSLIBS)
1686
1687	$(PROBE): $(ARCHS_PROBE_DEPEND:.a=.dummy) link_db
1688	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) config.makefile $(ARCHS_PROBE_ALL) \|\| ( \
1689	echo "$(SEP) Link $@"; \
1690	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_ALL)" ; \
1691	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_ALL) && \
1692	echo "$(SEP) Link $@ [done]"; \
1693	)
1694
1695	#********************************* arb_name_server ************************************
1696	NAMES = bin/arb_name_server
1697	ARCHS_NAMES = \
1698	NAMES/NAMES.a \
1699	SERVERCNTRL/SERVERCNTRL.a \
1700
1701	ARCHS_NAMES_ALL = $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS)
1702
1703	$(NAMES): $(ARCHS_NAMES:.a=.dummy) link_db
1704	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NAMES_ALL) \|\| ( \
1705	echo "$(SEP) Link $@"; \
1706	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES_ALL)" ; \
1707	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES_ALL) && \
1708	echo "$(SEP) Link $@ [done]"; \
1709	)
1710
1711	#********************************* SHARED LIBRARIES SECTION ************************************
1712
1713	prepare_libdir: addlibs
1714
1715	addlibs:
1716	(perl $(ARBHOME)/SOURCE_TOOLS/provide_libs.pl \
1717	"arbhome=$(ARBHOME)" \
1718	"opengl=$(OPENGL)" \
1719	"link_static=$(LINK_STATIC)" \
1720	)
1721
1722	#***************************************************************************************
1723	# Recursive calls to sub-makefiles
1724	#***************************************************************************************
1725
1726	%.depends: have_makedepend
1727	@cp -p $(@D)/Makefile $(@D)/Makefile.old # save old Makefile
1728	@$(MAKE) -C $(@D) -r \
1729	"AUTODEPENDS=1" \
1730	"MAIN=nothing" \
1731	"cflags=noCflagsHere_use_MAKEDEPENDFLAGS" \
1732	"cxxflags=noCxxflagsHere_use_MAKEDEPENDFLAGS" \
1733	depends
1734	@grep "^# DO NOT DELETE" $(@D)/Makefile >/dev/null
1735	@cat $(@D)/Makefile \
1736	\| SOURCE_TOOLS/fix_depends.pl "(from main)" \
1737	>$(@D)/Makefile.2
1738	@mv $(@D)/Makefile.old $(@D)/Makefile # restore old Makefile
1739	@$(ARBHOME)/SOURCE_TOOLS/mv_if_diff $(@D)/Makefile.2 $(@D)/Makefile # update Makefile if changed
1740
1741	%.proto:
1742	@($(MAKE) -C $(@D) \
1743	"AUTODEPENDS=0" \
1744	"MAIN=nothing" \
1745	"cflags=noCflags" \
1746	"cxxflags=noCxxflags" \
1747	proto 2>&1 ) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
1748
1749	%.clean:
1750	@$(MAKE) -C $(@D) \
1751	"AUTODEPENDS=0" \
1752	"MAIN=nothing" \
1753	"cflags=noCflags" \
1754	"cxxflags=noCxxflags" \
1755	clean
1756
1757
1758	# stop wrong targets:
1759	target_is_missing_lib_prefix:
1760	@echo "Error: Denied to build shared library target with missing 'lib'-prefix"
1761	false
1762
1763	ARBDB/ARBDB.dummy: target_is_missing_lib_prefix
1764	CORE/CORE.dummy: target_is_missing_lib_prefix
1765	AWT/AWT.dummy: target_is_missing_lib_prefix
1766	WINDOW/WINDOW.dummy: target_is_missing_lib_prefix
1767
1768	# rule to generate main target (normally a library):
1769	# @@@ check effect of setting LANG=C below
1770	%.dummy:
1771	@( export ID=$$$$; LANG=C; \
1772	(( \
1773	echo "$(SEP) Make $(@D)"; \
1774	$(MAKE) -C $(@D) -r \
1775	"AUTODEPENDS=1" \
1776	"MAIN=$(@F:.dummy=.a)" \
1777	"cflags=$(cflags) -DIN_ARB_$(subst /,_,$(@D))" \
1778	&& \
1779	echo "$(SEP) Make $(@D) [done]"; \
1780	) >$(@D).$$ID.log 2>&1 && (cat $(@D).$$ID.log;rm $(@D).$$ID.log)) \|\| (cat $(@D).$$ID.log;rm $(@D).$$ID.log;false))
1781
1782	# Additional dependencies for subtargets:
1783
1784	PROBE_COM/PROBE_COM.dummy : comtools
1785	NAMES_COM/NAMES_COM.dummy : comtools
1786
1787	com: PROBE_COM/PROBE_COM.dummy NAMES_COM/NAMES_COM.dummy
1788
1789	# stop wrong more targets:
1790	PROBE_COM/server.dummy:
1791	@echo Unwanted request to make target $<
1792	false
1793
1794	PROBE_COM/client.dummy:
1795	@echo Unwanted request to make target $<
1796	false
1797
1798	NAMES_COM/server.dummy:
1799	@echo Unwanted request to make target $<
1800	false
1801
1802	NAMES_COM/client.dummy:
1803	@echo Unwanted request to make target $<
1804	false
1805
1806
1807	ARBDB/libARBDB.dummy: links
1808	CORE/libCORE.dummy: links
1809
1810	PERLTOOLS/PERLTOOLS.dummy: core db
1811
1812	# all subdirs perl not depends on go here (ADD_links_non_perl)
1813	AWTI/AWTI.dummy: links_non_perl
1814	CONSENSUS_TREE/CONSENSUS_TREE.dummy: links_non_perl
1815	CONVERTALN/CONVERTALN.dummy: links_non_perl
1816	DBSERVER/DBSERVER.dummy: links_non_perl
1817	DIST/DIST.dummy: links_non_perl
1818	EDIT4/EDIT4.dummy: links_non_perl com
1819	EISPACK/EISPACK.dummy: links_non_perl
1820	GDE/GDE.dummy: links_non_perl
1821	GENOM/GENOM.dummy: links_non_perl
1822	GENOM_IMPORT/GENOM_IMPORT.dummy: links_non_perl
1823	ISLAND_HOPPING/ISLAND_HOPPING.dummy: links_non_perl
1824	MERGE/MERGE.dummy: links_non_perl
1825	NTREE/NTREE.dummy: links_non_perl
1826	PARSIMONY/PARSIMONY.dummy: links_non_perl
1827	PHYLO/PHYLO.dummy: links_non_perl
1828	PRIMER_DESIGN/PRIMER_DESIGN.dummy: links_non_perl
1829	PROBE_SET/PROBE_SET.dummy: links_non_perl link_db
1830	READSEQ/READSEQ.dummy: links_non_perl
1831	RNACMA/RNACMA.dummy: links_non_perl header_libs
1832	SECEDIT/SECEDIT.dummy: links_non_perl
1833	SEQ_QUALITY/SEQ_QUALITY.dummy: links_non_perl
1834	SERVERCNTRL/SERVERCNTRL.dummy: links_non_perl com
1835	SL/ALILINK/ALILINK.dummy: links_non_perl
1836	SL/ALIVIEW/ALIVIEW.dummy: links_non_perl
1837	SL/AP_TREE/AP_TREE.dummy: links_non_perl
1838	SL/APP/APP.dummy: links_non_perl
1839	SL/ARB_SPEC/ARB_SPEC.dummy: links_non_perl
1840	SL/ARB_TREE/ARB_TREE.dummy: links_non_perl
1841	SL/AW_HELIX/AW_HELIX.dummy: links_non_perl
1842	SL/CONSENSUS/CONSENSUS.dummy: links_non_perl
1843	SL/CANVAS/CANVAS.dummy: links_non_perl
1844	SL/DB_QUERY/DB_QUERY.dummy: links_non_perl
1845	SL/DB_SCANNER/DB_SCANNER.dummy: links_non_perl
1846	SL/DB_UI/DB_UI.dummy: links_non_perl
1847	SL/FAST_ALIGNER/FAST_ALIGNER.dummy: links_non_perl
1848	SL/FILTER/FILTER.dummy: links_non_perl
1849	SL/FILTSEQEXP/FILTSEQEXP.dummy: links_non_perl
1850	SL/GROUP_SEARCH/GROUP_SEARCH.dummy: links_non_perl
1851	SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy: links_non_perl
1852	SL/GUI_TK/GUI_TK.dummy: links_non_perl
1853	SL/HEADERTESTS/HEADERTESTS.dummy: links_non_perl
1854	SL/HELIX/HELIX.dummy: links_non_perl
1855	SL/INSDEL/INSDEL.dummy: links_non_perl
1856	SL/ITEM_SHADER/ITEM_SHADER.dummy: links_non_perl
1857	SL/ITEMS/ITEMS.dummy: links_non_perl
1858	SL/LOCATION/LOCATION.dummy: links_non_perl
1859	SL/MACROS/MACROS.dummy: links_non_perl
1860	SL/MASKS/MASKS.dummy: links_non_perl
1861	SL/MATRIX/MATRIX.dummy: links_non_perl
1862	SL/MAPKEY/MAPKEY.dummy: links_non_perl
1863	SL/NDS/NDS.dummy: links_non_perl
1864	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.dummy: links_non_perl
1865	SL/PRONUC/PRONUC.dummy: links_non_perl
1866	SL/PTCLEAN/PTCLEAN.dummy: links_non_perl link_db
1867	SL/PVP/PVP.dummy: links_non_perl
1868	SL/QUERY/QUERY.dummy: links_non_perl link_db
1869	SL/REFENTRIES/REFENTRIES.dummy: links_non_perl
1870	SL/REGEXPR/REGEXPR.dummy: links_non_perl
1871	SL/SAICALC/SAICALC.dummy: links_non_perl
1872	SL/SPECSEL/SPECSEL.dummy: links_non_perl
1873	SL/SEQIO/SEQIO.dummy: links_non_perl
1874	SL/SEQUENCE/SEQUENCE.dummy: links_non_perl
1875	SL/TRANSLATE/TRANSLATE.dummy: links_non_perl
1876	SL/TREE_ADMIN/TREE_ADMIN.dummy: links_non_perl
1877	SL/TREE_READ/TREE_READ.dummy: links_non_perl
1878	SL/TREE_WRITE/TREE_WRITE.dummy: links_non_perl
1879	SL/TREEDISP/TREEDISP.dummy: links_non_perl
1880	SL/XFERGUI/XFERGUI.dummy: links_non_perl
1881	SL/XFERSET/XFERSET.dummy: links_non_perl
1882	STAT/STAT.dummy: links_non_perl
1883	TREEGEN/TREEGEN.dummy: links_non_perl
1884	WETC/WETC.dummy: links_non_perl
1885	WINDOW/libWINDOW.dummy: links_non_perl
1886	XML/XML.dummy: links_non_perl
1887
1888	ifeq ($(OPENGL),1)
1889	GL/glAW/glAW.dummy: links_non_perl
1890	GL/glpng/glpng.dummy: links_non_perl
1891	GL/GL.dummy: GL/glAW/glAW.dummy GL/glpng/glpng.dummy
1892	RNA3D/RNA3D.dummy: links_non_perl gl
1893	endif
1894
1895	UNIT_TESTER/UNIT_TESTER.dummy: link_db \
1896	SERVERCNTRL/SERVERCNTRL.dummy \
1897
1898	# see also TOOLS/Makefile@TOOLSLIBDEPENDS
1899	TOOLS/TOOLS.dummy : links_non_perl link_db com \
1900	CONSENSUS_TREE/CONSENSUS_TREE.dummy \
1901	SERVERCNTRL/SERVERCNTRL.dummy \
1902	SL/FILTER/FILTER.dummy \
1903	SL/FILTSEQEXP/FILTSEQEXP.dummy \
1904	SL/INSDEL/INSDEL.dummy \
1905	SL/PRONUC/PRONUC.dummy \
1906	SL/PVP/PVP.dummy \
1907	SL/REGEXPR/REGEXPR.dummy \
1908	SL/SEQIO/SEQIO.dummy \
1909	SL/TREE_READ/TREE_READ.dummy \
1910	SL/TREE_WRITE/TREE_WRITE.dummy \
1911	SL/XFERSET/XFERSET.dummy \
1912	XML/XML.dummy \
1913
1914	AWTC/AWTC.dummy : com
1915
1916	NAMES/NAMES.dummy : com
1917	SL/AW_NAME/AW_NAME.dummy : com
1918
1919	PROBE/PROBE.dummy : com
1920	MULTI_PROBE/MULTI_PROBE.dummy : com
1921	PROBE_DESIGN/PROBE_DESIGN.dummy : com
1922
1923	ARB_GDE/ARB_GDE.dummy : proto_tools menus
1924
1925	compile_compatibility: SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.dummy
1926
1927	#***************************************************************************************
1928	# Short aliases to make targets
1929	#***************************************************************************************
1930
1931	show:
1932	@echo $(SEP)
1933	@echo 'Aliases for often needed targets:'
1934	@echo ''
1935	@echo ' executables:'
1936	@echo ''
1937	@echo ' nt arb_ntree'
1938	@echo ' e4 arb_edit4 (includes secedit)'
1939	@echo ' di arb_dist'
1940	@echo ' ph arb_phylo'
1941	@echo ' pa arb_parsimony'
1942	@echo ' tg arb_treegen'
1943	@echo ' ds arb_dbserver'
1944	@echo ' pt arb_pt_server'
1945	@echo ' na arb_name_server'
1946	@echo ''
1947	@echo ' libraries:'
1948	@echo ''
1949	@echo ' com communication libraries'
1950	@echo ' db ARB database'
1951	@echo ' aw GUI lib'
1952	@echo ' awt GUI toolkit'
1953	@echo ' awtc general purpose library'
1954	@echo ' awti import/export library'
1955	@echo ' mp multi probe library'
1956	@echo ' ge genome library'
1957	@echo ' pd probe design lib'
1958	@echo ' prd primer design lib'
1959	@echo ''
1960	@echo ' other targets:'
1961	@echo ''
1962	@echo ' help recompile help files'
1963	@echo ' tools make small tools used by arb'
1964	@echo ''
1965	@echo ' foreign targets:'
1966	@echo ''
1967	@echo ' gde GDE'
1968	@echo ' agde ARB_GDE'
1969	@echo ''
1970	@echo 'for other targets inspect $(ARBHOME)/Makefile'
1971	@echo ''
1972	@echo $(SEP)
1973
1974	source_doc:
1975	@echo "Remove some links (doxygen crashes otherwise):"
1976	find . $ -name "AISC" -o -name "C" -o -name "GDEHELP" $ -type l -exec rm {} \;
1977	doxygen 2>&1 1>/dev/null
1978	$(MAKE) forcelinks
1979
1980	dep_graph:
1981	@echo "Building some dependency graphs"
1982	SOURCE_TOOLS/dependency_graphs.pl
1983
1984	help: HELP_SOURCE/HELP_SOURCE.dummy
1985
1986	HELP_SOURCE/HELP_SOURCE.dummy: link_core xml menus
1987
1988	db: ARBDB/libARBDB.dummy
1989	core: CORE/libCORE.dummy
1990	aw: WINDOW/libWINDOW.dummy
1991	awtc: AWTC/AWTC.dummy
1992	awti: AWTI/AWTI.dummy
1993
1994	mp: MULTI_PROBE/MULTI_PROBE.dummy
1995	mg: MERGE/MERGE.dummy
1996	ge: GENOM/GENOM.dummy
1997	prd: PRIMER_DESIGN/PRIMER_DESIGN.dummy
1998
1999	nt: menus $(NTREE)
2000
2001	di: $(DIST)
2002	ph: $(PHYLO)
2003	pa: $(PARSIMONY)
2004	tg: $(TREEGEN)
2005
2006	ifeq ($(OPENGL),1)
2007	3d: RNA3D/RNA3D.dummy
2008	gl: GL/GL.dummy
2009	else
2010	noopengl:
2011	@echo "invalid target for OPENGL=0"
2012	3d: noopengl
2013	gl: noopengl
2014	endif
2015
2016	SL/SL.dummy: com
2017
2018	ds: $(DBSERVER)
2019	pt: $(PROBE)
2020	pst: PROBE_SET/PROBE_SET.dummy
2021	pd: PROBE_DESIGN/PROBE_DESIGN.dummy
2022	na: $(NAMES)
2023	sq: SEQ_QUALITY/SEQ_QUALITY.dummy
2024	cma: $(RNACMA)
2025
2026	sec: SECEDIT/SECEDIT.dummy
2027
2028	e4: $(EDIT4) readseq menus
2029
2030	gi: GENOM_IMPORT/GENOM_IMPORT.dummy
2031	wetc: $(WETC)
2032
2033	xml: XML/XML.dummy
2034	stat: STAT/STAT.dummy $(NTREE) $(EDIT4)
2035	fa: SL/FAST_ALIGNER/FAST_ALIGNER.dummy
2036
2037	#********************************************************************************
2038
2039	up_by_remake: depends proto vectorize_checks
2040
2041	up: up_by_remake tags valgrind_update
2042
2043	#********************************************************************************
2044
2045	touch:
2046	SOURCE_TOOLS/touch_modified.pl
2047
2048	modified: touch
2049	$(MAKE) all
2050
2051	#********************************************************************************
2052
2053	libdepends:
2054	$(MAKE) -C "SOURCE_TOOLS" \
2055	"RNA3D_LIB=$(RNA3D_LIB_4_DEPENDS)" \
2056	libdepends
2057
2058	#********************************************************************************
2059
2060	# create generated headers:
2061	genheaders: TEMPLATES/TEMPLATES.dummy
2062
2063	clrdotdepends:
2064	rm PROBE_COM/.depends \|\| true
2065	rm NAMES_COM/.depends \|\| true
2066	rm PERL2ARB/.depends \|\| true
2067
2068	comdepends: comtools clrdotdepends have_makedepend
2069	@echo "$(SEP) Partially build com interface"
2070	$(MAKE) PROBE_COM/PROBE_COM.depends NAMES_COM/NAMES_COM.depends
2071	$(MAKE) PROBE_COM/server.depends NAMES_COM/server.depends
2072
2073	depends: genheaders comdepends vectorize_checks have_makedepend
2074	@echo "$(SEP) Updating other dependencies"
2075	$(MAKE) $(subst NAMES_COM/server.depends,,$(subst PROBE_COM/server.depends,,$(SUBDIRS:.sub=.depends))) \
2076	HELP_SOURCE/HELP_SOURCE.depends \
2077	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.depends \
2078
2079	$(MAKE) libdepends
2080
2081	depend: depends
2082
2083	# ------------------------------------------------------------
2084	# dependency generation tests for AISC code
2085	#(all should work w/o creating wrong dependencies;
2086	# neither in XXX_COM/Makefile nor in code using AISC interface)
2087	dependstest1: silent_clean
2088	$(MAKE) depends
2089	dependstest2: silent_clean
2090	$(MAKE) com
2091	dependstest3: silent_clean
2092	$(MAKE) aw
2093	dependstest4: silent_clean
2094	$(MAKE) pt
2095	dependstest5: silent_clean
2096	$(MAKE) na
2097	dependstest6: silent_clean
2098	$(MAKE) nt
2099	dependstest7: silent_clean
2100	$(MAKE) all
2101	# ------------------------------------------------------------
2102
2103	vectorize_checks:
2104	$(MAKE) -C SOURCE_TOOLS -r vectorize_checks
2105
2106	clean_checked_vect: lib/lib.clean
2107	SOURCE_TOOLS/clean_checked_vectorizations.sh
2108
2109	# ------------------------------------------------------------
2110
2111	AISC_MKPTPS/AISC_MKPTPS.dummy: links
2112
2113	proto_tools: AISC_MKPTPS/AISC_MKPTPS.dummy
2114
2115	proto: proto_tools
2116	@echo $(SEP) Updating prototypes
2117	$(MAKE) \
2118	ARBDB/ARBDB.proto \
2119	AISC_COM/AISC_COM.proto \
2120	ARB_GDE/ARB_GDE.proto \
2121	CORE/CORE.proto \
2122	CONVERTALN/CONVERTALN.proto \
2123	NTREE/NTREE.proto \
2124	MERGE/MERGE.proto \
2125	PROBE/PROBE.proto \
2126	SERVERCNTRL/SERVERCNTRL.proto \
2127	SL/SL.proto \
2128
2129	#********************************************************************************
2130
2131	valgrind_update: links
2132	@echo $(SEP) Updating for valgrind
2133	$(MAKE) -C SOURCE_TOOLS valgrind_update
2134
2135	#********************************************************************************
2136
2137	TAGFILE=TAGS
2138	UTAGS=TAGS.$(ARBBID)
2139	TAGFILE_TMP=$(UTAGS).tmp
2140
2141	TAG_SOURCE_HEADERS=$(UTAGS).headers.tmp
2142	TAG_SOURCE_CODE=$(UTAGS).codefiles.tmp
2143	TAG_SOURCE_LISTS=$(TAG_SOURCE_HEADERS) $(TAG_SOURCE_CODE)
2144
2145	ETAGS_IGNORE_LIST=SOURCE_TOOLS/etags_ignore.lst
2146
2147	ETAGS=ctags -e -I @$(ETAGS_IGNORE_LIST) --sort=no --if0=no --extra=q
2148	ETAGS_TYPES=--C-kinds=cgnsut --C++-kinds=cgnsut
2149	ETAGS_FUN =--C-kinds=fm --C++-kinds=fm
2150	ETAGS_REST =--C-kinds=dev --C++-kinds=dev
2151
2152	FILTER_TAGS_SOURCES= \
2153	$(SED) -e 's/^.\///g' \| \
2154	grep -Pvi '^HEADERLIBS/\|^GDE/\|^UNIT_TESTER/tests(?:\.slow)?/' \| \
2155	grep -Pvi '/GEN[CH]/'
2156
2157	$(TAG_SOURCE_HEADERS): links
2158	@find . $ -name '.hxx' -o -name ".h" $ -type f \| $(FILTER_TAGS_SOURCES) > $@
2159
2160	$(TAG_SOURCE_CODE): links
2161	@find . $ -name '.cxx' -o -name ".c" $ -type f \| $(FILTER_TAGS_SOURCES) > $@
2162
2163	$(UTAGS).1.tmp: $(TAG_SOURCE_HEADERS)
2164	@$(ETAGS) -f $@ $(ETAGS_TYPES) -L $<
2165	$(UTAGS).2.tmp: $(TAG_SOURCE_HEADERS)
2166	@$(ETAGS) -f $@ $(ETAGS_FUN) -L $<
2167	$(UTAGS).3.tmp: $(TAG_SOURCE_HEADERS)
2168	@$(ETAGS) -f $@ $(ETAGS_REST) -L $<
2169	$(UTAGS).4.tmp: $(TAG_SOURCE_CODE)
2170	@$(ETAGS) -f $@ $(ETAGS_TYPES) -L $<
2171	$(UTAGS).5.tmp: $(TAG_SOURCE_CODE)
2172	@$(ETAGS) -f $@ $(ETAGS_FUN) -L $<
2173	$(UTAGS).6.tmp: $(TAG_SOURCE_CODE)
2174	@$(ETAGS) -f $@ $(ETAGS_REST) -L $<
2175
2176	TAGS_ALL_PARTS=$(UTAGS).1.tmp $(UTAGS).2.tmp $(UTAGS).3.tmp $(UTAGS).4.tmp $(UTAGS).5.tmp $(UTAGS).6.tmp
2177
2178	$(TAGFILE_TMP) : $(TAGS_ALL_PARTS)
2179	@cat $(TAGS_ALL_PARTS) > $@
2180	@rm $(TAGS_ALL_PARTS) $(TAG_SOURCE_LISTS)
2181
2182	cleanOldTags:
2183	@find $(ARBHOME) -name 'TAGS.*.tmp' -ctime +2 -exec rm {} \;
2184
2185	tags: $(TAGFILE_TMP) cleanOldTags
2186	@mv_if_diff $(TAGFILE_TMP) $(TAGFILE)
2187
2188	#********************************************************************************
2189
2190	LINKSTAMP=SOURCE_TOOLS/stamp.generate_all_links
2191
2192	links: checks $(LINKSTAMP) arbmainwrapper
2193	links_no_checks: $(LINKSTAMP) arbmainwrapper
2194
2195	forcelinks:
2196	-rm $(LINKSTAMP)
2197	$(MAKE) links
2198
2199	$(LINKSTAMP): SOURCE_TOOLS/generate_all_links.sh genheaders
2200	+SOURCE_TOOLS/generate_all_links.sh
2201	touch $(LINKSTAMP)
2202
2203	clean_links:
2204	# avoid to delete linked pts, nas or arb_tcp.dat:
2205	find . -path './lib' -prune -o -type l -exec rm {} \;
2206	# removed obsolete file - refuses to disappear due to 'prune' above
2207	@rm -f lib/help/GDEHELP
2208	@rm -f $(LINKSTAMP) lib/inputMasks/format.readme
2209
2210	redo_links: clean_links
2211	$(MAKE) links_no_checks
2212
2213	#********************************************************************************
2214
2215	header_libs:
2216	@(( \
2217	echo "$(SEP) Make HEADERLIBS"; \
2218	$(MAKE) -C HEADERLIBS all && \
2219	echo "$(SEP) Make HEADERLIBS [done]"; \
2220	) > HEADERLIBS.log 2>&1 && (cat HEADERLIBS.log;rm HEADERLIBS.log)) \|\| (cat HEADERLIBS.log;rm HEADERLIBS.log;false)
2221
2222	#********************************************************************************
2223
2224	gde: GDE/GDE.dummy
2225	GDE: gde
2226	agde: ARB_GDE/ARB_GDE.dummy
2227	tools: TOOLS/TOOLS.dummy
2228	convert: $(CONVERT_ALN)
2229	readseq: READSEQ/READSEQ.dummy
2230
2231	#***************************************************************************************
2232	# Some user commands
2233	#***************************************************************************************
2234
2235	menus: binlink links
2236	@(( \
2237	echo "$(SEP) Make GDEHELP"; \
2238	$(MAKE) -C GDEHELP -r all && \
2239	echo "$(SEP) Make GDEHELP [done]"; \
2240	) > GDEHELP.log 2>&1 && (cat GDEHELP.log;rm GDEHELP.log)) \|\| (cat GDEHELP.log;rm GDEHELP.log;false)
2241
2242	ifeq ($(DEBUG),1)
2243	BIN_TARGET=develall
2244	else
2245	BIN_TARGET=all
2246	endif
2247
2248
2249	binlink:
2250	$(MAKE) -C bin $(BIN_TARGET)
2251
2252	check_bin_dep: binlink
2253	SOURCE_TOOLS/check_bin_dependencies.pl
2254
2255	fig_cure:
2256	SOURCE_TOOLS/sortfig.pl doit
2257
2258	preplib:
2259	(cd lib;$(MAKE) all)
2260
2261	# --------------------------------------------------------------------------------
2262	# This section is quite tricky:
2263	#
2264	# make 'perl' is a BIG target, so when it has to be made, it has to be started
2265	# as early as possible to reduce overall compile time. Since 'make' does not
2266	# provide any priorities, i force it to build all 'perl'-prerequisites early, by
2267	# adding artificial dependencies to these prerequisites
2268	#
2269	# That behavior is likely to be system-dependent.
2270	# My goal was only to make it work on my current development system,
2271	# where this saves about 20% of overall build time.
2272
2273	ifeq ($(WITHPERL),1)
2274	links_non_perl: PERLTOOLS/PERLTOOLS.dummy
2275	perltools: links_non_perl
2276	perl: realperl
2277	else
2278	links_non_perl: links
2279	perl: links
2280	$(MAKE) "WITHPERL=1" perl
2281	endif
2282
2283	# ---------------------------------------- perl
2284
2285	realperl: perltools
2286	(( \
2287	echo "$(SEP) Make PERL2ARB" ; \
2288	$(TIME) $(MAKE) -C PERL2ARB -r -f Makefile.main \
2289	"AUTODEPENDS=1" \
2290	"dflags=$(dflags)" \
2291	"cflags4perl=$(cflags) $(cxxflags) $(dflags)" \
2292	"lflags4perl=$(lflags4perl)" \
2293	"COMPILER_VERSION=$(COMPILER_VERSION)" \
2294	all && \
2295	$(MAKE) -C PERL_SCRIPTS/test test && \
2296	echo "$(SEP) Make PERL2ARB [done]" ; \
2297	) > PERL2ARB.log 2>&1 && (cat PERL2ARB.log;rm PERL2ARB.log)) \|\| (cat PERL2ARB.log;rm PERL2ARB.log;false)
2298
2299	perl_clean:
2300	@$(MAKE) -C PERL2ARB -r -f Makefile.main \
2301	"AUTODEPENDS=0" \
2302	clean
2303
2304	PERL2ARB/PERL2ARB.clean:
2305	$(MAKE) perl_clean
2306	$(MAKE) -C PERL_SCRIPTS/test clean
2307
2308	# ---------------------------------------- bindings to script languages
2309
2310	bindings: lib/libCORE.so lib/libARBDB.so
2311	$(MAKE) -C BINDINGS all ARBDEPENDS="$(^:%=../%)" DFLAGS="$(dflags)"
2312
2313	bindings_clean:
2314	$(MAKE) -C BINDINGS clean
2315
2316	# ---------------------------------------- check resources
2317
2318	check_res:
2319	$(ARBHOME)/SOURCE_TOOLS/check_resources.pl
2320
2321	# ---------------------------------------- cleaning
2322
2323	rmbak:
2324	@echo "[cleanup backup/core files]"
2325	@find . \( -name '*%' \
2326	-o -name '*.bak' \
2327	-o -name '*~' \) \
2328	-o $ -name 'core' -a \! -type d $ \
2329	-exec rm -v {} \; \|\| \
2330	echo "Warning: target 'rmbak' reported problems when removing misc. backup files (ignored)"
2331	@echo "[cleanup done]"
2332
2333	bin_reinit:
2334	$(MAKE) bin/bin.clean
2335	$(MAKE) -C "bin" all
2336
2337	clean_directories:
2338	-rm -rf \
2339	$(ARBHOME)/PROBE_SET/bin \
2340	$(ARBHOME)/INCLUDE \
2341
2342	libclean:
2343	-find $(ARBHOME) -type f $ -name '*.a' ! -type l $ -exec rm -f {} \;
2344	-find $(ARBHOME) -type f $ -name 'lib*.so' ! -type l $ -exec rm -f {} \;
2345
2346	objclean:
2347	-find $(ARBHOME) -type f $ -name '*.o' ! -type l $ -exec rm -f {} \;
2348
2349	# bin.clean and HELP_SOURCE.clean interfere
2350	clean3:
2351	$(MAKE) bin/bin.clean
2352	$(MAKE) HELP_SOURCE/HELP_SOURCE.clean
2353
2354
2355	# delete all binaries (similar to 'cleanlinked')
2356	cleanRelinkable: libclean UNIT_TESTER/UNIT_TESTER.clean
2357	$(MAKE) -C bin cleanbinariesRelinkable
2358	$(MAKE) -C PROBE_SET cleanLinked
2359
2360
2361	clean2: $(SUBDIRS:.sub=.clean) \
2362	clean3 \
2363	rmbak \
2364	libclean \
2365	objclean \
2366	lib/lib.clean \
2367	GDEHELP/GDEHELP.clean \
2368	HEADERLIBS/HEADERLIBS.clean \
2369	SOURCE_TOOLS/SOURCE_TOOLS.clean \
2370	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.clean \
2371	UNIT_TESTER/UNIT_TESTER.clean \
2372	TEMPLATES/TEMPLATES.clean \
2373	perl_clean \
2374
2375	rm -f .last_gcc .last_compiler config.makefile.bak
2376	$(MAKE) clean_directories
2377
2378	# links are needed for cleanup
2379	clean: redo_links motif_xpm_hack_clean
2380	$(MAKE) clean2
2381	$(MAKE) clean_cov_all clean_links
2382
2383	silent_clean:
2384	$(MAKE) clean >/dev/null
2385
2386	# 'relocated' is about 50% faster than 'rebuild'
2387	reloc_clean: links
2388	@echo "---------------------------------------- Relocation cleanup"
2389	$(MAKE) \
2390	perl_clean \
2391	GDEHELP/GDEHELP.clean \
2392	HELP_SOURCE/genhelp/genhelp.clean \
2393	bin/bin.clean \
2394	libclean \
2395	objclean
2396
2397	relocated: links
2398	$(MAKE) reloc_clean
2399	@echo "---------------------------------------- and remake"
2400	$(MAKE) build
2401
2402	# -----------------------------------
2403	# some stress tests
2404	# (helpful to reveal race conditions with -j)
2405
2406	rebuild4ever: rebuild
2407	$(MAKE) rebuild4ever
2408
2409	build4ever: build
2410	$(MAKE) build4ever
2411
2412	clean4ever: clean
2413	$(MAKE) clean4ever
2414
2415	test4ever: ut
2416	$(MAKE) test4ever
2417
2418	perl4ever: clean
2419	$(MAKE) links
2420	$(MAKE) perl
2421	$(MAKE) perl4ever
2422
2423	help4ever: clean
2424	$(MAKE) help
2425	$(MAKE) help4ever
2426
2427	# -----------------------------------
2428
2429	cleanlinked: bin/bin.clean libclean
2430
2431	relink: cleanlinked
2432	$(MAKE) all
2433
2434	# --------------------------------------------------------------------------------
2435	# source related targets
2436
2437	CLOC=cloc
2438	CLOCFLAGS=--no3 --quiet --progress-rate=0
2439	CLOCARB=--exclude-dir=GDE .
2440	CLOCEXT=GDE
2441	CLOCCODE=--force-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.code.def
2442	CLOCREST=--force-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.rest.def
2443	CLOCFILT=tail --lines=+4
2444
2445	cloc:
2446	@echo 'Arb code:'
2447	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCARB) \| $(CLOCFILT)
2448	@echo 'Arb rest:'
2449	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCARB) \| $(CLOCFILT)
2450	@echo 'External code:'
2451	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCEXT) \| $(CLOCFILT)
2452	@echo 'External rest:'
2453	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCEXT) \| $(CLOCFILT)
2454
2455
2456	# patch generation
2457	patch:
2458	SOURCE_TOOLS/arb_create_patch.sh arbPatch --svn
2459
2460	# source tarball generation
2461	save: sourcetarfile
2462
2463	sourcetarfile: rmbak
2464	util/arb_save
2465
2466	# test early whether save will work
2467	savetest:
2468	@util/arb_srclst.pl >/dev/null
2469
2470	testsave: savetest
2471
2472	save2: rmbak
2473	util/arb_save ignore
2474
2475	save_test: rmbak
2476	@echo "Testing source list.."
2477	@util/arb_srclst.pl > /dev/null
2478
2479	save_test_no_error:
2480	@-$(MAKE) save_test
2481
2482	# --------------------------------------------------------------------------------
2483	# version management
2484
2485	inc_candi:
2486	touch SOURCE_TOOLS/inc_candi.stamp
2487	$(MAKE) do_version_update
2488
2489	inc_patch:
2490	touch SOURCE_TOOLS/inc_patch.stamp
2491	$(MAKE) do_version_update
2492
2493	inc_minor:
2494	touch SOURCE_TOOLS/inc_minor.stamp
2495	$(MAKE) do_version_update
2496
2497	inc_major:
2498	touch SOURCE_TOOLS/inc_major.stamp
2499	$(MAKE) do_version_update
2500
2501	do_version_update:
2502	@echo Incrementing version information
2503	$(MAKE) savetest
2504	$(MAKE) genheaders # auto upgrades version early
2505
2506	show_version:
2507	$(MAKE) genheaders # updates version info
2508	@echo "$(SEP) ARB version info"
2509	@grep ARB_VERSION TEMPLATES/arb_build.h
2510	@echo "$(SEP)"
2511
2512	# --------------------------------------------------------------------------------
2513	# special cleanups
2514
2515	clean_opengl_changed: RNA3D/RNA3D.clean EDIT4/EDIT4.clean WINDOW/WINDOW.clean GL/GL.clean
2516
2517	# --------------------------------------------------------------------------------
2518
2519	arbapplications: nt pa e4 wetc pt na di ph ds wetc cma
2520
2521	arb_external: convert tools gde readseq tg pst
2522
2523	arb_no_perl: arbapplications help arb_external
2524
2525	arb: motif_xpm_hack
2526	$(MAKE) "WITHPERL=1" perl arb_no_perl
2527
2528	motif_xpm_hack:
2529	$(MAKE) -r -C "lib/motifHack" all
2530
2531	motif_xpm_hack_clean:
2532	$(MAKE) -r -C "lib/motifHack" clean
2533
2534	# --------------------------------------------------------------------------------
2535	# special targets for SOURCE_TOOLS/remake_after_change.pl
2536
2537	rac_arb_dist: di
2538	rac_arb_edit4: e4
2539	rac_arb_ntree: nt
2540	rac_arb_pars: pa
2541	rac_arb_phylo: ph
2542	rac_arb_wetc: wetc
2543	rac_arb_pt_server: pt
2544	rac_arb_db_server: ds
2545	rac_arb_name_server: na
2546	rac_arb_convert_aln: convert
2547	rac_arb_treegen: tg
2548	rac_arb_rnacma: cma
2549	rac_arb_help2xml: help
2550
2551	rac_arb_a2ps: tools
2552	rac_arb_consensus_tree: tools
2553	rac_arb_dnarates: tools
2554	rac_arb_export_rates: tools
2555	rac_arb_export_tree: tools
2556	rac_arb_gene_probe: tools
2557	rac_arb_message: tools
2558	rac_arb_primer: tools
2559	rac_arb_probe: tools
2560	rac_arb_read_tree: tools
2561
2562	# --------------------------------------------------------------------------------
2563	# unit testing
2564	# @@@ work in progress
2565	#
2566	# goal is to automatically test all libraries/executables using TESTED_UNITS_AUTO
2567	# currently not all test executables link w/o error.
2568	# therefor units are organized in three sets:
2569	#
2570	# TESTED_UNITS = testable and contain tests
2571	# UNTESTED_UNITS = testable, but no tests written yet
2572	# UNTESTABLE_UNITS = not testable
2573
2574	# always define OPENGL units manually:
2575	OPENGL_TESTS :=
2576	ifeq ($(OPENGL),1)
2577	# this section defines RNA3D.test
2578	OPENGL_TESTS += \
2579	$(subst .a,.test,$(RNA3D_LIB)) \
2580	GL/glAW/libglAW.test \
2581	GL/glpng/libglpng_arb.test \
2582
2583	endif
2584
2585	UNITS_NOT_AUTODETECTED = \
2586	HELP_SOURCE/HELP_SOURCE.tooltests
2587
2588	TESTED_UNITS_AUTO = \
2589	$(OPENGL_TESTS) \
2590	$(TL_ARCHIVES:.a=.test) \
2591	$(TL_SHARED_ARCHIVES:.so=.test) \
2592	$(CL_ARCHIVES:.a=.test) \
2593	$(TL_TOOLS_COLLECTIONS:.toolColl=.tooltests) \
2594	$(UNITS_NOT_AUTODETECTED) \
2595
2596	UNTESTED_UNITS = \
2597	$(OPENGL_TESTS) \
2598	EISPACK/EISPACK.test \
2599	GENOM/GENOM.test \
2600	ISLAND_HOPPING/ISLAND_HOPPING.test \
2601	NAMES/NAMES.test \
2602	PHYLO/PHYLO.test \
2603	PRIMER_DESIGN/PRIMER_DESIGN.test \
2604	READSEQ/READSEQ.tooltests \
2605	SECEDIT/SECEDIT.test \
2606	SEQ_QUALITY/SEQ_QUALITY.test \
2607	SERVERCNTRL/SERVERCNTRL.test \
2608	SL/ALIVIEW/ALIVIEW.test \
2609	SL/AP_TREE/AP_TREE.test \
2610	SL/ARB_SPEC/ARB_SPEC.test \
2611	SL/ARB_TREE/ARB_TREE.test \
2612	SL/AW_HELIX/AW_HELIX.test \
2613	SL/AW_NAME/AW_NAME.test \
2614	SL/CANVAS/CANVAS.test \
2615	SL/DB_SCANNER/DB_SCANNER.test \
2616	SL/DB_UI/DB_UI.test \
2617	SL/GUI_ALIVIEW/GUI_ALIVIEW.test \
2618	SL/GUI_TK/GUI_TK.test \
2619	SL/HELIX/HELIX.test \
2620	SL/MASKS/MASKS.test \
2621	SL/MAPKEY/MAPKEY.test \
2622	SL/QUERY/QUERY.test \
2623	SL/REFENTRIES/REFENTRIES.test \
2624	SL/SEQUENCE/SEQUENCE.test \
2625	SL/TREE_ADMIN/TREE_ADMIN.test \
2626	SL/TREE_WRITE/TREE_WRITE.test \
2627	SL/XFERGUI/XFERGUI.test \
2628	STAT/STAT.test \
2629	TREEGEN/TREEGEN.test \
2630	WETC/WETC.test \
2631	XML/XML.test \
2632
2633	# untestable units
2634
2635	UNTESTABLE_UNITS = \
2636	AISC/AISC.test \
2637	NAMES_COM/server.test \
2638	PROBE_COM/server.test \
2639
2640	# --------------------
2641	# put all units containing tests into the following 4 sections (see also TESTED_UNITS below)
2642
2643	# recent development
2644	UNITS_TESTED_FIRST = \
2645	SL/SPECSEL/SPECSEL.test \
2646	SL/MATRIX/MATRIX.test \
2647	AWTI/AWTI.test \
2648	SL/FILTSEQEXP/FILTSEQEXP.test \
2649	SL/GROUP_SEARCH/GROUP_SEARCH.test \
2650	SL/PVP/PVP.test \
2651	SL/SAICALC/SAICALC.test \
2652	SL/TRANSLATE/TRANSLATE.test \
2653	SL/XFERSET/XFERSET.test \
2654
2655	# start units with long duration early
2656	UNITS_RUNNING_LONG = \
2657	ARBDB/libARBDB.test \
2658	AWTC/AWTC.test \
2659	TOOLS/TOOLS.tooltests \
2660
2661	# plain test-libaries that are not linked anywhere
2662	TEST_SANDBOXES = \
2663	SL/CB/CB.test \
2664	SL/HEADERTESTS/HEADERTESTS.test \
2665
2666	UNITS_TESTED = \
2667	AISC_MKPTPS/AISC_MKPTPS.tooltests \
2668	ARB_GDE/ARB_GDE.test \
2669	CONSENSUS_TREE/CONSENSUS_TREE.test \
2670	CONVERTALN/CONVERTALN.test \
2671	CORE/libCORE.test \
2672	DBSERVER/DBSERVER.test \
2673	DIST/DIST.test \
2674	EDIT4/EDIT4.test \
2675	GENOM_IMPORT/GENOM_IMPORT.test \
2676	HELP_SOURCE/HELP_SOURCE.tooltests \
2677	MERGE/MERGE.test \
2678	MULTI_PROBE/MULTI_PROBE.test \
2679	NTREE/NTREE.test \
2680	PARSIMONY/PARSIMONY.test \
2681	PERLTOOLS/PERLTOOLS.tooltests \
2682	PROBE/PROBE.test \
2683	PROBE_DESIGN/PROBE_DESIGN.test \
2684	PROBE_SET/PROBE_SET.tooltests \
2685	RNACMA/RNACMA.test \
2686	SL/ALILINK/ALILINK.test \
2687	SL/APP/APP.test \
2688	SL/CONSENSUS/CONSENSUS.test \
2689	SL/DB_QUERY/DB_QUERY.test \
2690	SL/FAST_ALIGNER/FAST_ALIGNER.test \
2691	SL/FILTER/FILTER.test \
2692	SL/INSDEL/INSDEL.test \
2693	SL/ITEM_SHADER/ITEM_SHADER.test \
2694	SL/ITEMS/ITEMS.test \
2695	SL/LOCATION/LOCATION.test \
2696	SL/MACROS/MACROS.test \
2697	SL/NDS/NDS.test \
2698	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.test \
2699	SL/PRONUC/PRONUC.test \
2700	SL/PTCLEAN/PTCLEAN.test \
2701	SL/REGEXPR/REGEXPR.test \
2702	SL/SEQIO/SEQIO.test \
2703	SL/TREE_READ/TREE_READ.test \
2704	SL/TREEDISP/TREEDISP.test \
2705	WINDOW/libWINDOW.test \
2706
2707	TESTED_UNITS = \
2708	$(UNITS_TESTED_FIRST) \
2709	$(UNITS_RUNNING_LONG) \
2710	$(TEST_SANDBOXES) \
2711	$(UNITS_TESTED) \
2712
2713	# ----------------------------------------
2714
2715	ifeq ($(DEVELOPER),RALF)
2716
2717	DEFINED_TEST_UNITS = \
2718	$(TESTED_UNITS) \
2719	$(UNTESTED_UNITS) \
2720	$(UNTESTABLE_UNITS) \
2721
2722	list_undefined_units:
2723	@UNIT_TESTER/list_undefined_units.pl $(DEFINED_TEST_UNITS) -- $(TESTED_UNITS_AUTO)
2724
2725	else
2726
2727	list_undefined_units:
2728
2729	endif
2730
2731	# ----------------------------------------
2732
2733	TEST_LOG_DIR = UNIT_TESTER/logs
2734	TEST_RUN_SUITE=$(MAKE) $(NODIR) -C UNIT_TESTER -f Makefile.suite -r
2735	# -> UNIT_TESTER/Makefile.suite
2736	TEST_MAKE_FLAGS=
2737	TEST_POST_CLEAN=
2738	ifeq ($(COVERAGE),1)
2739	TEST_POST_CLEAN=$(MAKE) clean_cov
2740	TEST_MAKE_FLAGS+=-j1
2741	endif
2742
2743
2744	%.test:
2745	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
2746	( \
2747	echo "take[1]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
2748	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
2749	"UNITDIR=$(@D)" \
2750	"UNITLIBNAME=$(@F:.test=)" \
2751	"COVERAGE=$(COVERAGE)" \
2752	"ARB_PID=$(ARB_PID)_$(@F)" \
2753	"DEVELOPER=$(DEVELOPER)" \
2754	runtest; \
2755	echo "take[1]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"; \
2756	$(TEST_POST_CLEAN) \
2757	) >$(TEST_LOG_DIR)/$(@F).log 2>&1; \
2758	UNIT_TESTER/log_result.pl $(TEST_LOG_DIR)/$(@F).log )
2759
2760	%.notest:
2761	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
2762	( \
2763	echo "take[4]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
2764	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
2765	"UNITDIR=$(@D)" \
2766	"UNITLIBNAME=$(@F:.notest=)" \
2767	"COVERAGE=0" \
2768	"ARB_PID=$(ARB_PID)_$(@F)" \
2769	"DEVELOPER=$(DEVELOPER)" \
2770	check_no_test; \
2771	echo "take[4]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'" \
2772	) >$(TEST_LOG_DIR)/$(@F).log 2>&1 )
2773
2774
2775	# tool test aliases (used to test one or multiple executable(s) in a single subdir):
2776	%.tooltests:
2777	$(error please define an explicit tooltest alias for $@)
2778
2779	AISC_MKPTPS/AISC_MKPTPS.tooltests : AISC_MKPTPS/mkptypes.test
2780	@echo "aliasing $@ -> $^"
2781	PERLTOOLS/PERLTOOLS.tooltests : PERLTOOLS/arb_proto_2_xsub.test
2782	@echo "aliasing $@ -> $^"
2783	PROBE_SET/PROBE_SET.tooltests : PROBE_SET/fb_test.test
2784	@echo "aliasing $@ -> $^"
2785	HELP_SOURCE/HELP_SOURCE.tooltests : HELP_SOURCE/arb_help2xml.test
2786	@echo "aliasing $@ -> $^"
2787	TOOLS/TOOLS.tooltests : TOOLS/arb_consensus_tree.test TOOLS/arb_probe.test TOOLS/arb_test.test
2788	@echo "aliasing $@ -> $^"
2789
2790	# aliases for tools w/o tests:
2791	READSEQ/READSEQ.tooltests:
2792	@echo "Note: no tests for $@"
2793
2794
2795	test_base: $(UNIT_TESTER_LIB:.a=.dummy) $(subst .test,.dummy,$(TEST_SANDBOXES))
2796
2797	clean_cov:
2798	find . $ -name ".gcda" -o -name ".gcov" -o -name "*.cov" $ -exec rm {} \;
2799
2800	clean_cov_all: clean_cov
2801	find . $ -name "*.gcno" $ -exec rm {} \;
2802
2803	cleanup_faked_arbpids:
2804	@rm ~/.arb_tmp/tmp/arb_pids_${USER}_${ARB_PID}_* \|\| true
2805
2806	cleanup_faked_arbpids_and_fail: cleanup_faked_arbpids
2807	@false
2808
2809	NOTESTS_IN_UNTESTED = $(subst .test,.notest,$(UNTESTED_UNITS))
2810
2811	run_tests_faked_arbpid:
2812	+@$(TEST_RUN_SUITE) init
2813	@echo "take[2]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2814	@$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(TESTED_UNITS) $(NOTESTS_IN_UNTESTED) \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2815	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2816	@echo "take[2]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2817	@$(MAKE) clean_cov >/dev/null
2818	@$(MAKE) cleanup_faked_arbpids
2819
2820	# @@@ instead of only running UNIT, this should as well run all tests this unit depends on? according to 'needs_libs'
2821	# @@@ '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
2822
2823	run_onetest_faked_arbpid:
2824	+@$(TEST_RUN_SUITE) init
2825	@echo "take[3]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2826	@test -n "$(UNIT)" \|\| (echo "Error: UNIT has to be defined for target 'run_onetest_faked_arbpid'!"; false)
2827	$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(UNIT).test \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2828	@echo "take[3]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2829	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2830	@$(MAKE) clean_cov >/dev/null
2831	@$(MAKE) cleanup_faked_arbpids
2832
2833	run_tests: test_base clean_cov
2834	$(MAKE) "ARB_PID=UT_$$$$" run_tests_faked_arbpid list_undefined_units
2835
2836	run_oneunitstests: test_base
2837	$(MAKE) "ARB_PID=UT_$$$$" run_onetest_faked_arbpid
2838
2839
2840	ut:
2841	ifeq ($(UNIT_TESTS),1)
2842	@echo $(MAKE) run_tests
2843	@$(MAKE) run_tests
2844	else
2845	@echo "Not compiled with unit tests"
2846	endif
2847
2848
2849	aut:
2850	+@$(TEST_RUN_SUITE) unskip
2851	$(MAKE) ut
2852
2853	# --------------------------------------------------------------------------------
2854
2855	TIMELOG=$(ARBHOME)/arb_time.log
2856	TIMEARGS=--append --output=$(TIMELOG) --format=" * %E(%S+%U) %P [%C]"
2857	TIMECMD=$(TIME) $(TIMEARGS)
2858
2859	time_one:
2860	ifeq ($(ONE_TIMED_TARGET),)
2861	@echo "Error: You have to pass ONE_TIMED_TARGET to $@"
2862	false
2863	else
2864	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET)"
2865	@$(TIMECMD) $(MAKE) $(ONE_TIMED_TARGET)
2866	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET) [done]"
2867	endif
2868
2869	timed_target:
2870	ifeq ($(TIMED_TARGET),)
2871	@echo "Error: You have to pass TIMED_TARGET to $@"
2872	false
2873	else
2874	@echo "Build time:" > $(TIMELOG)
2875	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2876	@cat $(TIMELOG)
2877	@rm $(TIMELOG)
2878	endif
2879
2880	timed_target_tested:
2881	ifeq ($(TIMED_TARGET),)
2882	@echo "Error: You have to pass TIMED_TARGET to $@"
2883	false
2884	else
2885	@echo "Build time:" > $(TIMELOG)
2886	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2887	$(MAKE) "ONE_TIMED_TARGET=ut" time_one
2888	@cat $(TIMELOG)
2889	@rm $(TIMELOG)
2890	endif
2891
2892	clean_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=clean" time_one
2899	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2900	@cat $(TIMELOG)
2901	@rm $(TIMELOG)
2902	endif
2903
2904	# --------------------------------------------------------------------------------
2905
2906	CHECKOUT_MODIFIED=0# # set to 1 to temporarily skip test for modifications (do not check in if set to 1)
2907
2908	check_svn_does_not_contain_generated:
2909	ifeq ($(CHECKOUT_MODIFIED),0)
2910	@echo "Testing that build does not modify files in SVN"
2911	@test 0 = `svn status \| wc -l` \|\| ( \
2912	echo "The checkout is not/no longer clean:"; \
2913	svn status; \
2914	echo "- if this fails instantly, your checkout is not clean"; \
2915	echo "- if this fails after other targets, these targets modify checked in data"; \
2916	echo " (a common cause may be that depends are not up to date)"; \
2917	false)
2918	else
2919	grep -Hn 'CHECKOUT_MODIFIED' Makefile
2920	endif
2921
2922	check_svn_ignores_generated:
2923	@test 0 = `svn status \| grep '^\?' \| wc -l` \|\| ( \
2924	echo "There are svn-unignored files:"; \
2925	svn status \| grep '^\?'; \
2926	echo "(all generated files should be svn-ignored)"; \
2927	false)
2928
2929	check_svn_state: check_svn_does_not_contain_generated
2930	$(MAKE) check_svn_ignores_generated
2931	$(MAKE) savetest
2932
2933	things_that_always_should_work: depends proto
2934
2935	post_commit_check:
2936	@echo "---------------------------------------- [Initial]"
2937	$(MAKE) check_svn_state
2938
2939	$(MAKE) clean
2940	@echo "---------------------------------------- [After 'make clean']"
2941	$(MAKE) check_svn_state
2942
2943	$(MAKE) things_that_always_should_work
2944	@echo "---------------------------------------- [After 'make things_that_always_should_work']"
2945	$(MAKE) check_svn_state
2946
2947	$(MAKE) all
2948	@echo "---------------------------------------- [After 'make all']"
2949	$(MAKE) check_svn_state
2950
2951	$(MAKE) things_that_always_should_work
2952	@echo "---------------------------------------- [Final]"
2953	$(MAKE) check_svn_state
2954
2955	# --------------------------------------------------------------------------------
2956	# sanitize arb_ntree; also works for clients (arb_edit4, ...) started from there.
2957
2958	sanitize: all
2959	( \
2960	export "LSAN_OPTIONS=max_leaks=30:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp"; \
2961	echo "sake[1]: Entering directory \`$(ARBHOME)'"; \
2962	$(ARBHOME)/bin/arb_ntree --execute _logged ~/data/test.arb 2>&1 ; \
2963	echo "sake[1]: Leaving directory \`$(ARBHOME)'" \
2964	) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
2965
2966	# --------------------------------------------------------------------------------
2967	# build and test one unit:
2968
2969	build_oneunit:
2970	$(MAKE) "WITHPERL=1" $(UNIT).dummy
2971
2972	oneunit:
2973	ifndef UNIT
2974	@echo "Please define UNIT, e.g. using"
2975	@echo " make \"UNIT=ARBDB/libARBDB\" oneunit"
2976	@echo " make \"UNIT=SL/TREEDISP/TREEDISP\" oneunit"
2977	@echo "(Note: 1st is a shared library, 2nd isn't)"
2978	false
2979	else
2980	@echo "Build time" > $(TIMELOG)
2981	@echo "$(SEP) $(MAKE) build_oneunit"
2982	@$(TIMECMD) $(MAKE) build_oneunit
2983	ifeq ($(UNIT_TESTS),1)
2984	@echo "$(SEP) $(MAKE) run_oneunitstests"
2985	@$(TIMECMD) $(MAKE) run_oneunitstests
2986	endif
2987	@cat $(TIMELOG)
2988	@rm $(TIMELOG)
2989	endif
2990
2991	# --------------------------------------------------------------------------------
2992	# Main targets:
2993
2994	tarfile: rebuild
2995	$(MAKE) prepare_libdir
2996	util/arb_compress
2997
2998	tarfile_quick: all
2999	$(MAKE) prepare_libdir
3000	util/arb_compress
3001
3002	# -----------------------------------
3003
3004	build: arb
3005	$(MAKE) check_bin_dep preplib compile_compatibility fig_cure
3006
3007	all:
3008	@echo "Build time" > $(TIMELOG)
3009	# $(MAKE) clean_checked_vect # uncomment to rebuild sources where expected vectorization gets tested
3010	@echo "$(SEP) $(MAKE) all"
3011	@$(TIMECMD) $(MAKE) build
3012	@echo $(SEP)
3013	@echo "made 'all' with success."
3014	@echo "to start arb enter 'arb'"
3015	ifeq ($(UNIT_TESTS),1)
3016	@echo "$(SEP) $(MAKE) run_tests"
3017	@$(TIMECMD) $(MAKE) run_tests
3018	endif
3019	@echo "$(SEP) $(MAKE) all [done]"
3020	ifeq ($(DEBUG),1)
3021	@$(MAKE) save_test_no_error >/dev/null # just show hints
3022	endif
3023	@cat $(TIMELOG)
3024	@rm $(TIMELOG)
3025
3026	rebuild: clean
3027	$(MAKE) all
3028
3029	# --------------------------------------------------------------------------------
3030	# special targets showing obvious error at bottom
3031	# (intended to be used from automated builds)
3032
3033	BUILD_LOG=build.log
3034	SHELL=bash
3035	REDIRECT_KEEP_EXITCODE = tee $(BUILD_LOG) ; exit "$${PIPESTATUS[0]}"
3036	EXTRACT_ERROR_SUMMARY = (./SOURCE_TOOLS/short_error_summary.pl $(BUILD_LOG); false)
3037
3038	REEXTRACT:
3039	@echo "Note: Re-extracting errors from $(BUILD_LOG):"
3040	@$(EXTRACT_ERROR_SUMMARY)
3041
3042	ALL:
3043	@(($(MAKE) all 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
3044
3045	REBUILD:
3046	@(($(MAKE) rebuild 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
3047
3048	TARFILE:
3049	@(($(MAKE) tarfile 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
3050
3051	TARFILE_QUICK:
3052	@(($(MAKE) tarfile_quick 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
3053

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