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Last change on this file was 19440, checked in by westram, 22 months ago
full update from 'trunk' into 'ali' fixes for debian11 version adds: log:trunk@19416:19424,19426:19439
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 87.4 KB

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

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