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Last change on this file was 18655, checked in by westram, 3 years ago
usage of libglut is no longer system dependent (thx to Jan).
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 84.3 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	# Read configuration
65	include config.makefile
66	CONFIG_MAKEFILE_FOUND=$(strip $(wildcard config.makefile))
67
68	# set defaults for variables commented out in config.makefile:
69	ifndef DARWIN
70	DARWIN:=0
71	endif
72	ifndef LINUX
73	LINUX:=0
74	endif
75	ifndef DEBIAN
76	DEBIAN:=0
77	endif
78	ifndef ARB_64
79	ARB_64=1#default to 64bit
80	endif
81
82	# Variables allowed for injection [InjectedEnvironment]
83	# (alternatively initialize them with '?=', e.g. done for XLIBS and XINCLUDES)
84	# In both cases add them to SOURCE_TOOLS/export2sub
85	ifndef XML_INCLUDES
86	XML_INCLUDES=
87	endif
88	ifndef XAW_LIBS
89	XAW_LIBS=
90	endif
91
92
93	ifneq ($(CONFIG_MAKEFILE_FOUND),)
94	ifneq ($(DARWIN)$(LINUX),10)
95	ifneq ($(DARWIN)$(LINUX),01)
96	$(error exactly one of DARWIN=1 or LINUX=1 has to be defined (got:$(DARWIN)$(LINUX)))
97	endif
98	endif
99	endif
100
101	# compiler settings:
102	ifneq ($(CC),use__A_CC__instead_of__CC)
103	A_CC:=$(CC)# compile C
104	A_CXX:=$(CXX)# compile C++
105
106	# uncomment to ensure no submakefile uses CC and CXX directly
107	override CC:=use__A_CC__instead_of__CC
108	override CXX:=use__A_CXX__instead_of__CXX
109	endif
110
111	export CC CXX A_CC A_CXX
112
113	# unconditionally prepend $(ARBHOME)/lib to LD_LIBRARY_PATH if not found
114	ifeq ($(findstring $(ARBHOME)/lib,$(LD_LIBRARY_PATH)),)
115	LD_LIBRARY_PATH:=${ARBHOME}/lib:$(LD_LIBRARY_PATH)
116	endif
117
118	# store LD_LIBRARY_PATH to circumvent SIP restrictions:
119	ARBBUILD_LIBRARY_PATH:=$(LD_LIBRARY_PATH)
120
121	FORCEMASK = umask 002
122	NODIR=--no-print-directory
123
124	SED:=$(ARBHOME)/SH/arb_sed
125	READLINK:=$(ARBHOME)/SH/arb_readlink
126
127	# ---------------------- compiler version detection
128
129	# supported gcc versions:
130	ALLOWED_gcc_VERSIONS=\
131	4.4.3 4.4.5 4.4.6 4.4.7 \
132	4.5.2 \
133	4.6.1 4.6.2 4.6.3 4.6.4 \
134	4.7.1 4.7.2 4.7.3 4.7.4 \
135	4.8.0 4.8.1 4.8.2 4.8.3 4.8.4 4.8.5 \
136	4.9.0 4.9.1 4.9.2 4.9.3 4.9.4 \
137	5.1.0 5.2.0 5.3.0 5.4.0 5.5.0 \
138	6.1.0 6.2.0 6.3.0 6.4.0 6.5.0 \
139	7.1.0 7.2.0 7.3.0 7.4.0 7.5.0 \
140	8.1.0 8.2.0 8.3.0 8.4.0 \
141	9.1.0 9.2.0 9.3.0 \
142
143	# Note: starting with version 5, arb silently accepts any subversion number
144	# above zero. See SOURCE_TOOLS/arb_compiler_version.pl@acceptSubVersions
145	#
146	# This may cause problems when manually checking for compiler versions in code
147	# (GCC_VERSION_CODE is not affected, GCC_PATCHLEVEL_CODE may cause problems!)
148	# ----------------------
149
150	COMPILER_INFO:=$(shell SOURCE_TOOLS/arb_compiler_version.pl $(A_CXX))
151	COMPILER_NAME:=$(word 1,$(COMPILER_INFO))
152	COMPILER_VERSION:=$(word 2,$(COMPILER_INFO))
153
154	USE_CLANG:=0
155	ifneq ($(COMPILER_NAME),gcc)
156	ifeq ($(COMPILER_NAME),clang)
157	USE_CLANG:=1
158	else
159	ifeq ($(COMPILER_VERSION),4.6.4)
160	# gcc version 4.6.4 segfaults when dumping symbols for detection (silently accept as gcc)
161	COMPILER_NAME:=gcc
162	else
163	$(error failed to detect COMPILER_NAME (got '$(COMPILER_NAME)', expected 'clang' or 'gcc'))
164	endif
165	endif
166	endif
167
168	ifeq ($(USE_CLANG),1)
169	# accept all clang versions:
170	ALLOWED_COMPILER_VERSIONS=$(COMPILER_VERSION)
171	else
172	ALLOWED_COMPILER_VERSIONS=$(ALLOWED_gcc_VERSIONS)
173	endif
174
175	COMPILER_VERSION_ALLOWED=$(strip $(subst ___,,$(foreach version,$(ALLOWED_COMPILER_VERSIONS),$(findstring ___$(version)___,___$(COMPILER_VERSION)___))))
176
177	#---------------------- split gcc version
178
179	SPLITTED_VERSION:=$(subst ., ,$(COMPILER_VERSION))
180
181	USE_GCC_MAJOR:=$(word 1,$(SPLITTED_VERSION))
182	USE_GCC_MINOR:=$(word 2,$(SPLITTED_VERSION))
183	USE_GCC_PATCHLEVEL:=$(word 3,$(SPLITTED_VERSION))
184
185	USE_GCC_452_OR_HIGHER:=
186	USE_GCC_46_OR_HIGHER:=
187	USE_GCC_47_OR_HIGHER:=
188	USE_GCC_48_OR_HIGHER:=
189	USE_GCC_49_OR_HIGHER:=
190	USE_GCC_50_OR_HIGHER:=
191	USE_GCC_60_OR_HIGHER:=
192	USE_GCC_70_OR_HIGHER:=
193	USE_GCC_80_OR_HIGHER:=
194	USE_GCC_90_OR_HIGHER:=
195
196	ifeq ($(USE_CLANG),0)
197	ifeq ($(USE_GCC_MAJOR),4)
198	ifeq ($(USE_GCC_MINOR),5)
199	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),23456789)','')
200	USE_GCC_452_OR_HIGHER:=yes
201	endif
202	else
203	ifneq ('$(findstring $(USE_GCC_MINOR),6789)','')
204	USE_GCC_452_OR_HIGHER:=yes
205	USE_GCC_46_OR_HIGHER:=yes
206	ifneq ($(USE_GCC_MINOR),6)
207	USE_GCC_47_OR_HIGHER:=yes
208	ifneq ($(USE_GCC_MINOR),7)
209	USE_GCC_48_OR_HIGHER:=yes
210	ifneq ($(USE_GCC_MINOR),8)
211	USE_GCC_49_OR_HIGHER:=yes
212	endif
213	endif
214	endif
215	endif
216	endif
217	else
218	# gcc 5.x or higher
219	USE_GCC_452_OR_HIGHER:=yes
220	USE_GCC_46_OR_HIGHER:=yes
221	USE_GCC_47_OR_HIGHER:=yes
222	USE_GCC_48_OR_HIGHER:=yes
223	USE_GCC_49_OR_HIGHER:=yes
224	USE_GCC_50_OR_HIGHER:=yes
225	ifneq ($(USE_GCC_MAJOR),5)
226	# gcc 6.x or higher
227	USE_GCC_60_OR_HIGHER:=yes
228	ifneq ($(USE_GCC_MAJOR),6)
229	# gcc 7.x or higher
230	USE_GCC_70_OR_HIGHER:=yes
231	ifneq ($(USE_GCC_MAJOR),7)
232	# gcc 8.x or higher
233	USE_GCC_80_OR_HIGHER:=yes
234	ifneq ($(USE_GCC_MAJOR),8)
235	# gcc 9.x or higher
236	USE_GCC_90_OR_HIGHER:=yes
237	endif
238	endif
239	endif
240	endif
241	endif
242	endif
243
244	#---------------------- define special directories for non standard builds
245
246	ifeq ($(DARWIN),1)
247	OSX_FW:=/System/Library/Frameworks
248	OSX_FW_OPENGL:=$(OSX_FW)/OpenGL.framework/Versions/A/Libraries
249	OSX_FW_GLUT:=$(OSX_FW)/GLUT.framework/Versions/A/Libraries
250	OSX_FW_IMAGEIO:=$(OSX_FW)/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources
251	endif
252
253	#---------------------- SSE vectorization
254	# for details about vectorization checks see SOURCE_TOOLS/vectorize.README
255
256	DISABLE_VECTORIZE_CHECK:=0# set to 1 to completely disable vectorization checks
257	TRACE_MISSED_VECTORIZATIONS:=0# set to 1 to activate detailed output about failed vectorizations
258	# (does also show details about successful vectorized loops, which are not optimal)
259	VECTORIZATION_CHECK_CANDIDATES:=0# set to 1 to show vectorizations that may be checked
260	# (for yet unchecked files)
261	# Note: TRACE_MISSED_VECTORIZATIONS and VECTORIZATION_CHECK_CANDIDATES cannot be used together!
262
263	#----------------------
264
265	ifeq ($(DARWIN),1)
266	LINK_STATIC=1# link static
267	else
268	LINK_STATIC=0# link dynamically
269	# LINK_STATIC=1# link static (testing only)
270	endif
271
272	shared_cflags :=# flags for shared lib compilation
273	clflags :=# linker flags (when passed through gcc)
274	extended_warnings :=# warning flags for C and C++-compiler
275	extended_cpp_warnings :=# warning flags for C++-compiler only
276
277	ifeq ($(DEBUG),0)
278	dflags := -DNDEBUG# defines
279	ifeq ($(USE_CLANG),1)
280	cflags := -O3# compiler flags (C and C++)
281	else
282	clflags += -Wl,-O2# passthrough linker flags
283	# ------- standard optimization:
284	cflags := -O3# compiler flags (C and C++)
285	# ------- test changed optimization (DISABLE_VECTORIZE_CHECK for -O2 or lower):
286	# cflags := -O2# do not commit uncommented!
287	# DISABLE_VECTORIZE_CHECK:=1
288	endif
289	endif
290
291	ifeq ($(DEBIAN),1)
292	clflags += -Wl,-rpath=/usr/lib/arb/lib -Wl,-z,relro
293	endif
294
295	ifeq ($(DEBUG),1)
296	dflags := -DDEBUG
297
298	gdb_common := -g -g3 -ggdb -ggdb3
299
300	DBGOPTI:=-O0
301	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
302	DBGOPTI:=-Og
303	endif
304
305	ifeq ($(STABS),1)
306	cflags := $(DBGOPTI) $(gdb_common) -gstabs+ # using stabs+ (enable this for bigger debug session: debugs inlines, quick var inspect, BUT valgrind stops working :/)
307	else
308	cflags := $(DBGOPTI) $(gdb_common) # (using dwarf - cant debug inlines here, incredible slow on showing variable content)
309	endif
310
311	# cflags := $(DBGOPTI) $(gdb_common) -gdwarf-3 # (specify explicit dwarf format)
312	# cflags := $(DBGOPTI) $(gdb_common) -gstabs # using stabs (same here IIRC)
313	# cflags := -O2 $(gdb_common) # use this for callgrind (force inlining)
314
315	ifeq ($(DARWIN),0)
316	clflags += -Wl,-g
317	# Note:
318	# Previously '-Wl,-noinhibit-exec' was added to 'clflags' here,
319	# to fix some issues with launchpad binutils (see [12972]).
320	# But that change also caused 'undefined symbols' NOT to be reported as errors
321	# at link time, producing executables that fail at runtime :/
322	endif
323
324	ifeq ($(DEBUG_GRAPHICS),1)
325	dflags += -DDEBUG_GRAPHICS
326	endif
327
328	endif # DEBUG only
329
330	# ------------------------------ POST_COMPILE - control how much you get spammed
331	# (please do not change default in SVN)
332	POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl
333
334	# POST_COMPILE += --original # dont modify compiler output
335	# POST_COMPILE += --hide-Noncopyable-advices
336	# POST_COMPILE += --show-useless-Weff++
337	# POST_COMPILE += --no-warnings
338	# POST_COMPILE += --only-first-error
339	# POST_COMPILE += --no-warnings --only-first-error
340
341	# always pass used compiler version to postcompile:
342	POST_COMPILE += --compiler=$(COMPILER_VERSION)
343
344	# ------------------------------
345
346	# Enable extra warnings
347	extended_warnings :=
348	extended_cpp_warnings :=
349
350	# C and C++
351	extended_warnings += -Wwrite-strings -Wunused -Wno-aggregate-return
352
353	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
354	# disable shadow warnings for gcc 4.8 (and lower)
355	# (does e.g. warn if a method-name is used as parameter in another method - even for derived classes. unusable!)
356	extended_warnings += -Wshadow
357	endif
358
359	# C++ only
360	extended_cpp_warnings += -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute
361	extended_cpp_warnings += -Wctor-dtor-privacy
362	# extended_cpp_warnings += -Wfloat-equal
363
364	extended_cpp_warnings += -Wmissing-noreturn
365	# extended_cpp_warnings += -Wold-style-cast# (warns about 28405 old-style casts)
366	extended_cpp_warnings += -Winit-self
367	extended_cpp_warnings += -Wstrict-aliasing
368	extended_cpp_warnings += -Wextra
369
370	# ------- above only warning-options already available in gcc 4.4.3
371
372	# -Weffc++ broken in 4.7.x series
373	# gcc 4.7.3 crashes on GenomeImport.cxx when -Weffc++ is active
374	# (bug reported https://gcc.gnu.org/bugzilla/show_bug.cgi?id=56923; apparently wont be fixed for 4.7-series)
375	# gcc 4.7.4 crashes on DBwriter.cxx when -Weffc++ is active
376	WEFFC_BROKEN:=0
377	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
378	ifneq ('$(USE_GCC_48_OR_HIGHER)','yes')
379	WEFFC_BROKEN:=1
380	endif
381	endif
382	ifeq ('$(WEFFC_BROKEN)','0')
383	extended_cpp_warnings += -Weffc++
384	endif
385
386	# turn off -Wmaybe-uninitialized in debug mode (gets activated with -Wextra). too many bogus warnings
387	ifeq ($(DEBUG),1)
388	ifeq ($(USE_CLANG),0)
389	extended_cpp_warnings += -Wno-maybe-uninitialized
390	endif
391	endif
392
393	SUGGEST_FINAL:=
394
395	ifeq ('$(USE_GCC_452_OR_HIGHER)','yes')
396	extended_cpp_warnings += -Wlogical-op# gcc 4.5.2
397	endif
398	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
399	extended_cpp_warnings += -Wzero-as-null-pointer-constant# gcc 4.7
400	endif
401	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
402	extended_cpp_warnings += -Wunused-local-typedefs# available since gcc 4.7 (but fails for each STATIC_ASSERT, so enable only for Cxx11)
403	endif
404	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
405	extended_cpp_warnings += -Wswitch-bool
406	extended_cpp_warnings += -Wlogical-not-parentheses
407	extended_cpp_warnings += -Wsizeof-array-argument
408	extended_cpp_warnings += -Wbool-compare
409
410	SUGGEST_FINAL:=yes
411	endif
412	ifeq ('$(USE_GCC_60_OR_HIGHER)','yes')
413	extended_cpp_warnings += -Wduplicated-cond
414	endif
415	ifeq ('$(USE_GCC_80_OR_HIGHER)','yes')
416	extended_cpp_warnings += -Wmultistatement-macros
417	endif
418
419	# switch off final suggestions for 8.3.0 and 8.4.0:
420	ifeq ('$(COMPILER_VERSION)','8.3.0')
421	SUGGEST_FINAL:=no
422	endif
423	ifeq ('$(COMPILER_VERSION)','8.4.0')
424	SUGGEST_FINAL:=no
425	endif
426
427	ifeq ($(DEVELOPER),RELEASE)
428	# switch off final suggestions in RELEASE:
429	SUGGEST_FINAL:=no
430	endif
431	# suggest final:
432	ifeq ('$(SUGGEST_FINAL)','yes')
433	extended_cpp_warnings += -Wsuggest-final-types
434	extended_cpp_warnings += -Wsuggest-final-methods
435	dflags += -DSUGGESTS_FINAL
436	endif
437
438	#---------------------- turn off clang bogus warnings
439
440	ifeq ($(USE_CLANG),1)
441	# -Wmismatched-tags warns about struct/class mismatch in forward declarations (which is explicitely allowed)
442	# -Wchar-subscripts reports too many bogus warnings for "array['x']" (when 'x' is known to be in range [0..128])
443	# -Wunused-private-field report too many false positives (currently ~ 2 of 3)
444	# -Wstring-plus-int warns about common ARB coding practice
445	# -Wgnu-static-float-init warns about accepted GNU extension
446	extended_cpp_warnings += -Wno-mismatched-tags -Wno-char-subscripts -Wno-unused-private-field -Wno-string-plus-int
447	ifeq ('$(COMPILER_VERSION)','4.2.1')
448	# jenkins build (doesn't know switch -Wno-gnu-static-float-init)
449	extended_cpp_warnings += -Wno-gnu
450	else
451	extended_cpp_warnings += -Wno-gnu-static-float-init
452	endif
453	endif
454
455	#---------------------- developer
456
457	ifneq ($(DEVELOPER),ANY) # ANY=default setting (skip all developer specific code)
458	dflags += -DDEVEL_$(DEVELOPER)# activate developer/release specific code
459	endif
460
461	#---------------------- activate TODO warnings?
462
463	ifndef SHOWTODO
464	ifeq ($(DEVELOPER),RALF)
465	SHOWTODO:=1
466	else
467	SHOWTODO:=0
468	endif
469	endif
470	ifeq ($(SHOWTODO),1)
471	dflags += -DWARN_TODO# activate "TODO" warnings
472	endif
473
474	#---------------------- activate threads?
475	# only useful if compiler is able to compile Cxx11 or better
476
477	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
478	# see also ./TEMPLATES/cxxforward.h@USE_Cxx11
479	cflags += -pthread
480	clflags += -pthread
481	endif
482
483	#---------------------- activate Sanitizers?
484
485	ifndef IGNORE_LEAKS
486	IGNORE_LEAKS:=0
487	endif
488
489	ASAN_OPTIONS:=handle_segv=0:color=0
490	ifeq ($(IGNORE_LEAKS),1)
491	ASAN_OPTIONS+=:detect_leaks=0 # disable leak-detection
492	else
493	ASAN_OPTIONS+=:detect_leaks=1 # detect leaks (normal setting)
494	endif
495	ASAN_OPTIONS+=:check_initialization_order=1
496	# ASAN_OPTIONS+=:abort_on_error=1
497
498	# suppressions: SOURCE_TOOLS/arb.leaksan.supp
499	LSAN_OPTIONS:=max_leaks=3:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp
500
501	UBSAN_OPTIONS:=print_stacktrace=1
502
503	ifndef SANITIZE
504	SANITIZE:=0
505	endif
506
507	SANITIZE_ADDRESS:=0
508	SANITIZE_UNDEFINED:=0
509
510	ifneq ($(SANITIZE),0)
511	ifeq ($(SANITIZE),all)
512	SANITIZE:=3
513	endif
514
515	ifeq ($(SANITIZE),1)
516	SANITIZE_ADDRESS:=1
517	else
518	ifeq ($(SANITIZE),2)
519	SANITIZE_UNDEFINED:=1
520	else
521	ifeq ($(SANITIZE),3)
522	SANITIZE_ADDRESS:=1
523	SANITIZE_UNDEFINED:=1
524	else
525	$(error Unknown value '$(SANITIZE)' specified for SANITIZE in config.makefile)
526	endif
527	endif
528	endif
529	endif
530
531	ifeq ($(SANITIZE_ADDRESS),1)
532	ifneq ('$(USE_GCC_48_OR_HIGHER)','yes')
533	$(info AddressSanitizer not usable with gcc $(COMPILER_VERSION) - disabled)
534	SANITIZE_ADDRESS:=0
535	else
536	ifneq ('$(USE_GCC_49_OR_HIGHER)','yes')
537	$(info LeakSanitizer does not work with gcc $(COMPILER_VERSION) - disabled)
538	# need to disable AddressSanitizer (otherwise build fails; only affects gcc 4.8.x series)
539	SANITIZE_ADDRESS:=0
540	endif
541	endif
542	endif
543
544	ifeq ($(SANITIZE_UNDEFINED),1)
545	ifneq ('$(USE_GCC_49_OR_HIGHER)','yes')
546	$(info UndefinedBehaviorSanitizer not usable with gcc $(COMPILER_VERSION) - disabled)
547	SANITIZE_UNDEFINED:=0
548	endif
549	endif
550
551	SANITIZE_ANY:=0
552	ifeq ($(SANITIZE_ADDRESS),1)
553	SANITIZE_ANY:=1
554	endif
555	ifeq ($(SANITIZE_UNDEFINED),1)
556	SANITIZE_ANY:=1
557	endif
558
559	# vectorization fails if sanitizer active where it normally succeeds -> disable check
560	ifeq ($(SANITIZE_ANY),1)
561	$(info disabling vectorize checks. would fail with sanitized code)
562	DISABLE_VECTORIZE_CHECK:=1
563	else
564	$(info no sanitizer enabled. reset: SANITIZE=0)
565	SANITIZE:=0
566	endif
567
568	# deactivate some bogus warnings occurring when sanitizing NDEBUG version
569	# (do not disable for future gcc-version >= 8.x -> test again when available)
570	ifeq ($(SANITIZE_ANY),1)
571	ifeq ($(DEBUG),0)
572	ifneq ('$(USE_GCC_80_OR_HIGHER)','yes')
573	extended_cpp_warnings += -Wno-format-overflow
574	extended_cpp_warnings += -Wno-maybe-uninitialized
575	endif
576	endif
577	endif
578
579	#---------------------- 32 or 64 bit
580
581	cross_cflags:=
582	cross_lflags:=
583	cross_clflags:=
584
585	ifeq ($(ARB_64),1)
586	dflags += -DARB_64
587	shared_cflags += -fPIC
588	CROSS_LIB:=# empty => autodetect below
589	ifeq ($(DARWIN),1)
590	cross_cflags += -arch x86_64
591	cross_lflags += -arch x86_64
592	cross_clflags += -arch x86_64
593	endif
594	else
595	CROSS_LIB:=/lib
596	endif
597
598	cflags += $(cross_cflags)
599	clflags += $(cross_clflags)
600
601	ifeq ('$(CROSS_LIB)','')
602	# autodetect libdir
603	ifeq ($(ARB_64),1)
604	CROSS_LIB:=$(shell (test -d /lib64 && echo lib64) \|\| echo lib)
605	else
606	CROSS_LIB:=$(shell (test -d /lib32 && echo lib32) \|\| echo lib)
607	endif
608	endif
609
610	#---------------------- unit tests
611
612	ifndef UNIT_TESTS
613	UNIT_TESTS=0#default is "no tests"
614	endif
615	ifeq ($(UNIT_TESTS),1)
616	dflags += -DUNIT_TESTS
617	UNIT_TESTER_LIB=UNIT_TESTER/UNIT_TESTER.a
618	else
619	UNIT_TESTER_LIB=
620	endif
621
622	#---------------------- use gcov
623
624	ifndef COVERAGE
625	COVERAGE=0#default is "no"
626	endif
627	ifneq ($(COVERAGE),0)
628	GCOV_FLAGS=--coverage
629	$(info disabling vectorize checks. would fail with COVERAGE on)
630	DISABLE_VECTORIZE_CHECK:=1
631	else
632	GCOV_FLAGS=
633	endif
634
635	cflags += $(GCOV_FLAGS)
636	clflags += $(GCOV_FLAGS)
637	cross_lflags += $(GCOV_FLAGS)
638
639	#---------------------- other flags
640
641	dflags += -D$(MACH) # define machine
642
643	ifeq ($(DARWIN),1)
644	shared_cflags += -fno-common
645	else
646	dflags += $(shell getconf LFS_CFLAGS)
647	endif
648
649	cflags += -pipe
650	cflags += -fmessage-length=0# dont wrap compiler output
651	cflags += -fshow-column# show columns
652	cflags += -funit-at-a-time
653	cflags += -fPIC
654	cflags += -fno-common# link all global data into one namespace
655	cflags += -fstrict-aliasing# gcc 3.4
656
657
658	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
659	cflags += -fno-diagnostics-show-caret#gcc 4.8 (4.7.?)
660	endif
661	#cflags += -save-temps# uncomment to see preprocessor output
662
663	#---------------------- various sanitizers
664	# There are some disabled tests in CORE/arb_misc.cxx@sanitizers
665	# which trigger sanitizer reports.
666
667	ifeq ($(SANITIZE_ANY),1)
668	cflags += -ggdb3 -fno-omit-frame-pointer
669	endif
670
671	# activate AddressSanitizer+LeakSanitizer?
672	ifeq ($(SANITIZE_ADDRESS),1)
673	cflags += -fsanitize=address
674	clflags += -fsanitize=address
675	dflags += -DLEAKS_SANITIZED
676	endif
677
678	# activate UndefinedBehaviorSanitizer?
679	ifeq ($(SANITIZE_UNDEFINED),1)
680	cflags += -fsanitize=undefined
681	clflags += -fsanitize=undefined
682	dflags += -DUNDEF_SANITIZED
683	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
684	# abort on runtime errors
685	cflags += -fno-sanitize-recover=all
686	endif
687	#
688	# Note: alignment-sanitizer is deactivated for ARBDB and PROBE!
689	ifeq ('$(DEBUG)','1')
690	ifeq ($(USE_GCC_MAJOR),4)
691	ifeq ($(USE_GCC_MINOR),9)
692	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),01)','')
693	# workaround https://gcc.gnu.org/bugzilla/show_bug.cgi?id=63531 for 4.9.0 + 4.9.1
694	# (problem is fixed in 4.9.2 release)
695	extended_cpp_warnings:=$(subst -Weffc++,,$(extended_cpp_warnings))
696	endif
697	endif
698	endif
699	endif
700	endif
701
702	#---------------------- X11 location
703
704	ifeq ($(DARWIN),1)
705	XHOME:=$(PREFIX)
706	else
707	ifeq ($(DEBIAN),1)
708	XHOME:=$(PREFIX)
709	else
710	XHOME:=/usr/X11R6
711	endif
712	endif
713
714	XINCLUDES ?= -I$(XHOME)/include
715	XLIBS ?= -L$(XHOME)/$(CROSS_LIB)
716	ifeq ($(DARWIN),1)
717	XINCLUDES += -I$(OSX_FW)/GLUT.framework/Headers -I$(OSX_FW)/OpenGL.framework/Headers -I$(OSX_SDK)/usr/include/krb5
718
719	XLIBS += -lXm -lpng -lz -lXt -lX11 -lXext -lXp -lXmu -lXi
720	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGL.dylib:$(OSX_FW_OPENGL)/libGL.dylib
721	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGLU.dylib:$(OSX_FW_OPENGL)/libGLU.dylib
722	else
723	XLIBS += -lXm -lXpm -lXt -lXext -lX11
724	endif
725
726	#---------------------- open GL
727
728	ifeq ($(OPENGL),1)
729	cflags += -DARB_OPENGL # activate OPENGL code
730	GL := gl # this is the name of the OPENGL base target
731	GL_LIB_SYS := -lGL -lGLU
732	GL_LIB_ARB := -L$(ARBHOME)/GL/glAW -lglAW
733
734	ifeq ($(DARWIN),1)
735	GL_LIB_SYS += -lpthread
736	endif
737
738	GL_PNGLIBS_ARB := -L$(ARBHOME)/GL/glpng -lglpng_arb
739	GL_PNGLIBS_SYS := -lpng
740
741	GLEWLIB := -lGLEW -lGLw
742	GLUTLIB := -lglut
743
744	GL_LIBS_SYS := $(GL_LIB_SYS) $(GL_PNGLIBS_SYS) $(GLEWLIB) $(GLUTLIB)
745	GL_LIBS_ARB := $(GL_LIB_ARB) $(GL_PNGLIBS_ARB)
746
747	RNA3D_LIB := RNA3D/RNA3D.a
748	else
749	GL_LIBS_SYS:=# no opengl -> no libs
750	GL_LIBS_ARB:=# no opengl -> no libs
751	GL:=# dont build ARB openGL libs
752
753	RNA3D_LIB :=
754	endif
755
756	RNA3D_LIB_4_DEPENDS := RNA3D/RNA3D.a
757
758	GL_LIBS:=$(GL_LIBS_ARB) $(GL_LIBS_SYS)
759
760	#---------------------- tiff lib:
761
762	TIFFLIBS := -ltiff
763
764	#---------------------- XML lib:
765
766	XMLLIBS := -lxerces-c
767
768	#---------------------- glib:
769
770	ARB_NEEDED_GLIB=glib-2.0
771
772	ARB_GLIB_INCLUDE:=$(strip $(shell pkg-config --cflags $(ARB_NEEDED_GLIB)))
773	ARB_GLIB_LIBS:=$(strip $(shell pkg-config --libs $(ARB_NEEDED_GLIB)))
774
775	#---------------------- basic libs:
776
777	SYSLIBS:=
778	ifeq ($(DARWIN),1)
779	SYSLIBS += -lstdc++
780	else
781	SYSLIBS += -lm $(ARB_GLIB_LIBS)
782	endif
783
784	#---------------------- system dependent commands
785
786	ifeq ($(DARWIN),1)
787	TIME:=gtime
788	else
789	TIME:=/usr/bin/time
790	endif
791
792	#---------------------- SSE vectorizer
793	# for details see SOURCE_TOOLS/vectorize.README
794
795	ifeq ($(DEBUG),0)
796	ifeq ($(USE_GCC_49_OR_HIGHER),yes)
797	ifeq ($(DISABLE_VECTORIZE_CHECK),0)
798	cflags += -fopt-info-vec
799	cflags += -fopt-info-vec-missed
800	ifeq ($(TRACE_MISSED_VECTORIZATIONS),1)
801	# Shows reasons for unsuccessful vectorization:
802	cflags += -ftree-vectorizer-verbose=10
803	POST_COMPILE += --dump-loop-optimization
804	ifeq ($(VECTORIZATION_CHECK_CANDIDATES),1)
805	$(error TRACE_MISSED_VECTORIZATIONS and VECTORIZATION_CHECK_CANDIDATES may not be used together!)
806	endif
807	endif
808	ifeq ($(VECTORIZATION_CHECK_CANDIDATES),1)
809	POST_COMPILE += --loop-optimization-candi
810	endif
811	POST_COMPILE += --check-loop-optimization
812	endif
813	else
814	ifeq ($(USE_GCC_48_OR_HIGHER),yes)
815	# no automatic vectorization-check for gcc<4.9.0
816	# -> uncomment the next 2 lines and grep the spam it will produce for 'vectorized.*loops'
817	# cflags += -fopt-info -fopt-info-vec-missed
818	# POST_COMPILE += --original
819	endif
820	endif
821	endif
822
823	#---------------------- stop early on broken flags/compiler combination
824
825	ifeq ($(DEBUG),0)
826	ifeq ($(SANITIZE_ANY),1)
827	ifeq ('$(COMPILER_VERSION)','4.9.1')
828	$(error compiling DEBUG=0 + SANITIZE!=0 crashes with gcc $(COMPILER_VERSION) (gcc 4.9.2 works))
829	endif
830	endif
831	endif
832
833	#---------------------- include symbols?
834
835	ifeq ($(TRACESYM),1)
836	ifeq ($(USE_CLANG),0)
837	cflags += -rdynamic
838	clflags += -rdynamic -Wl,--export-dynamic
839	endif
840	endif
841
842	#---------------------- warn about duplicate variable definitions
843
844	ifeq ($(DARWIN),1)
845	clflags += -Wl,-warn_commons
846	else
847	clflags += -Wl,--warn-common
848	endif
849
850	#---------------------- differences between linking executables and shared libs:
851
852	# executables:
853	ifeq ($(DARWIN),1)
854	blflags:=$(clflags)
855	else
856	blflags:=$(clflags) -Wl,--no-undefined
857	endif
858
859	# shared libraries
860	llflags:=$(clflags)
861
862	# dont use clflags below
863	clflags:=
864
865	# -------------------------------------------------------------------------
866	# Don't put any machine/version/etc conditionals below!
867	# (instead define variables above)
868	# -------------------------------------------------------------------------
869
870	cflags += -W -Wall $(dflags) $(extended_warnings)
871	cxxflags := $(extended_cpp_warnings)
872
873	# add CFLAGS + CPPFLAGS from environment for DEBIAN build
874	ifeq ($(DEBIAN),1)
875	cflags := $(CFLAGS) $(cflags)
876	cxxflags += $(CPPFLAGS)
877	endif
878
879	ifeq ('$(USE_CLANG)','1')
880	# none of the following standards works with clang3.3 (under linux) => dont use standard (as done before r15516)
881	# cxxflags += -std=gnu++11
882	# cxxflags += -std=gnu++0x
883	else
884	ifeq ('$(USE_GCC_60_OR_HIGHER)','yes')
885	cxxflags += -std=gnu++14# see also TEMPLATES/cxxforward.h@USE_Cxx14
886	else
887	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
888	cxxflags += -std=gnu++11# see also TEMPLATES/cxxforward.h@USE_Cxx11
889	else
890	# gcc versions between 4.3 (lowest supported) and <4.7
891	cxxflags += -std=gnu++0x
892	endif
893	endif
894	endif
895
896	LINK_STATIC_LIB := $(AR) -csq# link static lib
897	LINK_EXECUTABLE := $(A_CXX) $(blflags) -o# link executable (c++)
898
899	ifeq ($(LINK_STATIC),1)
900	SHARED_LIB_SUFFIX = a# static lib suffix
901	LINK_SHARED_LIB := $(LINK_STATIC_LIB)
902	else
903	SHARED_LIB_SUFFIX = so# shared lib suffix
904	LINK_SHARED_LIB := $(A_CXX) $(llflags) -shared -o# link shared lib
905	endif
906
907	ifeq ($(DARWIN),1)
908	lflags4perl:=
909	else
910	lflags4perl:=$(cross_lflags) -shared
911	endif
912
913	# delete variables unused below
914	blflags:=
915	llflags:=
916
917	# other used tools
918	MAKEDEPEND_PLAIN = makedepend
919	MAKEDEPEND = $(FORCEMASK);$(MAKEDEPEND_PLAIN)
920
921	#SEP:=--------------------------------------------------------------------------------
922	SEP=[`date +%M:%S.%N`] ------------------------------------------------
923	# to analyse timings run
924	# make -j9 clean; make -j9 all \| grep '^\[' \| sort
925	# make -j9 "TIMED_TARGET=perl" clean_timed_target \| grep '^\[' \| sort
926
927	# ------------------------------------------------------------ DYNLIBDEFS
928	# various dynamic library definitions for linking executables:
929	#
930	# SYSLIBS: system libraries needed by database lib
931	# ARBDB_LIB: database lib
932	# DBSYS_LIBS: executable using database (but no GUI)
933	# GUI_LIBS: executable using database and GUI (arb gui uses database)
934	#
935	# Note: definitions exported to sub-makefiles are described in SOURCE_TOOLS/parent_make.txt
936
937	CORE_LIB=-lCORE
938	ARBDB_LIB=-lARBDB $(CORE_LIB)
939	DBSYS_LIBS = $(ARBDB_LIB) $(SYSLIBS)
940
941	GUI_LIBS_PREFIX:=
942	ifeq ($(DARWIN),1)
943	# this seem to be added at wrong place, since opengl is only needed to link EDIT4
944	GUI_LIBS_PREFIX:=-framework GLUT -framework OpenGL
945	endif
946
947	GUI_LIBS=$(GUI_LIBS_PREFIX) $(DBSYS_LIBS) -lAWT -lWINDOW $(XLIBS)
948
949	LIBPATH = -L$(ARBHOME)/lib
950
951	DEST_LIB = lib
952	DEST_BIN = bin
953
954	CC_INCLUDES := -I. -I$(ARBHOME)/INCLUDE $(XINCLUDES) $(ARB_GLIB_INCLUDE)
955	CXX_INCLUDES := $(CC_INCLUDES)
956	MAKEDEPENDFLAGS := -- -DARB_OPENGL -DUNIT_TESTS -D__cplusplus -I. -Y$(ARBHOME)/INCLUDE
957
958	# ---------------------------------------
959	# wrap main()
960
961	use_ARB_main=$(ARBHOME)/SOURCE_TOOLS/arb_main_cpp.o
962	use_ARB_main_C=$(ARBHOME)/SOURCE_TOOLS/arb_main_c.o
963
964	# -----------------------------------------
965	# unique build-id
966	# - different for different calls of make
967	# - constant in recursive calls
968
969	ifndef ARBBID
970	ARBBID:=$(shell SOURCE_TOOLS/uniqueID.sh)
971	endif
972
973	# -----------------------------------------
974	# export variables to submakefiles
975
976	include SOURCE_TOOLS/export2sub
977
978	# do not define (exported) variables below this point
979
980	# -------------------------
981	# Main arb targets:
982	# -------------------------
983
984	first_target:
985	$(MAKE) checks
986	@echo $(SEP)
987	@echo 'Main targets:'
988	@echo ''
989	@echo ' all - Compile ARB + TOOLs + and copy shared libs + link foreign software'
990	@echo ' (That is most likely the target you want)'
991	@echo ''
992	@echo ' clean - remove generated files ("SUBDIR/SUBDIR.clean" to clean only SUBDIR)'
993	@echo ' rebuild - clean + all'
994	@echo ' cleanlinked - remove all binaries'
995	@echo ' relink - cleanlinked + all (=relink all from objects)'
996	@echo ''
997	@echo 'Some often used sub targets (make all makes them all):'
998	@echo ''
999	@echo ' arb - Just compile ARB (but none of the integrated tools)'
1000	@echo ' menus - create lib/gde/arb.menu from GDEHELP/ARB_GDEmenus.source'
1001	@echo ' perl - Compile the PERL XSUBS into lib/ARB.so and create links in lib to perl'
1002	@echo ' binlink - Create all links in the bin directory'
1003	@echo ''
1004	@echo 'Development targets:'
1005	@echo ''
1006	@echo ' depends - create or update dependencies ("SUBDIR/SUBDIR.depends" to update only SUBDIR)'
1007	@echo ' proto - create or update prototypes ("SUBDIR/SUBDIR.proto" to update only SUBDIR)'
1008	@echo ' tags - create tags for xemacs'
1009	@echo ' show - show available shortcuts (AKA subtargets)'
1010	@echo ' up - shortcut for depends+proto+tags'
1011	ifeq ($(UNIT_TESTS),1)
1012	@echo ' ut - only run tests'
1013	@echo ' "UNIT=..." oneunit - build one unit and run tests (see also UNIT_TESTER/Makefile.setup.local)'
1014	endif
1015	ifneq ($(SANITIZE),0)
1016	@echo ' sanitize - all + run arb_ntree with sanitizer (test.arb + execute _logged)'
1017	endif
1018	@echo ' modified - rebuild files modified in svn checkout (does touch)'
1019	@echo ' touch - touch files modified in svn checkout'
1020	@echo ''
1021	@echo 'Internal maintenance:'
1022	@echo ''
1023	@echo ' relinfo - show help on release targets'
1024	@echo ' tarfile - make rebuild and create arb version tarfile ("tarfile_quick" to skip rebuild)'
1025	@echo ' save - save all basic ARB sources into arbsrc_DATE ("savetest" to check filelist)'
1026	@echo ' patch - save svn diff to patchfile'
1027	@echo ' source_doc - create doxygen documentation'
1028	@echo ' relocated - rebuild partly (use when you have relocated ARBHOME)'
1029	@echo ' check_res - check resource usage'
1030	@echo ' dep_graph - Build dependency graphs'
1031	@echo ' clean_cov - Clean coverage results'
1032	@echo ''
1033	@echo ' clean_opengl_changed - clean after changing OPENGL setting in config.Makefile'
1034	@echo ' clean_checked_vect - clean units containing vectorization checks'
1035	@echo ' cleanRelinkable - similar to cleanlinked (but skips raxml8 to avoid rebuild)'
1036	@echo ''
1037	@echo ' post_commit_check - Checks whether'
1038	@echo ' * main make targets work,'
1039	@echo ' * dependencies and prototypes are up to date,'
1040	@echo ' * SVN-controlled files remain unaffected by called targets and'
1041	@echo ' * all generated files are ignored.'
1042	@echo ' (has to be called in a clean SVN checkout)'
1043	@echo $(SEP)
1044	@echo ''
1045
1046	relinfo:
1047	@echo ''
1048	@echo $(SEP)
1049	@echo 'Release targets:'
1050	@echo ''
1051	@echo ' inc_candi - increase RC candidate-number (only possible in "rc" branch, not needed for RC1)'
1052	@echo ' inc_patch - increase release patchlevel (only possible in "stable" branch)'
1053	@echo ' inc_minor - increase minor version number (only possible in "trunk")'
1054	@echo ' inc_major - increase MAJOR version number (only possible in "trunk")'
1055	@echo ''
1056	@echo ' show_version - show version tag'
1057	@echo ''
1058	@echo $(SEP)
1059	@echo ''
1060
1061	# auto-generate config.makefile:
1062
1063	config.makefile : config.makefile.template
1064	@echo --------------------------------------------------------------------------------
1065	ifeq ($(CONFIG_MAKEFILE_FOUND),)
1066	@cp $< $@
1067	@echo '$(ARBHOME)/$@:1: has been generated.'
1068	@echo 'Please edit $@ to configure your system!'
1069	@echo --------------------------------------------------------------------------------
1070	@false
1071	else
1072	@echo '$(ARBHOME)/$<:1: is more recent than'
1073	@echo '$(ARBHOME)/$@:1:'
1074	@ls -al config.makefile*
1075	@echo --------------------------------------------------------------------------------
1076	@echo "Updating $@ (if this fails, check manually)"
1077	SOURCE_TOOLS/update_config_makefile.pl
1078	@echo "Sucessfully updated $@"
1079	@echo --------------------------------------------------------------------------------
1080	@ls -al config.makefile*
1081	@echo --------------------------------------------------------------------------------
1082	@echo "Diff to your old config.makefile:"
1083	@echo --------------------------------------------------------------------------------
1084	-diff $@.bak $@
1085	@echo --------------------------------------------------------------------------------
1086	endif
1087
1088	# check if everything is configured correctly
1089
1090	check_DEVELOPER:
1091	ifndef DEVELOPER
1092	@echo 'config.makefile:1: DEVELOPER not defined'
1093	@false
1094	endif
1095
1096	check_DEBUG:
1097	ifndef dflags
1098	@echo 'config.makefile:1: DEBUG has to be defined. Valid values are 0 and 1'
1099	@false
1100	endif
1101
1102	check_ARB_64:
1103	ifndef ARB_64
1104	@echo 'config.makefile:1: ARB_64 has to be defined. Valid values are 0 and 1'
1105	@false
1106	endif
1107
1108	# ---------------------------------------- check gcc version
1109
1110	COMPILER_BROKEN:=0
1111
1112	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.6.4')
1113	COMPILER_BROKEN:=1
1114	endif
1115	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.8.0')
1116	COMPILER_BROKEN:=1
1117	endif
1118
1119	check_same_GCC_VERSION:
1120	$(ARBHOME)/SOURCE_TOOLS/check_same_compiler_version.pl $(COMPILER_NAME) $(COMPILER_VERSION_ALLOWED)
1121
1122	check_GCC_VERSION:
1123	@echo 'Compiler version check:'
1124	# see .@ALLOWED_gcc_VERSIONS
1125	ifeq ('$(COMPILER_VERSION_ALLOWED)', '')
1126	@echo " - Your compiler is '$(COMPILER_NAME)' version '$(COMPILER_VERSION)'"
1127	@echo ' This version is not in the list of supported $(COMPILER_NAME)-versions:'
1128	@$(foreach version,$(ALLOWED_COMPILER_VERSIONS),echo ' * $(version)';)
1129	@echo ' - You may either ..'
1130	@echo ' - add your version to ALLOWED_$(COMPILER_NAME)_VERSIONS in the Makefile and try it out or'
1131	@echo ' - switch to one of the allowed versions (see arb_README_gcc.txt for installing'
1132	@echo ' a different version of gcc)'
1133	$(error Unsupported compiler '$(COMPILER_NAME)' version '$(COMPILER_VERSION)')
1134	else
1135	ifeq ($(COMPILER_BROKEN),1)
1136	$(error compilation refused for $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)'. Refer to http://bugs.arb-home.de/wiki/GccVersionInfo for details.)
1137	else
1138	@echo " - Supported $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)' detected - fine!"
1139	@echo ''
1140	ifeq ($(USE_CLANG),1)
1141	@echo "Dump clang version:"
1142	$(A_CXX) -v
1143	endif
1144	$(MAKE) check_same_GCC_VERSION
1145	endif
1146	endif
1147
1148	#---------------------- check ARBHOME
1149
1150	# use arb_INSTALL.txt to determine whether ARBHOME points to correct directory
1151	ARB_INSTALL_FOUND=$(wildcard $(ARBHOME)/arb_INSTALL.txt)
1152
1153	check_ARBHOME:
1154	ifeq ($(strip $(ARB_INSTALL_FOUND)),)
1155	@echo ------------------------------------------------------------
1156	@echo "ARBHOME is set to '$(ARBHOME)'"
1157	@echo "The environment variable ARBHOME has to point to the top arb source directory."
1158	@echo "If you use bash enter:"
1159	@echo " export ARBHOME='`pwd`'"
1160	@echo ------------------------------------------------------------
1161	@false
1162	endif
1163
1164	ARB_PATH_SET=$(findstring $(ARBHOME)/bin,$(PATH))
1165
1166	check_PATH: check_ARBHOME
1167	ifeq ($(strip $(ARB_PATH_SET)),)
1168	@echo ------------------------------------------------------------
1169	@echo "The environment variable PATH has to contain $(ARBHOME)/bin"
1170	@echo "If you use bash enter:"
1171	@echo ' export PATH=$$ARBHOME/bin:$$PATH'
1172	@echo ------------------------------------------------------------
1173	@false
1174	endif
1175
1176	check_TOOLS:
1177	@util/arb_check_build_env.pl \
1178	"$(A_CC)" \
1179	"$(A_CXX)" \
1180	"$(MAKEDEPEND_PLAIN)" \
1181	"$(LINK_SHARED_LIB)" \
1182	"$(LINK_SHARED_LIB)" \
1183
1184	check_ENVIRONMENT : check_PATH check_TOOLS
1185	@echo "-------------------- Environment [start]"
1186	@echo "ARBHOME='$(ARBHOME)'"
1187	@echo "PATH='$(PATH)'"
1188	@echo "LD_LIBRARY_PATH='$(LD_LIBRARY_PATH)'"
1189	@echo "-------------------- Environment [end]"
1190
1191	check_tabs: check_setup
1192	ifeq ($(DEBUG),1)
1193	@SOURCE_TOOLS/tabBrake.pl
1194	endif
1195
1196	force_tab_check:
1197	@touch -t 198001010000 SOURCE_TOOLS/stamp.tabBrake
1198	@$(MAKE) check_tabs
1199
1200
1201	# ---------------------
1202
1203	check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION
1204	@echo Your setup seems to be ok.
1205
1206	checks: check_setup check_tabs
1207	@rm -f SOURCE_TOOLS/postcompile.sav
1208
1209
1210	# end test section ------------------------------
1211
1212	# ---------------------------------------
1213	# List of standard top level directories
1214	#
1215	# sub-makefiles have to define the targets
1216	# - 'depends' and
1217	# - 'clean'
1218	#
1219	# when adding new libraries/subdirs here, also add a dependency vs 'links' or 'links_non_perl' in .@DD_links_non_perl
1220
1221	TL_ARCHIVES = \
1222	AISC/AISC.a \
1223	ARB_GDE/ARB_GDE.a \
1224	AWTC/AWTC.a \
1225	AWTI/AWTI.a \
1226	CONSENSUS_TREE/CONSENSUS_TREE.a \
1227	CONVERTALN/CONVERTALN.a \
1228	DBSERVER/DBSERVER.a \
1229	DIST/DIST.a \
1230	EDIT4/EDIT4.a \
1231	EISPACK/EISPACK.a \
1232	GENOM/GENOM.a \
1233	GENOM_IMPORT/GENOM_IMPORT.a \
1234	ISLAND_HOPPING/ISLAND_HOPPING.a \
1235	MERGE/MERGE.a \
1236	MULTI_PROBE/MULTI_PROBE.a \
1237	NALIGNER/NALIGNER.a \
1238	NAMES/NAMES.a \
1239	NAMES_COM/server.a \
1240	NTREE/NTREE.a \
1241	PARSIMONY/PARSIMONY.a \
1242	PHYLO/PHYLO.a \
1243	PRIMER_DESIGN/PRIMER_DESIGN.a \
1244	PROBE/PROBE.a \
1245	PROBE_COM/server.a \
1246	PROBE_DESIGN/PROBE_DESIGN.a \
1247	$(RNA3D_LIB) \
1248	RNACMA/RNACMA.a \
1249	SECEDIT/SECEDIT.a \
1250	SEQ_QUALITY/SEQ_QUALITY.a \
1251	SERVERCNTRL/SERVERCNTRL.a \
1252	STAT/STAT.a \
1253	TREEGEN/TREEGEN.a \
1254	WETC/WETC.a \
1255	XML/XML.a \
1256
1257	TL_SHARED_ARCHIVES = \
1258	ARBDB/libARBDB.so \
1259	CORE/libCORE.so \
1260	AWT/libAWT.so \
1261	WINDOW/libWINDOW.so \
1262
1263	TL_ARCHIV_COLLECTIONS = \
1264	SL/SL.archColl \
1265
1266	TL_TOOLS_COLLECTIONS = \
1267	AISC_MKPTPS/AISC_MKPTPS.toolColl \
1268	TOOLS/TOOLS.toolColl \
1269	PERLTOOLS/PERLTOOLS.toolColl \
1270	PROBE_SET/PROBE_SET.toolColl \
1271	READSEQ/READSEQ.toolColl \
1272
1273	RECURSIVE_SUBS = \
1274	GDE/GDE.sub \
1275	UNIT_TESTER/UNIT_TESTER.sub \
1276
1277	SUBDIRS = \
1278	$(RECURSIVE_SUBS) \
1279	$(TL_ARCHIVES:.a=.sub) \
1280	$(TL_SHARED_ARCHIVES:.so=.sub) \
1281	$(TL_ARCHIV_COLLECTIONS:.archColl=.sub) \
1282	$(TL_TOOLS_COLLECTIONS:.toolColl=.sub) \
1283
1284	# sub directories inside TL_ARCHIV_COLLECTIONS
1285	CL_ARCH_DIRS = $(foreach coll,$(TL_ARCHIV_COLLECTIONS),$(shell find $(dir $(coll)) -maxdepth 1 -mindepth 1 -type d))
1286
1287	# archives inside CL_ARCH_DIRS:
1288	CL_ARCHIVES = $(foreach adir,$(CL_ARCH_DIRS),$(dir $(adir))$(notdir $(adir))/$(notdir $(adir)).a)
1289
1290	# -----------------------
1291	# library packets
1292
1293	ARCHS_CLIENT_PROBE = PROBE_COM/client.a
1294	ARCHS_CLIENT_NAMES = NAMES_COM/client.a
1295
1296	ARCHS_MAKEBIN = AISC_MKPTPS/AISC_MKPTPS.a AISC/AISC.a
1297
1298	# communication libs need aisc and aisc_mkpts:
1299
1300	AISC/AISC.dummy: proto_tools
1301
1302	comtools: AISC/AISC.dummy
1303
1304	ARCHS_SEQUENCE = \
1305	SL/SEQUENCE/SEQUENCE.a \
1306	SL/ALIVIEW/ALIVIEW.a \
1307	SL/PRONUC/PRONUC.a \
1308
1309	ARCHS_TREE = \
1310	SL/ARB_TREE/ARB_TREE.a \
1311	SL/FILTER/FILTER.a \
1312	$(ARCHS_SEQUENCE) \
1313
1314	# parsimony tree (used by NTREE, PARSIMONY, STAT(->EDIT4), DIST(obsolete!))
1315	ARCHS_AP_TREE = \
1316	SL/AP_TREE/AP_TREE.a \
1317	$(ARCHS_TREE) \
1318
1319	# --------------------------------------------------------------------------------
1320	# dependencies for linking shared libs
1321
1322	link_core: core
1323	link_db: db link_core
1324	link_aw: aw link_db
1325	link_awt: awt link_aw
1326
1327	#***************************************************************************************
1328	# Individual_Programs_Section
1329	#***************************************************************************************
1330
1331	arbmainwrapper:
1332	$(MAKE) -C SOURCE_TOOLS -r mainwrapper
1333
1334
1335	#********************************* arb_ntree ************************************
1336	NTREE = bin/arb_ntree
1337	ARCHS_NTREE = \
1338	NTREE/NTREE.a \
1339	ARB_GDE/ARB_GDE.a \
1340	SL/GROUP_SEARCH/GROUP_SEARCH.a \
1341	SL/SAICALC/SAICALC.a \
1342	SL/DB_UI/DB_UI.a \
1343	AWTC/AWTC.a \
1344	AWTI/AWTI.a \
1345	CONSENSUS_TREE/CONSENSUS_TREE.a \
1346	GENOM_IMPORT/GENOM_IMPORT.a \
1347	GENOM/GENOM.a \
1348	MERGE/MERGE.a \
1349	MULTI_PROBE/MULTI_PROBE.a \
1350	PRIMER_DESIGN/PRIMER_DESIGN.a \
1351	PROBE_DESIGN/PROBE_DESIGN.a \
1352	SEQ_QUALITY/SEQ_QUALITY.a \
1353	SERVERCNTRL/SERVERCNTRL.a \
1354	SL/ALILINK/ALILINK.a \
1355	SL/AW_NAME/AW_NAME.a \
1356	SL/CONSENSUS/CONSENSUS.a \
1357	SL/DB_SCANNER/DB_SCANNER.a \
1358	SL/DB_QUERY/DB_QUERY.a \
1359	SL/QUERY/QUERY.a \
1360	SL/SEQIO/SEQIO.a \
1361	STAT/STAT.a \
1362	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1363	SL/HELIX/HELIX.a \
1364	SL/REGEXPR/REGEXPR.a \
1365	SL/REFENTRIES/REFENTRIES.a \
1366	SL/NDS/NDS.a \
1367	SL/ITEM_SHADER/ITEM_SHADER.a \
1368	SL/ITEMS/ITEMS.a \
1369	SL/INSDEL/INSDEL.a \
1370	SL/LOCATION/LOCATION.a \
1371	SL/MACROS/MACROS.a \
1372	SL/PVP/PVP.a \
1373	SL/TRANSLATE/TRANSLATE.a \
1374	SL/TREEDISP/TREEDISP.a \
1375	SL/TREE_ADMIN/TREE_ADMIN.a \
1376	SL/TREE_READ/TREE_READ.a \
1377	SL/TREE_WRITE/TREE_WRITE.a \
1378	SL/XFERGUI/XFERGUI.a \
1379	SL/XFERSET/XFERSET.a \
1380	XML/XML.a \
1381	$(ARCHS_AP_TREE) \
1382
1383	ARCHS_NTREE_ALL = $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(XMLLIBS)
1384
1385	$(NTREE): $(ARCHS_NTREE:.a=.dummy) link_awt
1386	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NTREE_ALL) \|\| ( \
1387	echo "$(SEP) Link $@"; \
1388	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE_ALL)" ; \
1389	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE_ALL) && \
1390	echo "$(SEP) Link $@ [done]"; \
1391	)
1392
1393	#********************************* arb_edit4 ************************************
1394	EDIT4 = bin/arb_edit4
1395
1396	ARCHS_EDIT4 := \
1397	EDIT4/EDIT4.a \
1398	ARB_GDE/ARB_GDE.a \
1399	SL/FAST_ALIGNER/FAST_ALIGNER.a \
1400	AWTC/AWTC.a \
1401	ISLAND_HOPPING/ISLAND_HOPPING.a \
1402	SECEDIT/SECEDIT.a \
1403	SERVERCNTRL/SERVERCNTRL.a \
1404	SL/AW_HELIX/AW_HELIX.a \
1405	SL/AW_NAME/AW_NAME.a \
1406	SL/CONSENSUS/CONSENSUS.a \
1407	SL/ITEMS/ITEMS.a \
1408	STAT/STAT.a \
1409	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1410	SL/HELIX/HELIX.a \
1411	SL/TRANSLATE/TRANSLATE.a \
1412	SL/MACROS/MACROS.a \
1413	SL/NDS/NDS.a \
1414	$(ARCHS_AP_TREE) \
1415	XML/XML.a \
1416
1417	ifeq ($(OPENGL),1)
1418	ARCHS_EDIT4 += RNA3D/RNA3D.a
1419	endif
1420
1421	ARCHS_EDIT4_ALL = $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4)
1422
1423	LIBS_EDIT4 := $(GL_LIBS)
1424
1425	$(EDIT4): $(ARCHS_EDIT4:.a=.dummy) link_awt
1426	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_EDIT4_ALL) \|\| ( \
1427	echo "$(SEP) Link $@"; \
1428	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4_ALL)" ; \
1429	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4_ALL) && \
1430	echo "$(SEP) Link $@ [done]"; \
1431	)
1432
1433	#********************************* arb_rnacma ************************************
1434	RNACMA = bin/arb_rnacma
1435	ARCHS_RNACMA = \
1436	RNACMA/RNACMA.a \
1437
1438	ARCHS_RNACMA_ALL = $(ARCHS_RNACMA) $(DBSYS_LIBS)
1439
1440	$(RNACMA) : $(ARCHS_RNACMA:.a=.dummy) link_db
1441	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_RNACMA_ALL) \|\| ( \
1442	echo "$(SEP) Link $@"; \
1443	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_RNACMA_ALL)"; \
1444	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_RNACMA_ALL) && \
1445	echo "$(SEP) Link $@ [done]"; \
1446	)
1447
1448	#********************************* arb_wetc ************************************
1449	WETC = bin/arb_wetc
1450	ARCHS_WETC = \
1451	WETC/WETC.a \
1452	SL/HELIX/HELIX.a \
1453	SL/FILTER/FILTER.a \
1454	XML/XML.a \
1455
1456	ARCHS_WETC_ALL = $(ARCHS_WETC) $(GUI_LIBS)
1457
1458	$(WETC): $(ARCHS_WETC:.a=.dummy) link_awt
1459	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_WETC_ALL) \|\| ( \
1460	echo "$(SEP) Link $@"; \
1461	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC_ALL)" ; \
1462	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC_ALL) && \
1463	echo "$(SEP) Link $@ [done]"; \
1464	)
1465
1466	#********************************* arb_dist ************************************
1467	DIST = bin/arb_dist
1468	ARCHS_DIST = \
1469	DIST/DIST.a \
1470	CONSENSUS_TREE/CONSENSUS_TREE.a \
1471	EISPACK/EISPACK.a \
1472	SERVERCNTRL/SERVERCNTRL.a \
1473	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1474	SL/HELIX/HELIX.a \
1475	SL/MATRIX/MATRIX.a \
1476	SL/MACROS/MACROS.a \
1477	SL/NDS/NDS.a \
1478	SL/ITEMS/ITEMS.a \
1479	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.a \
1480	XML/XML.a \
1481	$(ARCHS_AP_TREE) \
1482
1483	ARCHS_DIST_ALL = $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS)
1484
1485	$(DIST): $(ARCHS_DIST:.a=.dummy) link_awt
1486	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_DIST_ALL) \|\| ( \
1487	echo "$(SEP) Link $@"; \
1488	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST_ALL)" ; \
1489	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST_ALL) && \
1490	echo "$(SEP) Link $@ [done]"; \
1491	)
1492
1493	#********************************* arb_pars ************************************
1494	PARSIMONY = bin/arb_pars
1495	ARCHS_PARSIMONY = \
1496	PARSIMONY/PARSIMONY.a \
1497	SERVERCNTRL/SERVERCNTRL.a \
1498	SL/AW_NAME/AW_NAME.a \
1499	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1500	SL/HELIX/HELIX.a \
1501	SL/MACROS/MACROS.a \
1502	SL/NDS/NDS.a \
1503	SL/ITEMS/ITEMS.a \
1504	SL/TRANSLATE/TRANSLATE.a \
1505	SL/TREEDISP/TREEDISP.a \
1506	XML/XML.a \
1507	$(ARCHS_AP_TREE) \
1508
1509	ARCHS_PARSIMONY_ALL = $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS)
1510
1511	$(PARSIMONY): $(ARCHS_PARSIMONY:.a=.dummy) link_awt
1512	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_PARSIMONY_ALL) \|\| ( \
1513	echo "$(SEP) Link $@"; \
1514	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY_ALL)" ; \
1515	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY_ALL) && \
1516	echo "$(SEP) Link $@ [done]"; \
1517	)
1518
1519	#********************************* arb_convert_aln ************************************
1520	CONVERT_ALN = bin/arb_convert_aln
1521	ARCHS_CONVERT_ALN = \
1522	CONVERTALN/CONVERTALN.a \
1523
1524	ARCHS_CONVERT_ALN_ALL = $(ARCHS_CONVERT_ALN) $(DBSYS_LIBS)
1525
1526	$(CONVERT_ALN) : $(ARCHS_CONVERT_ALN:.a=.dummy) link_db
1527	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_CONVERT_ALN_ALL) \|\| ( \
1528	echo "$(SEP) Link $@"; \
1529	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN_ALL)"; \
1530	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN_ALL) && \
1531	echo "$(SEP) Link $@ [done]"; \
1532	)
1533
1534	#********************************* arb_treegen ************************************
1535
1536	TREEGEN = bin/arb_treegen
1537	ARCHS_TREEGEN = \
1538	TREEGEN/TREEGEN.a \
1539
1540	ARCHS_TREEGEN_ALL = $(ARCHS_TREEGEN)
1541
1542	$(TREEGEN) : $(ARCHS_TREEGEN:.a=.dummy)
1543	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main_C) $(ARCHS_TREEGEN_ALL) \|\| ( \
1544	echo "$(SEP) Link $@"; \
1545	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN_ALL)" ; \
1546	$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN_ALL) && \
1547	echo "$(SEP) Link $@ [done]"; \
1548	)
1549
1550	#********************************* arb_naligner ************************************
1551	NALIGNER = bin/arb_naligner
1552	ARCHS_NALIGNER = \
1553	NALIGNER/NALIGNER.a \
1554	SERVERCNTRL/SERVERCNTRL.a \
1555	SL/HELIX/HELIX.a \
1556
1557	ARCHS_NALIGNER_ALL = $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(DBSYS_LIBS)
1558
1559	$(NALIGNER): $(ARCHS_NALIGNER:.a=.dummy) link_db
1560	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NALIGNER_ALL) \|\| ( \
1561	echo "$(SEP) Link $@"; \
1562	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER_ALL)" ; \
1563	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER_ALL) && \
1564	echo "$(SEP) Link $@ [done]"; \
1565	)
1566
1567	#********************************* arb_phylo ************************************
1568	PHYLO = bin/arb_phylo
1569	ARCHS_PHYLO = \
1570	PHYLO/PHYLO.a \
1571	SL/HELIX/HELIX.a \
1572	SL/FILTER/FILTER.a \
1573	SL/MACROS/MACROS.a \
1574	XML/XML.a \
1575
1576	ARCHS_PHYLO_ALL = $(ARCHS_PHYLO) $(GUI_LIBS)
1577
1578	$(PHYLO): $(ARCHS_PHYLO:.a=.dummy) link_awt
1579	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_PHYLO_ALL) \|\| ( \
1580	echo "$(SEP) Link $@"; \
1581	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO_ALL)" ; \
1582	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO_ALL) && \
1583	echo "$(SEP) Link $@ [done]"; \
1584	)
1585
1586	#***************************************************************************************
1587	# SERVER SECTION
1588	#***************************************************************************************
1589
1590	#********************************* arb_db_server ************************************
1591	DBSERVER = bin/arb_db_server
1592	ARCHS_DBSERVER = \
1593	DBSERVER/DBSERVER.a \
1594	SERVERCNTRL/SERVERCNTRL.a \
1595
1596	ARCHS_DBSERVER_ALL = $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS)
1597
1598	$(DBSERVER): $(ARCHS_DBSERVER:.a=.dummy) link_db
1599	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_DBSERVER_ALL) \|\| ( \
1600	echo "$(SEP) Link $@"; \
1601	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER_ALL)" ; \
1602	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER_ALL) && \
1603	echo "$(SEP) Link $@ [done]"; \
1604	)
1605
1606	#********************************* arb_pt_server ************************************
1607	PROBE = bin/arb_pt_server
1608
1609	ARCHS_PROBE_DEPEND = \
1610	PROBE/PROBE.a \
1611	SL/PTCLEAN/PTCLEAN.a \
1612	SERVERCNTRL/SERVERCNTRL.a \
1613	SL/HELIX/HELIX.a \
1614
1615	ARCHS_PROBE_ALL = $(ARCHS_PROBE_DEPEND) $(ARCHS_CLIENT_PROBE) $(ARBDB_LIB) $(SYSLIBS)
1616
1617	$(PROBE): $(ARCHS_PROBE_DEPEND:.a=.dummy) link_db
1618	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) config.makefile $(ARCHS_PROBE_ALL) \|\| ( \
1619	echo "$(SEP) Link $@"; \
1620	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_ALL)" ; \
1621	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_ALL) && \
1622	echo "$(SEP) Link $@ [done]"; \
1623	)
1624
1625	#********************************* arb_name_server ************************************
1626	NAMES = bin/arb_name_server
1627	ARCHS_NAMES = \
1628	NAMES/NAMES.a \
1629	SERVERCNTRL/SERVERCNTRL.a \
1630
1631	ARCHS_NAMES_ALL = $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS)
1632
1633	$(NAMES): $(ARCHS_NAMES:.a=.dummy) link_db
1634	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NAMES_ALL) \|\| ( \
1635	echo "$(SEP) Link $@"; \
1636	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES_ALL)" ; \
1637	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES_ALL) && \
1638	echo "$(SEP) Link $@ [done]"; \
1639	)
1640
1641	#********************************* SHARED LIBRARIES SECTION ************************************
1642
1643	prepare_libdir: addlibs
1644
1645	addlibs:
1646	(perl $(ARBHOME)/SOURCE_TOOLS/provide_libs.pl \
1647	"arbhome=$(ARBHOME)" \
1648	"opengl=$(OPENGL)" \
1649	"link_static=$(LINK_STATIC)" \
1650	)
1651
1652	#***************************************************************************************
1653	# Recursive calls to sub-makefiles
1654	#***************************************************************************************
1655
1656	%.depends:
1657	@cp -p $(@D)/Makefile $(@D)/Makefile.old # save old Makefile
1658	@$(MAKE) -C $(@D) -r \
1659	"AUTODEPENDS=1" \
1660	"MAIN=nothing" \
1661	"cflags=noCflagsHere_use_MAKEDEPENDFLAGS" \
1662	"cxxflags=noCxxflagsHere_use_MAKEDEPENDFLAGS" \
1663	depends
1664	@grep "^# DO NOT DELETE" $(@D)/Makefile >/dev/null
1665	@cat $(@D)/Makefile \
1666	\| SOURCE_TOOLS/fix_depends.pl "(from main)" \
1667	>$(@D)/Makefile.2
1668	@mv $(@D)/Makefile.old $(@D)/Makefile # restore old Makefile
1669	@$(ARBHOME)/SOURCE_TOOLS/mv_if_diff $(@D)/Makefile.2 $(@D)/Makefile # update Makefile if changed
1670
1671	%.proto:
1672	@($(MAKE) -C $(@D) \
1673	"AUTODEPENDS=0" \
1674	"MAIN=nothing" \
1675	"cflags=noCflags" \
1676	"cxxflags=noCxxflags" \
1677	proto 2>&1 ) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
1678
1679	%.clean:
1680	@$(MAKE) -C $(@D) \
1681	"AUTODEPENDS=0" \
1682	"MAIN=nothing" \
1683	"cflags=noCflags" \
1684	"cxxflags=noCxxflags" \
1685	clean
1686
1687
1688	# stop wrong targets:
1689	target_is_missing_lib_prefix:
1690	@echo "Error: Denied to build shared library target with missing 'lib'-prefix"
1691	false
1692
1693	ARBDB/ARBDB.dummy: target_is_missing_lib_prefix
1694	CORE/CORE.dummy: target_is_missing_lib_prefix
1695	AWT/AWT.dummy: target_is_missing_lib_prefix
1696	WINDOW/WINDOW.dummy: target_is_missing_lib_prefix
1697
1698	# rule to generate main target (normally a library):
1699	# @@@ check effect of setting LANG=C below
1700	%.dummy:
1701	@( export ID=$$$$; LANG=C; \
1702	(( \
1703	echo "$(SEP) Make $(@D)"; \
1704	$(MAKE) -C $(@D) -r \
1705	"AUTODEPENDS=1" \
1706	"MAIN=$(@F:.dummy=.a)" \
1707	"cflags=$(cflags) -DIN_ARB_$(subst /,_,$(@D))" \
1708	&& \
1709	echo "$(SEP) Make $(@D) [done]"; \
1710	) >$(@D).$$ID.log 2>&1 && (cat $(@D).$$ID.log;rm $(@D).$$ID.log)) \|\| (cat $(@D).$$ID.log;rm $(@D).$$ID.log;false))
1711
1712	# Additional dependencies for subtargets:
1713
1714	PROBE_COM/PROBE_COM.dummy : comtools
1715	NAMES_COM/NAMES_COM.dummy : comtools
1716
1717	com: PROBE_COM/PROBE_COM.dummy NAMES_COM/NAMES_COM.dummy
1718
1719	# stop wrong more targets:
1720	PROBE_COM/server.dummy:
1721	@echo Unwanted request to make target $<
1722	false
1723
1724	PROBE_COM/client.dummy:
1725	@echo Unwanted request to make target $<
1726	false
1727
1728	NAMES_COM/server.dummy:
1729	@echo Unwanted request to make target $<
1730	false
1731
1732	NAMES_COM/client.dummy:
1733	@echo Unwanted request to make target $<
1734	false
1735
1736
1737	ARBDB/libARBDB.dummy: links
1738	CORE/libCORE.dummy: links
1739
1740	PERLTOOLS/PERLTOOLS.dummy: core db
1741
1742	# all subdirs perl not depends on go here (ADD_links_non_perl)
1743	AWT/libAWT.dummy: links_non_perl
1744	AWTI/AWTI.dummy: links_non_perl
1745	CONSENSUS_TREE/CONSENSUS_TREE.dummy: links_non_perl
1746	CONVERTALN/CONVERTALN.dummy: links_non_perl
1747	DBSERVER/DBSERVER.dummy: links_non_perl
1748	DIST/DIST.dummy: links_non_perl
1749	EDIT4/EDIT4.dummy: links_non_perl com
1750	EISPACK/EISPACK.dummy: links_non_perl
1751	GDE/GDE.dummy: links_non_perl
1752	GENOM/GENOM.dummy: links_non_perl
1753	GENOM_IMPORT/GENOM_IMPORT.dummy: links_non_perl
1754	ISLAND_HOPPING/ISLAND_HOPPING.dummy: links_non_perl
1755	MERGE/MERGE.dummy: links_non_perl
1756	NTREE/NTREE.dummy: links_non_perl
1757	PARSIMONY/PARSIMONY.dummy: links_non_perl
1758	PHYLO/PHYLO.dummy: links_non_perl
1759	PRIMER_DESIGN/PRIMER_DESIGN.dummy: links_non_perl
1760	PROBE_SET/PROBE_SET.dummy: links_non_perl link_db
1761	READSEQ/READSEQ.dummy: links_non_perl
1762	RNACMA/RNACMA.dummy: links_non_perl header_libs
1763	SECEDIT/SECEDIT.dummy: links_non_perl
1764	SEQ_QUALITY/SEQ_QUALITY.dummy: links_non_perl
1765	SERVERCNTRL/SERVERCNTRL.dummy: links_non_perl com
1766	SL/ALILINK/ALILINK.dummy: links_non_perl
1767	SL/ALIVIEW/ALIVIEW.dummy: links_non_perl
1768	SL/AP_TREE/AP_TREE.dummy: links_non_perl
1769	SL/ARB_TREE/ARB_TREE.dummy: links_non_perl
1770	SL/AW_HELIX/AW_HELIX.dummy: links_non_perl
1771	SL/CONSENSUS/CONSENSUS.dummy: links_non_perl
1772	SL/DB_QUERY/DB_QUERY.dummy: links_non_perl
1773	SL/DB_SCANNER/DB_SCANNER.dummy: links_non_perl
1774	SL/DB_UI/DB_UI.dummy: links_non_perl
1775	SL/FAST_ALIGNER/FAST_ALIGNER.dummy: links_non_perl
1776	SL/FILTER/FILTER.dummy: links_non_perl
1777	SL/FILTSEQEXP/FILTSEQEXP.dummy: links_non_perl
1778	SL/GROUP_SEARCH/GROUP_SEARCH.dummy: links_non_perl
1779	SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy: links_non_perl
1780	SL/HELIX/HELIX.dummy: links_non_perl
1781	SL/INSDEL/INSDEL.dummy: links_non_perl
1782	SL/ITEM_SHADER/ITEM_SHADER.dummy: links_non_perl
1783	SL/ITEMS/ITEMS.dummy: links_non_perl
1784	SL/LOCATION/LOCATION.dummy: links_non_perl
1785	SL/MACROS/MACROS.dummy: links_non_perl
1786	SL/MATRIX/MATRIX.dummy: links_non_perl
1787	SL/NDS/NDS.dummy: links_non_perl
1788	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.dummy: links_non_perl
1789	SL/PRONUC/PRONUC.dummy: links_non_perl
1790	SL/PTCLEAN/PTCLEAN.dummy: links_non_perl link_db
1791	SL/PVP/PVP.dummy: links_non_perl
1792	SL/QUERY/QUERY.dummy: links_non_perl link_db
1793	SL/REFENTRIES/REFENTRIES.dummy: links_non_perl
1794	SL/REGEXPR/REGEXPR.dummy: links_non_perl
1795	SL/SAICALC/SAICALC.dummy: links_non_perl
1796	SL/SEQIO/SEQIO.dummy: links_non_perl
1797	SL/SEQUENCE/SEQUENCE.dummy: links_non_perl
1798	SL/TRANSLATE/TRANSLATE.dummy: links_non_perl
1799	SL/TREE_ADMIN/TREE_ADMIN.dummy: links_non_perl
1800	SL/TREE_READ/TREE_READ.dummy: links_non_perl
1801	SL/TREE_WRITE/TREE_WRITE.dummy: links_non_perl
1802	SL/TREEDISP/TREEDISP.dummy: links_non_perl
1803	SL/XFERGUI/XFERGUI.dummy: links_non_perl
1804	SL/XFERSET/XFERSET.dummy: links_non_perl
1805	STAT/STAT.dummy: links_non_perl
1806	TREEGEN/TREEGEN.dummy: links_non_perl
1807	WETC/WETC.dummy: links_non_perl
1808	WINDOW/libWINDOW.dummy: links_non_perl
1809	XML/XML.dummy: links_non_perl
1810
1811	ifeq ($(OPENGL),1)
1812	GL/glAW/glAW.dummy: links_non_perl
1813	GL/glpng/glpng.dummy: links_non_perl
1814	GL/GL.dummy: GL/glAW/glAW.dummy GL/glpng/glpng.dummy
1815	RNA3D/RNA3D.dummy: links_non_perl gl
1816	endif
1817
1818	UNIT_TESTER/UNIT_TESTER.dummy: link_db \
1819	SERVERCNTRL/SERVERCNTRL.dummy \
1820
1821	# see also TOOLS/Makefile@TOOLSLIBDEPENDS
1822	TOOLS/TOOLS.dummy : links_non_perl link_db \
1823	CONSENSUS_TREE/CONSENSUS_TREE.dummy \
1824	SERVERCNTRL/SERVERCNTRL.dummy \
1825	SL/FILTER/FILTER.dummy \
1826	SL/FILTSEQEXP/FILTSEQEXP.dummy \
1827	SL/INSDEL/INSDEL.dummy \
1828	SL/REGEXPR/REGEXPR.dummy \
1829	SL/SEQIO/SEQIO.dummy \
1830	SL/TREE_READ/TREE_READ.dummy \
1831	SL/TREE_WRITE/TREE_WRITE.dummy \
1832	XML/XML.dummy \
1833
1834	AWTC/AWTC.dummy : com
1835
1836	NAMES/NAMES.dummy : com
1837	SL/AW_NAME/AW_NAME.dummy : com
1838
1839	PROBE/PROBE.dummy : com
1840	MULTI_PROBE/MULTI_PROBE.dummy : com
1841	PROBE_DESIGN/PROBE_DESIGN.dummy : com
1842	NALIGNER/NALIGNER.dummy : com
1843
1844	ARB_GDE/ARB_GDE.dummy : proto_tools
1845
1846	compile_compatibility: SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.dummy
1847
1848	#***************************************************************************************
1849	# Short aliases to make targets
1850	#***************************************************************************************
1851
1852	show:
1853	@echo $(SEP)
1854	@echo 'Aliases for often needed targets:'
1855	@echo ''
1856	@echo ' executables:'
1857	@echo ''
1858	@echo ' nt arb_ntree'
1859	@echo ' e4 arb_edit4 (includes secedit)'
1860	@echo ' di arb_dist'
1861	@echo ' ph arb_phylo'
1862	@echo ' pa arb_parsimony'
1863	@echo ' tg arb_treegen'
1864	@echo ' ds arb_dbserver'
1865	@echo ' pt arb_pt_server'
1866	@echo ' na arb_name_server'
1867	@echo ''
1868	@echo ' libraries:'
1869	@echo ''
1870	@echo ' com communication libraries'
1871	@echo ' db ARB database'
1872	@echo ' aw GUI lib'
1873	@echo ' awt GUI toolkit'
1874	@echo ' awtc general purpose library'
1875	@echo ' awti import/export library'
1876	@echo ' mp multi probe library'
1877	@echo ' ge genome library'
1878	@echo ' pd probe design lib'
1879	@echo ' prd primer design lib'
1880	@echo ''
1881	@echo ' other targets:'
1882	@echo ''
1883	@echo ' help recompile help files'
1884	@echo ' tools make small tools used by arb'
1885	@echo ''
1886	@echo ' foreign targets:'
1887	@echo ''
1888	@echo ' gde GDE'
1889	@echo ' agde ARB_GDE'
1890	@echo ''
1891	@echo 'for other targets inspect $(ARBHOME)/Makefile'
1892	@echo ''
1893	@echo $(SEP)
1894
1895	source_doc:
1896	@echo "Remove some links (doxygen crashes otherwise):"
1897	find . \( -name "AISC" -o -name "C" -o -name "GDEHELP" \) -type l -exec rm {} \;
1898	doxygen 2>&1 1>/dev/null
1899	$(MAKE) forcelinks
1900
1901	dep_graph:
1902	@echo "Building some dependency graphs"
1903	SOURCE_TOOLS/dependency_graphs.pl
1904
1905	help: HELP_SOURCE/HELP_SOURCE.dummy
1906
1907	HELP_SOURCE/HELP_SOURCE.dummy: link_core xml menus
1908
1909	db: ARBDB/libARBDB.dummy
1910	core: CORE/libCORE.dummy
1911	aw: WINDOW/libWINDOW.dummy
1912	awt: AWT/libAWT.dummy
1913	awtc: AWTC/AWTC.dummy
1914	awti: AWTI/AWTI.dummy
1915
1916	mp: MULTI_PROBE/MULTI_PROBE.dummy
1917	mg: MERGE/MERGE.dummy
1918	ge: GENOM/GENOM.dummy
1919	prd: PRIMER_DESIGN/PRIMER_DESIGN.dummy
1920
1921	nt: menus $(NTREE)
1922
1923	nal: $(NALIGNER)
1924
1925	di: $(DIST)
1926	ph: $(PHYLO)
1927	pa: $(PARSIMONY)
1928	tg: $(TREEGEN)
1929
1930	ifeq ($(OPENGL),1)
1931	3d: RNA3D/RNA3D.dummy
1932	gl: GL/GL.dummy
1933	else
1934	noopengl:
1935	@echo "invalid target for OPENGL=0"
1936	3d: noopengl
1937	gl: noopengl
1938	endif
1939
1940	SL/SL.dummy: com
1941
1942	ds: $(DBSERVER)
1943	pt: $(PROBE)
1944	pst: PROBE_SET/PROBE_SET.dummy
1945	pd: PROBE_DESIGN/PROBE_DESIGN.dummy
1946	na: $(NAMES)
1947	sq: SEQ_QUALITY/SEQ_QUALITY.dummy
1948	cma: $(RNACMA)
1949
1950	sec: SECEDIT/SECEDIT.dummy
1951
1952	e4: $(EDIT4) readseq menus
1953
1954	gi: GENOM_IMPORT/GENOM_IMPORT.dummy
1955	wetc: $(WETC)
1956
1957	xml: XML/XML.dummy
1958	stat: STAT/STAT.dummy $(NTREE) $(EDIT4)
1959	fa: SL/FAST_ALIGNER/FAST_ALIGNER.dummy
1960
1961	#********************************************************************************
1962
1963	up_by_remake: depends proto vectorize_checks
1964
1965	up: up_by_remake tags valgrind_update
1966
1967	#********************************************************************************
1968
1969	touch:
1970	SOURCE_TOOLS/touch_modified.pl
1971
1972	modified: touch
1973	$(MAKE) all
1974
1975	#********************************************************************************
1976
1977	libdepends:
1978	$(MAKE) -C "SOURCE_TOOLS" \
1979	"RNA3D_LIB=$(RNA3D_LIB_4_DEPENDS)" \
1980	libdepends
1981
1982	#********************************************************************************
1983
1984	# create generated headers:
1985	genheaders: TEMPLATES/TEMPLATES.dummy
1986
1987	clrdotdepends:
1988	rm PROBE_COM/.depends \|\| true
1989	rm NAMES_COM/.depends \|\| true
1990	rm PERL2ARB/.depends \|\| true
1991
1992	comdepends: comtools clrdotdepends
1993	@echo "$(SEP) Partially build com interface"
1994	$(MAKE) PROBE_COM/PROBE_COM.depends NAMES_COM/NAMES_COM.depends
1995	$(MAKE) PROBE_COM/server.depends NAMES_COM/server.depends
1996
1997	depends: genheaders comdepends vectorize_checks
1998	@echo "$(SEP) Updating other dependencies"
1999	$(MAKE) $(subst NAMES_COM/server.depends,,$(subst PROBE_COM/server.depends,,$(SUBDIRS:.sub=.depends))) \
2000	HELP_SOURCE/HELP_SOURCE.depends \
2001	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.depends \
2002
2003	$(MAKE) libdepends
2004
2005	depend: depends
2006
2007	# ------------------------------------------------------------
2008	# dependency generation tests for AISC code
2009	#(all should work w/o creating wrong dependencies;
2010	# neither in XXX_COM/Makefile nor in code using AISC interface)
2011	dependstest1: silent_clean
2012	$(MAKE) depends
2013	dependstest2: silent_clean
2014	$(MAKE) com
2015	dependstest3: silent_clean
2016	$(MAKE) aw
2017	dependstest4: silent_clean
2018	$(MAKE) pt
2019	dependstest5: silent_clean
2020	$(MAKE) na
2021	dependstest6: silent_clean
2022	$(MAKE) nt
2023	dependstest7: silent_clean
2024	$(MAKE) all
2025	# ------------------------------------------------------------
2026
2027	vectorize_checks:
2028	$(MAKE) -C SOURCE_TOOLS -r vectorize_checks
2029
2030	clean_checked_vect: lib/lib.clean
2031	SOURCE_TOOLS/clean_checked_vectorizations.sh
2032
2033	# ------------------------------------------------------------
2034
2035	AISC_MKPTPS/AISC_MKPTPS.dummy: links
2036
2037	proto_tools: AISC_MKPTPS/AISC_MKPTPS.dummy
2038
2039	proto: proto_tools
2040	@echo $(SEP) Updating prototypes
2041	$(MAKE) \
2042	ARBDB/ARBDB.proto \
2043	AISC_COM/AISC_COM.proto \
2044	ARB_GDE/ARB_GDE.proto \
2045	CORE/CORE.proto \
2046	CONVERTALN/CONVERTALN.proto \
2047	NTREE/NTREE.proto \
2048	MERGE/MERGE.proto \
2049	PROBE/PROBE.proto \
2050	SERVERCNTRL/SERVERCNTRL.proto \
2051	SL/SL.proto \
2052
2053	#********************************************************************************
2054
2055	valgrind_update: links
2056	@echo $(SEP) Updating for valgrind
2057	$(MAKE) -C SOURCE_TOOLS valgrind_update
2058
2059	#********************************************************************************
2060
2061	TAGFILE=TAGS
2062	UTAGS=TAGS.$(ARBBID)
2063	TAGFILE_TMP=$(UTAGS).tmp
2064
2065	TAG_SOURCE_HEADERS=$(UTAGS).headers.tmp
2066	TAG_SOURCE_CODE=$(UTAGS).codefiles.tmp
2067	TAG_SOURCE_LISTS=$(TAG_SOURCE_HEADERS) $(TAG_SOURCE_CODE)
2068
2069	ETAGS_IGNORE_LIST=SOURCE_TOOLS/etags_ignore.lst
2070
2071	ETAGS=ctags -e -I @$(ETAGS_IGNORE_LIST) --sort=no --if0=no --extra=q
2072	ETAGS_TYPES=--C-kinds=cgnsut --C++-kinds=cgnsut
2073	ETAGS_FUN =--C-kinds=fm --C++-kinds=fm
2074	ETAGS_REST =--C-kinds=dev --C++-kinds=dev
2075
2076	FILTER_TAGS_SOURCES= \
2077	$(SED) -e 's/^.\///g' \| \
2078	grep -vi '^HEADERLIBS\\|^GDE/\\|/GEN[CH]/'
2079
2080	$(TAG_SOURCE_HEADERS): links
2081	@find . \( -name '.hxx' -o -name ".h" \) -type f \| $(FILTER_TAGS_SOURCES) > $@
2082
2083	$(TAG_SOURCE_CODE): links
2084	@find . \( -name '.cxx' -o -name ".c" \) -type f \| $(FILTER_TAGS_SOURCES) > $@
2085
2086	$(UTAGS).1.tmp: $(TAG_SOURCE_HEADERS)
2087	@$(ETAGS) -f $@ $(ETAGS_TYPES) -L $<
2088	$(UTAGS).2.tmp: $(TAG_SOURCE_HEADERS)
2089	@$(ETAGS) -f $@ $(ETAGS_FUN) -L $<
2090	$(UTAGS).3.tmp: $(TAG_SOURCE_HEADERS)
2091	@$(ETAGS) -f $@ $(ETAGS_REST) -L $<
2092	$(UTAGS).4.tmp: $(TAG_SOURCE_CODE)
2093	@$(ETAGS) -f $@ $(ETAGS_TYPES) -L $<
2094	$(UTAGS).5.tmp: $(TAG_SOURCE_CODE)
2095	@$(ETAGS) -f $@ $(ETAGS_FUN) -L $<
2096	$(UTAGS).6.tmp: $(TAG_SOURCE_CODE)
2097	@$(ETAGS) -f $@ $(ETAGS_REST) -L $<
2098
2099	TAGS_ALL_PARTS=$(UTAGS).1.tmp $(UTAGS).2.tmp $(UTAGS).3.tmp $(UTAGS).4.tmp $(UTAGS).5.tmp $(UTAGS).6.tmp
2100
2101	$(TAGFILE_TMP) : $(TAGS_ALL_PARTS)
2102	@cat $(TAGS_ALL_PARTS) > $@
2103	@rm $(TAGS_ALL_PARTS) $(TAG_SOURCE_LISTS)
2104
2105	cleanOldTags:
2106	@find $(ARBHOME) -name 'TAGS.*.tmp' -ctime +2 -exec rm {} \;
2107
2108	tags: $(TAGFILE_TMP) cleanOldTags
2109	@mv_if_diff $(TAGFILE_TMP) $(TAGFILE)
2110
2111	#********************************************************************************
2112
2113	LINKSTAMP=SOURCE_TOOLS/stamp.generate_all_links
2114
2115	links: checks $(LINKSTAMP) arbmainwrapper
2116	links_no_checks: $(LINKSTAMP) arbmainwrapper
2117
2118	forcelinks:
2119	-rm $(LINKSTAMP)
2120	$(MAKE) links
2121
2122	$(LINKSTAMP): SOURCE_TOOLS/generate_all_links.sh genheaders
2123	+SOURCE_TOOLS/generate_all_links.sh
2124	touch $(LINKSTAMP)
2125
2126	clean_links:
2127	# avoid to delete linked pts, nas or arb_tcp.dat:
2128	find . -path './lib' -prune -o -type l -exec rm {} \;
2129	# removed obsolete file - refuses to disappear due to 'prune' above
2130	@rm -f lib/help/GDEHELP
2131	@rm -f $(LINKSTAMP) lib/inputMasks/format.readme
2132
2133	redo_links: clean_links
2134	$(MAKE) links_no_checks
2135
2136	#********************************************************************************
2137
2138	header_libs:
2139	@(( \
2140	echo "$(SEP) Make HEADERLIBS"; \
2141	$(MAKE) -C HEADERLIBS all && \
2142	echo "$(SEP) Make HEADERLIBS [done]"; \
2143	) > HEADERLIBS.log 2>&1 && (cat HEADERLIBS.log;rm HEADERLIBS.log)) \|\| (cat HEADERLIBS.log;rm HEADERLIBS.log;false)
2144
2145	#********************************************************************************
2146
2147	gde: GDE/GDE.dummy
2148	GDE: gde
2149	agde: ARB_GDE/ARB_GDE.dummy
2150	tools: TOOLS/TOOLS.dummy
2151	convert: $(CONVERT_ALN)
2152	readseq: READSEQ/READSEQ.dummy
2153
2154	#***************************************************************************************
2155	# Some user commands
2156	#***************************************************************************************
2157
2158	menus: binlink links
2159	@(( \
2160	echo "$(SEP) Make GDEHELP"; \
2161	$(MAKE) -C GDEHELP -r all && \
2162	echo "$(SEP) Make GDEHELP [done]"; \
2163	) > GDEHELP.log 2>&1 && (cat GDEHELP.log;rm GDEHELP.log)) \|\| (cat GDEHELP.log;rm GDEHELP.log;false)
2164
2165	ifeq ($(DEBUG),1)
2166	BIN_TARGET=develall
2167	else
2168	BIN_TARGET=all
2169	endif
2170
2171
2172	binlink:
2173	$(MAKE) -C bin $(BIN_TARGET)
2174
2175	check_bin_dep: binlink
2176	SOURCE_TOOLS/check_bin_dependencies.pl
2177
2178	fig_cure:
2179	SOURCE_TOOLS/sortfig.pl doit
2180
2181	preplib:
2182	(cd lib;$(MAKE) all)
2183
2184	# --------------------------------------------------------------------------------
2185	# This section is quite tricky:
2186	#
2187	# make 'perl' is a BIG target, so when it has to be made, it has to be started
2188	# as early as possible to reduce overall compile time. Since 'make' does not
2189	# provide any priorities, i force it to build all 'perl'-prerequisites early, by
2190	# adding artificial dependencies to these prerequisites
2191	#
2192	# That behavior is likely to be system-dependent.
2193	# My goal was only to make it work on my current development system,
2194	# where this saves about 20% of overall build time.
2195
2196	ifeq ($(WITHPERL),1)
2197	links_non_perl: PERLTOOLS/PERLTOOLS.dummy
2198	perltools: links_non_perl
2199	perl: realperl
2200	else
2201	links_non_perl: links
2202	perl:
2203	$(MAKE) "WITHPERL=1" perl
2204	endif
2205
2206	# ---------------------------------------- perl
2207
2208	realperl: perltools
2209	(( \
2210	echo "$(SEP) Make PERL2ARB" ; \
2211	$(TIME) $(MAKE) -C PERL2ARB -r -f Makefile.main \
2212	"AUTODEPENDS=1" \
2213	"dflags=$(dflags)" \
2214	"cflags4perl=$(cflags) $(cxxflags) $(dflags)" \
2215	"lflags4perl=$(lflags4perl)" \
2216	"COMPILER_VERSION=$(COMPILER_VERSION)" \
2217	all && \
2218	$(MAKE) -C PERL_SCRIPTS/test test && \
2219	echo "$(SEP) Make PERL2ARB [done]" ; \
2220	) > PERL2ARB.log 2>&1 && (cat PERL2ARB.log;rm PERL2ARB.log)) \|\| (cat PERL2ARB.log;rm PERL2ARB.log;false)
2221
2222	perl_clean:
2223	@$(MAKE) -C PERL2ARB -r -f Makefile.main \
2224	"AUTODEPENDS=0" \
2225	clean
2226
2227	PERL2ARB/PERL2ARB.clean:
2228	$(MAKE) perl_clean
2229	$(MAKE) -C PERL_SCRIPTS/test clean
2230
2231	# ---------------------------------------- bindings to script languages
2232
2233	bindings: lib/libCORE.so lib/libARBDB.so
2234	$(MAKE) -C BINDINGS all ARBDEPENDS="$(^:%=../%)" DFLAGS="$(dflags)"
2235
2236	bindings_clean:
2237	$(MAKE) -C BINDINGS clean
2238
2239	# ----------------------------------------
2240
2241	CLOC=cloc-1.08.pl
2242	CLOCFLAGS=--no3 --quiet --progress-rate=0
2243	CLOCARB=--exclude-dir=GDE .
2244	CLOCEXT=GDE
2245	CLOCCODE=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.code.def
2246	CLOCREST=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.rest.def
2247	CLOCFILT=tail --lines=+4
2248
2249	cloc:
2250	@echo 'Arb code:'
2251	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCARB) \| $(CLOCFILT)
2252	@echo 'Arb rest:'
2253	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCARB) \| $(CLOCFILT)
2254	@echo 'External code:'
2255	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCEXT) \| $(CLOCFILT)
2256	@echo 'External rest:'
2257	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCEXT) \| $(CLOCFILT)
2258
2259	# ---------------------------------------- check resources
2260
2261	check_res:
2262	$(ARBHOME)/SOURCE_TOOLS/check_resources.pl
2263
2264	# ---------------------------------------- cleaning
2265
2266	rmbak:
2267	@echo "[cleanup backup/core files]"
2268	@find . \( -name '*%' \
2269	-o -name '*.bak' \
2270	-o -name '*~' \) \
2271	-o \( -name 'core' -a \! -type d \) \
2272	-exec rm -v {} \; \|\| \
2273	echo "Warning: target 'rmbak' reported problems when removing misc. backup files (ignored)"
2274	@echo "[cleanup done]"
2275
2276	bin_reinit:
2277	$(MAKE) bin/bin.clean
2278	$(MAKE) -C "bin" all
2279
2280	clean_directories:
2281	-rm -rf \
2282	$(ARBHOME)/PROBE_SET/bin \
2283	$(ARBHOME)/INCLUDE \
2284
2285	libclean:
2286	-find $(ARBHOME) -type f \( -name '*.a' ! -type l \) -exec rm -f {} \;
2287	-find $(ARBHOME) -type f \( -name 'lib*.so' ! -type l \) -exec rm -f {} \;
2288
2289	objclean:
2290	-find $(ARBHOME) -type f \( -name '*.o' ! -type l \) -exec rm -f {} \;
2291
2292	# bin.clean and HELP_SOURCE.clean interfere
2293	clean3:
2294	$(MAKE) bin/bin.clean
2295	$(MAKE) HELP_SOURCE/HELP_SOURCE.clean
2296
2297
2298	# delete all binaries (similar to 'cleanlinked')
2299	cleanRelinkable: libclean UNIT_TESTER/UNIT_TESTER.clean
2300	$(MAKE) -C bin cleanbinariesRelinkable
2301	$(MAKE) -C PROBE_SET cleanLinked
2302
2303
2304	clean2: $(SUBDIRS:.sub=.clean) \
2305	clean3 \
2306	rmbak \
2307	libclean \
2308	objclean \
2309	lib/lib.clean \
2310	GDEHELP/GDEHELP.clean \
2311	HEADERLIBS/HEADERLIBS.clean \
2312	SOURCE_TOOLS/SOURCE_TOOLS.clean \
2313	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.clean \
2314	UNIT_TESTER/UNIT_TESTER.clean \
2315	TEMPLATES/TEMPLATES.clean \
2316	perl_clean \
2317	clean_directories \
2318
2319	rm -f .last_gcc .last_compiler config.makefile.bak
2320
2321	# links are needed for cleanup
2322	clean: redo_links motif_xpm_hack_clean
2323	$(MAKE) clean2
2324	$(MAKE) clean_cov_all clean_links
2325
2326	silent_clean:
2327	$(MAKE) clean >/dev/null
2328
2329	# 'relocated' is about 50% faster than 'rebuild'
2330	reloc_clean: links
2331	@echo "---------------------------------------- Relocation cleanup"
2332	$(MAKE) \
2333	perl_clean \
2334	GDEHELP/GDEHELP.clean \
2335	HELP_SOURCE/genhelp/genhelp.clean \
2336	bin/bin.clean \
2337	libclean \
2338	objclean
2339
2340	relocated: links
2341	$(MAKE) reloc_clean
2342	@echo "---------------------------------------- and remake"
2343	$(MAKE) build
2344
2345	# -----------------------------------
2346	# some stress tests
2347	# (helpful to reveal race conditions with -j)
2348
2349	rebuild4ever: rebuild
2350	$(MAKE) rebuild4ever
2351
2352	build4ever: build
2353	$(MAKE) build4ever
2354
2355	clean4ever: clean
2356	$(MAKE) clean4ever
2357
2358	test4ever: ut
2359	$(MAKE) test4ever
2360
2361	perl4ever: clean
2362	$(MAKE) links
2363	$(MAKE) perl
2364	$(MAKE) perl4ever
2365
2366	help4ever: clean
2367	$(MAKE) help
2368	$(MAKE) help4ever
2369
2370	# -----------------------------------
2371
2372	rebuild: clean
2373	$(MAKE) all
2374
2375	cleanlinked: bin/bin.clean libclean
2376
2377	relink: cleanlinked
2378	$(MAKE) all
2379
2380	tarfile: rebuild
2381	$(MAKE) prepare_libdir
2382	util/arb_compress
2383
2384	tarfile_quick: build
2385	$(MAKE) prepare_libdir
2386	util/arb_compress
2387
2388	save: sourcetarfile
2389
2390	patch:
2391	SOURCE_TOOLS/arb_create_patch.sh arbPatch
2392
2393	# test early whether save will work
2394	savetest:
2395	@util/arb_srclst.pl >/dev/null
2396
2397	testsave: savetest
2398
2399	sourcetarfile: rmbak
2400	util/arb_save
2401
2402	save2: rmbak
2403	util/arb_save ignore
2404
2405	save_test: rmbak
2406	@echo "Testing source list.."
2407	@util/arb_srclst.pl > /dev/null
2408
2409	save_test_no_error:
2410	@-$(MAKE) save_test
2411
2412	inc_candi:
2413	touch SOURCE_TOOLS/inc_candi.stamp
2414	$(MAKE) do_version_update
2415
2416	inc_patch:
2417	touch SOURCE_TOOLS/inc_patch.stamp
2418	$(MAKE) do_version_update
2419
2420	inc_minor:
2421	touch SOURCE_TOOLS/inc_minor.stamp
2422	$(MAKE) do_version_update
2423
2424	inc_major:
2425	touch SOURCE_TOOLS/inc_major.stamp
2426	$(MAKE) do_version_update
2427
2428	do_version_update:
2429	@echo Incrementing version information
2430	$(MAKE) savetest
2431	$(MAKE) genheaders # auto upgrades version early
2432
2433	show_version:
2434	$(MAKE) genheaders # updates version info
2435	@echo "$(SEP) ARB version info"
2436	@grep ARB_VERSION TEMPLATES/arb_build.h
2437	@echo "$(SEP)"
2438
2439	release_quick:
2440	-rm arb.tgz arbsrc.tgz
2441	$(MAKE) tarfile_quick
2442	$(MAKE) sourcetarfile
2443
2444	# --------------------------------------------------------------------------------
2445	# special cleanups
2446
2447	clean_opengl_changed: RNA3D/RNA3D.clean EDIT4/EDIT4.clean WINDOW/WINDOW.clean GL/GL.clean
2448
2449	# --------------------------------------------------------------------------------
2450
2451	MAKE_IF_COMMITTED=$(MAKE) -C SOURCE_TOOLS -f Makefile.commitbuild
2452
2453	build_CTARGET:
2454	+$(MAKE_IF_COMMITTED) "CTARGET=$(CTARGET)" build_CTARGET
2455
2456	reset_committed_build:
2457	+$(MAKE_IF_COMMITTED) reset
2458
2459	# --------------------------------------------------------------------------------
2460
2461	arbapplications: nt pa e4 wetc pt na nal di ph ds wetc cma
2462
2463	arb_external: convert tools gde readseq tg pst
2464
2465	arb_no_perl: arbapplications help arb_external
2466
2467	arb: motif_xpm_hack
2468	$(MAKE) "WITHPERL=1" perl arb_no_perl
2469
2470	motif_xpm_hack:
2471	$(MAKE) -r -C "lib/motifHack" all
2472
2473	motif_xpm_hack_clean:
2474	$(MAKE) -r -C "lib/motifHack" clean
2475
2476	# --------------------------------------------------------------------------------
2477	# special targets for SOURCE_TOOLS/remake_after_change.pl
2478
2479	rac_arb_dist: di
2480	rac_arb_edit4: e4
2481	rac_arb_ntree: nt
2482	rac_arb_pars: pa
2483	rac_arb_phylo: ph
2484	rac_arb_wetc: wetc
2485	rac_arb_naligner: nal
2486	rac_arb_pt_server: pt
2487	rac_arb_db_server: ds
2488	rac_arb_name_server: na
2489	rac_arb_convert_aln: convert
2490	rac_arb_treegen: tg
2491	rac_arb_rnacma: cma
2492	rac_arb_help2xml: help
2493
2494	rac_arb_a2ps: tools
2495	rac_arb_consensus_tree: tools
2496	rac_arb_dnarates: tools
2497	rac_arb_export_rates: tools
2498	rac_arb_export_tree: tools
2499	rac_arb_gene_probe: tools
2500	rac_arb_message: tools
2501	rac_arb_primer: tools
2502	rac_arb_probe: tools
2503	rac_arb_read_tree: tools
2504
2505	# --------------------------------------------------------------------------------
2506	# unit testing
2507	# @@@ work in progress
2508	#
2509	# goal is to automatically test all libraries/executables using TESTED_UNITS_AUTO
2510	# currently not all test executables link w/o error.
2511	# therefor units are organized in three sets:
2512	#
2513	# TESTED_UNITS = testable and contain tests
2514	# UNTESTED_UNITS = testable, but no tests written yet
2515	# UNTESTABLE_UNITS = not testable
2516
2517	# always define OPENGL units manually:
2518	OPENGL_TESTS :=
2519	ifeq ($(OPENGL),1)
2520	OPENGL_TESTS += \
2521	$(subst .a,.test,$(RNA3D_LIB)) \
2522	GL/glAW/libglAW.test \
2523	GL/glpng/libglpng_arb.test \
2524
2525	endif
2526
2527	UNITS_NOT_AUTODETECTED = \
2528	HELP_SOURCE/HELP_SOURCE.tooltests
2529
2530	TESTED_UNITS_AUTO = \
2531	$(OPENGL_TESTS) \
2532	$(TL_ARCHIVES:.a=.test) \
2533	$(TL_SHARED_ARCHIVES:.so=.test) \
2534	$(CL_ARCHIVES:.a=.test) \
2535	$(TL_TOOLS_COLLECTIONS:.toolColl=.tooltests) \
2536	$(UNITS_NOT_AUTODETECTED) \
2537
2538	UNTESTED_UNITS = \
2539	$(OPENGL_TESTS) \
2540	EISPACK/EISPACK.test \
2541	GENOM/GENOM.test \
2542	ISLAND_HOPPING/ISLAND_HOPPING.test \
2543	NALIGNER/NALIGNER.test \
2544	NAMES/NAMES.test \
2545	PHYLO/PHYLO.test \
2546	PRIMER_DESIGN/PRIMER_DESIGN.test \
2547	PROBE_DESIGN/PROBE_DESIGN.test \
2548	READSEQ/READSEQ.tooltests \
2549	SECEDIT/SECEDIT.test \
2550	SEQ_QUALITY/SEQ_QUALITY.test \
2551	SERVERCNTRL/SERVERCNTRL.test \
2552	SL/ALIVIEW/ALIVIEW.test \
2553	SL/AP_TREE/AP_TREE.test \
2554	SL/ARB_TREE/ARB_TREE.test \
2555	SL/AW_HELIX/AW_HELIX.test \
2556	SL/AW_NAME/AW_NAME.test \
2557	SL/DB_SCANNER/DB_SCANNER.test \
2558	SL/DB_UI/DB_UI.test \
2559	SL/GUI_ALIVIEW/GUI_ALIVIEW.test \
2560	SL/HELIX/HELIX.test \
2561	SL/QUERY/QUERY.test \
2562	SL/REFENTRIES/REFENTRIES.test \
2563	SL/SEQUENCE/SEQUENCE.test \
2564	SL/TREE_ADMIN/TREE_ADMIN.test \
2565	SL/TREE_WRITE/TREE_WRITE.test \
2566	SL/XFERGUI/XFERGUI.test \
2567	STAT/STAT.test \
2568	TREEGEN/TREEGEN.test \
2569	WETC/WETC.test \
2570	XML/XML.test \
2571
2572	# untestable units
2573
2574	UNTESTABLE_UNITS = \
2575	AISC/AISC.test \
2576	NAMES_COM/server.test \
2577	PROBE_COM/server.test \
2578
2579	# --------------------
2580	# put all units containing tests into the following 4 sections (see also TESTED_UNITS below)
2581
2582	# recent development
2583	UNITS_TESTED_FIRST = \
2584	SL/MATRIX/MATRIX.test \
2585	AWTI/AWTI.test \
2586	SL/FILTSEQEXP/FILTSEQEXP.test \
2587	SL/GROUP_SEARCH/GROUP_SEARCH.test \
2588	SL/PVP/PVP.test \
2589	SL/SAICALC/SAICALC.test \
2590	SL/TRANSLATE/TRANSLATE.test \
2591	SL/XFERSET/XFERSET.test \
2592
2593	# start units with long duration early
2594	UNITS_RUNNING_LONG = \
2595	ARBDB/libARBDB.test \
2596	AWTC/AWTC.test \
2597	TOOLS/TOOLS.tooltests \
2598
2599	# plain test-libaries that are not linked anywhere
2600	TEST_SANDBOXES = \
2601	SL/CB/CB.test \
2602
2603	UNITS_TESTED = \
2604	AISC_MKPTPS/AISC_MKPTPS.tooltests \
2605	ARB_GDE/ARB_GDE.test \
2606	AWT/libAWT.test \
2607	CONSENSUS_TREE/CONSENSUS_TREE.test \
2608	CONVERTALN/CONVERTALN.test \
2609	CORE/libCORE.test \
2610	DBSERVER/DBSERVER.test \
2611	DIST/DIST.test \
2612	EDIT4/EDIT4.test \
2613	GENOM_IMPORT/GENOM_IMPORT.test \
2614	HELP_SOURCE/HELP_SOURCE.tooltests \
2615	MERGE/MERGE.test \
2616	MULTI_PROBE/MULTI_PROBE.test \
2617	NTREE/NTREE.test \
2618	PARSIMONY/PARSIMONY.test \
2619	PERLTOOLS/PERLTOOLS.tooltests \
2620	PROBE/PROBE.test \
2621	PROBE_SET/PROBE_SET.tooltests \
2622	RNACMA/RNACMA.test \
2623	SL/ALILINK/ALILINK.test \
2624	SL/CONSENSUS/CONSENSUS.test \
2625	SL/DB_QUERY/DB_QUERY.test \
2626	SL/FAST_ALIGNER/FAST_ALIGNER.test \
2627	SL/FILTER/FILTER.test \
2628	SL/INSDEL/INSDEL.test \
2629	SL/ITEM_SHADER/ITEM_SHADER.test \
2630	SL/ITEMS/ITEMS.test \
2631	SL/LOCATION/LOCATION.test \
2632	SL/MACROS/MACROS.test \
2633	SL/NDS/NDS.test \
2634	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.test \
2635	SL/PRONUC/PRONUC.test \
2636	SL/PTCLEAN/PTCLEAN.test \
2637	SL/REGEXPR/REGEXPR.test \
2638	SL/SEQIO/SEQIO.test \
2639	SL/TREE_READ/TREE_READ.test \
2640	SL/TREEDISP/TREEDISP.test \
2641	WINDOW/libWINDOW.test \
2642
2643	TESTED_UNITS = \
2644	$(UNITS_TESTED_FIRST) \
2645	$(UNITS_RUNNING_LONG) \
2646	$(TEST_SANDBOXES) \
2647	$(UNITS_TESTED) \
2648
2649	# ----------------------------------------
2650
2651	ifeq ($(DEVELOPER),RALF)
2652
2653	DEFINED_TEST_UNITS = \
2654	$(TESTED_UNITS) \
2655	$(UNTESTED_UNITS) \
2656	$(UNTESTABLE_UNITS) \
2657
2658	list_undefined_units:
2659	@UNIT_TESTER/list_undefined_units.pl $(DEFINED_TEST_UNITS) -- $(TESTED_UNITS_AUTO)
2660
2661	else
2662
2663	list_undefined_units:
2664
2665	endif
2666
2667	# ----------------------------------------
2668
2669	TEST_LOG_DIR = UNIT_TESTER/logs
2670	TEST_RUN_SUITE=$(MAKE) $(NODIR) -C UNIT_TESTER -f Makefile.suite -r
2671	# -> UNIT_TESTER/Makefile.suite
2672	TEST_MAKE_FLAGS=
2673	TEST_POST_CLEAN=
2674	ifeq ($(COVERAGE),1)
2675	TEST_POST_CLEAN=$(MAKE) clean_cov
2676	TEST_MAKE_FLAGS+=-j1
2677	endif
2678
2679
2680	%.test:
2681	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
2682	( \
2683	echo "take[1]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
2684	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
2685	"UNITDIR=$(@D)" \
2686	"UNITLIBNAME=$(@F:.test=)" \
2687	"COVERAGE=$(COVERAGE)" \
2688	"ARB_PID=$(ARB_PID)_$(@F)" \
2689	runtest; \
2690	echo "take[1]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"; \
2691	$(TEST_POST_CLEAN) \
2692	) >$(TEST_LOG_DIR)/$(@F).log 2>&1; \
2693	UNIT_TESTER/log_result.pl $(TEST_LOG_DIR)/$(@F).log )
2694
2695	%.notest:
2696	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
2697	( \
2698	echo "take[4]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
2699	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
2700	"UNITDIR=$(@D)" \
2701	"UNITLIBNAME=$(@F:.notest=)" \
2702	"COVERAGE=0" \
2703	"ARB_PID=$(ARB_PID)_$(@F)" \
2704	check_no_test; \
2705	echo "take[4]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'" \
2706	) >$(TEST_LOG_DIR)/$(@F).log 2>&1 )
2707
2708
2709	# tool test aliases (used to test one or multiple executable(s) in a single subdir):
2710	%.tooltests:
2711	$(error please define an explicit tooltest alias for $@)
2712
2713	AISC_MKPTPS/AISC_MKPTPS.tooltests : AISC_MKPTPS/mkptypes.test
2714	@echo "aliasing $@ -> $^"
2715	PERLTOOLS/PERLTOOLS.tooltests : PERLTOOLS/arb_proto_2_xsub.test
2716	@echo "aliasing $@ -> $^"
2717	PROBE_SET/PROBE_SET.tooltests : PROBE_SET/fb_test.test
2718	@echo "aliasing $@ -> $^"
2719	HELP_SOURCE/HELP_SOURCE.tooltests : HELP_SOURCE/arb_help2xml.test
2720	@echo "aliasing $@ -> $^"
2721	TOOLS/TOOLS.tooltests : TOOLS/arb_consensus_tree.test TOOLS/arb_probe.test TOOLS/arb_test.test
2722	@echo "aliasing $@ -> $^"
2723
2724	# aliases for tools w/o tests:
2725	READSEQ/READSEQ.tooltests:
2726	@echo "Note: no tests for $@"
2727
2728
2729	test_base: $(UNIT_TESTER_LIB:.a=.dummy) $(subst .test,.dummy,$(TEST_SANDBOXES))
2730
2731	clean_cov:
2732	find . \( -name ".gcda" -o -name ".gcov" -o -name "*.cov" \) -exec rm {} \;
2733
2734	clean_cov_all: clean_cov
2735	find . \( -name "*.gcno" \) -exec rm {} \;
2736
2737	cleanup_faked_arbpids:
2738	@rm ~/.arb_tmp/tmp/arb_pids_${USER}_${ARB_PID}_* \|\| true
2739
2740	cleanup_faked_arbpids_and_fail: cleanup_faked_arbpids
2741	@false
2742
2743	NOTESTS_IN_UNTESTED = $(subst .test,.notest,$(UNTESTED_UNITS))
2744
2745	run_tests_faked_arbpid:
2746	+@$(TEST_RUN_SUITE) init
2747	@echo "take[2]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2748	@$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(TESTED_UNITS) $(NOTESTS_IN_UNTESTED) \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2749	@echo "take[2]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2750	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2751	@$(MAKE) clean_cov >/dev/null
2752	@$(MAKE) cleanup_faked_arbpids
2753
2754	# @@@ instead of only running UNIT, this should as well run all tests this unit depends on? according to 'needs_libs'
2755	# @@@ 'run_tests_faked_arbpid' does not work for UNIT=ARBDB/libARBDB or UNIT=PARS/PARS -> could be solved via extra suffix, e.g. ARBDB/libARBDB.unit
2756
2757	run_onetest_faked_arbpid:
2758	+@$(TEST_RUN_SUITE) init
2759	@echo "take[3]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2760	test -n "$(UNIT)" \|\| (echo "Error: UNIT has to be defined for target 'run_onetest_faked_arbpid'!"; false)
2761	$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(UNIT).test \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2762	@echo "take[3]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2763	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2764	@$(MAKE) clean_cov >/dev/null
2765	@$(MAKE) cleanup_faked_arbpids
2766
2767	run_tests: test_base clean_cov
2768	$(MAKE) "ARB_PID=UT_$$$$" run_tests_faked_arbpid list_undefined_units
2769
2770	run_oneunitstests: test_base
2771	$(MAKE) "ARB_PID=UT_$$$$" run_onetest_faked_arbpid
2772
2773
2774	ut:
2775	ifeq ($(UNIT_TESTS),1)
2776	@echo $(MAKE) run_tests
2777	@$(MAKE) run_tests
2778	else
2779	@echo "Not compiled with unit tests"
2780	endif
2781
2782
2783	aut:
2784	+@$(TEST_RUN_SUITE) unskip
2785	$(MAKE) ut
2786
2787	# --------------------------------------------------------------------------------
2788
2789	TIMELOG=$(ARBHOME)/arb_time.log
2790	TIMEARGS=--append --output=$(TIMELOG) --format=" * %E(%S+%U) %P [%C]"
2791	TIMECMD=$(TIME) $(TIMEARGS)
2792
2793	time_one:
2794	ifeq ($(ONE_TIMED_TARGET),)
2795	@echo "Error: You have to pass ONE_TIMED_TARGET to $@"
2796	false
2797	else
2798	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET)"
2799	@$(TIMECMD) $(MAKE) $(ONE_TIMED_TARGET)
2800	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET) [done]"
2801	endif
2802
2803	timed_target:
2804	ifeq ($(TIMED_TARGET),)
2805	@echo "Error: You have to pass TIMED_TARGET to $@"
2806	false
2807	else
2808	@echo "Build time:" > $(TIMELOG)
2809	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2810	@cat $(TIMELOG)
2811	@rm $(TIMELOG)
2812	endif
2813
2814	timed_target_tested:
2815	ifeq ($(TIMED_TARGET),)
2816	@echo "Error: You have to pass TIMED_TARGET to $@"
2817	false
2818	else
2819	@echo "Build time:" > $(TIMELOG)
2820	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2821	$(MAKE) "ONE_TIMED_TARGET=ut" time_one
2822	@cat $(TIMELOG)
2823	@rm $(TIMELOG)
2824	endif
2825
2826	clean_timed_target:
2827	ifeq ($(TIMED_TARGET),)
2828	@echo "Error: You have to pass TIMED_TARGET to $@"
2829	false
2830	else
2831	@echo "Build time:" > $(TIMELOG)
2832	$(MAKE) "ONE_TIMED_TARGET=clean" time_one
2833	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2834	@cat $(TIMELOG)
2835	@rm $(TIMELOG)
2836	endif
2837
2838	# --------------------------------------------------------------------------------
2839
2840	CHECKOUT_MODIFIED=0# set to 1 to temporarily skip test for modifications (do not check in if set to 1)
2841
2842	check_svn_does_not_contain_generated:
2843	ifeq ($(CHECKOUT_MODIFIED),0)
2844	@echo "Testing that build does not modify files in SVN"
2845	@test 0 = `svn status \| wc -l` \|\| ( \
2846	echo "The checkout is not/no longer clean:"; \
2847	svn status; \
2848	echo "- if this fails instantly, your checkout is not clean"; \
2849	echo "- if this fails after other targets, these targets modify checked in data"; \
2850	echo " (a common cause may be that depends are not up to date)"; \
2851	false)
2852	else
2853	grep -Hn 'CHECKOUT_MODIFIED' Makefile
2854	endif
2855
2856	check_svn_ignores_generated:
2857	@test 0 = `svn status \| grep '^\?' \| wc -l` \|\| ( \
2858	echo "There are svn-unignored files:"; \
2859	svn status \| grep '^\?'; \
2860	echo "(all generated files should be svn-ignored)"; \
2861	false)
2862
2863	check_svn_state: check_svn_does_not_contain_generated
2864	$(MAKE) check_svn_ignores_generated
2865	$(MAKE) savetest
2866
2867	things_that_always_should_work: depends proto
2868
2869	post_commit_check:
2870	@echo "---------------------------------------- [Initial]"
2871	$(MAKE) check_svn_state
2872
2873	$(MAKE) clean
2874	@echo "---------------------------------------- [After 'make clean']"
2875	$(MAKE) check_svn_state
2876
2877	$(MAKE) things_that_always_should_work
2878	@echo "---------------------------------------- [After 'make things_that_always_should_work']"
2879	$(MAKE) check_svn_state
2880
2881	$(MAKE) all
2882	@echo "---------------------------------------- [After 'make all']"
2883	$(MAKE) check_svn_state
2884
2885	$(MAKE) things_that_always_should_work
2886	@echo "---------------------------------------- [Final]"
2887	$(MAKE) check_svn_state
2888
2889	# --------------------------------------------------------------------------------
2890	# sanitize arb_ntree; also works for clients (arb_edit4, ...) started from there.
2891
2892	sanitize: all
2893	( \
2894	export "LSAN_OPTIONS=max_leaks=30:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp"; \
2895	echo "sake[1]: Entering directory \`$(ARBHOME)'"; \
2896	$(ARBHOME)/bin/arb_ntree --execute _logged ~/data/test.arb 2>&1 ; \
2897	echo "sake[1]: Leaving directory \`$(ARBHOME)'" \
2898	) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
2899
2900	# --------------------------------------------------------------------------------
2901	# build and test one unit:
2902
2903	build_oneunit:
2904	$(MAKE) "WITHPERL=1" $(UNIT).dummy
2905
2906	oneunit:
2907	ifndef UNIT
2908	@echo "Please define UNIT, e.g. using"
2909	@echo " make \"UNIT=ARBDB/libARBDB\" oneunit"
2910	@echo " make \"UNIT=SL/TREEDISP/TREEDISP\" oneunit"
2911	@echo "(Note: 1st is a shared library, 2nd isn't)"
2912	false
2913	else
2914	@echo "Build time" > $(TIMELOG)
2915	@echo "$(SEP) $(MAKE) build_oneunit"
2916	@$(TIMECMD) $(MAKE) build_oneunit
2917	ifeq ($(UNIT_TESTS),1)
2918	@echo "$(SEP) $(MAKE) run_oneunitstests"
2919	@$(TIMECMD) $(MAKE) run_oneunitstests
2920	endif
2921	@cat $(TIMELOG)
2922	@rm $(TIMELOG)
2923	endif
2924
2925	# --------------------------------------------------------------------------------
2926
2927	build: arb
2928	$(MAKE) check_bin_dep preplib compile_compatibility fig_cure
2929
2930	all:
2931	@echo "Build time" > $(TIMELOG)
2932	# $(MAKE) clean_checked_vect # uncomment to rebuild sources where expected vectorization gets tested
2933	@echo "$(SEP) $(MAKE) all"
2934	@$(TIMECMD) $(MAKE) build
2935	@echo $(SEP)
2936	@echo "made 'all' with success."
2937	@echo "to start arb enter 'arb'"
2938	ifeq ($(UNIT_TESTS),1)
2939	@echo "$(SEP) $(MAKE) run_tests"
2940	@$(TIMECMD) $(MAKE) run_tests
2941	endif
2942	@echo "$(SEP) $(MAKE) all [done]"
2943	ifeq ($(DEBUG),1)
2944	@$(MAKE) save_test_no_error >/dev/null # just show hints
2945	endif
2946	@cat $(TIMELOG)
2947	@rm $(TIMELOG)
2948

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