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Last change on this file was 18311, checked in by westram, 4 years ago
reintegrates 'saicalc' into 'trunk' implements #730 adds: log:branches/saicalc@18141:18310
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 81.2 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	# $(MACH) name of the machine (LINUX or DARWIN; see config.makefile)
40	# DEBUG compiles the DEBUG sections
41	# DEBUG_GRAPHICS all X-graphics are flushed immediately (for debugging)
42	# ARB_64=0/1 1=>compile 64 bit version
43	# UNIT_TESTS=0/1 1=>compile in unit tests and call them after build
44	# COVERAGE=0/1/2 compile in gcov support (useful together with UNIT_TESTS=1)
45	# 0=no, 1+2=compile in, 1=show
46	# STABS=0/1 force stabs format? (0 = "use default format")
47	# SANITIZE=0/#/all use Sanitizer? (defaults to 0,
48	# 1=AddressSanitizer+LeakSanitizer,
49	# 2=UndefinedBehaviorSanitizer,
50	# combine bit-values to activate multiple Sanitizers,
51	# specify 'all' to activate all)
52	# SHOWTODO=0/1 activate TODO-warnings? (defaults to 0, except for ralf)
53	#
54	# -----------------------------------------------------
55	# The ARB source code is aware of the following defines:
56	#
57	# NDEBUG doesn't compile the DEBUG sections
58	# DEVEL_$(DEVELOPER) developer-dependent flag (enables you to have private sections in code)
59	# DEVELOPER='ANY' (default setting) will be ignored
60	# configurable in config.makefile
61	#
62	# -----------------------------------------------------
63	# Read configuration
64	include config.makefile
65	CONFIG_MAKEFILE_FOUND=$(strip $(wildcard config.makefile))
66
67	# set defaults for variables commented out in config.makefile:
68	ifndef DARWIN
69	DARWIN:=0
70	endif
71	ifndef LINUX
72	LINUX:=0
73	endif
74	ifndef DEBIAN
75	DEBIAN:=0
76	endif
77	ifndef REDHAT
78	REDHAT:=0
79	endif
80	ifndef ARB_64
81	ARB_64=1#default to 64bit
82	endif
83
84	# Variables allowed for injection [InjectedEnvironment]
85	# (alternatively initialize them with '?=', e.g. done for XLIBS and XINCLUDES)
86	# In both cases add them to SOURCE_TOOLS/export2sub
87	ifndef XML_INCLUDES
88	XML_INCLUDES=
89	endif
90	ifndef XAW_LIBS
91	XAW_LIBS=
92	endif
93
94
95	ifneq ($(CONFIG_MAKEFILE_FOUND),)
96	ifneq ($(DARWIN)$(LINUX),10)
97	ifneq ($(DARWIN)$(LINUX),01)
98	$(error exactly one of DARWIN=1 or LINUX=1 has to be defined (got:$(DARWIN)$(LINUX)))
99	endif
100	endif
101	endif
102
103	# compiler settings:
104	ifneq ($(CC),use__A_CC__instead_of__CC)
105	A_CC:=$(CC)# compile C
106	A_CXX:=$(CXX)# compile C++
107
108	# uncomment to ensure no submakefile uses CC and CXX directly
109	override CC:=use__A_CC__instead_of__CC
110	override CXX:=use__A_CXX__instead_of__CXX
111	endif
112
113	export CC CXX A_CC A_CXX
114
115	# unconditionally prepend $(ARBHOME)/lib to LD_LIBRARY_PATH if not found
116	ifeq ($(findstring $(ARBHOME)/lib,$(LD_LIBRARY_PATH)),)
117	LD_LIBRARY_PATH:=${ARBHOME}/lib:$(LD_LIBRARY_PATH)
118	endif
119
120	# store LD_LIBRARY_PATH to circumvent SIP restrictions:
121	ARBBUILD_LIBRARY_PATH:=$(LD_LIBRARY_PATH)
122
123	FORCEMASK = umask 002
124	NODIR=--no-print-directory
125
126	SED:=$(ARBHOME)/SH/arb_sed
127	READLINK:=$(ARBHOME)/SH/arb_readlink
128
129	# ---------------------- compiler version detection
130
131	# supported gcc versions:
132	ALLOWED_gcc_VERSIONS=\
133	4.4.3 4.4.5 4.4.6 4.4.7 \
134	4.5.2 \
135	4.6.1 4.6.2 4.6.3 4.6.4 \
136	4.7.1 4.7.2 4.7.3 4.7.4 \
137	4.8.0 4.8.1 4.8.2 4.8.3 4.8.4 4.8.5 \
138	4.9.0 4.9.1 4.9.2 4.9.3 4.9.4 \
139	5.1.0 5.2.0 5.3.0 5.4.0 5.5.0 \
140	6.1.0 6.2.0 6.3.0 6.4.0 6.5.0 \
141	7.1.0 7.2.0 7.3.0 7.4.0 7.5.0 \
142	8.1.0 8.2.0 8.3.0 \
143	9.1.0 9.2.0 \
144
145	# Note: starting with version 5, arb silently accepts any subversion number
146	# above zero. See SOURCE_TOOLS/arb_compiler_version.pl@acceptSubVersions
147	#
148	# This may cause problems when manually checking for compiler versions in code
149	# (GCC_VERSION_CODE is not affected, GCC_PATCHLEVEL_CODE may cause problems!)
150	# ----------------------
151
152	COMPILER_INFO:=$(shell SOURCE_TOOLS/arb_compiler_version.pl $(A_CXX))
153	COMPILER_NAME:=$(word 1,$(COMPILER_INFO))
154	COMPILER_VERSION:=$(word 2,$(COMPILER_INFO))
155
156	USE_CLANG:=0
157	ifneq ($(COMPILER_NAME),gcc)
158	ifeq ($(COMPILER_NAME),clang)
159	USE_CLANG:=1
160	else
161	ifeq ($(COMPILER_VERSION),4.6.4)
162	# gcc version 4.6.4 segfaults when dumping symbols for detection (silently accept as gcc)
163	COMPILER_NAME:=gcc
164	else
165	$(error failed to detect COMPILER_NAME (got '$(COMPILER_NAME)', expected 'clang' or 'gcc'))
166	endif
167	endif
168	endif
169
170	ifeq ($(USE_CLANG),1)
171	# accept all clang versions:
172	ALLOWED_COMPILER_VERSIONS=$(COMPILER_VERSION)
173	else
174	ALLOWED_COMPILER_VERSIONS=$(ALLOWED_gcc_VERSIONS)
175	endif
176
177	COMPILER_VERSION_ALLOWED=$(strip $(subst ___,,$(foreach version,$(ALLOWED_COMPILER_VERSIONS),$(findstring ___$(version)___,___$(COMPILER_VERSION)___))))
178
179	#---------------------- split gcc version
180
181	SPLITTED_VERSION:=$(subst ., ,$(COMPILER_VERSION))
182
183	USE_GCC_MAJOR:=$(word 1,$(SPLITTED_VERSION))
184	USE_GCC_MINOR:=$(word 2,$(SPLITTED_VERSION))
185	USE_GCC_PATCHLEVEL:=$(word 3,$(SPLITTED_VERSION))
186
187	USE_GCC_452_OR_HIGHER:=
188	USE_GCC_46_OR_HIGHER:=
189	USE_GCC_47_OR_HIGHER:=
190	USE_GCC_48_OR_HIGHER:=
191	USE_GCC_49_OR_HIGHER:=
192	USE_GCC_50_OR_HIGHER:=
193	USE_GCC_60_OR_HIGHER:=
194	USE_GCC_70_OR_HIGHER:=
195	USE_GCC_80_OR_HIGHER:=
196	USE_GCC_90_OR_HIGHER:=
197
198	ifeq ($(USE_CLANG),0)
199	ifeq ($(USE_GCC_MAJOR),4)
200	ifeq ($(USE_GCC_MINOR),5)
201	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),23456789)','')
202	USE_GCC_452_OR_HIGHER:=yes
203	endif
204	else
205	ifneq ('$(findstring $(USE_GCC_MINOR),6789)','')
206	USE_GCC_452_OR_HIGHER:=yes
207	USE_GCC_46_OR_HIGHER:=yes
208	ifneq ($(USE_GCC_MINOR),6)
209	USE_GCC_47_OR_HIGHER:=yes
210	ifneq ($(USE_GCC_MINOR),7)
211	USE_GCC_48_OR_HIGHER:=yes
212	ifneq ($(USE_GCC_MINOR),8)
213	USE_GCC_49_OR_HIGHER:=yes
214	endif
215	endif
216	endif
217	endif
218	endif
219	else
220	# gcc 5.x or higher
221	USE_GCC_452_OR_HIGHER:=yes
222	USE_GCC_46_OR_HIGHER:=yes
223	USE_GCC_47_OR_HIGHER:=yes
224	USE_GCC_48_OR_HIGHER:=yes
225	USE_GCC_49_OR_HIGHER:=yes
226	USE_GCC_50_OR_HIGHER:=yes
227	ifneq ($(USE_GCC_MAJOR),5)
228	# gcc 6.x or higher
229	USE_GCC_60_OR_HIGHER:=yes
230	ifneq ($(USE_GCC_MAJOR),6)
231	# gcc 7.x or higher
232	USE_GCC_70_OR_HIGHER:=yes
233	ifneq ($(USE_GCC_MAJOR),7)
234	# gcc 8.x or higher
235	USE_GCC_80_OR_HIGHER:=yes
236	ifneq ($(USE_GCC_MAJOR),8)
237	# gcc 9.x or higher
238	USE_GCC_90_OR_HIGHER:=yes
239	endif
240	endif
241	endif
242	endif
243	endif
244	endif
245
246	#---------------------- define special directories for non standard builds
247
248	ifeq ($(DARWIN),1)
249	OSX_FW:=/System/Library/Frameworks
250	OSX_FW_OPENGL:=$(OSX_FW)/OpenGL.framework/Versions/A/Libraries
251	OSX_FW_GLUT:=$(OSX_FW)/GLUT.framework/Versions/A/Libraries
252	OSX_FW_IMAGEIO:=$(OSX_FW)/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources
253	endif
254
255	#---------------------- SSE vectorization
256	# for details about vectorization checks see SOURCE_TOOLS/vectorize.README
257
258	DISABLE_VECTORIZE_CHECK:=0# set to 1 to completely disable vectorization checks
259	TRACE_MISSED_VECTORIZATIONS:=0# set to 1 to activate detailed output about failed vectorizations
260	# (does also show details about successful vectorized loops, which are not optimal)
261	VECTORIZATION_CHECK_CANDIDATES:=0# set to 1 to show vectorizations that may be checked
262	# (for yet unchecked files)
263	# Note: TRACE_MISSED_VECTORIZATIONS and VECTORIZATION_CHECK_CANDIDATES cannot be used together!
264
265	#----------------------
266
267	ifeq ($(DARWIN),1)
268	LINK_STATIC=1# link static
269	else
270	LINK_STATIC=0# link dynamically
271	# LINK_STATIC=1# link static (testing only)
272	endif
273
274	shared_cflags :=# flags for shared lib compilation
275	clflags :=# linker flags (when passed through gcc)
276	extended_warnings :=# warning flags for C and C++-compiler
277	extended_cpp_warnings :=# warning flags for C++-compiler only
278
279	ifeq ($(DEBUG),0)
280	dflags := -DNDEBUG# defines
281	ifeq ($(USE_CLANG),1)
282	cflags := -O3# compiler flags (C and C++)
283	else
284	clflags += -Wl,-O2# passthrough linker flags
285	# ------- standard optimization:
286	cflags := -O3# compiler flags (C and C++)
287	# ------- test changed optimization (DISABLE_VECTORIZE_CHECK for -O2 or lower):
288	# cflags := -O2# do not commit uncommented!
289	# DISABLE_VECTORIZE_CHECK:=1
290	endif
291	endif
292
293	ifeq ($(DEBIAN),1)
294	clflags += -Wl,-rpath=/usr/lib/arb/lib -Wl,-z,relro
295	endif
296
297	ifeq ($(DEBUG),1)
298	dflags := -DDEBUG
299
300	gdb_common := -g -g3 -ggdb -ggdb3
301
302	DBGOPTI:=-O0
303	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
304	DBGOPTI:=-Og
305	endif
306
307	ifeq ($(STABS),1)
308	cflags := $(DBGOPTI) $(gdb_common) -gstabs+ # using stabs+ (enable this for bigger debug session: debugs inlines, quick var inspect, BUT valgrind stops working :/)
309	else
310	cflags := $(DBGOPTI) $(gdb_common) # (using dwarf - cant debug inlines here, incredible slow on showing variable content)
311	endif
312
313	# cflags := $(DBGOPTI) $(gdb_common) -gdwarf-3 # (specify explicit dwarf format)
314	# cflags := $(DBGOPTI) $(gdb_common) -gstabs # using stabs (same here IIRC)
315	# cflags := -O2 $(gdb_common) # use this for callgrind (force inlining)
316
317	ifeq ($(DARWIN),0)
318	clflags += -Wl,-g
319	# Note:
320	# Previously '-Wl,-noinhibit-exec' was added to 'clflags' here,
321	# to fix some issues with launchpad binutils (see [12972]).
322	# But that change also caused 'undefined symbols' NOT to be reported as errors
323	# at link time, producing executables that fail at runtime :/
324	endif
325
326	ifeq ($(DEBUG_GRAPHICS),1)
327	dflags += -DDEBUG_GRAPHICS
328	endif
329
330	endif # DEBUG only
331
332	# ------------------------------ POST_COMPILE - control how much you get spammed
333	# (please do not change default in SVN)
334	POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl
335
336	# POST_COMPILE += --original # dont modify compiler output
337	# POST_COMPILE += --hide-Noncopyable-advices
338	# POST_COMPILE += --show-useless-Weff++
339	# POST_COMPILE += --no-warnings
340	# POST_COMPILE += --only-first-error
341	# POST_COMPILE += --no-warnings --only-first-error
342
343	# always pass used compiler version to postcompile:
344	POST_COMPILE += --compiler=$(COMPILER_VERSION)
345
346	# ------------------------------
347
348	# Enable extra warnings
349	extended_warnings :=
350	extended_cpp_warnings :=
351
352	# C and C++
353	extended_warnings += -Wwrite-strings -Wunused -Wno-aggregate-return -Wshadow
354
355	# C++ only
356	extended_cpp_warnings += -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute
357	extended_cpp_warnings += -Wctor-dtor-privacy
358	# extended_cpp_warnings += -Wfloat-equal
359
360	extended_cpp_warnings += -Wmissing-noreturn
361	# extended_cpp_warnings += -Wold-style-cast# (warns about 28405 old-style casts)
362	extended_cpp_warnings += -Winit-self
363	extended_cpp_warnings += -Wstrict-aliasing
364	extended_cpp_warnings += -Wextra
365
366	# ------- above only warning-options already available in gcc 4.4.3
367
368	# -Weffc++ broken in 4.7.x series
369	# gcc 4.7.3 crashes on GenomeImport.cxx when -Weffc++ is active
370	# (bug reported https://gcc.gnu.org/bugzilla/show_bug.cgi?id=56923; apparently wont be fixed for 4.7-series)
371	# gcc 4.7.4 crashes on DBwriter.cxx when -Weffc++ is active
372	WEFFC_BROKEN:=0
373	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
374	ifneq ('$(USE_GCC_48_OR_HIGHER)','yes')
375	WEFFC_BROKEN:=1
376	endif
377	endif
378	ifeq ('$(WEFFC_BROKEN)','0')
379	extended_cpp_warnings += -Weffc++
380	endif
381
382	# turn off -Wmaybe-uninitialized in debug mode (gets activated with -Wextra). too many bogus warnings
383	ifeq ($(DEBUG),1)
384	ifeq ($(USE_CLANG),0)
385	extended_cpp_warnings += -Wno-maybe-uninitialized
386	endif
387	endif
388
389	SUGGEST_FINAL:=
390
391	ifeq ('$(USE_GCC_452_OR_HIGHER)','yes')
392	extended_cpp_warnings += -Wlogical-op# gcc 4.5.2
393	endif
394	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
395	extended_cpp_warnings += -Wzero-as-null-pointer-constant# gcc 4.7
396	endif
397	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
398	extended_cpp_warnings += -Wunused-local-typedefs# available since gcc 4.7 (but fails for each STATIC_ASSERT, so enable only for Cxx11)
399	endif
400	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
401	extended_cpp_warnings += -Wswitch-bool
402	extended_cpp_warnings += -Wlogical-not-parentheses
403	extended_cpp_warnings += -Wsizeof-array-argument
404	extended_cpp_warnings += -Wbool-compare
405
406	SUGGEST_FINAL:=yes
407	endif
408	ifeq ('$(USE_GCC_60_OR_HIGHER)','yes')
409	extended_cpp_warnings += -Wduplicated-cond
410	endif
411	ifeq ('$(USE_GCC_80_OR_HIGHER)','yes')
412	extended_cpp_warnings += -Wmultistatement-macros
413	endif
414
415	ifeq ('$(COMPILER_VERSION)','8.3.0')
416	# switch off final suggestions for 8.3.0:
417	SUGGEST_FINAL:=no
418	endif
419
420	ifeq ('$(USE_GCC_90_OR_HIGHER)','yes')
421	# have a workaround for suggest-final -> activate
422	SUGGEST_FINAL:=yes
423	endif
424
425	ifeq ($(DEVELOPER),RELEASE)
426	# switch off final suggestions in RELEASE:
427	SUGGEST_FINAL:=no
428	endif
429	# suggest final:
430	ifeq ('$(SUGGEST_FINAL)','yes')
431	extended_cpp_warnings += -Wsuggest-final-types
432	extended_cpp_warnings += -Wsuggest-final-methods
433	dflags += -DSUGGESTS_FINAL
434	endif
435
436	#---------------------- turn off clang bogus warnings
437
438	ifeq ($(USE_CLANG),1)
439	# -Wmismatched-tags warns about struct/class mismatch in forward declarations (which is explicitely allowed)
440	# -Wchar-subscripts reports too many bogus warnings for "array['x']" (when 'x' is known to be in range [0..128])
441	# -Wunused-private-field report too many false positives (currently ~ 2 of 3)
442	# -Wstring-plus-int warns about common ARB coding practice
443	# -Wgnu-static-float-init warns about accepted GNU extension
444	extended_cpp_warnings += -Wno-mismatched-tags -Wno-char-subscripts -Wno-unused-private-field -Wno-string-plus-int
445	ifeq ('$(COMPILER_VERSION)','4.2.1')
446	# jenkins build (doesn't know switch -Wno-gnu-static-float-init)
447	extended_cpp_warnings += -Wno-gnu
448	else
449	extended_cpp_warnings += -Wno-gnu-static-float-init
450	endif
451	endif
452
453	#---------------------- developer
454
455	ifneq ($(DEVELOPER),ANY) # ANY=default setting (skip all developer specific code)
456	dflags += -DDEVEL_$(DEVELOPER)# activate developer/release specific code
457	endif
458
459	#---------------------- activate TODO warnings?
460
461	ifndef SHOWTODO
462	ifeq ($(DEVELOPER),RALF)
463	SHOWTODO:=1
464	else
465	SHOWTODO:=0
466	endif
467	endif
468	ifeq ($(SHOWTODO),1)
469	dflags += -DWARN_TODO# activate "TODO" warnings
470	endif
471
472	#---------------------- activate threads?
473	# only useful if compiler is able to compile Cxx11 or better
474
475	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
476	# see also ./TEMPLATES/cxxforward.h@USE_Cxx11
477	cflags += -pthread
478	clflags += -pthread
479	endif
480
481	#---------------------- activate Sanitizers?
482
483	ASAN_OPTIONS:=handle_segv=0:color=0
484	ASAN_OPTIONS+=:detect_leaks=1 # comment-out to disable leak-detection
485	ASAN_OPTIONS+=:check_initialization_order=1
486	# ASAN_OPTIONS+=:abort_on_error=1
487
488	# suppressions: SOURCE_TOOLS/arb.leaksan.supp
489	LSAN_OPTIONS:=max_leaks=3:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp
490
491	UBSAN_OPTIONS:=print_stacktrace=1
492
493	ifndef SANITIZE
494	SANITIZE:=0
495	endif
496
497	SANITIZE_ADDRESS:=0
498	SANITIZE_UNDEFINED:=0
499
500	ifneq ($(SANITIZE),0)
501	ifeq ($(SANITIZE),all)
502	SANITIZE:=3
503	endif
504
505	ifeq ($(SANITIZE),1)
506	SANITIZE_ADDRESS:=1
507	else
508	ifeq ($(SANITIZE),2)
509	SANITIZE_UNDEFINED:=1
510	else
511	ifeq ($(SANITIZE),3)
512	SANITIZE_ADDRESS:=1
513	SANITIZE_UNDEFINED:=1
514	else
515	$(error Unknown value '$(SANITIZE)' specified for SANITIZE in config.makefile)
516	endif
517	endif
518	endif
519	endif
520
521	ifeq ($(SANITIZE_ADDRESS),1)
522	ifneq ('$(USE_GCC_48_OR_HIGHER)','yes')
523	$(info AddressSanitizer not usable with gcc $(COMPILER_VERSION) - disabled)
524	SANITIZE_ADDRESS:=0
525	else
526	ifneq ('$(USE_GCC_49_OR_HIGHER)','yes')
527	$(info LeakSanitizer does not work with gcc $(COMPILER_VERSION) - disabled)
528	# need to disable AddressSanitizer (otherwise build fails; only affects gcc 4.8.x series)
529	SANITIZE_ADDRESS:=0
530	endif
531	endif
532	endif
533
534	ifeq ($(SANITIZE_UNDEFINED),1)
535	ifneq ('$(USE_GCC_49_OR_HIGHER)','yes')
536	$(info UndefinedBehaviorSanitizer not usable with gcc $(COMPILER_VERSION) - disabled)
537	SANITIZE_UNDEFINED:=0
538	endif
539	endif
540
541	SANITIZE_ANY:=0
542	ifeq ($(SANITIZE_ADDRESS),1)
543	SANITIZE_ANY:=1
544	endif
545	ifeq ($(SANITIZE_UNDEFINED),1)
546	SANITIZE_ANY:=1
547	endif
548
549	# vectorization fails if sanitizer active where it normally succeeds -> disable check
550	ifeq ($(SANITIZE_ANY),1)
551	$(info disabling vectorize checks. would fail with sanitized code)
552	DISABLE_VECTORIZE_CHECK:=1
553	else
554	$(info no sanitizer enabled. reset: SANITIZE=0)
555	SANITIZE:=0
556	endif
557
558	# deactivate some bogus warnings occurring when sanitizing NDEBUG version
559	# (do not disable for future gcc-version >= 8.x -> test again when available)
560	ifeq ($(SANITIZE_ANY),1)
561	ifeq ($(DEBUG),0)
562	ifneq ('$(USE_GCC_80_OR_HIGHER)','yes')
563	extended_cpp_warnings += -Wno-format-overflow
564	extended_cpp_warnings += -Wno-maybe-uninitialized
565	endif
566	endif
567	endif
568
569	#---------------------- 32 or 64 bit
570
571	cross_cflags:=
572	cross_lflags:=
573	cross_clflags:=
574
575	ifeq ($(ARB_64),1)
576	dflags += -DARB_64
577	shared_cflags += -fPIC
578	CROSS_LIB:=# empty => autodetect below
579	ifeq ($(DARWIN),1)
580	cross_cflags += -arch x86_64
581	cross_lflags += -arch x86_64
582	cross_clflags += -arch x86_64
583	endif
584	else
585	CROSS_LIB:=/lib
586	endif
587
588	cflags += $(cross_cflags)
589	clflags += $(cross_clflags)
590
591	ifeq ('$(CROSS_LIB)','')
592	# autodetect libdir
593	ifeq ($(ARB_64),1)
594	CROSS_LIB:=$(shell (test -d /lib64 && echo lib64) \|\| echo lib)
595	else
596	CROSS_LIB:=$(shell (test -d /lib32 && echo lib32) \|\| echo lib)
597	endif
598	endif
599
600	#---------------------- unit tests
601
602	ifndef UNIT_TESTS
603	UNIT_TESTS=0#default is "no tests"
604	endif
605	ifeq ($(UNIT_TESTS),1)
606	dflags += -DUNIT_TESTS
607	UNIT_TESTER_LIB=UNIT_TESTER/UNIT_TESTER.a
608	else
609	UNIT_TESTER_LIB=
610	endif
611
612	#---------------------- use gcov
613
614	ifndef COVERAGE
615	COVERAGE=0#default is "no"
616	endif
617	ifneq ($(COVERAGE),0)
618	GCOV_FLAGS=--coverage
619	else
620	GCOV_FLAGS=
621	endif
622
623	cflags += $(GCOV_FLAGS)
624	clflags += $(GCOV_FLAGS)
625	cross_lflags += $(GCOV_FLAGS)
626
627	#---------------------- other flags
628
629	dflags += -D$(MACH) # define machine
630
631	ifeq ($(DARWIN),1)
632	shared_cflags += -fno-common
633	else
634	dflags += $(shell getconf LFS_CFLAGS)
635	endif
636
637	cflags += -pipe
638	cflags += -fmessage-length=0# dont wrap compiler output
639	cflags += -fshow-column# show columns
640	cflags += -funit-at-a-time
641	cflags += -fPIC
642	cflags += -fno-common# link all global data into one namespace
643	cflags += -fstrict-aliasing# gcc 3.4
644
645
646	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
647	cflags += -fno-diagnostics-show-caret#gcc 4.8 (4.7.?)
648	endif
649	#cflags += -save-temps# uncomment to see preprocessor output
650
651	#---------------------- various sanitizers
652	# There are some disabled tests in CORE/arb_misc.cxx@sanitizers
653	# which trigger sanitizer reports.
654
655	ifeq ($(SANITIZE_ANY),1)
656	cflags += -ggdb3 -fno-omit-frame-pointer
657	endif
658
659	# activate AddressSanitizer+LeakSanitizer?
660	ifeq ($(SANITIZE_ADDRESS),1)
661	cflags += -fsanitize=address
662	clflags += -fsanitize=address
663	dflags += -DLEAKS_SANITIZED
664	endif
665
666	# activate UndefinedBehaviorSanitizer?
667	ifeq ($(SANITIZE_UNDEFINED),1)
668	cflags += -fsanitize=undefined
669	clflags += -fsanitize=undefined
670	dflags += -DUNDEF_SANITIZED
671	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
672	# abort on runtime errors
673	cflags += -fno-sanitize-recover=all
674	endif
675	#
676	# Note: alignment-sanitizer is deactivated for ARBDB and PROBE!
677	ifeq ('$(DEBUG)','1')
678	ifeq ($(USE_GCC_MAJOR),4)
679	ifeq ($(USE_GCC_MINOR),9)
680	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),01)','')
681	# workaround https://gcc.gnu.org/bugzilla/show_bug.cgi?id=63531 for 4.9.0 + 4.9.1
682	# (problem is fixed in 4.9.2 release)
683	extended_cpp_warnings:=$(subst -Weffc++,,$(extended_cpp_warnings))
684	endif
685	endif
686	endif
687	endif
688	endif
689
690	#---------------------- X11 location
691
692	ifeq ($(DARWIN),1)
693	XHOME:=$(PREFIX)
694	else
695	ifeq ($(DEBIAN),1)
696	XHOME:=$(PREFIX)
697	else
698	XHOME:=/usr/X11R6
699	endif
700	endif
701
702	XINCLUDES ?= -I$(XHOME)/include
703	XLIBS ?= -L$(XHOME)/$(CROSS_LIB)
704	ifeq ($(DARWIN),1)
705	XINCLUDES += -I$(OSX_FW)/GLUT.framework/Headers -I$(OSX_FW)/OpenGL.framework/Headers -I$(OSX_SDK)/usr/include/krb5
706
707	XLIBS += -lXm -lpng -lz -lXt -lX11 -lXext -lXp -lXmu -lXi
708	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGL.dylib:$(OSX_FW_OPENGL)/libGL.dylib
709	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGLU.dylib:$(OSX_FW_OPENGL)/libGLU.dylib
710	else
711	XLIBS += -lXm -lXpm -lXt -lXext -lX11
712	endif
713
714	#---------------------- open GL
715
716	ifeq ($(OPENGL),1)
717	cflags += -DARB_OPENGL # activate OPENGL code
718	GL := gl # this is the name of the OPENGL base target
719	GL_LIB_SYS := -lGL -lGLU
720	GL_LIB_ARB := -L$(ARBHOME)/GL/glAW -lglAW
721
722	ifeq ($(DARWIN),1)
723	GL_LIB_SYS += -lpthread
724	endif
725
726	GL_PNGLIBS_ARB := -L$(ARBHOME)/GL/glpng -lglpng_arb
727	GL_PNGLIBS_SYS := -lpng
728
729	GLEWLIB := -lGLEW -lGLw
730	ifeq ($(DARWIN),1)
731	GLUTLIB := -glut
732	else
733	GLUTLIB := -lglut
734	endif
735
736	GL_LIBS_SYS := $(GL_LIB_SYS) $(GL_PNGLIBS_SYS) $(GLEWLIB) $(GLUTLIB)
737	GL_LIBS_ARB := $(GL_LIB_ARB) $(GL_PNGLIBS_ARB)
738
739	RNA3D_LIB := RNA3D/RNA3D.a
740	else
741	GL_LIBS_ARB:=# no opengl -> no libs
742	GL_LIBS_SYS:=# no opengl -> no libs
743	GL:=# dont build ARB openGL libs
744
745	RNA3D_LIB :=
746	endif
747
748	RNA3D_LIB_4_DEPENDS := RNA3D/RNA3D.a
749
750	GL_LIBS:=$(GL_LIBS_ARB) $(GL_LIBS_SYS)
751
752	#---------------------- tiff lib:
753
754	TIFFLIBS := -ltiff
755
756	#---------------------- XML lib:
757
758	XMLLIBS := -lxerces-c
759
760	#---------------------- glib:
761
762	ARB_NEEDED_GLIB=glib-2.0
763
764	ARB_GLIB_INCLUDE:=$(strip $(shell pkg-config --cflags $(ARB_NEEDED_GLIB)))
765	ARB_GLIB_LIBS:=$(strip $(shell pkg-config --libs $(ARB_NEEDED_GLIB)))
766
767	#---------------------- basic libs:
768
769	SYSLIBS:=
770	ifeq ($(DARWIN),1)
771	SYSLIBS += -lstdc++
772	else
773	SYSLIBS += -lm $(ARB_GLIB_LIBS)
774	endif
775
776	#---------------------- include symbols?
777
778	ifeq ($(TRACESYM),1)
779	ifeq ($(USE_CLANG),0)
780	cflags += -rdynamic
781	clflags += -rdynamic -Wl,--export-dynamic
782	endif
783	endif
784
785	#---------------------- system dependent commands
786
787	ifeq ($(DARWIN),1)
788	TIME:=gtime
789	else
790	TIME:=/usr/bin/time
791	endif
792
793	#---------------------- SSE vectorizer
794	# for details see SOURCE_TOOLS/vectorize.README
795
796	ifeq ($(DEBUG),0)
797	ifeq ($(USE_GCC_49_OR_HIGHER),yes)
798	ifeq ($(DISABLE_VECTORIZE_CHECK),0)
799	cflags += -fopt-info-vec
800	cflags += -fopt-info-vec-missed
801	ifeq ($(TRACE_MISSED_VECTORIZATIONS),1)
802	# Shows reasons for unsuccessful vectorization:
803	cflags += -ftree-vectorizer-verbose=10
804	POST_COMPILE += --dump-loop-optimization
805	ifeq ($(VECTORIZATION_CHECK_CANDIDATES),1)
806	$(error TRACE_MISSED_VECTORIZATIONS and VECTORIZATION_CHECK_CANDIDATES may not be used together!)
807	endif
808	endif
809	ifeq ($(VECTORIZATION_CHECK_CANDIDATES),1)
810	POST_COMPILE += --loop-optimization-candi
811	endif
812	POST_COMPILE += --check-loop-optimization
813	endif
814	else
815	ifeq ($(USE_GCC_48_OR_HIGHER),yes)
816	# no automatic vectorization-check for gcc<4.9.0
817	# -> uncomment the next 2 lines and grep the spam it will produce for 'vectorized.*loops'
818	# cflags += -fopt-info -fopt-info-vec-missed
819	# POST_COMPILE += --original
820	endif
821	endif
822	endif
823
824	#---------------------- stop early on broken flags/compiler combination
825
826	ifeq ($(DEBUG),0)
827	ifeq ($(SANITIZE_ANY),1)
828	ifeq ('$(COMPILER_VERSION)','4.9.1')
829	$(error compiling DEBUG=0 + SANITIZE!=0 crashes with gcc $(COMPILER_VERSION) (gcc 4.9.2 works))
830	endif
831	endif
832	endif
833
834	#---------------------- differences between linking executables and shared libs:
835
836	# executables:
837	ifeq ($(DARWIN),1)
838	blflags:=$(clflags)
839	else
840	blflags:=$(clflags) -Wl,--no-undefined
841	endif
842
843	# shared libraries
844	llflags:=$(clflags)
845
846	# dont use clflags below
847	clflags:=
848
849	# -------------------------------------------------------------------------
850	# Don't put any machine/version/etc conditionals below!
851	# (instead define variables above)
852	# -------------------------------------------------------------------------
853
854	cflags += -W -Wall $(dflags) $(extended_warnings)
855	cxxflags := $(extended_cpp_warnings)
856
857	# add CFLAGS + CPPFLAGS from environment for DEBIAN build
858	ifeq ($(DEBIAN),1)
859	cflags := $(CFLAGS) $(cflags)
860	cxxflags += $(CPPFLAGS)
861	endif
862
863	ifeq ('$(USE_CLANG)','1')
864	# none of the following standards works with clang3.3 (under linux) => dont use standard (as done before r15516)
865	# cxxflags += -std=gnu++11
866	# cxxflags += -std=gnu++0x
867	else
868	ifeq ('$(USE_GCC_60_OR_HIGHER)','yes')
869	cxxflags += -std=gnu++14# see also TEMPLATES/cxxforward.h@USE_Cxx14
870	else
871	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
872	cxxflags += -std=gnu++11# see also TEMPLATES/cxxforward.h@USE_Cxx11
873	else
874	# gcc versions between 4.3 (lowest supported) and <4.7
875	cxxflags += -std=gnu++0x
876	endif
877	endif
878	endif
879
880	LINK_STATIC_LIB := $(AR) -csq# link static lib
881	LINK_EXECUTABLE := $(A_CXX) $(blflags) -o# link executable (c++)
882
883	ifeq ($(LINK_STATIC),1)
884	SHARED_LIB_SUFFIX = a# static lib suffix
885	LINK_SHARED_LIB := $(LINK_STATIC_LIB)
886	else
887	SHARED_LIB_SUFFIX = so# shared lib suffix
888	LINK_SHARED_LIB := $(A_CXX) $(llflags) -shared -o# link shared lib
889	endif
890
891	ifeq ($(DARWIN),1)
892	lflags4perl:=
893	else
894	lflags4perl:=$(cross_lflags) -shared
895	endif
896
897	# delete variables unused below
898	blflags:=
899	llflags:=
900
901	# other used tools
902	MAKEDEPEND_PLAIN = makedepend
903	MAKEDEPEND = $(FORCEMASK);$(MAKEDEPEND_PLAIN)
904
905	#SEP:=--------------------------------------------------------------------------------
906	SEP=[`date +%M:%S.%N`] ------------------------------------------------
907	# to analyse timings run
908	# make -j9 clean; make -j9 all \| grep '^\[' \| sort
909	# make -j9 "TIMED_TARGET=perl" clean_timed_target \| grep '^\[' \| sort
910
911	# ------------------------------------------------------------ DYNLIBDEFS
912	# various dynamic library definitions for linking executables:
913	#
914	# SYSLIBS: system libraries needed by database lib
915	# ARBDB_LIB: database lib
916	# DBSYS_LIBS: executable using database (but no GUI)
917	# GUI_LIBS: executable using database and GUI (arb gui uses database)
918	#
919	# Note: definitions exported to sub-makefiles are described in SOURCE_TOOLS/parent_make.txt
920
921	CORE_LIB=-lCORE
922	ARBDB_LIB=-lARBDB $(CORE_LIB)
923	DBSYS_LIBS = $(ARBDB_LIB) $(SYSLIBS)
924
925	GUI_LIBS_PREFIX:=
926	ifeq ($(DARWIN),1)
927	# this seem to be added at wrong place, since opengl is only needed to link EDIT4
928	GUI_LIBS_PREFIX:=-framework GLUT -framework OpenGL
929	endif
930
931	GUI_LIBS=$(GUI_LIBS_PREFIX) $(DBSYS_LIBS) -lAWT -lWINDOW $(XLIBS)
932
933	LIBPATH = -L$(ARBHOME)/lib
934
935	DEST_LIB = lib
936	DEST_BIN = bin
937
938	CC_INCLUDES := -I. -I$(ARBHOME)/INCLUDE $(XINCLUDES) $(ARB_GLIB_INCLUDE)
939	CXX_INCLUDES := $(CC_INCLUDES)
940	MAKEDEPENDFLAGS := -- -DARB_OPENGL -DUNIT_TESTS -D__cplusplus -I. -Y$(ARBHOME)/INCLUDE
941
942	# ---------------------------------------
943	# wrap main()
944
945	use_ARB_main=$(ARBHOME)/SOURCE_TOOLS/arb_main_cpp.o
946	use_ARB_main_C=$(ARBHOME)/SOURCE_TOOLS/arb_main_c.o
947
948	# -----------------------------------------
949	# unique build-id
950	# - different for different calls of make
951	# - constant in recursive calls
952
953	ifndef ARBBID
954	ARBBID:=$(shell SOURCE_TOOLS/uniqueID.sh)
955	endif
956
957	# -----------------------------------------
958	# export variables to submakefiles
959
960	include SOURCE_TOOLS/export2sub
961
962	# do not define (exported) variables below this point
963
964	# -------------------------
965	# Main arb targets:
966	# -------------------------
967
968	first_target:
969	$(MAKE) checks
970	@echo $(SEP)
971	@echo 'Main targets:'
972	@echo ''
973	@echo ' all - Compile ARB + TOOLs + and copy shared libs + link foreign software'
974	@echo ' (That is most likely the target you want)'
975	@echo ''
976	@echo ' clean - remove generated files ("SUBDIR/SUBDIR.clean" to clean only SUBDIR)'
977	@echo ' rebuild - clean + all'
978	@echo ' cleanlinked - remove all binaries'
979	@echo ' relink - cleanlinked + all (=relink all from objects)'
980	@echo ''
981	@echo 'Some often used sub targets (make all makes them all):'
982	@echo ''
983	@echo ' arb - Just compile ARB (but none of the integrated tools)'
984	@echo ' menus - create lib/gde/arb.menu from GDEHELP/ARB_GDEmenus.source'
985	@echo ' perl - Compile the PERL XSUBS into lib/ARB.so and create links in lib to perl'
986	@echo ' binlink - Create all links in the bin directory'
987	@echo ''
988	@echo 'Development targets:'
989	@echo ''
990	@echo ' depends - create or update dependencies ("SUBDIR/SUBDIR.depends" to update only SUBDIR)'
991	@echo ' proto - create or update prototypes ("SUBDIR/SUBDIR.proto" to update only SUBDIR)'
992	@echo ' tags - create tags for xemacs'
993	@echo ' show - show available shortcuts (AKA subtargets)'
994	@echo ' up - shortcut for depends+proto+tags'
995	ifeq ($(UNIT_TESTS),1)
996	@echo ' ut - only run tests'
997	@echo ' "UNIT=..." oneunit - build one unit and run tests (see also UNIT_TESTER/Makefile.setup.local)'
998	endif
999	ifneq ($(SANITIZE),0)
1000	@echo ' sanitize - all + run arb_ntree with sanitizer (test.arb + execute _logged)'
1001	endif
1002	@echo ' modified - rebuild files modified in svn checkout (does touch)'
1003	@echo ' touch - touch files modified in svn checkout'
1004	@echo ''
1005	@echo 'Internal maintenance:'
1006	@echo ''
1007	@echo ' relinfo - show help on release targets'
1008	@echo ' tarfile - make rebuild and create arb version tarfile ("tarfile_quick" to skip rebuild)'
1009	@echo ' save - save all basic ARB sources into arbsrc_DATE ("savetest" to check filelist)'
1010	@echo ' patch - save svn diff to patchfile'
1011	@echo ' source_doc - create doxygen documentation'
1012	@echo ' relocated - rebuild partly (use when you have relocated ARBHOME)'
1013	@echo ' check_res - check resource usage'
1014	@echo ' dep_graph - Build dependency graphs'
1015	@echo ' clean_cov - Clean coverage results'
1016	@echo ''
1017	@echo ' clean_opengl_changed - clean after changing OPENGL setting in config.Makefile'
1018	@echo ' clean_checked_vect - clean units containing vectorization checks'
1019	@echo ' cleanRelinkable - similar to cleanlinked (but skips raxml8 to avoid rebuild)'
1020	@echo ''
1021	@echo ' post_commit_check - Checks whether'
1022	@echo ' * main make targets work,'
1023	@echo ' * dependencies and prototypes are up to date,'
1024	@echo ' * SVN-controlled files remain unaffected by called targets and'
1025	@echo ' * all generated files are ignored.'
1026	@echo ' (has to be called in a clean SVN checkout)'
1027	@echo $(SEP)
1028	@echo ''
1029
1030	relinfo:
1031	@echo ''
1032	@echo $(SEP)
1033	@echo 'Release targets:'
1034	@echo ''
1035	@echo ' inc_candi - increase RC candidate-number (only possible in "rc" branch, not needed for RC1)'
1036	@echo ' inc_patch - increase release patchlevel (only possible in "stable" branch)'
1037	@echo ' inc_minor - increase minor version number (only possible in "trunk")'
1038	@echo ' inc_major - increase MAJOR version number (only possible in "trunk")'
1039	@echo ''
1040	@echo ' show_version - show version tag'
1041	@echo ''
1042	@echo $(SEP)
1043	@echo ''
1044
1045	# auto-generate config.makefile:
1046
1047	config.makefile : config.makefile.template
1048	@echo --------------------------------------------------------------------------------
1049	ifeq ($(CONFIG_MAKEFILE_FOUND),)
1050	@cp $< $@
1051	@echo '$(ARBHOME)/$@:1: has been generated.'
1052	@echo 'Please edit $@ to configure your system!'
1053	@echo --------------------------------------------------------------------------------
1054	@false
1055	else
1056	@echo '$(ARBHOME)/$<:1: is more recent than'
1057	@echo '$(ARBHOME)/$@:1:'
1058	@ls -al config.makefile*
1059	@echo --------------------------------------------------------------------------------
1060	@echo "Updating $@ (if this fails, check manually)"
1061	SOURCE_TOOLS/update_config_makefile.pl
1062	@echo "Sucessfully updated $@"
1063	@echo --------------------------------------------------------------------------------
1064	@ls -al config.makefile*
1065	@echo --------------------------------------------------------------------------------
1066	@echo "Diff to your old config.makefile:"
1067	@echo --------------------------------------------------------------------------------
1068	-diff $@.bak $@
1069	@echo --------------------------------------------------------------------------------
1070	endif
1071
1072	# check if everything is configured correctly
1073
1074	check_DEVELOPER:
1075	ifndef DEVELOPER
1076	@echo 'config.makefile:1: DEVELOPER not defined'
1077	@false
1078	endif
1079
1080	check_DEBUG:
1081	ifndef dflags
1082	@echo 'config.makefile:1: DEBUG has to be defined. Valid values are 0 and 1'
1083	@false
1084	endif
1085
1086	check_ARB_64:
1087	ifndef ARB_64
1088	@echo 'config.makefile:1: ARB_64 has to be defined. Valid values are 0 and 1'
1089	@false
1090	endif
1091
1092	# ---------------------------------------- check gcc version
1093
1094	COMPILER_BROKEN:=0
1095
1096	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.6.4')
1097	COMPILER_BROKEN:=1
1098	endif
1099	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.8.0')
1100	COMPILER_BROKEN:=1
1101	endif
1102
1103	check_same_GCC_VERSION:
1104	$(ARBHOME)/SOURCE_TOOLS/check_same_compiler_version.pl $(COMPILER_NAME) $(COMPILER_VERSION_ALLOWED)
1105
1106	check_GCC_VERSION:
1107	@echo 'Compiler version check:'
1108	# see .@ALLOWED_gcc_VERSIONS
1109	ifeq ('$(COMPILER_VERSION_ALLOWED)', '')
1110	@echo " - Your compiler is '$(COMPILER_NAME)' version '$(COMPILER_VERSION)'"
1111	@echo ' This version is not in the list of supported $(COMPILER_NAME)-versions:'
1112	@$(foreach version,$(ALLOWED_COMPILER_VERSIONS),echo ' * $(version)';)
1113	@echo ' - You may either ..'
1114	@echo ' - add your version to ALLOWED_$(COMPILER_NAME)_VERSIONS in the Makefile and try it out or'
1115	@echo ' - switch to one of the allowed versions (see arb_README_gcc.txt for installing'
1116	@echo ' a different version of gcc)'
1117	$(error Unsupported compiler '$(COMPILER_NAME)' version '$(COMPILER_VERSION)')
1118	else
1119	ifeq ($(COMPILER_BROKEN),1)
1120	$(error compilation refused for $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)'. Refer to http://bugs.arb-home.de/wiki/GccVersionInfo for details.)
1121	else
1122	@echo " - Supported $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)' detected - fine!"
1123	@echo ''
1124	ifeq ($(USE_CLANG),1)
1125	@echo "Dump clang version:"
1126	$(A_CXX) -v
1127	endif
1128	$(MAKE) check_same_GCC_VERSION
1129	endif
1130	endif
1131
1132	#---------------------- check ARBHOME
1133
1134	# use arb_INSTALL.txt to determine whether ARBHOME points to correct directory
1135	ARB_INSTALL_FOUND=$(wildcard $(ARBHOME)/arb_INSTALL.txt)
1136
1137	check_ARBHOME:
1138	ifeq ($(strip $(ARB_INSTALL_FOUND)),)
1139	@echo ------------------------------------------------------------
1140	@echo "ARBHOME is set to '$(ARBHOME)'"
1141	@echo "The environment variable ARBHOME has to point to the top arb source directory."
1142	@echo "If you use bash enter:"
1143	@echo " export ARBHOME='`pwd`'"
1144	@echo ------------------------------------------------------------
1145	@false
1146	endif
1147
1148	ARB_PATH_SET=$(findstring $(ARBHOME)/bin,$(PATH))
1149
1150	check_PATH: check_ARBHOME
1151	ifeq ($(strip $(ARB_PATH_SET)),)
1152	@echo ------------------------------------------------------------
1153	@echo "The environment variable PATH has to contain $(ARBHOME)/bin"
1154	@echo "If you use bash enter:"
1155	@echo ' export PATH=$$ARBHOME/bin:$$PATH'
1156	@echo ------------------------------------------------------------
1157	@false
1158	endif
1159
1160	check_TOOLS:
1161	@util/arb_check_build_env.pl \
1162	"$(A_CC)" \
1163	"$(A_CXX)" \
1164	"$(MAKEDEPEND_PLAIN)" \
1165	"$(LINK_SHARED_LIB)" \
1166	"$(LINK_SHARED_LIB)" \
1167
1168	check_ENVIRONMENT : check_PATH check_TOOLS
1169	@echo "-------------------- Environment [start]"
1170	@echo "ARBHOME='$(ARBHOME)'"
1171	@echo "PATH='$(PATH)'"
1172	@echo "LD_LIBRARY_PATH='$(LD_LIBRARY_PATH)'"
1173	@echo "-------------------- Environment [end]"
1174
1175	check_tabs: check_setup
1176	ifeq ($(DEBUG),1)
1177	@SOURCE_TOOLS/tabBrake.pl
1178	endif
1179
1180	force_tab_check:
1181	@touch -t 198001010000 SOURCE_TOOLS/stamp.tabBrake
1182	@$(MAKE) check_tabs
1183
1184
1185	# ---------------------
1186
1187	check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION
1188	@echo Your setup seems to be ok.
1189
1190	checks: check_setup check_tabs
1191	@rm -f SOURCE_TOOLS/postcompile.sav
1192
1193
1194	# end test section ------------------------------
1195
1196	# ---------------------------------------
1197	# List of standard top level directories
1198	#
1199	# sub-makefiles have to define the targets
1200	# - 'depends' and
1201	# - 'clean'
1202	#
1203	# when adding new libs here, also add a dependency vs 'links' or 'links_non_perl' in .@DD_links_non_perl
1204
1205	ARCHS = \
1206	AISC/AISC.a \
1207	AISC_MKPTPS/AISC_MKPTPS.a \
1208	ARBDB/libARBDB.a \
1209	CORE/libCORE.a \
1210	ARB_GDE/ARB_GDE.a \
1211	AWT/libAWT.a \
1212	AWTC/AWTC.a \
1213	AWTI/AWTI.a \
1214	CONSENSUS_TREE/CONSENSUS_TREE.a \
1215	CONVERTALN/CONVERTALN.a \
1216	DBSERVER/DBSERVER.a \
1217	DIST/DIST.a \
1218	EDIT4/EDIT4.a \
1219	EISPACK/EISPACK.a \
1220	GDE/GDE.a \
1221	GENOM/GENOM.a \
1222	GENOM_IMPORT/GENOM_IMPORT.a \
1223	GL/GL.a \
1224	ISLAND_HOPPING/ISLAND_HOPPING.a \
1225	MERGE/MERGE.a \
1226	MULTI_PROBE/MULTI_PROBE.a \
1227	NALIGNER/NALIGNER.a \
1228	NAMES/NAMES.a \
1229	NAMES_COM/server.a \
1230	NTREE/NTREE.a \
1231	PARSIMONY/PARSIMONY.a \
1232	PERLTOOLS/PERLTOOLS.a \
1233	PHYLO/PHYLO.a \
1234	PRIMER_DESIGN/PRIMER_DESIGN.a \
1235	PROBE/PROBE.a \
1236	PROBE_COM/server.a \
1237	PROBE_DESIGN/PROBE_DESIGN.a \
1238	PROBE_SET/PROBE_SET.a \
1239	READSEQ/READSEQ.a \
1240	RNA3D/RNA3D.a \
1241	RNACMA/RNACMA.a \
1242	SECEDIT/SECEDIT.a \
1243	SEQ_QUALITY/SEQ_QUALITY.a \
1244	SERVERCNTRL/SERVERCNTRL.a \
1245	SL/SL.a \
1246	STAT/STAT.a \
1247	TOOLS/TOOLS.a \
1248	TREEGEN/TREEGEN.a \
1249	UNIT_TESTER/UNIT_TESTER.a \
1250	WETC/WETC.a \
1251	WINDOW/libWINDOW.a \
1252	XML/XML.a \
1253
1254	# -----------------------
1255	# library packets
1256
1257	ARCHS_CLIENT_PROBE = PROBE_COM/client.a
1258	ARCHS_CLIENT_NAMES = NAMES_COM/client.a
1259
1260	ARCHS_MAKEBIN = AISC_MKPTPS/AISC_MKPTPS.a AISC/AISC.a
1261
1262	# communication libs need aisc and aisc_mkpts:
1263
1264	AISC/AISC.dummy: proto_tools
1265
1266	comtools: AISC/AISC.dummy
1267
1268	ARCHS_SEQUENCE = \
1269	SL/SEQUENCE/SEQUENCE.a \
1270	SL/ALIVIEW/ALIVIEW.a \
1271	SL/PRONUC/PRONUC.a \
1272
1273	ARCHS_TREE = \
1274	SL/ARB_TREE/ARB_TREE.a \
1275	SL/FILTER/FILTER.a \
1276	$(ARCHS_SEQUENCE) \
1277
1278	# parsimony tree (used by NTREE, PARSIMONY, STAT(->EDIT4), DIST(obsolete!))
1279	ARCHS_AP_TREE = \
1280	SL/AP_TREE/AP_TREE.a \
1281	$(ARCHS_TREE) \
1282
1283	# --------------------------------------------------------------------------------
1284	# dependencies for linking shared libs
1285
1286	link_core: core
1287	link_db: db link_core
1288	link_aw: aw link_db
1289	link_awt: awt link_aw
1290
1291	#***************************************************************************************
1292	# Individual_Programs_Section
1293	#***************************************************************************************
1294
1295	arbmainwrapper:
1296	$(MAKE) -C SOURCE_TOOLS -r mainwrapper
1297
1298
1299	#********************************* arb_ntree ************************************
1300	NTREE = bin/arb_ntree
1301	ARCHS_NTREE = \
1302	NTREE/NTREE.a \
1303	ARB_GDE/ARB_GDE.a \
1304	SL/GROUP_SEARCH/GROUP_SEARCH.a \
1305	SL/SAICALC/SAICALC.a \
1306	SL/DB_UI/DB_UI.a \
1307	AWTC/AWTC.a \
1308	AWTI/AWTI.a \
1309	CONSENSUS_TREE/CONSENSUS_TREE.a \
1310	GENOM_IMPORT/GENOM_IMPORT.a \
1311	GENOM/GENOM.a \
1312	MERGE/MERGE.a \
1313	MULTI_PROBE/MULTI_PROBE.a \
1314	PRIMER_DESIGN/PRIMER_DESIGN.a \
1315	PROBE_DESIGN/PROBE_DESIGN.a \
1316	SEQ_QUALITY/SEQ_QUALITY.a \
1317	SERVERCNTRL/SERVERCNTRL.a \
1318	SL/ALILINK/ALILINK.a \
1319	SL/AW_NAME/AW_NAME.a \
1320	SL/CONSENSUS/CONSENSUS.a \
1321	SL/DB_SCANNER/DB_SCANNER.a \
1322	SL/DB_QUERY/DB_QUERY.a \
1323	SL/QUERY/QUERY.a \
1324	SL/SEQIO/SEQIO.a \
1325	STAT/STAT.a \
1326	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1327	SL/HELIX/HELIX.a \
1328	SL/REGEXPR/REGEXPR.a \
1329	SL/REFENTRIES/REFENTRIES.a \
1330	SL/NDS/NDS.a \
1331	SL/ITEM_SHADER/ITEM_SHADER.a \
1332	SL/ITEMS/ITEMS.a \
1333	SL/INSDEL/INSDEL.a \
1334	SL/LOCATION/LOCATION.a \
1335	SL/MACROS/MACROS.a \
1336	SL/PVP/PVP.a \
1337	SL/TRANSLATE/TRANSLATE.a \
1338	SL/TREEDISP/TREEDISP.a \
1339	SL/TREE_ADMIN/TREE_ADMIN.a \
1340	SL/TREE_READ/TREE_READ.a \
1341	SL/TREE_WRITE/TREE_WRITE.a \
1342	SL/XFERGUI/XFERGUI.a \
1343	SL/XFERSET/XFERSET.a \
1344	XML/XML.a \
1345	$(ARCHS_AP_TREE) \
1346
1347	ARCHS_NTREE_ALL = $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(XMLLIBS)
1348
1349	$(NTREE): $(ARCHS_NTREE:.a=.dummy) link_awt
1350	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NTREE_ALL) \|\| ( \
1351	echo "$(SEP) Link $@"; \
1352	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE_ALL)" ; \
1353	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE_ALL) && \
1354	echo "$(SEP) Link $@ [done]"; \
1355	)
1356
1357	#********************************* arb_edit4 ************************************
1358	EDIT4 = bin/arb_edit4
1359
1360	ARCHS_EDIT4 := \
1361	EDIT4/EDIT4.a \
1362	ARB_GDE/ARB_GDE.a \
1363	SL/FAST_ALIGNER/FAST_ALIGNER.a \
1364	AWTC/AWTC.a \
1365	ISLAND_HOPPING/ISLAND_HOPPING.a \
1366	SECEDIT/SECEDIT.a \
1367	SERVERCNTRL/SERVERCNTRL.a \
1368	SL/AW_HELIX/AW_HELIX.a \
1369	SL/AW_NAME/AW_NAME.a \
1370	SL/CONSENSUS/CONSENSUS.a \
1371	SL/ITEMS/ITEMS.a \
1372	STAT/STAT.a \
1373	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1374	SL/HELIX/HELIX.a \
1375	SL/TRANSLATE/TRANSLATE.a \
1376	SL/MACROS/MACROS.a \
1377	SL/NDS/NDS.a \
1378	$(ARCHS_AP_TREE) \
1379	XML/XML.a \
1380
1381	ifeq ($(OPENGL),1)
1382	ARCHS_EDIT4 += RNA3D/RNA3D.a
1383	endif
1384
1385	ARCHS_EDIT4_ALL = $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4)
1386
1387	LIBS_EDIT4 := $(GL_LIBS)
1388
1389	$(EDIT4): $(ARCHS_EDIT4:.a=.dummy) link_awt
1390	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_EDIT4_ALL) \|\| ( \
1391	echo "$(SEP) Link $@"; \
1392	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4_ALL)" ; \
1393	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4_ALL) && \
1394	echo "$(SEP) Link $@ [done]"; \
1395	)
1396
1397	#********************************* arb_rnacma ************************************
1398	RNACMA = bin/arb_rnacma
1399	ARCHS_RNACMA = \
1400	RNACMA/RNACMA.a \
1401
1402	ARCHS_RNACMA_ALL = $(ARCHS_RNACMA) $(DBSYS_LIBS)
1403
1404	$(RNACMA) : $(ARCHS_RNACMA:.a=.dummy) link_db
1405	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_RNACMA_ALL) \|\| ( \
1406	echo "$(SEP) Link $@"; \
1407	echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_RNACMA_ALL)"; \
1408	$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_RNACMA_ALL) && \
1409	echo "$(SEP) Link $@ [done]"; \
1410	)
1411
1412	#********************************* arb_wetc ************************************
1413	WETC = bin/arb_wetc
1414	ARCHS_WETC = \
1415	WETC/WETC.a \
1416	SL/HELIX/HELIX.a \
1417	SL/FILTER/FILTER.a \
1418	XML/XML.a \
1419
1420	ARCHS_WETC_ALL = $(ARCHS_WETC) $(GUI_LIBS)
1421
1422	$(WETC): $(ARCHS_WETC:.a=.dummy) link_awt
1423	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_WETC_ALL) \|\| ( \
1424	echo "$(SEP) Link $@"; \
1425	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC_ALL)" ; \
1426	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC_ALL) && \
1427	echo "$(SEP) Link $@ [done]"; \
1428	)
1429
1430	#********************************* arb_dist ************************************
1431	DIST = bin/arb_dist
1432	ARCHS_DIST = \
1433	DIST/DIST.a \
1434	CONSENSUS_TREE/CONSENSUS_TREE.a \
1435	EISPACK/EISPACK.a \
1436	SERVERCNTRL/SERVERCNTRL.a \
1437	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1438	SL/HELIX/HELIX.a \
1439	SL/MATRIX/MATRIX.a \
1440	SL/MACROS/MACROS.a \
1441	SL/NDS/NDS.a \
1442	SL/ITEMS/ITEMS.a \
1443	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.a \
1444	XML/XML.a \
1445	$(ARCHS_AP_TREE) \
1446
1447	ARCHS_DIST_ALL = $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS)
1448
1449	$(DIST): $(ARCHS_DIST:.a=.dummy) link_awt
1450	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_DIST_ALL) \|\| ( \
1451	echo "$(SEP) Link $@"; \
1452	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST_ALL)" ; \
1453	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST_ALL) && \
1454	echo "$(SEP) Link $@ [done]"; \
1455	)
1456
1457	#********************************* arb_pars ************************************
1458	PARSIMONY = bin/arb_pars
1459	ARCHS_PARSIMONY = \
1460	PARSIMONY/PARSIMONY.a \
1461	SERVERCNTRL/SERVERCNTRL.a \
1462	SL/AW_NAME/AW_NAME.a \
1463	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1464	SL/HELIX/HELIX.a \
1465	SL/MACROS/MACROS.a \
1466	SL/NDS/NDS.a \
1467	SL/ITEMS/ITEMS.a \
1468	SL/TRANSLATE/TRANSLATE.a \
1469	SL/TREEDISP/TREEDISP.a \
1470	XML/XML.a \
1471	$(ARCHS_AP_TREE) \
1472
1473	ARCHS_PARSIMONY_ALL = $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS)
1474
1475	$(PARSIMONY): $(ARCHS_PARSIMONY:.a=.dummy) link_awt
1476	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_PARSIMONY_ALL) \|\| ( \
1477	echo "$(SEP) Link $@"; \
1478	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY_ALL)" ; \
1479	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY_ALL) && \
1480	echo "$(SEP) Link $@ [done]"; \
1481	)
1482
1483	#********************************* arb_convert_aln ************************************
1484	CONVERT_ALN = bin/arb_convert_aln
1485	ARCHS_CONVERT_ALN = \
1486	CONVERTALN/CONVERTALN.a \
1487
1488	ARCHS_CONVERT_ALN_ALL = $(ARCHS_CONVERT_ALN) $(DBSYS_LIBS)
1489
1490	$(CONVERT_ALN) : $(ARCHS_CONVERT_ALN:.a=.dummy) link_db
1491	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_CONVERT_ALN_ALL) \|\| ( \
1492	echo "$(SEP) Link $@"; \
1493	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN_ALL)"; \
1494	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN_ALL) && \
1495	echo "$(SEP) Link $@ [done]"; \
1496	)
1497
1498	#********************************* arb_treegen ************************************
1499
1500	TREEGEN = bin/arb_treegen
1501	ARCHS_TREEGEN = \
1502	TREEGEN/TREEGEN.a \
1503
1504	ARCHS_TREEGEN_ALL = $(ARCHS_TREEGEN)
1505
1506	$(TREEGEN) : $(ARCHS_TREEGEN:.a=.dummy)
1507	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main_C) $(ARCHS_TREEGEN_ALL) \|\| ( \
1508	echo "$(SEP) Link $@"; \
1509	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN_ALL)" ; \
1510	$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN_ALL) && \
1511	echo "$(SEP) Link $@ [done]"; \
1512	)
1513
1514	#********************************* arb_naligner ************************************
1515	NALIGNER = bin/arb_naligner
1516	ARCHS_NALIGNER = \
1517	NALIGNER/NALIGNER.a \
1518	SERVERCNTRL/SERVERCNTRL.a \
1519	SL/HELIX/HELIX.a \
1520
1521	ARCHS_NALIGNER_ALL = $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(DBSYS_LIBS)
1522
1523	$(NALIGNER): $(ARCHS_NALIGNER:.a=.dummy) link_db
1524	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NALIGNER_ALL) \|\| ( \
1525	echo "$(SEP) Link $@"; \
1526	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER_ALL)" ; \
1527	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER_ALL) && \
1528	echo "$(SEP) Link $@ [done]"; \
1529	)
1530
1531	#********************************* arb_phylo ************************************
1532	PHYLO = bin/arb_phylo
1533	ARCHS_PHYLO = \
1534	PHYLO/PHYLO.a \
1535	SL/HELIX/HELIX.a \
1536	SL/FILTER/FILTER.a \
1537	SL/MACROS/MACROS.a \
1538	XML/XML.a \
1539
1540	ARCHS_PHYLO_ALL = $(ARCHS_PHYLO) $(GUI_LIBS)
1541
1542	$(PHYLO): $(ARCHS_PHYLO:.a=.dummy) link_awt
1543	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_PHYLO_ALL) \|\| ( \
1544	echo "$(SEP) Link $@"; \
1545	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO_ALL)" ; \
1546	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO_ALL) && \
1547	echo "$(SEP) Link $@ [done]"; \
1548	)
1549
1550	#***************************************************************************************
1551	# SERVER SECTION
1552	#***************************************************************************************
1553
1554	#********************************* arb_db_server ************************************
1555	DBSERVER = bin/arb_db_server
1556	ARCHS_DBSERVER = \
1557	DBSERVER/DBSERVER.a \
1558	SERVERCNTRL/SERVERCNTRL.a \
1559
1560	ARCHS_DBSERVER_ALL = $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS)
1561
1562	$(DBSERVER): $(ARCHS_DBSERVER:.a=.dummy) link_db
1563	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_DBSERVER_ALL) \|\| ( \
1564	echo "$(SEP) Link $@"; \
1565	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER_ALL)" ; \
1566	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER_ALL) && \
1567	echo "$(SEP) Link $@ [done]"; \
1568	)
1569
1570	#********************************* arb_pt_server ************************************
1571	PROBE = bin/arb_pt_server
1572
1573	ARCHS_PROBE_DEPEND = \
1574	PROBE/PROBE.a \
1575	SL/PTCLEAN/PTCLEAN.a \
1576	SERVERCNTRL/SERVERCNTRL.a \
1577	SL/HELIX/HELIX.a \
1578
1579	ARCHS_PROBE_ALL = $(ARCHS_PROBE_DEPEND) $(ARCHS_CLIENT_PROBE) $(ARBDB_LIB) $(SYSLIBS)
1580
1581	$(PROBE): $(ARCHS_PROBE_DEPEND:.a=.dummy) link_db
1582	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) config.makefile $(ARCHS_PROBE_ALL) \|\| ( \
1583	echo "$(SEP) Link $@"; \
1584	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_ALL)" ; \
1585	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_ALL) && \
1586	echo "$(SEP) Link $@ [done]"; \
1587	)
1588
1589	#********************************* arb_name_server ************************************
1590	NAMES = bin/arb_name_server
1591	ARCHS_NAMES = \
1592	NAMES/NAMES.a \
1593	SERVERCNTRL/SERVERCNTRL.a \
1594
1595	ARCHS_NAMES_ALL = $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS)
1596
1597	$(NAMES): $(ARCHS_NAMES:.a=.dummy) link_db
1598	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NAMES_ALL) \|\| ( \
1599	echo "$(SEP) Link $@"; \
1600	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES_ALL)" ; \
1601	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES_ALL) && \
1602	echo "$(SEP) Link $@ [done]"; \
1603	)
1604
1605	#********************************* SHARED LIBRARIES SECTION ************************************
1606
1607	prepare_libdir: addlibs
1608
1609	addlibs:
1610	(perl $(ARBHOME)/SOURCE_TOOLS/provide_libs.pl \
1611	"arbhome=$(ARBHOME)" \
1612	"opengl=$(OPENGL)" \
1613	"link_static=$(LINK_STATIC)" \
1614	)
1615
1616	#***************************************************************************************
1617	# Recursive calls to sub-makefiles
1618	#***************************************************************************************
1619
1620	%.depends:
1621	@cp -p $(@D)/Makefile $(@D)/Makefile.old # save old Makefile
1622	@$(MAKE) -C $(@D) -r \
1623	"AUTODEPENDS=1" \
1624	"MAIN=nothing" \
1625	"cflags=noCflagsHere_use_MAKEDEPENDFLAGS" \
1626	"cxxflags=noCxxflagsHere_use_MAKEDEPENDFLAGS" \
1627	depends
1628	@grep "^# DO NOT DELETE" $(@D)/Makefile >/dev/null
1629	@cat $(@D)/Makefile \
1630	\| SOURCE_TOOLS/fix_depends.pl "(from main)" \
1631	>$(@D)/Makefile.2
1632	@mv $(@D)/Makefile.old $(@D)/Makefile # restore old Makefile
1633	@$(ARBHOME)/SOURCE_TOOLS/mv_if_diff $(@D)/Makefile.2 $(@D)/Makefile # update Makefile if changed
1634
1635	%.proto:
1636	@($(MAKE) -C $(@D) \
1637	"AUTODEPENDS=0" \
1638	"MAIN=nothing" \
1639	"cflags=noCflags" \
1640	"cxxflags=noCxxflags" \
1641	proto 2>&1 ) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
1642
1643	%.clean:
1644	@$(MAKE) -C $(@D) \
1645	"AUTODEPENDS=0" \
1646	"MAIN=nothing" \
1647	"cflags=noCflags" \
1648	"cxxflags=noCxxflags" \
1649	clean
1650
1651
1652	# stop wrong targets
1653	target_is_missing_lib_prefix:
1654	@echo "Error: Denied to build shared library target with missing 'lib'-prefix"
1655	false
1656
1657	ARBDB/ARBDB.dummy: target_is_missing_lib_prefix
1658	CORE/CORE.dummy: target_is_missing_lib_prefix
1659	AWT/AWT.dummy: target_is_missing_lib_prefix
1660	WINDOW/WINDOW.dummy: target_is_missing_lib_prefix
1661
1662	# rule to generate main target (normally a library):
1663	# @@@ check effect of setting LANG=C below
1664	%.dummy:
1665	@( export ID=$$$$; LANG=C; \
1666	(( \
1667	echo "$(SEP) Make $(@D)"; \
1668	$(MAKE) -C $(@D) -r \
1669	"AUTODEPENDS=1" \
1670	"MAIN=$(@F:.dummy=.a)" \
1671	"cflags=$(cflags) -DIN_ARB_$(subst /,_,$(@D))" \
1672	&& \
1673	echo "$(SEP) Make $(@D) [done]"; \
1674	) >$(@D).$$ID.log 2>&1 && (cat $(@D).$$ID.log;rm $(@D).$$ID.log)) \|\| (cat $(@D).$$ID.log;rm $(@D).$$ID.log;false))
1675
1676	# Additional dependencies for subtargets:
1677
1678	PROBE_COM/PROBE_COM.dummy : comtools
1679	NAMES_COM/NAMES_COM.dummy : comtools
1680
1681	com: PROBE_COM/PROBE_COM.dummy NAMES_COM/NAMES_COM.dummy
1682
1683	PROBE_COM/server.dummy:
1684	@echo Unwanted request to make target $<
1685	false
1686
1687	PROBE_COM/client.dummy:
1688	@echo Unwanted request to make target $<
1689	false
1690
1691	NAMES_COM/server.dummy:
1692	@echo Unwanted request to make target $<
1693	false
1694
1695	NAMES_COM/client.dummy:
1696	@echo Unwanted request to make target $<
1697	false
1698
1699
1700	ARBDB/libARBDB.dummy: links
1701	CORE/libCORE.dummy: links
1702
1703	PERLTOOLS/PERLTOOLS.dummy: core db
1704
1705	# all subdirs perl not depends on go here (ADD_links_non_perl)
1706	AWT/libAWT.dummy: links_non_perl
1707	AWTI/AWTI.dummy: links_non_perl
1708	CONSENSUS_TREE/CONSENSUS_TREE.dummy: links_non_perl
1709	CONVERTALN/CONVERTALN.dummy: links_non_perl
1710	DBSERVER/DBSERVER.dummy: links_non_perl
1711	DIST/DIST.dummy: links_non_perl
1712	EDIT4/EDIT4.dummy: links_non_perl com
1713	EISPACK/EISPACK.dummy: links_non_perl
1714	GDE/GDE.dummy: links_non_perl
1715	GENOM/GENOM.dummy: links_non_perl
1716	GENOM_IMPORT/GENOM_IMPORT.dummy: links_non_perl
1717	ISLAND_HOPPING/ISLAND_HOPPING.dummy: links_non_perl
1718	MERGE/MERGE.dummy: links_non_perl
1719	NTREE/NTREE.dummy: links_non_perl
1720	PARSIMONY/PARSIMONY.dummy: links_non_perl
1721	PHYLO/PHYLO.dummy: links_non_perl
1722	PRIMER_DESIGN/PRIMER_DESIGN.dummy: links_non_perl
1723	PROBE_SET/PROBE_SET.dummy: links_non_perl link_db
1724	READSEQ/READSEQ.dummy: links_non_perl
1725	RNACMA/RNACMA.dummy: links_non_perl header_libs
1726	SECEDIT/SECEDIT.dummy: links_non_perl
1727	SEQ_QUALITY/SEQ_QUALITY.dummy: links_non_perl
1728	SERVERCNTRL/SERVERCNTRL.dummy: links_non_perl com
1729	SL/ALILINK/ALILINK.dummy: links_non_perl
1730	SL/ALIVIEW/ALIVIEW.dummy: links_non_perl
1731	SL/AP_TREE/AP_TREE.dummy: links_non_perl
1732	SL/ARB_TREE/ARB_TREE.dummy: links_non_perl
1733	SL/AW_HELIX/AW_HELIX.dummy: links_non_perl
1734	SL/CONSENSUS/CONSENSUS.dummy: links_non_perl
1735	SL/DB_QUERY/DB_QUERY.dummy: links_non_perl
1736	SL/DB_SCANNER/DB_SCANNER.dummy: links_non_perl
1737	SL/DB_UI/DB_UI.dummy: links_non_perl
1738	SL/FAST_ALIGNER/FAST_ALIGNER.dummy: links_non_perl
1739	SL/FILTER/FILTER.dummy: links_non_perl
1740	SL/FILTSEQEXP/FILTSEQEXP.dummy: links_non_perl
1741	SL/GROUP_SEARCH/GROUP_SEARCH.dummy: links_non_perl
1742	SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy: links_non_perl
1743	SL/HELIX/HELIX.dummy: links_non_perl
1744	SL/INSDEL/INSDEL.dummy: links_non_perl
1745	SL/ITEM_SHADER/ITEM_SHADER.dummy: links_non_perl
1746	SL/ITEMS/ITEMS.dummy: links_non_perl
1747	SL/LOCATION/LOCATION.dummy: links_non_perl
1748	SL/MACROS/MACROS.dummy: links_non_perl
1749	SL/MATRIX/MATRIX.dummy: links_non_perl
1750	SL/NDS/NDS.dummy: links_non_perl
1751	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.dummy: links_non_perl
1752	SL/PRONUC/PRONUC.dummy: links_non_perl
1753	SL/PTCLEAN/PTCLEAN.dummy: links_non_perl link_db
1754	SL/PVP/PVP.dummy: links_non_perl
1755	SL/QUERY/QUERY.dummy: links_non_perl link_db
1756	SL/REFENTRIES/REFENTRIES.dummy: links_non_perl
1757	SL/REGEXPR/REGEXPR.dummy: links_non_perl
1758	SL/SAICALC/SAICALC.dummy: links_non_perl
1759	SL/SEQIO/SEQIO.dummy: links_non_perl
1760	SL/SEQUENCE/SEQUENCE.dummy: links_non_perl
1761	SL/TRANSLATE/TRANSLATE.dummy: links_non_perl
1762	SL/TREE_ADMIN/TREE_ADMIN.dummy: links_non_perl
1763	SL/TREE_READ/TREE_READ.dummy: links_non_perl
1764	SL/TREE_WRITE/TREE_WRITE.dummy: links_non_perl
1765	SL/TREEDISP/TREEDISP.dummy: links_non_perl
1766	SL/XFERGUI/XFERGUI.dummy: links_non_perl
1767	SL/XFERSET/XFERSET.dummy: links_non_perl
1768	STAT/STAT.dummy: links_non_perl
1769	TREEGEN/TREEGEN.dummy: links_non_perl
1770	WETC/WETC.dummy: links_non_perl
1771	WINDOW/libWINDOW.dummy: links_non_perl
1772	XML/XML.dummy: links_non_perl
1773
1774	ifeq ($(OPENGL),1)
1775	GL/glAW/glAW.dummy: links_non_perl
1776	GL/glpng/glpng.dummy: links_non_perl
1777	GL/GL.dummy: GL/glAW/glAW.dummy GL/glpng/glpng.dummy
1778	RNA3D/RNA3D.dummy: links_non_perl gl
1779	endif
1780
1781	UNIT_TESTER/UNIT_TESTER.dummy: link_db \
1782	SERVERCNTRL/SERVERCNTRL.dummy \
1783
1784	# see also TOOLS/Makefile@TOOLSLIBDEPENDS
1785	TOOLS/TOOLS.dummy : links_non_perl link_db \
1786	CONSENSUS_TREE/CONSENSUS_TREE.dummy \
1787	SERVERCNTRL/SERVERCNTRL.dummy \
1788	SL/FILTER/FILTER.dummy \
1789	SL/FILTSEQEXP/FILTSEQEXP.dummy \
1790	SL/INSDEL/INSDEL.dummy \
1791	SL/REGEXPR/REGEXPR.dummy \
1792	SL/SEQIO/SEQIO.dummy \
1793	SL/TREE_READ/TREE_READ.dummy \
1794	SL/TREE_WRITE/TREE_WRITE.dummy \
1795	XML/XML.dummy \
1796
1797	AWTC/AWTC.dummy : com
1798
1799	NAMES/NAMES.dummy : com
1800	SL/AW_NAME/AW_NAME.dummy : com
1801
1802	PROBE/PROBE.dummy : com
1803	ptpan/PROBE.dummy : com
1804	MULTI_PROBE/MULTI_PROBE.dummy : com
1805	PROBE_DESIGN/PROBE_DESIGN.dummy : com
1806	NALIGNER/NALIGNER.dummy : com
1807
1808	ARB_GDE/ARB_GDE.dummy : proto_tools
1809
1810	compile_compatibility: SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.dummy
1811
1812	#***************************************************************************************
1813	# Short aliases to make targets
1814	#***************************************************************************************
1815
1816	show:
1817	@echo $(SEP)
1818	@echo 'Aliases for often needed targets:'
1819	@echo ''
1820	@echo ' executables:'
1821	@echo ''
1822	@echo ' nt arb_ntree'
1823	@echo ' e4 arb_edit4 (includes secedit)'
1824	@echo ' di arb_dist'
1825	@echo ' ph arb_phylo'
1826	@echo ' pa arb_parsimony'
1827	@echo ' tg arb_treegen'
1828	@echo ' ds arb_dbserver'
1829	@echo ' pt arb_pt_server'
1830	@echo ' na arb_name_server'
1831	@echo ''
1832	@echo ' libraries:'
1833	@echo ''
1834	@echo ' com communication libraries'
1835	@echo ' db ARB database'
1836	@echo ' aw GUI lib'
1837	@echo ' awt GUI toolkit'
1838	@echo ' awtc general purpose library'
1839	@echo ' awti import/export library'
1840	@echo ' mp multi probe library'
1841	@echo ' ge genome library'
1842	@echo ' pd probe design lib'
1843	@echo ' prd primer design lib'
1844	@echo ''
1845	@echo ' other targets:'
1846	@echo ''
1847	@echo ' help recompile help files'
1848	@echo ' tools make small tools used by arb'
1849	@echo ''
1850	@echo ' foreign targets:'
1851	@echo ''
1852	@echo ' gde GDE'
1853	@echo ' agde ARB_GDE'
1854	@echo ''
1855	@echo 'for other targets inspect $(ARBHOME)/Makefile'
1856	@echo ''
1857	@echo $(SEP)
1858
1859	source_doc:
1860	@echo "Remove some links (doxygen crashes otherwise):"
1861	find . \( -name "AISC" -o -name "C" -o -name "GDEHELP" \) -type l -exec rm {} \;
1862	doxygen 2>&1 1>/dev/null
1863	$(MAKE) forcelinks
1864
1865	dep_graph:
1866	@echo "Building some dependency graphs"
1867	SOURCE_TOOLS/dependency_graphs.pl
1868
1869	help: HELP_SOURCE/HELP_SOURCE.dummy
1870
1871	HELP_SOURCE/HELP_SOURCE.dummy: link_core xml menus
1872
1873	db: ARBDB/libARBDB.dummy
1874	core: CORE/libCORE.dummy
1875	aw: WINDOW/libWINDOW.dummy
1876	awt: AWT/libAWT.dummy
1877	awtc: AWTC/AWTC.dummy
1878	awti: AWTI/AWTI.dummy
1879
1880	mp: MULTI_PROBE/MULTI_PROBE.dummy
1881	mg: MERGE/MERGE.dummy
1882	ge: GENOM/GENOM.dummy
1883	prd: PRIMER_DESIGN/PRIMER_DESIGN.dummy
1884
1885	nt: menus $(NTREE)
1886
1887	nal: $(NALIGNER)
1888
1889	di: $(DIST)
1890	ph: $(PHYLO)
1891	pa: $(PARSIMONY)
1892	tg: $(TREEGEN)
1893
1894	ifeq ($(OPENGL),1)
1895	3d: RNA3D/RNA3D.dummy
1896	gl: GL/GL.dummy
1897	else
1898	noopengl:
1899	@echo "invalid target for OPENGL=0"
1900	3d: noopengl
1901	gl: noopengl
1902	endif
1903
1904	SL/SL.dummy: com
1905
1906	ds: $(DBSERVER)
1907	pt: $(PROBE)
1908	pst: PROBE_SET/PROBE_SET.dummy
1909	pd: PROBE_DESIGN/PROBE_DESIGN.dummy
1910	na: $(NAMES)
1911	sq: SEQ_QUALITY/SEQ_QUALITY.dummy
1912	cma: $(RNACMA)
1913
1914	sec: SECEDIT/SECEDIT.dummy
1915
1916	e4: $(EDIT4) readseq menus
1917
1918	gi: GENOM_IMPORT/GENOM_IMPORT.dummy
1919	wetc: $(WETC)
1920
1921	xml: XML/XML.dummy
1922	xmlin: XML_IMPORT/XML_IMPORT.dummy# broken
1923	stat: STAT/STAT.dummy $(NTREE) $(EDIT4)
1924	fa: SL/FAST_ALIGNER/FAST_ALIGNER.dummy
1925
1926	#********************************************************************************
1927
1928	up_by_remake: depends proto vectorize_checks
1929
1930	up: up_by_remake tags valgrind_update
1931
1932	#********************************************************************************
1933
1934	touch:
1935	SOURCE_TOOLS/touch_modified.pl
1936
1937	modified: touch
1938	$(MAKE) all
1939
1940	#********************************************************************************
1941
1942	libdepends:
1943	$(MAKE) -C "SOURCE_TOOLS" \
1944	"RNA3D_LIB=$(RNA3D_LIB_4_DEPENDS)" \
1945	libdepends
1946
1947	#********************************************************************************
1948
1949	# create generated headers:
1950	genheaders: TEMPLATES/TEMPLATES.dummy
1951
1952	clrdotdepends:
1953	rm PROBE_COM/.depends \|\| true
1954	rm NAMES_COM/.depends \|\| true
1955	rm PERL2ARB/.depends \|\| true
1956
1957	comdepends: comtools clrdotdepends
1958	@echo "$(SEP) Partially build com interface"
1959	$(MAKE) PROBE_COM/PROBE_COM.depends NAMES_COM/NAMES_COM.depends
1960	$(MAKE) PROBE_COM/server.depends NAMES_COM/server.depends
1961
1962	depends: genheaders comdepends vectorize_checks
1963	@echo "$(SEP) Updating other dependencies"
1964	$(MAKE) $(subst NAMES_COM/server.depends,,$(subst PROBE_COM/server.depends,,$(ARCHS:.a=.depends))) \
1965	HELP_SOURCE/HELP_SOURCE.depends \
1966	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.depends \
1967
1968	$(MAKE) libdepends
1969
1970	depend: depends
1971
1972	# ------------------------------------------------------------
1973	# dependency generation tests for AISC code
1974	#(all should work w/o creating wrong dependencies;
1975	# neither in XXX_COM/Makefile nor in code using AISC interface)
1976	dependstest1: silent_clean
1977	$(MAKE) depends
1978	dependstest2: silent_clean
1979	$(MAKE) com
1980	dependstest3: silent_clean
1981	$(MAKE) aw
1982	dependstest4: silent_clean
1983	$(MAKE) pt
1984	dependstest5: silent_clean
1985	$(MAKE) na
1986	dependstest6: silent_clean
1987	$(MAKE) nt
1988	dependstest7: silent_clean
1989	$(MAKE) all
1990	# ------------------------------------------------------------
1991
1992	vectorize_checks:
1993	$(MAKE) -C SOURCE_TOOLS -r vectorize_checks
1994
1995	clean_checked_vect: lib/lib.clean
1996	SOURCE_TOOLS/clean_checked_vectorizations.sh
1997
1998	# ------------------------------------------------------------
1999
2000	AISC_MKPTPS/AISC_MKPTPS.dummy: links
2001
2002	proto_tools: AISC_MKPTPS/AISC_MKPTPS.dummy
2003
2004	proto: proto_tools
2005	@echo $(SEP) Updating prototypes
2006	$(MAKE) \
2007	ARBDB/ARBDB.proto \
2008	AISC_COM/AISC_COM.proto \
2009	ARB_GDE/ARB_GDE.proto \
2010	CORE/CORE.proto \
2011	CONVERTALN/CONVERTALN.proto \
2012	NTREE/NTREE.proto \
2013	MERGE/MERGE.proto \
2014	PROBE/PROBE.proto \
2015	SERVERCNTRL/SERVERCNTRL.proto \
2016	SL/SL.proto \
2017
2018	#********************************************************************************
2019
2020	valgrind_update: links
2021	@echo $(SEP) Updating for valgrind
2022	$(MAKE) -C SOURCE_TOOLS valgrind_update
2023
2024	#********************************************************************************
2025
2026	TAGFILE=TAGS
2027	UTAGS=TAGS.$(ARBBID)
2028	TAGFILE_TMP=$(UTAGS).tmp
2029
2030	TAG_SOURCE_HEADERS=$(UTAGS).headers.tmp
2031	TAG_SOURCE_CODE=$(UTAGS).codefiles.tmp
2032	TAG_SOURCE_LISTS=$(TAG_SOURCE_HEADERS) $(TAG_SOURCE_CODE)
2033
2034	ETAGS_IGNORE_LIST=SOURCE_TOOLS/etags_ignore.lst
2035
2036	ETAGS=ctags -e -I @$(ETAGS_IGNORE_LIST) --sort=no --if0=no --extra=q
2037	ETAGS_TYPES=--C-kinds=cgnsut --C++-kinds=cgnsut
2038	ETAGS_FUN =--C-kinds=fm --C++-kinds=fm
2039	ETAGS_REST =--C-kinds=dev --C++-kinds=dev
2040
2041	FILTER_TAGS_SOURCES= \
2042	$(SED) -e 's/^.\///g' \| \
2043	grep -vi '^HEADERLIBS\\|^GDE/\\|/GEN[CH]/'
2044
2045	$(TAG_SOURCE_HEADERS): links
2046	@find . \( -name '.hxx' -o -name ".h" \) -type f \| $(FILTER_TAGS_SOURCES) > $@
2047
2048	$(TAG_SOURCE_CODE): links
2049	@find . \( -name '.cxx' -o -name ".c" \) -type f \| $(FILTER_TAGS_SOURCES) > $@
2050
2051	$(UTAGS).1.tmp: $(TAG_SOURCE_HEADERS)
2052	@$(ETAGS) -f $@ $(ETAGS_TYPES) -L $<
2053	$(UTAGS).2.tmp: $(TAG_SOURCE_HEADERS)
2054	@$(ETAGS) -f $@ $(ETAGS_FUN) -L $<
2055	$(UTAGS).3.tmp: $(TAG_SOURCE_HEADERS)
2056	@$(ETAGS) -f $@ $(ETAGS_REST) -L $<
2057	$(UTAGS).4.tmp: $(TAG_SOURCE_CODE)
2058	@$(ETAGS) -f $@ $(ETAGS_TYPES) -L $<
2059	$(UTAGS).5.tmp: $(TAG_SOURCE_CODE)
2060	@$(ETAGS) -f $@ $(ETAGS_FUN) -L $<
2061	$(UTAGS).6.tmp: $(TAG_SOURCE_CODE)
2062	@$(ETAGS) -f $@ $(ETAGS_REST) -L $<
2063
2064	TAGS_ALL_PARTS=$(UTAGS).1.tmp $(UTAGS).2.tmp $(UTAGS).3.tmp $(UTAGS).4.tmp $(UTAGS).5.tmp $(UTAGS).6.tmp
2065
2066	$(TAGFILE_TMP) : $(TAGS_ALL_PARTS)
2067	@cat $(TAGS_ALL_PARTS) > $@
2068	@rm $(TAGS_ALL_PARTS) $(TAG_SOURCE_LISTS)
2069
2070	cleanOldTags:
2071	@find $(ARBHOME) -name 'TAGS.*.tmp' -ctime +2 -exec rm {} \;
2072
2073	tags: $(TAGFILE_TMP) cleanOldTags
2074	@mv_if_diff $(TAGFILE_TMP) $(TAGFILE)
2075
2076	#********************************************************************************
2077
2078	LINKSTAMP=SOURCE_TOOLS/stamp.generate_all_links
2079
2080	links: checks $(LINKSTAMP) arbmainwrapper
2081	links_no_checks: $(LINKSTAMP) arbmainwrapper
2082
2083	forcelinks:
2084	-rm $(LINKSTAMP)
2085	$(MAKE) links
2086
2087	$(LINKSTAMP): SOURCE_TOOLS/generate_all_links.sh genheaders
2088	+SOURCE_TOOLS/generate_all_links.sh
2089	touch $(LINKSTAMP)
2090
2091	clean_links:
2092	# avoid to delete linked pts, nas or arb_tcp.dat:
2093	find . -path './lib' -prune -o -type l -exec rm {} \;
2094	# removed obsolete file - refuses to disappear due to 'prune' above
2095	@rm -f lib/help/GDEHELP
2096	@rm -f $(LINKSTAMP) lib/inputMasks/format.readme
2097
2098	redo_links: clean_links
2099	$(MAKE) links_no_checks
2100
2101	#********************************************************************************
2102
2103	header_libs:
2104	@(( \
2105	echo "$(SEP) Make HEADERLIBS"; \
2106	$(MAKE) -C HEADERLIBS all && \
2107	echo "$(SEP) Make HEADERLIBS [done]"; \
2108	) > HEADERLIBS.log 2>&1 && (cat HEADERLIBS.log;rm HEADERLIBS.log)) \|\| (cat HEADERLIBS.log;rm HEADERLIBS.log;false)
2109
2110	#********************************************************************************
2111
2112	gde: GDE/GDE.dummy
2113	GDE: gde
2114	agde: ARB_GDE/ARB_GDE.dummy
2115	tools: TOOLS/TOOLS.dummy
2116	convert: $(CONVERT_ALN)
2117	readseq: READSEQ/READSEQ.dummy
2118
2119	#***************************************************************************************
2120	# Some user commands
2121	#***************************************************************************************
2122
2123	menus: binlink links
2124	@(( \
2125	echo "$(SEP) Make GDEHELP"; \
2126	$(MAKE) -C GDEHELP -r all && \
2127	echo "$(SEP) Make GDEHELP [done]"; \
2128	) > GDEHELP.log 2>&1 && (cat GDEHELP.log;rm GDEHELP.log)) \|\| (cat GDEHELP.log;rm GDEHELP.log;false)
2129
2130	ifeq ($(DEBUG),1)
2131	BIN_TARGET=develall
2132	else
2133	BIN_TARGET=all
2134	endif
2135
2136
2137	binlink:
2138	$(MAKE) -C bin $(BIN_TARGET)
2139
2140	check_bin_dep: binlink
2141	SOURCE_TOOLS/check_bin_dependencies.pl
2142
2143	fig_cure:
2144	SOURCE_TOOLS/sortfig.pl doit
2145
2146	preplib:
2147	(cd lib;$(MAKE) all)
2148
2149	# --------------------------------------------------------------------------------
2150	# This section is quite tricky:
2151	#
2152	# make 'perl' is a BIG target, so when it has to be made, it has to be started
2153	# as early as possible to reduce overall compile time. Since 'make' does not
2154	# provide any priorities, i force it to build all 'perl'-prerequisites early, by
2155	# adding artificial dependencies to these prerequisites
2156	#
2157	# That behavior is likely to be system-dependent.
2158	# My goal was only to make it work on my current development system,
2159	# where this saves about 20% of overall build time.
2160
2161	ifeq ($(WITHPERL),1)
2162	links_non_perl: PERLTOOLS/PERLTOOLS.dummy
2163	perltools: links_non_perl
2164	perl: realperl
2165	else
2166	links_non_perl: links
2167	perl:
2168	$(MAKE) "WITHPERL=1" perl
2169	endif
2170
2171	# ---------------------------------------- perl
2172
2173	realperl: perltools
2174	(( \
2175	echo "$(SEP) Make PERL2ARB" ; \
2176	$(TIME) $(MAKE) -C PERL2ARB -r -f Makefile.main \
2177	"AUTODEPENDS=1" \
2178	"dflags=$(dflags)" \
2179	"cflags4perl=$(cflags) $(cxxflags) $(dflags)" \
2180	"lflags4perl=$(lflags4perl)" \
2181	"COMPILER_VERSION=$(COMPILER_VERSION)" \
2182	all && \
2183	$(MAKE) -C PERL_SCRIPTS/test test && \
2184	echo "$(SEP) Make PERL2ARB [done]" ; \
2185	) > PERL2ARB.log 2>&1 && (cat PERL2ARB.log;rm PERL2ARB.log)) \|\| (cat PERL2ARB.log;rm PERL2ARB.log;false)
2186
2187	perl_clean:
2188	@$(MAKE) -C PERL2ARB -r -f Makefile.main \
2189	"AUTODEPENDS=0" \
2190	clean
2191
2192	PERL2ARB/PERL2ARB.clean:
2193	$(MAKE) perl_clean
2194	$(MAKE) -C PERL_SCRIPTS/test clean
2195
2196	# ---------------------------------------- bindings to script languages
2197
2198	bindings: lib/libCORE.so lib/libARBDB.so
2199	$(MAKE) -C BINDINGS all ARBDEPENDS="$(^:%=../%)" DFLAGS="$(dflags)"
2200
2201	bindings_clean:
2202	$(MAKE) -C BINDINGS clean
2203
2204	# ----------------------------------------
2205
2206	CLOC=cloc-1.08.pl
2207	CLOCFLAGS=--no3 --quiet --progress-rate=0
2208	CLOCARB=--exclude-dir=GDE .
2209	CLOCEXT=GDE
2210	CLOCCODE=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.code.def
2211	CLOCREST=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.rest.def
2212	CLOCFILT=tail --lines=+4
2213
2214	cloc:
2215	@echo 'Arb code:'
2216	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCARB) \| $(CLOCFILT)
2217	@echo 'Arb rest:'
2218	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCARB) \| $(CLOCFILT)
2219	@echo 'External code:'
2220	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCEXT) \| $(CLOCFILT)
2221	@echo 'External rest:'
2222	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCEXT) \| $(CLOCFILT)
2223
2224	# ---------------------------------------- check resources
2225
2226	check_res:
2227	$(ARBHOME)/SOURCE_TOOLS/check_resources.pl
2228
2229	# ---------------------------------------- cleaning
2230
2231	rmbak:
2232	@echo "[cleanup backup/core files]"
2233	@find . \( -name '*%' \
2234	-o -name '*.bak' \
2235	-o -name '*~' \) \
2236	-o \( -name 'core' -a \! -type d \) \
2237	-exec rm -v {} \; \|\| \
2238	echo "Warning: target 'rmbak' reported problems when removing misc. backup files (ignored)"
2239	@echo "[cleanup done]"
2240
2241	bin_reinit:
2242	$(MAKE) bin/bin.clean
2243	$(MAKE) -C "bin" all
2244
2245	clean_directories:
2246	-rm -rf \
2247	$(ARBHOME)/PROBE_SET/bin \
2248	$(ARBHOME)/INCLUDE \
2249
2250	libclean:
2251	-find $(ARBHOME) -type f \( -name '*.a' ! -type l \) -exec rm -f {} \;
2252	-find $(ARBHOME) -type f \( -name 'lib*.so' ! -type l \) -exec rm -f {} \;
2253
2254	objclean:
2255	-find $(ARBHOME) -type f \( -name '*.o' ! -type l \) -exec rm -f {} \;
2256
2257	# bin.clean and HELP_SOURCE.clean interfere
2258	clean3:
2259	$(MAKE) bin/bin.clean
2260	$(MAKE) HELP_SOURCE/HELP_SOURCE.clean
2261
2262
2263	# delete all binaries (similar to 'cleanlinked')
2264	cleanRelinkable: libclean UNIT_TESTER/UNIT_TESTER.clean
2265	$(MAKE) -C bin cleanbinariesRelinkable
2266	$(MAKE) -C PROBE_SET cleanLinked
2267
2268
2269	clean2: $(ARCHS:.a=.clean) \
2270	clean3 \
2271	rmbak \
2272	libclean \
2273	objclean \
2274	lib/lib.clean \
2275	GDEHELP/GDEHELP.clean \
2276	HEADERLIBS/HEADERLIBS.clean \
2277	SOURCE_TOOLS/SOURCE_TOOLS.clean \
2278	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.clean \
2279	UNIT_TESTER/UNIT_TESTER.clean \
2280	TEMPLATES/TEMPLATES.clean \
2281	perl_clean \
2282	clean_directories \
2283
2284	rm -f .last_gcc .last_compiler config.makefile.bak
2285
2286	# links are needed for cleanup
2287	clean: redo_links motif_xpm_hack_clean
2288	$(MAKE) clean2
2289	$(MAKE) clean_cov_all clean_links
2290
2291	silent_clean:
2292	$(MAKE) clean >/dev/null
2293
2294	# 'relocated' is about 50% faster than 'rebuild'
2295	reloc_clean: links
2296	@echo "---------------------------------------- Relocation cleanup"
2297	$(MAKE) \
2298	perl_clean \
2299	GDEHELP/GDEHELP.clean \
2300	HELP_SOURCE/genhelp/genhelp.clean \
2301	bin/bin.clean \
2302	libclean \
2303	objclean
2304
2305	relocated: links
2306	$(MAKE) reloc_clean
2307	@echo "---------------------------------------- and remake"
2308	$(MAKE) build
2309
2310	# -----------------------------------
2311	# some stress tests
2312	# (helpful to reveal race conditions with -j)
2313
2314	rebuild4ever: rebuild
2315	$(MAKE) rebuild4ever
2316
2317	build4ever: build
2318	$(MAKE) build4ever
2319
2320	clean4ever: clean
2321	$(MAKE) clean4ever
2322
2323	test4ever: ut
2324	$(MAKE) test4ever
2325
2326	perl4ever: clean
2327	$(MAKE) links
2328	$(MAKE) perl
2329	$(MAKE) perl4ever
2330
2331	help4ever: clean
2332	$(MAKE) help
2333	$(MAKE) help4ever
2334
2335	# -----------------------------------
2336
2337	rebuild: clean
2338	$(MAKE) all
2339
2340	cleanlinked: bin/bin.clean libclean
2341
2342	relink: cleanlinked
2343	$(MAKE) all
2344
2345	tarfile: rebuild
2346	$(MAKE) prepare_libdir
2347	util/arb_compress
2348
2349	tarfile_quick: build
2350	$(MAKE) prepare_libdir
2351	util/arb_compress
2352
2353	save: sourcetarfile
2354
2355	patch:
2356	SOURCE_TOOLS/arb_create_patch.sh arbPatch
2357
2358	# test early whether save will work
2359	savetest:
2360	@util/arb_srclst.pl >/dev/null
2361
2362	testsave: savetest
2363
2364	sourcetarfile: rmbak
2365	util/arb_save
2366
2367	save2: rmbak
2368	util/arb_save ignore
2369
2370	save_test: rmbak
2371	@echo "Testing source list.."
2372	@util/arb_srclst.pl > /dev/null
2373
2374	save_test_no_error:
2375	@-$(MAKE) save_test
2376
2377	inc_candi:
2378	touch SOURCE_TOOLS/inc_candi.stamp
2379	$(MAKE) do_version_update
2380
2381	inc_patch:
2382	touch SOURCE_TOOLS/inc_patch.stamp
2383	$(MAKE) do_version_update
2384
2385	inc_minor:
2386	touch SOURCE_TOOLS/inc_minor.stamp
2387	$(MAKE) do_version_update
2388
2389	inc_major:
2390	touch SOURCE_TOOLS/inc_major.stamp
2391	$(MAKE) do_version_update
2392
2393	do_version_update:
2394	@echo Incrementing version information
2395	$(MAKE) savetest
2396	$(MAKE) genheaders # auto upgrades version early
2397
2398	show_version:
2399	$(MAKE) genheaders # updates version info
2400	@echo "$(SEP) ARB version info"
2401	@grep ARB_VERSION TEMPLATES/arb_build.h
2402	@echo "$(SEP)"
2403
2404	release_quick:
2405	-rm arb.tgz arbsrc.tgz
2406	$(MAKE) tarfile_quick
2407	$(MAKE) sourcetarfile
2408
2409	# --------------------------------------------------------------------------------
2410	# special cleanups
2411
2412	clean_opengl_changed: RNA3D/RNA3D.clean EDIT4/EDIT4.clean WINDOW/WINDOW.clean GL/GL.clean
2413
2414	# --------------------------------------------------------------------------------
2415
2416	MAKE_IF_COMMITTED=$(MAKE) -C SOURCE_TOOLS -f Makefile.commitbuild
2417
2418	build_CTARGET:
2419	+$(MAKE_IF_COMMITTED) "CTARGET=$(CTARGET)" build_CTARGET
2420
2421	reset_committed_build:
2422	+$(MAKE_IF_COMMITTED) reset
2423
2424	# --------------------------------------------------------------------------------
2425
2426	arbapplications: nt pa e4 wetc pt na nal di ph ds wetc cma
2427
2428	arb_external: convert tools gde readseq tg pst xmlin
2429
2430	arb_no_perl: arbapplications help arb_external
2431
2432	arb: motif_xpm_hack
2433	$(MAKE) "WITHPERL=1" perl arb_no_perl
2434
2435	motif_xpm_hack:
2436	$(MAKE) -r -C "lib/motifHack" all
2437
2438	motif_xpm_hack_clean:
2439	$(MAKE) -r -C "lib/motifHack" clean
2440
2441	# --------------------------------------------------------------------------------
2442	# special targets for SOURCE_TOOLS/remake_after_change.pl
2443
2444	rac_arb_dist: di
2445	rac_arb_edit4: e4
2446	rac_arb_ntree: nt
2447	rac_arb_pars: pa
2448	rac_arb_phylo: ph
2449	rac_arb_wetc: wetc
2450	rac_arb_naligner: nal
2451	rac_arb_pt_server: pt
2452	rac_arb_db_server: ds
2453	rac_arb_name_server: na
2454	rac_arb_convert_aln: convert
2455	rac_arb_treegen: tg
2456	rac_arb_rnacma: cma
2457	rac_arb_help2xml: help
2458
2459	rac_arb_a2ps: tools
2460	rac_arb_consensus_tree: tools
2461	rac_arb_dnarates: tools
2462	rac_arb_export_rates: tools
2463	rac_arb_export_tree: tools
2464	rac_arb_gene_probe: tools
2465	rac_arb_message: tools
2466	rac_arb_primer: tools
2467	rac_arb_probe: tools
2468	rac_arb_read_tree: tools
2469
2470	# --------------------------------------------------------------------------------
2471	# unit testing
2472	# @@@ work in progress
2473	#
2474	# goal is to automatically test all libraries/executables using TESTED_UNITS_AUTO
2475	#
2476	# currently not all test executables link w/o error
2477	# (see UNITS_WORKING, UNITS_UNTESTABLE_ATM and UNITS_NEED_FIX)
2478
2479	# define RNA3D/RNA3D.test
2480	RNA3D_TEST := $(subst .a,.test,$(RNA3D_LIB))
2481
2482	TESTED_UNITS_AUTO = $(ARCHS:.a=.test)
2483
2484	UNITS_WORKING = \
2485	$(RNA3D_TEST) \
2486	EISPACK/EISPACK.test \
2487	GENOM/GENOM.test \
2488	GL/glAW/libglAW.test \
2489	GL/glpng/libglpng_arb.test \
2490	ISLAND_HOPPING/ISLAND_HOPPING.test \
2491	NALIGNER/NALIGNER.test \
2492	NAMES/NAMES.test \
2493	PHYLO/PHYLO.test \
2494	PRIMER_DESIGN/PRIMER_DESIGN.test \
2495	PROBE_DESIGN/PROBE_DESIGN.test \
2496	SECEDIT/SECEDIT.test \
2497	SEQ_QUALITY/SEQ_QUALITY.test \
2498	SERVERCNTRL/SERVERCNTRL.test \
2499	SL/ALIVIEW/ALIVIEW.test \
2500	SL/AP_TREE/AP_TREE.test \
2501	SL/ARB_TREE/ARB_TREE.test \
2502	SL/AW_HELIX/AW_HELIX.test \
2503	SL/AW_NAME/AW_NAME.test \
2504	SL/DB_SCANNER/DB_SCANNER.test \
2505	SL/GUI_ALIVIEW/GUI_ALIVIEW.test \
2506	SL/HELIX/HELIX.test \
2507	SL/LOCATION/LOCATION.test \
2508	SL/MATRIX/MATRIX.test \
2509	SL/QUERY/QUERY.test \
2510	SL/REFENTRIES/REFENTRIES.test \
2511	SL/SEQUENCE/SEQUENCE.test \
2512	SL/TREE_ADMIN/TREE_ADMIN.test \
2513	SL/TREE_WRITE/TREE_WRITE.test \
2514	SL/XFERGUI/XFERGUI.test \
2515	STAT/STAT.test \
2516	TREEGEN/TREEGEN.test \
2517	WETC/WETC.test \
2518	XML/XML.test \
2519
2520	# untestable units
2521
2522	UNITS_NEED_FIX = \
2523	ptpan/PROBE.test \
2524
2525	UNITS_UNTESTABLE_ATM = \
2526	XML_IMPORT/XML_IMPORT.test \
2527
2528	# for the moment, put all units containing tests into the following 4 sections (see also TESTED_UNITS below)
2529
2530	# recent development
2531	UNITS_TESTED_FIRST = \
2532	SL/SAICALC/SAICALC.test \
2533	SL/XFERSET/XFERSET.test \
2534	SL/TRANSLATE/TRANSLATE.test \
2535	SL/PVP/PVP.test \
2536	AWTI/AWTI.test \
2537	SL/FILTSEQEXP/FILTSEQEXP.test \
2538	SL/GROUP_SEARCH/GROUP_SEARCH.test \
2539
2540	# start units with long duration early
2541	UNITS_RUNNING_LONG = \
2542	ARBDB/libARBDB.test \
2543	AWTC/AWTC.test \
2544	TOOLS/arb_test.test \
2545
2546	# plain test-libaries that are not linked anywhere
2547	TEST_SANDBOXES = \
2548	SL/CB/CB.test \
2549
2550	UNITS_TESTED = \
2551	AISC_MKPTPS/mkptypes.test \
2552	ARB_GDE/ARB_GDE.test \
2553	AWT/libAWT.test \
2554	CONSENSUS_TREE/CONSENSUS_TREE.test \
2555	CONVERTALN/CONVERTALN.test \
2556	CORE/libCORE.test \
2557	DBSERVER/DBSERVER.test \
2558	DIST/DIST.test \
2559	EDIT4/EDIT4.test \
2560	GENOM_IMPORT/GENOM_IMPORT.test \
2561	HELP_SOURCE/arb_help2xml.test \
2562	MERGE/MERGE.test \
2563	MULTI_PROBE/MULTI_PROBE.test \
2564	NTREE/NTREE.test \
2565	PARSIMONY/PARSIMONY.test \
2566	PERLTOOLS/arb_proto_2_xsub.test \
2567	PROBE/PROBE.test \
2568	PROBE_SET/fb_test.test \
2569	SERVERCNTRL/SERVERCNTRL.test \
2570	SL/ALILINK/ALILINK.test \
2571	SL/CONSENSUS/CONSENSUS.test \
2572	SL/DB_QUERY/DB_QUERY.test \
2573	SL/FAST_ALIGNER/FAST_ALIGNER.test \
2574	SL/FILTER/FILTER.test \
2575	SL/INSDEL/INSDEL.test \
2576	SL/ITEM_SHADER/ITEM_SHADER.test \
2577	SL/ITEMS/ITEMS.test \
2578	SL/MACROS/MACROS.test \
2579	SL/NDS/NDS.test \
2580	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.test \
2581	SL/PRONUC/PRONUC.test \
2582	SL/PTCLEAN/PTCLEAN.test \
2583	SL/REGEXPR/REGEXPR.test \
2584	SL/SEQIO/SEQIO.test \
2585	SL/TREE_READ/TREE_READ.test \
2586	SL/TREEDISP/TREEDISP.test \
2587	TOOLS/arb_consensus_tree.test \
2588	TOOLS/arb_probe.test \
2589	WINDOW/libWINDOW.test \
2590
2591	TESTED_UNITS = \
2592	$(UNITS_TESTED_FIRST) \
2593	$(UNITS_RUNNING_LONG) \
2594	$(TEST_SANDBOXES) \
2595	$(UNITS_TESTED) \
2596
2597	# see UNIT_TESTER/sym2testcode.pl@disableErrorOnUnitsWithoutTests
2598
2599	# ----------------------------------------
2600
2601	TEST_LOG_DIR = UNIT_TESTER/logs
2602	TEST_RUN_SUITE=$(MAKE) $(NODIR) -C UNIT_TESTER -f Makefile.suite -r
2603	TEST_MAKE_FLAGS=
2604	TEST_POST_CLEAN=
2605	ifeq ($(COVERAGE),1)
2606	TEST_POST_CLEAN=$(MAKE) clean_cov
2607	TEST_MAKE_FLAGS+=-j1
2608	endif
2609
2610
2611	%.test:
2612	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
2613	( \
2614	echo "fake[1]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
2615	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
2616	"UNITDIR=$(@D)" \
2617	"UNITLIBNAME=$(@F:.test=)" \
2618	"COVERAGE=$(COVERAGE)" \
2619	"ARB_PID=$(ARB_PID)_$(@F)" \
2620	runtest; \
2621	echo "fake[1]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"; \
2622	$(TEST_POST_CLEAN) \
2623	) >$(TEST_LOG_DIR)/$(@F).log 2>&1; \
2624	UNIT_TESTER/log_result.pl $(TEST_LOG_DIR)/$(@F).log )
2625
2626
2627	test_base: $(UNIT_TESTER_LIB:.a=.dummy) $(subst .test,.dummy,$(TEST_SANDBOXES))
2628
2629	clean_cov:
2630	find . \( -name ".gcda" -o -name ".gcov" -o -name "*.cov" \) -exec rm {} \;
2631
2632	clean_cov_all: clean_cov
2633	find . \( -name "*.gcno" \) -exec rm {} \;
2634
2635	cleanup_faked_arbpids:
2636	@rm ~/.arb_tmp/tmp/arb_pids_${USER}_${ARB_PID}_* \|\| true
2637
2638	cleanup_faked_arbpids_and_fail: cleanup_faked_arbpids
2639	@false
2640
2641
2642	run_tests_faked_arbpid:
2643	+@$(TEST_RUN_SUITE) init
2644	@echo "fake[2]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2645	$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(TESTED_UNITS) \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2646	@echo "fake[2]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2647	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2648	@$(MAKE) clean_cov >/dev/null
2649	@$(MAKE) cleanup_faked_arbpids
2650
2651	# @@@ instead of only running UNIT, this should as well run all tests this unit depends on? according to 'needs_libs'
2652	# @@@ 'run_tests_faked_arbpid' does not work for UNIT=ARBDB/libARBDB or UNIT=PARS/PARS -> could be solved via extra suffix, e.g. ARBDB/libARBDB.unit
2653
2654	run_onetest_faked_arbpid:
2655	+@$(TEST_RUN_SUITE) init
2656	@echo "fake[2]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2657	test -n "$(UNIT)" \|\| (echo "Error: UNIT has to be defined for target 'run_onetest_faked_arbpid'!"; false)
2658	$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(UNIT).test \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2659	@echo "fake[2]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2660	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2661	@$(MAKE) clean_cov >/dev/null
2662	@$(MAKE) cleanup_faked_arbpids
2663
2664
2665	run_tests: test_base clean_cov
2666	$(MAKE) "ARB_PID=UT_$$$$" run_tests_faked_arbpid
2667
2668	run_oneunitstests: test_base
2669	$(MAKE) "ARB_PID=UT_$$$$" run_onetest_faked_arbpid
2670
2671
2672	ut:
2673	ifeq ($(UNIT_TESTS),1)
2674	@echo $(MAKE) run_tests
2675	@$(MAKE) run_tests
2676	else
2677	@echo "Not compiled with unit tests"
2678	endif
2679
2680
2681	aut:
2682	+@$(TEST_RUN_SUITE) unskip
2683	$(MAKE) ut
2684
2685	# --------------------------------------------------------------------------------
2686
2687	TIMELOG=$(ARBHOME)/arb_time.log
2688	TIMEARGS=--append --output=$(TIMELOG) --format=" * %E(%S+%U) %P [%C]"
2689	TIMECMD=$(TIME) $(TIMEARGS)
2690
2691	time_one:
2692	ifeq ($(ONE_TIMED_TARGET),)
2693	@echo "Error: You have to pass ONE_TIMED_TARGET to $@"
2694	false
2695	else
2696	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET)"
2697	@$(TIMECMD) $(MAKE) $(ONE_TIMED_TARGET)
2698	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET) [done]"
2699	endif
2700
2701	timed_target:
2702	ifeq ($(TIMED_TARGET),)
2703	@echo "Error: You have to pass TIMED_TARGET to $@"
2704	false
2705	else
2706	@echo "Build time:" > $(TIMELOG)
2707	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2708	@cat $(TIMELOG)
2709	@rm $(TIMELOG)
2710	endif
2711
2712	timed_target_tested:
2713	ifeq ($(TIMED_TARGET),)
2714	@echo "Error: You have to pass TIMED_TARGET to $@"
2715	false
2716	else
2717	@echo "Build time:" > $(TIMELOG)
2718	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2719	$(MAKE) "ONE_TIMED_TARGET=ut" time_one
2720	@cat $(TIMELOG)
2721	@rm $(TIMELOG)
2722	endif
2723
2724	clean_timed_target:
2725	ifeq ($(TIMED_TARGET),)
2726	@echo "Error: You have to pass TIMED_TARGET to $@"
2727	false
2728	else
2729	@echo "Build time:" > $(TIMELOG)
2730	$(MAKE) "ONE_TIMED_TARGET=clean" time_one
2731	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2732	@cat $(TIMELOG)
2733	@rm $(TIMELOG)
2734	endif
2735
2736	# --------------------------------------------------------------------------------
2737
2738	CHECKOUT_MODIFIED=0# set to 1 to temporarily skip test for modifications (do not check in if set to 1)
2739
2740	check_svn_does_not_contain_generated:
2741	ifeq ($(CHECKOUT_MODIFIED),0)
2742	@echo "Testing that build does not modify files in SVN"
2743	@test 0 = `svn status \| wc -l` \|\| ( \
2744	echo "The checkout is not/no longer clean:"; \
2745	svn status; \
2746	echo "- if this fails instantly, your checkout is not clean"; \
2747	echo "- if this fails after other targets, these targets modify checked in data"; \
2748	echo " (a common cause may be that depends are not up to date)"; \
2749	false)
2750	else
2751	grep -Hn 'CHECKOUT_MODIFIED' Makefile
2752	endif
2753
2754	check_svn_ignores_generated:
2755	@test 0 = `svn status \| grep '^\?' \| wc -l` \|\| ( \
2756	echo "There are svn-unignored files:"; \
2757	svn status \| grep '^\?'; \
2758	echo "(all generated files should be svn-ignored)"; \
2759	false)
2760
2761	check_svn_state: check_svn_does_not_contain_generated
2762	$(MAKE) check_svn_ignores_generated
2763	$(MAKE) savetest
2764
2765	things_that_always_should_work: depends proto
2766
2767	post_commit_check:
2768	@echo "---------------------------------------- [Initial]"
2769	$(MAKE) check_svn_state
2770
2771	$(MAKE) clean
2772	@echo "---------------------------------------- [After 'make clean']"
2773	$(MAKE) check_svn_state
2774
2775	$(MAKE) things_that_always_should_work
2776	@echo "---------------------------------------- [After 'make things_that_always_should_work']"
2777	$(MAKE) check_svn_state
2778
2779	$(MAKE) all
2780	@echo "---------------------------------------- [After 'make all']"
2781	$(MAKE) check_svn_state
2782
2783	$(MAKE) things_that_always_should_work
2784	@echo "---------------------------------------- [Final]"
2785	$(MAKE) check_svn_state
2786
2787	# --------------------------------------------------------------------------------
2788	# sanitize arb_ntree; also works for clients (arb_edit4, ...) started from there.
2789
2790	sanitize: all
2791	( \
2792	export "LSAN_OPTIONS=max_leaks=30:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp"; \
2793	echo "sake[1]: Entering directory \`$(ARBHOME)'"; \
2794	$(ARBHOME)/bin/arb_ntree --execute _logged ~/data/test.arb 2>&1 ; \
2795	echo "sake[1]: Leaving directory \`$(ARBHOME)'" \
2796	) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
2797
2798	# --------------------------------------------------------------------------------
2799	# build and test one unit:
2800
2801	build_oneunit:
2802	$(MAKE) "WITHPERL=1" $(UNIT).dummy
2803
2804	oneunit:
2805	ifndef UNIT
2806	@echo "Please define UNIT, e.g. using"
2807	@echo " make \"UNIT=ARBDB/libARBDB\" oneunit"
2808	@echo " make \"UNIT=SL/TREEDISP/TREEDISP\" oneunit"
2809	@echo "(Note: 1st is a shared library, 2nd isn't)"
2810	false
2811	else
2812	@echo "Build time" > $(TIMELOG)
2813	@echo "$(SEP) $(MAKE) build_oneunit"
2814	@$(TIMECMD) $(MAKE) build_oneunit
2815	ifeq ($(UNIT_TESTS),1)
2816	@echo "$(SEP) $(MAKE) run_oneunitstests"
2817	@$(TIMECMD) $(MAKE) run_oneunitstests
2818	endif
2819	@cat $(TIMELOG)
2820	@rm $(TIMELOG)
2821	endif
2822
2823	# --------------------------------------------------------------------------------
2824
2825	build: arb
2826	$(MAKE) check_bin_dep preplib compile_compatibility fig_cure
2827
2828	all:
2829	@echo "Build time" > $(TIMELOG)
2830	# $(MAKE) clean_checked_vect # uncomment to rebuild sources where expected vectorization gets tested
2831	@echo "$(SEP) $(MAKE) all"
2832	@$(TIMECMD) $(MAKE) build
2833	@echo $(SEP)
2834	@echo "made 'all' with success."
2835	@echo "to start arb enter 'arb'"
2836	ifeq ($(UNIT_TESTS),1)
2837	@echo "$(SEP) $(MAKE) run_tests"
2838	@$(TIMECMD) $(MAKE) run_tests
2839	endif
2840	@echo "$(SEP) $(MAKE) all [done]"
2841	ifeq ($(DEBUG),1)
2842	@$(MAKE) save_test_no_error >/dev/null # just show hints
2843	endif
2844	@cat $(TIMELOG)
2845	@rm $(TIMELOG)
2846

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