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Last change on this file was 16986, checked in by westram, 7 years ago

reintegrates 'gcc' into 'trunk'
- ports arb to gcc 8.1 (fixing warnings)
adds: log:branches/gcc@16965:16985

Update: continued by [17178]

Property svn:eol-style set to native
Property svn:keywords set to Author Date Id Revision

File size: 78.7 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	# BUILDHOST_64=0/1 1=>compile on 64 bit platform (defaults to ARB_64)
17	# DEVELOPER=name special compilation (values: ANY,RELEASE,your name)
18	# OPENGL=0/1 whether OPENGL is available
19	#
20	# -----------------------------------------------------
21	# Paths for several libraries may be set from config.makefile by using:
22	#
23	# export XLIBS=$(shell pkg-config --libs xpm xerces-c)
24	# export XINCLUDES=$(shell pkg-config --cflags x11)
25	# export XAW_LIBS=$(shell pkg-config --libs xaw7)
26	# export XML_INCLUDES=$(shell pkg-config --cflags xerces-c)
27	#
28	# You make have to explicitely point pkg-config to the *.pc files needed.
29	# For example, Xquartz X11 libraries on macos can be located by adding
30	# the following line before those given above:
31	#
32	# export PKG_CONFIG_PATH=/usr/X11/lib/pkgconfig
33	#
34	# -----------------------------------------------------
35	# ARB Makefile and ARB source code are aware of the following defines:
36	#
37	# $(MACH) name of the machine (LINUX or DARWIN; see config.makefile)
38	# DEBUG compiles the DEBUG sections
39	# DEBUG_GRAPHICS all X-graphics are flushed immediately (for debugging)
40	# ARB_64=0/1 1=>compile 64 bit version
41	# UNIT_TESTS=0/1 1=>compile in unit tests and call them after build
42	# COVERAGE=0/1/2 compile in gcov support (useful together with UNIT_TESTS=1)
43	# 0=no, 1+2=compile in, 1=show
44	# STABS=0/1 force stabs format? (0 = "use default format")
45	# SANITIZE=0/#/all use Sanitizer? (defaults to 0,
46	# 1=AddressSanitizer+LeakSanitizer,
47	# 2=UndefinedBehaviorSanitizer,
48	# combine bit-values to activate multiple Sanitizers,
49	# specify 'all' to activate all)
50	# SHOWTODO=0/1 activate TODO-warnings? (defaults to 0, except for ralf)
51	#
52	# -----------------------------------------------------
53	# The ARB source code is aware of the following defines:
54	#
55	# NDEBUG doesn't compile the DEBUG sections
56	# DEVEL_$(DEVELOPER) developer-dependent flag (enables you to have private sections in code)
57	# DEVELOPER='ANY' (default setting) will be ignored
58	# configurable in config.makefile
59	#
60	# -----------------------------------------------------
61	# Read configuration
62	include config.makefile
63
64	# set defaults for variables commented out in config.makefile:
65	ifndef DARWIN
66	DARWIN:=0
67	endif
68	ifndef LINUX
69	LINUX:=0
70	endif
71	ifndef DEBIAN
72	DEBIAN:=0
73	endif
74	ifndef REDHAT
75	REDHAT:=0
76	endif
77	ifndef ARB_64
78	ARB_64=1#default to 64bit
79	endif
80
81	# compiler settings:
82	ifneq ($(CC),use__A_CC__instead_of__CC)
83	A_CC:=$(CC)# compile C
84	A_CXX:=$(CXX)# compile C++
85
86	# uncomment to ensure no submakefile uses CC and CXX directly
87	override CC:=use__A_CC__instead_of__CC
88	override CXX:=use__A_CXX__instead_of__CXX
89	endif
90
91	export CC CXX A_CC A_CXX
92
93	# unconditionally prepend $(ARBHOME)/lib to LD_LIBRARY_PATH if not found
94	ifeq ($(findstring $(ARBHOME)/lib,$(LD_LIBRARY_PATH)),)
95	LD_LIBRARY_PATH:=${ARBHOME}/lib:$(LD_LIBRARY_PATH)
96	endif
97
98	# store LD_LIBRARY_PATH to circumvent SIP restrictions:
99	ARBBUILD_LIBRARY_PATH:=$(LD_LIBRARY_PATH)
100
101	FORCEMASK = umask 002
102	NODIR=--no-print-directory
103
104	SED:=$(ARBHOME)/SH/arb_sed
105	READLINK:=$(ARBHOME)/SH/arb_readlink
106
107	# ---------------------- compiler version detection
108
109	# supported gcc versions:
110	ALLOWED_gcc_VERSIONS=\
111	4.4.3 4.4.5 4.4.6 4.4.7 \
112	4.5.2 \
113	4.6.1 4.6.2 4.6.3 4.6.4 \
114	4.7.1 4.7.2 4.7.3 4.7.4 \
115	4.8.0 4.8.1 4.8.2 4.8.3 4.8.4 4.8.5 \
116	4.9.0 4.9.1 4.9.2 4.9.3 4.9.4 \
117	5.1.0 5.2.0 5.3.0 5.3.1 5.4.0 5.5.0 \
118	6.1.0 6.2.0 6.3.0 6.4.0 \
119	7.1.0 7.2.0 7.3.0 \
120	8.1.0 \
121
122	# ----------------------
123
124	COMPILER_INFO:=$(shell SOURCE_TOOLS/arb_compiler_version.pl $(A_CXX))
125	COMPILER_NAME:=$(word 1,$(COMPILER_INFO))
126	COMPILER_VERSION:=$(word 2,$(COMPILER_INFO))
127
128	USE_CLANG:=0
129	ifneq ($(COMPILER_NAME),gcc)
130	ifeq ($(COMPILER_NAME),clang)
131	USE_CLANG:=1
132	else
133	ifeq ($(COMPILER_VERSION),4.6.4)
134	# gcc version 4.6.4 segfaults when dumping symbols for detection (silently accept as gcc)
135	COMPILER_NAME:=gcc
136	else
137	$(error failed to detect COMPILER_NAME (got '$(COMPILER_NAME)', expected 'clang' or 'gcc'))
138	endif
139	endif
140	endif
141
142	ifeq ($(USE_CLANG),1)
143	# accept all clang versions:
144	ALLOWED_COMPILER_VERSIONS=$(COMPILER_VERSION)
145	else
146	ALLOWED_COMPILER_VERSIONS=$(ALLOWED_gcc_VERSIONS)
147	endif
148
149	COMPILER_VERSION_ALLOWED=$(strip $(subst ___,,$(foreach version,$(ALLOWED_COMPILER_VERSIONS),$(findstring ___$(version)___,___$(COMPILER_VERSION)___))))
150
151	#---------------------- split gcc version
152
153	SPLITTED_VERSION:=$(subst ., ,$(COMPILER_VERSION))
154
155	USE_GCC_MAJOR:=$(word 1,$(SPLITTED_VERSION))
156	USE_GCC_MINOR:=$(word 2,$(SPLITTED_VERSION))
157	USE_GCC_PATCHLEVEL:=$(word 3,$(SPLITTED_VERSION))
158
159	USE_GCC_452_OR_HIGHER:=
160	USE_GCC_46_OR_HIGHER:=
161	USE_GCC_47_OR_HIGHER:=
162	USE_GCC_48_OR_HIGHER:=
163	USE_GCC_49_OR_HIGHER:=
164	USE_GCC_50_OR_HIGHER:=
165	USE_GCC_60_OR_HIGHER:=
166	USE_GCC_70_OR_HIGHER:=
167	USE_GCC_80_OR_HIGHER:=
168
169	ifeq ($(USE_CLANG),0)
170	ifeq ($(USE_GCC_MAJOR),4)
171	ifeq ($(USE_GCC_MINOR),5)
172	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),23456789)','')
173	USE_GCC_452_OR_HIGHER:=yes
174	endif
175	else
176	ifneq ('$(findstring $(USE_GCC_MINOR),6789)','')
177	USE_GCC_452_OR_HIGHER:=yes
178	USE_GCC_46_OR_HIGHER:=yes
179	ifneq ($(USE_GCC_MINOR),6)
180	USE_GCC_47_OR_HIGHER:=yes
181	ifneq ($(USE_GCC_MINOR),7)
182	USE_GCC_48_OR_HIGHER:=yes
183	ifneq ($(USE_GCC_MINOR),8)
184	USE_GCC_49_OR_HIGHER:=yes
185	endif
186	endif
187	endif
188	endif
189	endif
190	else
191	# gcc 5.x or higher
192	USE_GCC_452_OR_HIGHER:=yes
193	USE_GCC_46_OR_HIGHER:=yes
194	USE_GCC_47_OR_HIGHER:=yes
195	USE_GCC_48_OR_HIGHER:=yes
196	USE_GCC_49_OR_HIGHER:=yes
197	USE_GCC_50_OR_HIGHER:=yes
198	ifneq ($(USE_GCC_MAJOR),5)
199	# gcc 6.x or higher
200	USE_GCC_60_OR_HIGHER:=yes
201	ifneq ($(USE_GCC_MAJOR),6)
202	# gcc 7.x or higher
203	USE_GCC_70_OR_HIGHER:=yes
204	ifneq ($(USE_GCC_MAJOR),7)
205	# gcc 8.x or higher
206	USE_GCC_80_OR_HIGHER:=yes
207	endif
208	endif
209	endif
210	endif
211	endif
212
213	#---------------------- define special directories for non standard builds
214
215	ifeq ($(DARWIN),1)
216	OSX_FW:=/System/Library/Frameworks
217	OSX_FW_OPENGL:=$(OSX_FW)/OpenGL.framework/Versions/A/Libraries
218	OSX_FW_GLUT:=$(OSX_FW)/GLUT.framework/Versions/A/Libraries
219	OSX_FW_IMAGEIO:=$(OSX_FW)/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources
220	endif
221
222	#----------------------
223
224	ifeq ($(DARWIN),1)
225	LINK_STATIC=1# link static
226	else
227	LINK_STATIC=0# link dynamically
228	# LINK_STATIC=1# link static (testing only)
229	endif
230
231	shared_cflags :=# flags for shared lib compilation
232	clflags :=# linker flags (when passed through gcc)
233	extended_warnings :=# warning flags for C and C++-compiler
234	extended_cpp_warnings :=# warning flags for C++-compiler only
235
236	DISABLE_VECTORIZE_CHECK:=0# for details about vectorization checks see SOURCE_TOOLS/vectorize.README
237
238	ifeq ($(DEBUG),0)
239	dflags := -DNDEBUG# defines
240	ifeq ($(USE_CLANG),1)
241	cflags := -O3# compiler flags (C and C++)
242	else
243	clflags += -Wl,-O2# passthrough linker flags
244	# ------- standard optimization:
245	cflags := -O3# compiler flags (C and C++)
246	# ------- test changed optimization (DISABLE_VECTORIZE_CHECK for -O2 or lower):
247	# cflags := -O2# do not commit uncommented!
248	# DISABLE_VECTORIZE_CHECK:=1
249	endif
250	endif
251
252	ifeq ($(DEBIAN),1)
253	clflags += -Wl,-rpath=/usr/lib/arb/lib -Wl,-z,relro
254	endif
255
256	ifeq ($(DEBUG),1)
257	dflags := -DDEBUG
258
259	gdb_common := -g -g3 -ggdb -ggdb3
260
261	DBGOPTI:=-O0
262	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
263	DBGOPTI:=-Og
264	endif
265
266	ifeq ($(STABS),1)
267	cflags := $(DBGOPTI) $(gdb_common) -gstabs+ # using stabs+ (enable this for bigger debug session: debugs inlines, quick var inspect, BUT valgrind stops working :/)
268	else
269	cflags := $(DBGOPTI) $(gdb_common) # (using dwarf - cant debug inlines here, incredible slow on showing variable content)
270	endif
271
272	# cflags := $(DBGOPTI) $(gdb_common) -gdwarf-3 # (specify explicit dwarf format)
273	# cflags := $(DBGOPTI) $(gdb_common) -gstabs # using stabs (same here IIRC)
274	# cflags := -O2 $(gdb_common) # use this for callgrind (force inlining)
275
276	ifeq ($(DARWIN),0)
277	clflags += -Wl,-g
278	# Note:
279	# Previously '-Wl,-noinhibit-exec' was added to 'clflags' here,
280	# to fix some issues with launchpad binutils (see [12972]).
281	# But that change also caused 'undefined symbols' NOT to be reported as errors
282	# at link time, producing executables that fail at runtime :/
283	endif
284
285	ifeq ($(DEBUG_GRAPHICS),1)
286	dflags += -DDEBUG_GRAPHICS
287	endif
288
289	endif # DEBUG only
290
291	# control how much you get spammed
292	# (please do not change default in SVN, use developer specific setting as below)
293	POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl
294	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --original# dont modify compiler output
295	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --loop-optimization-candi# show candidates for vectorization check
296	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --dump-loop-optimization# useful while optimizing code for vectorization
297	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --hide-Noncopyable-advices
298	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --show-useless-Weff++
299	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --no-warnings
300	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --only-first-error
301	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --no-warnings --only-first-error
302	#
303	# for details about vectorization checks see SOURCE_TOOLS/vectorize.README
304
305	ifeq ($(DEVELOPER),ELMAR)
306	POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --only-first-error
307	endif
308
309	# always pass used compiler version to postcompile:
310	POST_COMPILE += --compiler=$(COMPILER_VERSION)
311
312	# Enable extra warnings
313	extended_warnings :=
314	extended_cpp_warnings :=
315
316	# C and C++
317	extended_warnings += -Wwrite-strings -Wunused -Wno-aggregate-return -Wshadow
318
319	# C++ only
320	extended_cpp_warnings += -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute
321	extended_cpp_warnings += -Wctor-dtor-privacy
322	# extended_cpp_warnings += -Wfloat-equal
323
324	extended_cpp_warnings += -Wmissing-noreturn
325	# extended_cpp_warnings += -Wold-style-cast# (warns about 28405 old-style casts)
326	extended_cpp_warnings += -Winit-self
327	extended_cpp_warnings += -Wstrict-aliasing
328	extended_cpp_warnings += -Wextra
329
330	# ------- above only warning-options already available in gcc 4.4.3
331
332	# -Weffc++ broken in 4.7.x series
333	# gcc 4.7.3 crashes on GenomeImport.cxx when -Weffc++ is active
334	# (bug reported https://gcc.gnu.org/bugzilla/show_bug.cgi?id=56923; apparently wont be fixed for 4.7-series)
335	# gcc 4.7.4 crashes on DBwriter.cxx when -Weffc++ is active
336	WEFFC_BROKEN:=0
337	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
338	ifneq ('$(USE_GCC_48_OR_HIGHER)','yes')
339	WEFFC_BROKEN:=1
340	endif
341	endif
342	ifeq ('$(WEFFC_BROKEN)','0')
343	extended_cpp_warnings += -Weffc++
344	endif
345
346	# turn off -Wmaybe-uninitialized in debug mode (gets activated with -Wextra). too many bogus warnings
347	ifeq ($(DEBUG),1)
348	ifeq ($(USE_CLANG),0)
349	extended_cpp_warnings += -Wno-maybe-uninitialized
350	endif
351	endif
352
353	ifeq ('$(USE_GCC_452_OR_HIGHER)','yes')
354	extended_cpp_warnings += -Wlogical-op# gcc 4.5.2
355	endif
356	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
357	extended_cpp_warnings += -Wzero-as-null-pointer-constant# gcc 4.7
358	endif
359	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
360	extended_cpp_warnings += -Wunused-local-typedefs# available since gcc 4.7 (but fails for each STATIC_ASSERT, so enable only for Cxx11)
361	endif
362	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
363	extended_cpp_warnings += -Wswitch-bool
364	extended_cpp_warnings += -Wlogical-not-parentheses
365	extended_cpp_warnings += -Wsizeof-array-argument
366	extended_cpp_warnings += -Wbool-compare
367
368	ifneq ($(DEVELOPER),RELEASE)
369	# suggest final:
370	extended_cpp_warnings += -Wsuggest-final-types
371	extended_cpp_warnings += -Wsuggest-final-methods
372	dflags += -DSUGGESTS_FINAL
373	endif
374	endif
375	ifeq ('$(USE_GCC_60_OR_HIGHER)','yes')
376	extended_cpp_warnings += -Wduplicated-cond
377	endif
378
379	#---------------------- turn off clang bogus warnings
380
381	ifeq ($(USE_CLANG),1)
382	# -Wmismatched-tags warns about struct/class mismatch in forward declarations (which is explicitely allowed)
383	# -Wchar-subscripts reports too many bogus warnings for "array['x']" (when 'x' is known to be in range [0..128])
384	# -Wunused-private-field report too many false positives (currently ~ 2 of 3)
385	# -Wstring-plus-int warns about common ARB coding practice
386	# -Wgnu-static-float-init warns about accepted GNU extension
387	extended_cpp_warnings += -Wno-mismatched-tags -Wno-char-subscripts -Wno-unused-private-field -Wno-string-plus-int
388	ifeq ('$(COMPILER_VERSION)','4.2.1')
389	# jenkins build (doesn't know switch -Wno-gnu-static-float-init)
390	extended_cpp_warnings += -Wno-gnu
391	else
392	extended_cpp_warnings += -Wno-gnu-static-float-init
393	endif
394	endif
395
396	#---------------------- developer
397
398	ifneq ($(DEVELOPER),ANY) # ANY=default setting (skip all developer specific code)
399	dflags += -DDEVEL_$(DEVELOPER)# activate developer/release specific code
400	endif
401
402	#---------------------- activate TODO warnings?
403
404	ifndef SHOWTODO
405	ifeq ($(DEVELOPER),RALF)
406	SHOWTODO:=1
407	else
408	SHOWTODO:=0
409	endif
410	endif
411	ifeq ($(SHOWTODO),1)
412	dflags += -DWARN_TODO# activate "TODO" warnings
413	endif
414
415	#---------------------- activate threads?
416	# only useful if compiler is able to compile Cxx11 or better
417
418	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
419	# see also ./TEMPLATES/cxxforward.h@USE_Cxx11
420	cflags += -pthread
421	clflags += -pthread
422	endif
423
424	#---------------------- activate Sanitizers?
425
426	ASAN_OPTIONS:=handle_segv=0:color=0
427	ASAN_OPTIONS+=:detect_leaks=1 # comment-out to disable leak-detection
428	ASAN_OPTIONS+=:check_initialization_order=1
429	# ASAN_OPTIONS+=:abort_on_error=1
430
431	# suppressions: SOURCE_TOOLS/arb.leaksan.supp
432	LSAN_OPTIONS:=max_leaks=3:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp
433
434
435	ifndef SANITIZE
436	SANITIZE:=0
437	endif
438
439	SANITIZE_ADDRESS:=0
440	SANITIZE_UNDEFINED:=0
441
442	ifneq ($(SANITIZE),0)
443	ifeq ($(SANITIZE),all)
444	SANITIZE:=3
445	endif
446
447	ifeq ($(SANITIZE),1)
448	SANITIZE_ADDRESS:=1
449	else
450	ifeq ($(SANITIZE),2)
451	SANITIZE_UNDEFINED:=1
452	else
453	ifeq ($(SANITIZE),3)
454	SANITIZE_ADDRESS:=1
455	SANITIZE_UNDEFINED:=1
456	else
457	$(error Unknown value '$(SANITIZE)' specified for SANITIZE in config.makefile)
458	endif
459	endif
460	endif
461	endif
462
463	ifeq ($(SANITIZE_ADDRESS),1)
464	ifneq ('$(USE_GCC_48_OR_HIGHER)','yes')
465	$(info AddressSanitizer not usable with gcc $(COMPILER_VERSION) - disabled)
466	SANITIZE_ADDRESS:=0
467	else
468	ifneq ('$(USE_GCC_49_OR_HIGHER)','yes')
469	$(warning note that LeakSanitizer does not work with gcc $(COMPILER_VERSION))
470	endif
471	endif
472	endif
473
474	ifeq ($(SANITIZE_UNDEFINED),1)
475	ifneq ('$(USE_GCC_49_OR_HIGHER)','yes')
476	$(info UndefinedBehaviorSanitizer not usable with gcc $(COMPILER_VERSION) - disabled)
477	SANITIZE_UNDEFINED:=0
478	endif
479	endif
480
481	SANITIZE_ANY:=0
482	ifeq ($(SANITIZE_ADDRESS),1)
483	SANITIZE_ANY:=1
484	endif
485	ifeq ($(SANITIZE_UNDEFINED),1)
486	SANITIZE_ANY:=1
487	endif
488
489	# vectorization fails if sanitizer active where it normally succeeds -> disable check
490	ifeq ($(SANITIZE_ANY),1)
491	DISABLE_VECTORIZE_CHECK:=1
492	endif
493
494	# deactivate some bogus warnings occurring when sanitizing NDEBUG version
495	# (do not disable for future gcc-version >= 8.x -> test again when available)
496	ifeq ($(SANITIZE_ANY),1)
497	ifeq ($(DEBUG),0)
498	ifneq ('$(USE_GCC_80_OR_HIGHER)','yes')
499	extended_cpp_warnings += -Wno-format-overflow
500	extended_cpp_warnings += -Wno-maybe-uninitialized
501	endif
502	endif
503	endif
504
505	#---------------------- 32 or 64 bit
506
507	ifndef BUILDHOST_64
508	BUILDHOST_64:=$(ARB_64)# assume build host is same as version (see config.makefile)
509	endif
510
511	cross_cflags:=
512	cross_lflags:=
513	cross_clflags:=
514
515	ifeq ($(ARB_64),1)
516	dflags += -DARB_64 #-fPIC
517	shared_cflags += -fPIC
518
519	ifeq ($(BUILDHOST_64),1)
520	# build 64-bit ARB version on 64-bit host
521	CROSS_LIB:=# empty = autodetect below
522	ifeq ($(DARWIN),1)
523	cross_cflags += -arch x86_64
524	cross_lflags += -arch x86_64
525	cross_clflags += -arch x86_64
526	endif
527	else
528	# build 64-bit ARB version on 32-bit host
529	CROSS_LIB:=/lib64
530	cross_cflags += -m64
531	cross_lflags += -m64 -m elf_x86_64
532	cross_clflags += -m64 -Wl,-m64,-m,elf_x86_64
533	endif
534	else
535	ifeq ($(BUILDHOST_64),1)
536	# build 32-bit ARB version on 64-bit host
537	CROSS_LIB:=# empty = autodetect below
538	cross_cflags += -m32
539	cross_lflags += -m32 -m elf_i386
540	cross_clflags += -m32 -Wl,-m32,-m,elf_i386
541	else
542	# build 32-bit ARB version on 32-bit host
543	CROSS_LIB:=/lib
544	endif
545	endif
546
547	cflags += $(cross_cflags)
548	clflags += $(cross_clflags)
549
550	ifeq ('$(CROSS_LIB)','')
551	# autodetect libdir
552	ifeq ($(ARB_64),1)
553	CROSS_LIB:=$(shell (test -d /lib64 && echo lib64) \|\| echo lib)
554	else
555	CROSS_LIB:=$(shell (test -d /lib32 && echo lib32) \|\| echo lib)
556	endif
557	endif
558
559	#---------------------- unit tests
560
561	ifndef UNIT_TESTS
562	UNIT_TESTS=0#default is "no tests"
563	endif
564	ifeq ($(UNIT_TESTS),1)
565	dflags += -DUNIT_TESTS
566	UNIT_TESTER_LIB=UNIT_TESTER/UNIT_TESTER.a
567	else
568	UNIT_TESTER_LIB=
569	endif
570
571	#---------------------- use gcov
572
573	ifndef COVERAGE
574	COVERAGE=0#default is "no"
575	endif
576	ifneq ($(COVERAGE),0)
577	GCOV_FLAGS=--coverage
578	else
579	GCOV_FLAGS=
580	endif
581
582	cflags += $(GCOV_FLAGS)
583	clflags += $(GCOV_FLAGS)
584	cross_lflags += $(GCOV_FLAGS)
585
586	#---------------------- other flags
587
588	dflags += -D$(MACH) # define machine
589
590	ifeq ($(DARWIN),1)
591	shared_cflags += -fno-common
592	else
593	dflags += $(shell getconf LFS_CFLAGS)
594	endif
595
596	cflags += -pipe
597	cflags += -fmessage-length=0# don't wrap compiler output
598	cflags += -fshow-column# show columns
599	cflags += -funit-at-a-time
600	cflags += -fPIC
601	cflags += -fno-common# link all global data into one namespace
602	cflags += -fstrict-aliasing# gcc 3.4
603	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
604	cflags += -fno-diagnostics-show-caret#gcc 4.8 (4.7.?)
605	endif
606	#cflags += -save-temps# uncomment to see preprocessor output
607
608	#---------------------- various sanitizers
609	# There are some disabled tests in CORE/arb_misc.cxx@sanitizers
610	# which trigger sanitizer reports.
611
612	ifeq ($(SANITIZE_ANY),1)
613	cflags += -ggdb3 -fno-omit-frame-pointer
614	endif
615
616	# activate AddressSanitizer+LeakSanitizer?
617	ifeq ($(SANITIZE_ADDRESS),1)
618	cflags += -fsanitize=address
619	clflags += -fsanitize=address
620	dflags += -DLEAKS_SANITIZED
621	endif
622
623	# activate UndefinedBehaviorSanitizer?
624	ifeq ($(SANITIZE_UNDEFINED),1)
625	cflags += -fsanitize=undefined
626	clflags += -fsanitize=undefined
627	dflags += -DUNDEF_SANITIZED
628	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
629	# abort on runtime errors
630	cflags += -fno-sanitize-recover=all
631	endif
632	#
633	# Note: alignment-sanitizer is deactivated for ARBDB and PROBE!
634	ifeq ('$(DEBUG)','1')
635	ifeq ($(USE_GCC_MAJOR),4)
636	ifeq ($(USE_GCC_MINOR),9)
637	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),01)','')
638	# workaround https://gcc.gnu.org/bugzilla/show_bug.cgi?id=63531 for 4.9.0 + 4.9.1
639	# (problem is fixed in 4.9.2 release)
640	extended_cpp_warnings:=$(subst -Weffc++,,$(extended_cpp_warnings))
641	endif
642	endif
643	endif
644	endif
645	endif
646
647	#---------------------- X11 location
648
649	ifeq ($(DARWIN),1)
650	XHOME:=$(PREFIX)
651	else
652	ifeq ($(DEBIAN),1)
653	XHOME:=$(PREFIX)
654	else
655	XHOME:=/usr/X11R6
656	endif
657	endif
658
659	XINCLUDES ?= -I$(XHOME)/include
660	XLIBS ?= -L$(XHOME)/$(CROSS_LIB)
661	ifeq ($(DARWIN),1)
662	XINCLUDES += -I$(OSX_FW)/GLUT.framework/Headers -I$(OSX_FW)/OpenGL.framework/Headers -I$(OSX_SDK)/usr/include/krb5
663
664	XLIBS += -lXm -lpng -lz -lXt -lX11 -lXext -lXp -lXmu -lXi
665	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGL.dylib:$(OSX_FW_OPENGL)/libGL.dylib
666	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGLU.dylib:$(OSX_FW_OPENGL)/libGLU.dylib
667	else
668	XLIBS += -lXm -lXpm -lXt -lXext -lX11
669	endif
670
671	#---------------------- open GL
672
673	ifeq ($(OPENGL),1)
674	cflags += -DARB_OPENGL # activate OPENGL code
675	GL := gl # this is the name of the OPENGL base target
676	GL_LIB_SYS := -lGL -lGLU
677	GL_LIB_ARB := -L$(ARBHOME)/GL/glAW -lglAW
678
679	ifeq ($(DARWIN),1)
680	GL_LIB_SYS += -lpthread
681	endif
682
683	GL_PNGLIBS_ARB := -L$(ARBHOME)/GL/glpng -lglpng_arb
684	GL_PNGLIBS_SYS := -lpng
685
686	GLEWLIB := -lGLEW -lGLw
687	ifeq ($(DARWIN),1)
688	GLUTLIB := -glut
689	else
690	GLUTLIB := -lglut
691	endif
692
693	GL_LIBS_SYS := $(GL_LIB_SYS) $(GL_PNGLIBS_SYS) $(GLEWLIB) $(GLUTLIB)
694	GL_LIBS_ARB := $(GL_LIB_ARB) $(GL_PNGLIBS_ARB)
695
696	RNA3D_LIB := RNA3D/RNA3D.a
697	else
698	GL_LIBS_ARB:=# no opengl -> no libs
699	GL_LIBS_SYS:=# no opengl -> no libs
700	GL:=# don't build ARB openGL libs
701
702	RNA3D_LIB :=
703	endif
704
705	RNA3D_LIB_4_DEPENDS := RNA3D/RNA3D.a
706
707	GL_LIBS:=$(GL_LIBS_ARB) $(GL_LIBS_SYS)
708
709	#---------------------- tiff lib:
710
711	TIFFLIBS := -ltiff
712
713	#---------------------- XML lib:
714
715	XMLLIBS := -lxerces-c
716
717	#---------------------- glib:
718
719	ARB_NEEDED_GLIB=glib-2.0
720
721	ARB_GLIB_INCLUDE:=$(strip $(shell pkg-config --cflags $(ARB_NEEDED_GLIB)))
722	ARB_GLIB_LIBS:=$(strip $(shell pkg-config --libs $(ARB_NEEDED_GLIB)))
723
724	#---------------------- basic libs:
725
726	SYSLIBS:=
727	ifeq ($(DARWIN),1)
728	SYSLIBS += -lstdc++
729	else
730	SYSLIBS += -lm $(ARB_GLIB_LIBS)
731	endif
732
733	#---------------------- include symbols?
734
735	ifeq ($(TRACESYM),1)
736	ifeq ($(USE_CLANG),0)
737	cflags += -rdynamic
738	clflags += -rdynamic -Wl,--export-dynamic
739	endif
740	endif
741
742	#---------------------- system dependent commands
743
744	ifeq ($(DARWIN),1)
745	TIME:=gtime
746	else
747	TIME:=/usr/bin/time
748	endif
749
750	#---------------------- SSE vectorizer
751	# for details see SOURCE_TOOLS/vectorize.README
752
753	ifeq ($(DEBUG),0)
754	ifeq ($(USE_GCC_49_OR_HIGHER),yes)
755	ifeq ($(DISABLE_VECTORIZE_CHECK),0)
756	# cflags += -fopt-info
757	cflags += -fopt-info-vec
758	# Shows reasons for unsuccessful vectorization:
759	# cflags += -fopt-info-vec-missed
760	POST_COMPILE += --check-loop-optimization
761	endif
762	else
763	ifeq ($(USE_GCC_48_OR_HIGHER),yes)
764	# no automatic vectorization-check for gcc<4.9.0
765	# -> uncomment the next 2 lines and grep the spam it will produce for 'vectorized.*loops'
766	# cflags += -fopt-info -fopt-info-vec-missed
767	# POST_COMPILE += --original
768	endif
769	endif
770	endif
771
772	#---------------------- stop early on broken flags/compiler combination
773
774	ifeq ($(DEBUG),0)
775	ifeq ($(SANITIZE_ANY),1)
776	ifeq ('$(COMPILER_VERSION)','4.9.1')
777	$(error compiling DEBUG=0 + SANITIZE!=0 crashes with gcc $(COMPILER_VERSION) (gcc 4.9.2 works))
778	endif
779	endif
780	endif
781
782	#---------------------- differences between linking executables and shared libs:
783
784	# executables:
785	ifeq ($(DARWIN),1)
786	blflags:=$(clflags)
787	else
788	blflags:=$(clflags) -Wl,--no-undefined
789	endif
790
791	# shared libraries
792	llflags:=$(clflags)
793
794	# dont use clflags below
795	clflags:=
796
797	# -------------------------------------------------------------------------
798	# Don't put any machine/version/etc conditionals below!
799	# (instead define variables above)
800	# -------------------------------------------------------------------------
801
802	cflags += -W -Wall $(dflags) $(extended_warnings)
803	cxxflags := $(extended_cpp_warnings)
804
805	# add CFLAGS + CPPFLAGS from environment for DEBIAN build
806	ifeq ($(DEBIAN),1)
807	cflags := $(CFLAGS) $(cflags)
808	cxxflags += $(CPPFLAGS)
809	endif
810
811	ifeq ('$(USE_CLANG)','1')
812	# none of the following standards works with clang3.3 (under linux) => dont use standard (as done before r15516)
813	# cxxflags += -std=gnu++11
814	# cxxflags += -std=gnu++0x
815	else
816	ifeq ('$(USE_GCC_60_OR_HIGHER)','yes')
817	cxxflags += -std=gnu++14# see also TEMPLATES/cxxforward.h@USE_Cxx14
818	else
819	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
820	cxxflags += -std=gnu++11# see also TEMPLATES/cxxforward.h@USE_Cxx11
821	else
822	# gcc versions between 4.3 (lowest supported) and <4.7
823	cxxflags += -std=gnu++0x
824	endif
825	endif
826	endif
827
828	LINK_STATIC_LIB := ar -csq# link static lib
829	LINK_EXECUTABLE := $(A_CXX) $(blflags) -o# link executable (c++)
830
831	ifeq ($(LINK_STATIC),1)
832	SHARED_LIB_SUFFIX = a# static lib suffix
833	LINK_SHARED_LIB := $(LINK_STATIC_LIB)
834	else
835	SHARED_LIB_SUFFIX = so# shared lib suffix
836	LINK_SHARED_LIB := $(A_CXX) $(llflags) -shared -o# link shared lib
837	endif
838
839	ifeq ($(DARWIN),1)
840	lflags4perl:=
841	else
842	lflags4perl:=$(cross_lflags) -shared
843	endif
844
845	# delete variables unused below
846	blflags:=
847	llflags:=
848
849	# other used tools
850	MAKEDEPEND_PLAIN = makedepend
851	MAKEDEPEND = $(FORCEMASK);$(MAKEDEPEND_PLAIN)
852
853	#SEP:=--------------------------------------------------------------------------------
854	SEP=[`date +%M:%S.%N`] ------------------------------------------------
855	# to analyse timings run
856	# make -j9 clean; make -j9 all \| grep '^\[' \| sort
857	# make -j9 "TIMED_TARGET=perl" clean_timed_target \| grep '^\[' \| sort
858
859	# ------------------------------------------------------------ DYNLIBDEFS
860	# various dynamic library definitions for linking executables:
861	#
862	# SYSLIBS: system libraries needed by database lib
863	# ARBDB_LIB: database lib
864	# DBSYS_LIBS: executable using database (but no GUI)
865	# GUI_LIBS: executable using database and GUI (arb gui uses database)
866	#
867	# Note: definitions exported to sub-makefiles are described in SOURCE_TOOLS/parent_make.txt
868
869	CORE_LIB=-lCORE
870	ARBDB_LIB=-lARBDB $(CORE_LIB)
871	DBSYS_LIBS = $(ARBDB_LIB) $(SYSLIBS)
872
873	GUI_LIBS_PREFIX:=
874	ifeq ($(DARWIN),1)
875	# this seem to be added at wrong place, since opengl is only needed to link EDIT4
876	GUI_LIBS_PREFIX:=-framework GLUT -framework OpenGL
877	endif
878
879	GUI_LIBS=$(GUI_LIBS_PREFIX) $(DBSYS_LIBS) -lAWT -lWINDOW $(XLIBS)
880
881	LIBPATH = -L$(ARBHOME)/lib
882
883	DEST_LIB = lib
884	DEST_BIN = bin
885
886	CC_INCLUDES := -I. -I$(ARBHOME)/INCLUDE $(XINCLUDES) $(ARB_GLIB_INCLUDE)
887	CXX_INCLUDES := $(CC_INCLUDES)
888	MAKEDEPENDFLAGS := -- -DARB_OPENGL -DUNIT_TESTS -D__cplusplus -I. -Y$(ARBHOME)/INCLUDE
889
890	# -------------------------------
891	# old PTSERVER or PTPAN?
892
893	ifeq ($(PTPAN),1)
894	# PTPAN only libs
895	ARCHS_PT_SERVER = \
896	ptpan/PROBE.a
897	else
898	ifeq ($(PTPAN),2)
899	# special mode to compile both servers (developers only!)
900	ARCHS_PT_SERVER = \
901	ptpan/PROBE.a \
902	PROBE/PROBE.a
903	ARCHS_PT_SERVER_LINK = PROBE/PROBE.a# default to old ptserver
904	else
905	# PT-server only libs
906	ARCHS_PT_SERVER = \
907	PROBE/PROBE.a
908	endif
909	endif
910
911	ifndef ARCHS_PT_SERVER_LINK
912	ARCHS_PT_SERVER_LINK = $(ARCHS_PT_SERVER)
913	endif
914
915	# ---------------------------------------
916	# wrap main()
917
918	use_ARB_main=$(ARBHOME)/SOURCE_TOOLS/arb_main_cpp.o
919	use_ARB_main_C=$(ARBHOME)/SOURCE_TOOLS/arb_main_c.o
920
921	# -----------------------------------------
922	# export variables to submakefiles
923
924	include SOURCE_TOOLS/export2sub
925
926	# do not define (exported) variables below this point
927
928	# -------------------------
929	# Main arb targets:
930	# -------------------------
931
932	first_target:
933	$(MAKE) checks
934	@echo $(SEP)
935	@echo 'Main targets:'
936	@echo ''
937	@echo ' all - Compile ARB + TOOLs + and copy shared libs + link foreign software'
938	@echo ' (That is most likely the target you want)'
939	@echo ''
940	@echo ' clean - remove generated files ("SUBDIR/SUBDIR.clean" to clean only SUBDIR)'
941	@echo ' rebuild - clean + all'
942	@echo ' cleanlinked - remove all binaries'
943	@echo ' relink - cleanlinked + all (=relink all from objects)'
944	@echo ''
945	@echo 'Some often used sub targets (make all makes them all):'
946	@echo ''
947	@echo ' arb - Just compile ARB (but none of the integrated tools)'
948	@echo ' menus - create lib/gde/arb.menu from GDEHELP/ARB_GDEmenus.source'
949	@echo ' perl - Compile the PERL XSUBS into lib/ARB.so and create links in lib to perl'
950	@echo ' binlink - Create all links in the bin directory'
951	@echo ''
952	@echo 'Development targets:'
953	@echo ''
954	@echo ' depends - create or update dependencies ("SUBDIR/SUBDIR.depends" to update only SUBDIR)'
955	@echo ' proto - create or update prototypes ("SUBDIR/SUBDIR.proto" to update only SUBDIR)'
956	@echo ' tags - create tags for xemacs'
957	@echo ' show - show available shortcuts (AKA subtargets)'
958	@echo ' up - shortcut for depends+proto+tags'
959	ifeq ($(UNIT_TESTS),1)
960	@echo ' ut - only run tests'
961	@echo ' "UNIT=..." oneunit - build one unit and run tests (see also UNIT_TESTER/Makefile.setup.local)'
962	endif
963	ifneq ($(SANITIZE),0)
964	@echo ' sanitize - all + run arb_ntree with sanitizer (test.arb + execute _logged)'
965	endif
966	@echo ' modified - rebuild files modified in svn checkout (does touch)'
967	@echo ' touch - touch files modified in svn checkout'
968	@echo ''
969	@echo 'Internal maintenance:'
970	@echo ''
971	@echo ' relinfo - show help on release targets'
972	@echo ' tarfile - make rebuild and create arb version tarfile ("tarfile_quick" to skip rebuild)'
973	@echo ' save - save all basic ARB sources into arbsrc_DATE ("savetest" to check filelist)'
974	@echo ' patch - save svn diff to patchfile'
975	@echo ' source_doc - create doxygen documentation'
976	@echo ' relocated - rebuild partly (use when you have relocated ARBHOME)'
977	@echo ' check_res - check resource usage'
978	@echo ' dep_graph - Build dependency graphs'
979	@echo ' clean_cov - Clean coverage results'
980	@echo ''
981	@echo ' clean_opengl_changed - clean after changing OPENGL setting in config.Makefile'
982	@echo ' clean_checked_vect - clean units containing vectorization checks'
983	@echo ''
984	@echo ' post_commit_check - Checks whether'
985	@echo ' * main make targets work,'
986	@echo ' * dependencies and prototypes are up to date,'
987	@echo ' * SVN-controlled files remain unaffected by called targets and'
988	@echo ' * all generated files are ignored.'
989	@echo ' (has to be called in a clean SVN checkout)'
990	@echo $(SEP)
991	@echo ''
992
993	relinfo:
994	@echo ''
995	@echo $(SEP)
996	@echo 'Release targets:'
997	@echo ''
998	@echo ' inc_candi - increase RC candidate-number (only possible in "rc" branch, not needed for RC1)'
999	@echo ' inc_patch - increase release patchlevel (only possible in "stable" branch)'
1000	@echo ' inc_minor - increase minor version number (only possible in "trunk")'
1001	@echo ' inc_major - increase MAJOR version number (only possible in "trunk")'
1002	@echo ''
1003	@echo ' show_version - show version tag'
1004	@echo ''
1005	@echo $(SEP)
1006	@echo ''
1007
1008	# auto-generate config.makefile:
1009
1010	CONFIG_MAKEFILE_FOUND=$(wildcard config.makefile)
1011
1012	config.makefile : config.makefile.template
1013	@echo --------------------------------------------------------------------------------
1014	ifeq ($(strip $(CONFIG_MAKEFILE_FOUND)),)
1015	@cp $< $@
1016	@echo '$(ARBHOME)/$@:1: has been generated.'
1017	@echo 'Please edit $@ to configure your system!'
1018	@echo --------------------------------------------------------------------------------
1019	@false
1020	else
1021	@echo '$(ARBHOME)/$<:1: is more recent than'
1022	@echo '$(ARBHOME)/$@:1:'
1023	@ls -al config.makefile*
1024	@echo --------------------------------------------------------------------------------
1025	@echo "Updating $@ (if this fails, check manually)"
1026	SOURCE_TOOLS/update_config_makefile.pl
1027	@echo "Sucessfully updated $@"
1028	@echo --------------------------------------------------------------------------------
1029	@ls -al config.makefile*
1030	@echo --------------------------------------------------------------------------------
1031	@echo "Diff to your old config.makefile:"
1032	@echo --------------------------------------------------------------------------------
1033	-diff $@.bak $@
1034	@echo --------------------------------------------------------------------------------
1035	endif
1036
1037	# check if everything is configured correctly
1038
1039	check_DEVELOPER:
1040	ifndef DEVELOPER
1041	@echo 'config.makefile:1: DEVELOPER not defined'
1042	@false
1043	endif
1044
1045	check_DEBUG:
1046	ifndef dflags
1047	@echo 'config.makefile:1: DEBUG has to be defined. Valid values are 0 and 1'
1048	@false
1049	endif
1050
1051	check_ARB_64:
1052	ifndef ARB_64
1053	@echo 'config.makefile:1: ARB_64 has to be defined. Valid values are 0 and 1'
1054	@false
1055	endif
1056
1057	# ---------------------------------------- check gcc version
1058
1059	COMPILER_BROKEN:=0
1060
1061	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.6.4')
1062	COMPILER_BROKEN:=1
1063	endif
1064	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.8.0')
1065	COMPILER_BROKEN:=1
1066	endif
1067
1068	check_same_GCC_VERSION:
1069	$(ARBHOME)/SOURCE_TOOLS/check_same_compiler_version.pl $(COMPILER_NAME) $(COMPILER_VERSION_ALLOWED)
1070
1071	check_GCC_VERSION:
1072	@echo 'Compiler version check:'
1073	# see .@ALLOWED_gcc_VERSIONS
1074	ifeq ('$(COMPILER_VERSION_ALLOWED)', '')
1075	@echo " - Your compiler is '$(COMPILER_NAME)' version '$(COMPILER_VERSION)'"
1076	@echo ' This version is not in the list of supported $(COMPILER_NAME)-versions:'
1077	@$(foreach version,$(ALLOWED_COMPILER_VERSIONS),echo ' * $(version)';)
1078	@echo ' - You may either ..'
1079	@echo ' - add your version to ALLOWED_$(COMPILER_NAME)_VERSIONS in the Makefile and try it out or'
1080	@echo ' - switch to one of the allowed versions (see arb_README_gcc.txt for installing'
1081	@echo ' a different version of gcc)'
1082	$(error Unsupported compiler '$(COMPILER_NAME)' version '$(COMPILER_VERSION)')
1083	else
1084	ifeq ($(COMPILER_BROKEN),1)
1085	$(error compilation refused for $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)'. Refer to http://bugs.arb-home.de/wiki/GccVersionInfo for details.)
1086	else
1087	@echo " - Supported $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)' detected - fine!"
1088	@echo ''
1089	ifeq ($(USE_CLANG),1)
1090	@echo "Dump clang version:"
1091	$(A_CXX) -v
1092	endif
1093	$(MAKE) check_same_GCC_VERSION
1094	endif
1095	endif
1096
1097	#---------------------- check ARBHOME
1098
1099	# use arb_INSTALL.txt to determine whether ARBHOME points to correct directory
1100	ARB_INSTALL_FOUND=$(wildcard $(ARBHOME)/arb_INSTALL.txt)
1101
1102	check_ARBHOME:
1103	ifeq ($(strip $(ARB_INSTALL_FOUND)),)
1104	@echo ------------------------------------------------------------
1105	@echo "ARBHOME is set to '$(ARBHOME)'"
1106	@echo "The environment variable ARBHOME has to point to the top arb source directory."
1107	@echo "If you use bash enter:"
1108	@echo " export ARBHOME='`pwd`'"
1109	@echo ------------------------------------------------------------
1110	@false
1111	endif
1112
1113	ARB_PATH_SET=$(findstring $(ARBHOME)/bin,$(PATH))
1114
1115	check_PATH: check_ARBHOME
1116	ifeq ($(strip $(ARB_PATH_SET)),)
1117	@echo ------------------------------------------------------------
1118	@echo "The environment variable PATH has to contain $(ARBHOME)/bin"
1119	@echo "If you use bash enter:"
1120	@echo ' export PATH=$$ARBHOME/bin:$$PATH'
1121	@echo ------------------------------------------------------------
1122	@false
1123	endif
1124
1125	check_TOOLS:
1126	@util/arb_check_build_env.pl \
1127	"$(A_CC)" \
1128	"$(A_CXX)" \
1129	"$(MAKEDEPEND_PLAIN)" \
1130	"$(LINK_SHARED_LIB)" \
1131	"$(LINK_SHARED_LIB)" \
1132
1133	check_ENVIRONMENT : check_PATH check_TOOLS
1134	@echo "-------------------- Environment [start]"
1135	@echo "ARBHOME='$(ARBHOME)'"
1136	@echo "PATH='$(PATH)'"
1137	@echo "LD_LIBRARY_PATH='$(LD_LIBRARY_PATH)'"
1138	@echo "-------------------- Environment [end]"
1139
1140	check_tabs: check_setup
1141	ifeq ($(DEBUG),1)
1142	@SOURCE_TOOLS/tabBrake.pl
1143	endif
1144
1145	force_tab_check:
1146	@touch -t 198001010000 SOURCE_TOOLS/stamp.tabBrake
1147	@$(MAKE) check_tabs
1148
1149
1150	# ---------------------
1151
1152	check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION
1153	@echo Your setup seems to be ok.
1154
1155	checks: check_setup check_tabs
1156	@rm -f SOURCE_TOOLS/postcompile.sav
1157
1158
1159	# end test section ------------------------------
1160
1161	# ---------------------------------------
1162	# List of standard top level directories
1163	#
1164	# sub-makefiles have to define the targets
1165	# - 'depends' and
1166	# - 'clean'
1167	#
1168	# when adding new libs here, also add a dependency vs 'links' or 'links_non_perl' in .@DD_links_non_perl
1169
1170	ARCHS = \
1171	$(ARCHS_PT_SERVER) \
1172	AISC/AISC.a \
1173	AISC_MKPTPS/AISC_MKPTPS.a \
1174	ARBDB/libARBDB.a \
1175	CORE/libCORE.a \
1176	ARB_GDE/ARB_GDE.a \
1177	AWT/libAWT.a \
1178	AWTC/AWTC.a \
1179	AWTI/AWTI.a \
1180	CONSENSUS_TREE/CONSENSUS_TREE.a \
1181	CONVERTALN/CONVERTALN.a \
1182	DBSERVER/DBSERVER.a \
1183	DIST/DIST.a \
1184	EDIT4/EDIT4.a \
1185	EISPACK/EISPACK.a \
1186	GDE/GDE.a \
1187	GENOM/GENOM.a \
1188	GENOM_IMPORT/GENOM_IMPORT.a \
1189	GL/GL.a \
1190	ISLAND_HOPPING/ISLAND_HOPPING.a \
1191	MERGE/MERGE.a \
1192	MULTI_PROBE/MULTI_PROBE.a \
1193	NALIGNER/NALIGNER.a \
1194	NAMES/NAMES.a \
1195	NAMES_COM/server.a \
1196	NTREE/NTREE.a \
1197	PARSIMONY/PARSIMONY.a \
1198	PERLTOOLS/PERLTOOLS.a \
1199	PHYLO/PHYLO.a \
1200	PRIMER_DESIGN/PRIMER_DESIGN.a \
1201	PROBE_COM/server.a \
1202	PROBE_DESIGN/PROBE_DESIGN.a \
1203	PROBE_SET/PROBE_SET.a \
1204	READSEQ/READSEQ.a \
1205	RNA3D/RNA3D.a \
1206	RNACMA/RNACMA.a \
1207	SECEDIT/SECEDIT.a \
1208	SEQ_QUALITY/SEQ_QUALITY.a \
1209	SERVERCNTRL/SERVERCNTRL.a \
1210	SL/SL.a \
1211	STAT/STAT.a \
1212	TOOLS/TOOLS.a \
1213	TREEGEN/TREEGEN.a \
1214	UNIT_TESTER/UNIT_TESTER.a \
1215	WETC/WETC.a \
1216	WINDOW/libWINDOW.a \
1217	XML/XML.a \
1218
1219	# -----------------------
1220	# library packets
1221
1222	ARCHS_CLIENT_PROBE = PROBE_COM/client.a
1223	ARCHS_CLIENT_NAMES = NAMES_COM/client.a
1224
1225	ARCHS_MAKEBIN = AISC_MKPTPS/AISC_MKPTPS.a AISC/AISC.a
1226
1227	# communication libs need aisc and aisc_mkpts:
1228
1229	AISC/AISC.dummy: proto_tools
1230
1231	comtools: AISC/AISC.dummy
1232
1233	ARCHS_SEQUENCE = \
1234	SL/SEQUENCE/SEQUENCE.a \
1235	SL/ALIVIEW/ALIVIEW.a \
1236	SL/PRONUC/PRONUC.a \
1237
1238	ARCHS_TREE = \
1239	SL/ARB_TREE/ARB_TREE.a \
1240	SL/FILTER/FILTER.a \
1241	$(ARCHS_SEQUENCE) \
1242
1243	# parsimony tree (used by NTREE, PARSIMONY, STAT(->EDIT4), DIST(obsolete!))
1244	ARCHS_AP_TREE = \
1245	SL/AP_TREE/AP_TREE.a \
1246	$(ARCHS_TREE) \
1247
1248	# --------------------------------------------------------------------------------
1249	# dependencies for linking shared libs
1250
1251	link_core: core
1252	link_db: db link_core
1253	link_aw: aw link_db
1254	link_awt: awt link_aw
1255
1256	#***************************************************************************************
1257	# Individual_Programs_Section
1258	#***************************************************************************************
1259
1260	arbmainwrapper:
1261	$(MAKE) -C SOURCE_TOOLS -r mainwrapper
1262
1263
1264	#********************************* arb_ntree ************************************
1265	NTREE = bin/arb_ntree
1266	ARCHS_NTREE = \
1267	NTREE/NTREE.a \
1268	ARB_GDE/ARB_GDE.a \
1269	SL/GROUP_SEARCH/GROUP_SEARCH.a \
1270	SL/DB_UI/DB_UI.a \
1271	AWTC/AWTC.a \
1272	AWTI/AWTI.a \
1273	CONSENSUS_TREE/CONSENSUS_TREE.a \
1274	GENOM_IMPORT/GENOM_IMPORT.a \
1275	GENOM/GENOM.a \
1276	MERGE/MERGE.a \
1277	MULTI_PROBE/MULTI_PROBE.a \
1278	PRIMER_DESIGN/PRIMER_DESIGN.a \
1279	PROBE_DESIGN/PROBE_DESIGN.a \
1280	SEQ_QUALITY/SEQ_QUALITY.a \
1281	SERVERCNTRL/SERVERCNTRL.a \
1282	SL/ALILINK/ALILINK.a \
1283	SL/AW_NAME/AW_NAME.a \
1284	SL/CONSENSUS/CONSENSUS.a \
1285	SL/DB_SCANNER/DB_SCANNER.a \
1286	SL/DB_QUERY/DB_QUERY.a \
1287	SL/QUERY/QUERY.a \
1288	SL/SEQIO/SEQIO.a \
1289	STAT/STAT.a \
1290	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1291	SL/HELIX/HELIX.a \
1292	SL/REGEXPR/REGEXPR.a \
1293	SL/REFENTRIES/REFENTRIES.a \
1294	SL/NDS/NDS.a \
1295	SL/ITEM_SHADER/ITEM_SHADER.a \
1296	SL/ITEMS/ITEMS.a \
1297	SL/INSDEL/INSDEL.a \
1298	SL/LOCATION/LOCATION.a \
1299	SL/MACROS/MACROS.a \
1300	SL/PVP/PVP.a \
1301	SL/TRANSLATE/TRANSLATE.a \
1302	SL/TREEDISP/TREEDISP.a \
1303	SL/TREE_ADMIN/TREE_ADMIN.a \
1304	SL/TREE_READ/TREE_READ.a \
1305	SL/TREE_WRITE/TREE_WRITE.a \
1306	XML/XML.a \
1307	$(ARCHS_AP_TREE) \
1308
1309	$(NTREE): $(ARCHS_NTREE:.a=.dummy) link_awt
1310	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NTREE) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1311	echo "$(SEP) Link $@"; \
1312	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(XMLLIBS)" ; \
1313	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(XMLLIBS) && \
1314	echo "$(SEP) Link $@ [done]"; \
1315	)
1316
1317	#********************************* arb_edit4 ************************************
1318	EDIT4 = bin/arb_edit4
1319
1320	ARCHS_EDIT4 := \
1321	EDIT4/EDIT4.a \
1322	ARB_GDE/ARB_GDE.a \
1323	SL/FAST_ALIGNER/FAST_ALIGNER.a \
1324	AWTC/AWTC.a \
1325	ISLAND_HOPPING/ISLAND_HOPPING.a \
1326	SECEDIT/SECEDIT.a \
1327	SERVERCNTRL/SERVERCNTRL.a \
1328	SL/AW_HELIX/AW_HELIX.a \
1329	SL/AW_NAME/AW_NAME.a \
1330	SL/CONSENSUS/CONSENSUS.a \
1331	SL/ITEMS/ITEMS.a \
1332	STAT/STAT.a \
1333	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1334	SL/HELIX/HELIX.a \
1335	SL/TRANSLATE/TRANSLATE.a \
1336	SL/MACROS/MACROS.a \
1337	SL/NDS/NDS.a \
1338	$(ARCHS_AP_TREE) \
1339	XML/XML.a \
1340
1341	ifeq ($(OPENGL),1)
1342	ARCHS_EDIT4 += RNA3D/RNA3D.a
1343	endif
1344
1345	LIBS_EDIT4 := $(GL_LIBS)
1346
1347	$(EDIT4): $(ARCHS_EDIT4:.a=.dummy) link_awt
1348	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_EDIT4) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1349	echo "$(SEP) Link $@"; \
1350	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4)" ; \
1351	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4) && \
1352	echo "$(SEP) Link $@ [done]"; \
1353	)
1354
1355	#********************************* arb_rnacma ************************************
1356	RNACMA = bin/arb_rnacma
1357	ARCHS_RNACMA = \
1358	RNACMA/RNACMA.a \
1359
1360	$(RNACMA) : $(ARCHS_RNACMA:.a=.dummy) link_db
1361	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_RNACMA) \|\| ( \
1362	echo "$(SEP) Link $@"; \
1363	echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_RNACMA) $(DBSYS_LIBS)"; \
1364	$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_RNACMA) $(DBSYS_LIBS) && \
1365	echo "$(SEP) Link $@ [done]"; \
1366	)
1367
1368	#********************************* arb_wetc ************************************
1369	WETC = bin/arb_wetc
1370	ARCHS_WETC = \
1371	WETC/WETC.a \
1372	SL/HELIX/HELIX.a \
1373	SL/FILTER/FILTER.a \
1374	XML/XML.a \
1375
1376	$(WETC): $(ARCHS_WETC:.a=.dummy) link_awt
1377	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_WETC) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1378	echo "$(SEP) Link $@"; \
1379	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC) $(GUI_LIBS)" ; \
1380	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC) $(GUI_LIBS) && \
1381	echo "$(SEP) Link $@ [done]"; \
1382	)
1383
1384	#********************************* arb_dist ************************************
1385	DIST = bin/arb_dist
1386	ARCHS_DIST = \
1387	DIST/DIST.a \
1388	CONSENSUS_TREE/CONSENSUS_TREE.a \
1389	EISPACK/EISPACK.a \
1390	SERVERCNTRL/SERVERCNTRL.a \
1391	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1392	SL/HELIX/HELIX.a \
1393	SL/MATRIX/MATRIX.a \
1394	SL/MACROS/MACROS.a \
1395	SL/NDS/NDS.a \
1396	SL/ITEMS/ITEMS.a \
1397	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.a \
1398	XML/XML.a \
1399	$(ARCHS_AP_TREE) \
1400
1401	$(DIST): $(ARCHS_DIST:.a=.dummy) link_awt
1402	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_DIST) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1403	echo "$(SEP) Link $@"; \
1404	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS)" ; \
1405	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) && \
1406	echo "$(SEP) Link $@ [done]"; \
1407	)
1408
1409	#********************************* arb_pars ************************************
1410	PARSIMONY = bin/arb_pars
1411	ARCHS_PARSIMONY = \
1412	PARSIMONY/PARSIMONY.a \
1413	SERVERCNTRL/SERVERCNTRL.a \
1414	SL/AW_NAME/AW_NAME.a \
1415	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1416	SL/HELIX/HELIX.a \
1417	SL/MACROS/MACROS.a \
1418	SL/NDS/NDS.a \
1419	SL/ITEMS/ITEMS.a \
1420	SL/TRANSLATE/TRANSLATE.a \
1421	SL/TREEDISP/TREEDISP.a \
1422	XML/XML.a \
1423	$(ARCHS_AP_TREE) \
1424
1425	$(PARSIMONY): $(ARCHS_PARSIMONY:.a=.dummy) link_awt
1426	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PARSIMONY) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1427	echo "$(SEP) Link $@"; \
1428	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS)" ; \
1429	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) && \
1430	echo "$(SEP) Link $@ [done]"; \
1431	)
1432
1433	#********************************* arb_convert_aln ************************************
1434	CONVERT_ALN = bin/arb_convert_aln
1435	ARCHS_CONVERT_ALN = \
1436	CONVERTALN/CONVERTALN.a \
1437
1438	$(CONVERT_ALN) : $(ARCHS_CONVERT_ALN:.a=.dummy) link_db
1439	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_CONVERT_ALN) $(use_ARB_main) \|\| ( \
1440	echo "$(SEP) Link $@"; \
1441	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN) $(DBSYS_LIBS)"; \
1442	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN) $(DBSYS_LIBS) && \
1443	echo "$(SEP) Link $@ [done]"; \
1444	)
1445
1446	#********************************* arb_treegen ************************************
1447
1448	TREEGEN = bin/arb_treegen
1449	ARCHS_TREEGEN = \
1450	TREEGEN/TREEGEN.a \
1451
1452	$(TREEGEN) : $(ARCHS_TREEGEN:.a=.dummy)
1453	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_TREEGEN) $(use_ARB_main_C) \|\| ( \
1454	echo "$(SEP) Link $@"; \
1455	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN)" ; \
1456	$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN) && \
1457	echo "$(SEP) Link $@ [done]"; \
1458	)
1459
1460	#********************************* arb_naligner ************************************
1461	NALIGNER = bin/arb_naligner
1462	ARCHS_NALIGNER = \
1463	NALIGNER/NALIGNER.a \
1464	SERVERCNTRL/SERVERCNTRL.a \
1465	SL/HELIX/HELIX.a \
1466
1467	$(NALIGNER): $(ARCHS_NALIGNER:.a=.dummy) link_db
1468	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NALIGNER) $(use_ARB_main) \|\| ( \
1469	echo "$(SEP) Link $@"; \
1470	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(DBSYS_LIBS)" ; \
1471	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(DBSYS_LIBS) && \
1472	echo "$(SEP) Link $@ [done]"; \
1473	)
1474
1475	#********************************* arb_phylo ************************************
1476	PHYLO = bin/arb_phylo
1477	ARCHS_PHYLO = \
1478	PHYLO/PHYLO.a \
1479	SL/HELIX/HELIX.a \
1480	SL/FILTER/FILTER.a \
1481	SL/MACROS/MACROS.a \
1482	XML/XML.a \
1483
1484	$(PHYLO): $(ARCHS_PHYLO:.a=.dummy) link_awt
1485	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PHYLO) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1486	echo "$(SEP) Link $@"; \
1487	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO) $(GUI_LIBS)" ; \
1488	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO) $(GUI_LIBS) && \
1489	echo "$(SEP) Link $@ [done]"; \
1490	)
1491
1492	#***************************************************************************************
1493	# SERVER SECTION
1494	#***************************************************************************************
1495
1496	#********************************* arb_db_server ************************************
1497	DBSERVER = bin/arb_db_server
1498	ARCHS_DBSERVER = \
1499	DBSERVER/DBSERVER.a \
1500	SERVERCNTRL/SERVERCNTRL.a \
1501
1502	$(DBSERVER): $(ARCHS_DBSERVER:.a=.dummy) link_db
1503	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_DBSERVER) $(ARBDB_LIB) $(use_ARB_main) \|\| ( \
1504	echo "$(SEP) Link $@"; \
1505	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS)" ; \
1506	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS) && \
1507	echo "$(SEP) Link $@ [done]"; \
1508	)
1509
1510	#********************************* arb_pt_server ************************************
1511	PROBE = bin/arb_pt_server
1512	ARCHS_PROBE_COMMON = \
1513	SL/PTCLEAN/PTCLEAN.a \
1514	SERVERCNTRL/SERVERCNTRL.a \
1515	SL/HELIX/HELIX.a \
1516
1517	ARCHS_PROBE_LINK = \
1518	$(ARCHS_PT_SERVER_LINK) \
1519	$(ARCHS_PROBE_COMMON) \
1520
1521	ARCHS_PROBE_DEPEND = \
1522	$(ARCHS_PT_SERVER) \
1523	$(ARCHS_PROBE_COMMON) \
1524
1525	$(PROBE): $(ARCHS_PROBE_DEPEND:.a=.dummy) link_db
1526	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_SERVER_PROBE) config.makefile $(use_ARB_main) \|\| ( \
1527	echo "$(SEP) Link $@"; \
1528	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_LINK) $(ARCHS_CLIENT_PROBE) $(ARBDB_LIB) $(SYSLIBS)" ; \
1529	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_LINK) $(ARCHS_CLIENT_PROBE) $(ARBDB_LIB) $(SYSLIBS) && \
1530	echo "$(SEP) Link $@ [done]"; \
1531	)
1532
1533	#********************************* arb_name_server ************************************
1534	NAMES = bin/arb_name_server
1535	ARCHS_NAMES = \
1536	NAMES/NAMES.a \
1537	SERVERCNTRL/SERVERCNTRL.a \
1538
1539	$(NAMES): $(ARCHS_NAMES:.a=.dummy) link_db
1540	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) $(use_ARB_main) \|\| ( \
1541	echo "$(SEP) Link $@"; \
1542	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS)" ; \
1543	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS) && \
1544	echo "$(SEP) Link $@ [done]"; \
1545	)
1546
1547	#********************************* SHARED LIBRARIES SECTION ************************************
1548
1549	prepare_libdir: addlibs
1550
1551	addlibs:
1552	(perl $(ARBHOME)/SOURCE_TOOLS/provide_libs.pl \
1553	"arbhome=$(ARBHOME)" \
1554	"opengl=$(OPENGL)" \
1555	"link_static=$(LINK_STATIC)" \
1556	)
1557
1558	#***************************************************************************************
1559	# Recursive calls to sub-makefiles
1560	#***************************************************************************************
1561
1562	%.depends:
1563	@cp -p $(@D)/Makefile $(@D)/Makefile.old # save old Makefile
1564	@$(MAKE) -C $(@D) -r \
1565	"AUTODEPENDS=1" \
1566	"MAIN=nothing" \
1567	"cflags=noCflagsHere_use_MAKEDEPENDFLAGS" \
1568	"cxxflags=noCxxflagsHere_use_MAKEDEPENDFLAGS" \
1569	depends
1570	@grep "^# DO NOT DELETE" $(@D)/Makefile >/dev/null
1571	@cat $(@D)/Makefile \
1572	\| SOURCE_TOOLS/fix_depends.pl "(from main)" \
1573	>$(@D)/Makefile.2
1574	@mv $(@D)/Makefile.old $(@D)/Makefile # restore old Makefile
1575	@$(ARBHOME)/SOURCE_TOOLS/mv_if_diff $(@D)/Makefile.2 $(@D)/Makefile # update Makefile if changed
1576
1577	%.proto:
1578	@($(MAKE) -C $(@D) \
1579	"AUTODEPENDS=0" \
1580	"MAIN=nothing" \
1581	"cflags=noCflags" \
1582	"cxxflags=noCxxflags" \
1583	proto 2>&1 ) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
1584
1585	%.clean:
1586	@$(MAKE) -C $(@D) \
1587	"AUTODEPENDS=0" \
1588	"MAIN=nothing" \
1589	"cflags=noCflags" \
1590	"cxxflags=noCxxflags" \
1591	clean
1592
1593
1594	# stop wrong targets
1595	target_is_missing_lib_prefix:
1596	@echo "Error: Denied to build shared library target with missing 'lib'-prefix"
1597	false
1598
1599	ARBDB/ARBDB.dummy: target_is_missing_lib_prefix
1600	CORE/CORE.dummy: target_is_missing_lib_prefix
1601	AWT/AWT.dummy: target_is_missing_lib_prefix
1602	WINDOW/WINDOW.dummy: target_is_missing_lib_prefix
1603
1604	# rule to generate main target (normally a library):
1605	# @@@ check effect of setting LANG=C below
1606	%.dummy:
1607	@( export ID=$$$$; LANG=C; \
1608	(( \
1609	echo "$(SEP) Make $(@D)"; \
1610	$(MAKE) -C $(@D) -r \
1611	"AUTODEPENDS=1" \
1612	"MAIN=$(@F:.dummy=.a)" \
1613	"cflags=$(cflags) -DIN_ARB_$(subst /,_,$(@D))" \
1614	&& \
1615	echo "$(SEP) Make $(@D) [done]"; \
1616	) >$(@D).$$ID.log 2>&1 && (cat $(@D).$$ID.log;rm $(@D).$$ID.log)) \|\| (cat $(@D).$$ID.log;rm $(@D).$$ID.log;false))
1617
1618	# Additional dependencies for subtargets:
1619
1620	PROBE_COM/PROBE_COM.dummy : comtools
1621	NAMES_COM/NAMES_COM.dummy : comtools
1622
1623	com: PROBE_COM/PROBE_COM.dummy NAMES_COM/NAMES_COM.dummy
1624
1625	PROBE_COM/server.dummy:
1626	@echo Unwanted request to make target $<
1627	false
1628
1629	PROBE_COM/client.dummy:
1630	@echo Unwanted request to make target $<
1631	false
1632
1633	NAMES_COM/server.dummy:
1634	@echo Unwanted request to make target $<
1635	false
1636
1637	NAMES_COM/client.dummy:
1638	@echo Unwanted request to make target $<
1639	false
1640
1641
1642	ARBDB/libARBDB.dummy: links
1643	CORE/libCORE.dummy: links
1644
1645	PERLTOOLS/PERLTOOLS.dummy: core db
1646
1647	# all subdirs perl not depends on go here (ADD_links_non_perl)
1648	AWT/libAWT.dummy: links_non_perl
1649	AWTI/AWTI.dummy: links_non_perl
1650	CONSENSUS_TREE/CONSENSUS_TREE.dummy: links_non_perl
1651	CONVERTALN/CONVERTALN.dummy: links_non_perl
1652	DBSERVER/DBSERVER.dummy: links_non_perl
1653	DIST/DIST.dummy: links_non_perl
1654	EDIT4/EDIT4.dummy: links_non_perl com
1655	EISPACK/EISPACK.dummy: links_non_perl
1656	GDE/GDE.dummy: links_non_perl
1657	GENOM/GENOM.dummy: links_non_perl
1658	GENOM_IMPORT/GENOM_IMPORT.dummy: links_non_perl
1659	ISLAND_HOPPING/ISLAND_HOPPING.dummy: links_non_perl
1660	MERGE/MERGE.dummy: links_non_perl
1661	NTREE/NTREE.dummy: links_non_perl
1662	PARSIMONY/PARSIMONY.dummy: links_non_perl
1663	PHYLO/PHYLO.dummy: links_non_perl
1664	PRIMER_DESIGN/PRIMER_DESIGN.dummy: links_non_perl
1665	PROBE_SET/PROBE_SET.dummy: links_non_perl link_db
1666	READSEQ/READSEQ.dummy: links_non_perl
1667	RNACMA/RNACMA.dummy: links_non_perl header_libs
1668	SECEDIT/SECEDIT.dummy: links_non_perl
1669	SEQ_QUALITY/SEQ_QUALITY.dummy: links_non_perl
1670	SERVERCNTRL/SERVERCNTRL.dummy: links_non_perl com
1671	SL/ALILINK/ALILINK.dummy: links_non_perl
1672	SL/ALIVIEW/ALIVIEW.dummy: links_non_perl
1673	SL/AP_TREE/AP_TREE.dummy: links_non_perl
1674	SL/ARB_TREE/ARB_TREE.dummy: links_non_perl
1675	SL/AW_HELIX/AW_HELIX.dummy: links_non_perl
1676	SL/CONSENSUS/CONSENSUS.dummy: links_non_perl
1677	SL/DB_QUERY/DB_QUERY.dummy: links_non_perl
1678	SL/DB_SCANNER/DB_SCANNER.dummy: links_non_perl
1679	SL/DB_UI/DB_UI.dummy: links_non_perl
1680	SL/FAST_ALIGNER/FAST_ALIGNER.dummy: links_non_perl
1681	SL/FILTER/FILTER.dummy: links_non_perl
1682	SL/FILTSEQEXP/FILTSEQEXP.dummy: links_non_perl
1683	SL/GROUP_SEARCH/GROUP_SEARCH.dummy: links_non_perl
1684	SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy: links_non_perl
1685	SL/HELIX/HELIX.dummy: links_non_perl
1686	SL/INSDEL/INSDEL.dummy: links_non_perl
1687	SL/ITEM_SHADER/ITEM_SHADER.dummy: links_non_perl
1688	SL/ITEMS/ITEMS.dummy: links_non_perl
1689	SL/LOCATION/LOCATION.dummy: links_non_perl
1690	SL/MACROS/MACROS.dummy: links_non_perl
1691	SL/MATRIX/MATRIX.dummy: links_non_perl
1692	SL/NDS/NDS.dummy: links_non_perl
1693	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.dummy: links_non_perl
1694	SL/PRONUC/PRONUC.dummy: links_non_perl
1695	SL/PTCLEAN/PTCLEAN.dummy: links_non_perl link_db
1696	SL/PVP/PVP.dummy: links_non_perl
1697	SL/QUERY/QUERY.dummy: links_non_perl link_db
1698	SL/REFENTRIES/REFENTRIES.dummy: links_non_perl
1699	SL/REGEXPR/REGEXPR.dummy: links_non_perl
1700	SL/SEQIO/SEQIO.dummy: links_non_perl
1701	SL/SEQUENCE/SEQUENCE.dummy: links_non_perl
1702	SL/TRANSLATE/TRANSLATE.dummy: links_non_perl
1703	SL/TREE_ADMIN/TREE_ADMIN.dummy: links_non_perl
1704	SL/TREE_READ/TREE_READ.dummy: links_non_perl
1705	SL/TREE_WRITE/TREE_WRITE.dummy: links_non_perl
1706	SL/TREEDISP/TREEDISP.dummy: links_non_perl
1707	STAT/STAT.dummy: links_non_perl
1708	TREEGEN/TREEGEN.dummy: links_non_perl
1709	WETC/WETC.dummy: links_non_perl
1710	WINDOW/libWINDOW.dummy: links_non_perl
1711	XML/XML.dummy: links_non_perl
1712
1713	ifeq ($(OPENGL),1)
1714	GL/glAW/glAW.dummy: links_non_perl
1715	GL/glpng/glpng.dummy: links_non_perl
1716	GL/GL.dummy: GL/glAW/glAW.dummy GL/glpng/glpng.dummy
1717	RNA3D/RNA3D.dummy: links_non_perl gl
1718	endif
1719
1720	UNIT_TESTER/UNIT_TESTER.dummy: link_db \
1721	SERVERCNTRL/SERVERCNTRL.dummy \
1722
1723	# see also TOOLS/Makefile@TOOLSLIBDEPENDS
1724	TOOLS/TOOLS.dummy : links_non_perl link_db \
1725	CONSENSUS_TREE/CONSENSUS_TREE.dummy \
1726	SERVERCNTRL/SERVERCNTRL.dummy \
1727	SL/FILTER/FILTER.dummy \
1728	SL/FILTSEQEXP/FILTSEQEXP.dummy \
1729	SL/INSDEL/INSDEL.dummy \
1730	SL/REGEXPR/REGEXPR.dummy \
1731	SL/SEQIO/SEQIO.dummy \
1732	SL/TREE_READ/TREE_READ.dummy \
1733	SL/TREE_WRITE/TREE_WRITE.dummy \
1734	XML/XML.dummy \
1735
1736	AWTC/AWTC.dummy : com
1737
1738	NAMES/NAMES.dummy : com
1739	SL/AW_NAME/AW_NAME.dummy : com
1740
1741	PROBE/PROBE.dummy : com
1742	ptpan/PROBE.dummy : com
1743	MULTI_PROBE/MULTI_PROBE.dummy : com
1744	PROBE_DESIGN/PROBE_DESIGN.dummy : com
1745	NALIGNER/NALIGNER.dummy : com
1746
1747	ARB_GDE/ARB_GDE.dummy : proto_tools
1748
1749	compile_compatibility: SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.dummy
1750
1751	#***************************************************************************************
1752	# Short aliases to make targets
1753	#***************************************************************************************
1754
1755	show:
1756	@echo $(SEP)
1757	@echo 'Aliases for often needed targets:'
1758	@echo ''
1759	@echo ' executables:'
1760	@echo ''
1761	@echo ' nt arb_ntree'
1762	@echo ' e4 arb_edit4 (includes secedit)'
1763	@echo ' di arb_dist'
1764	@echo ' ph arb_phylo'
1765	@echo ' pa arb_parsimony'
1766	@echo ' tg arb_treegen'
1767	@echo ' ds arb_dbserver'
1768	@echo ' pt arb_pt_server'
1769	@echo ' na arb_name_server'
1770	@echo ''
1771	@echo ' libraries:'
1772	@echo ''
1773	@echo ' com communication libraries'
1774	@echo ' db ARB database'
1775	@echo ' aw GUI lib'
1776	@echo ' awt GUI toolkit'
1777	@echo ' awtc general purpose library'
1778	@echo ' awti import/export library'
1779	@echo ' mp multi probe library'
1780	@echo ' ge genome library'
1781	@echo ' pd probe design lib'
1782	@echo ' prd primer design lib'
1783	@echo ''
1784	@echo ' other targets:'
1785	@echo ''
1786	@echo ' help recompile help files'
1787	@echo ' tools make small tools used by arb'
1788	@echo ''
1789	@echo ' foreign targets:'
1790	@echo ''
1791	@echo ' gde GDE'
1792	@echo ' agde ARB_GDE'
1793	@echo ''
1794	@echo 'for other targets inspect $(ARBHOME)/Makefile'
1795	@echo ''
1796	@echo $(SEP)
1797
1798	source_doc:
1799	@echo "Remove some links (doxygen crashes otherwise):"
1800	find . \( -name "AISC" -o -name "C" -o -name "GDEHELP" \) -type l -exec rm {} \;
1801	doxygen 2>&1 1>/dev/null
1802	$(MAKE) forcelinks
1803
1804	dep_graph:
1805	@echo "Building some dependency graphs"
1806	SOURCE_TOOLS/dependency_graphs.pl
1807
1808	help: HELP_SOURCE/HELP_SOURCE.dummy
1809
1810	HELP_SOURCE/HELP_SOURCE.dummy: link_core xml menus
1811
1812	db: ARBDB/libARBDB.dummy
1813	core: CORE/libCORE.dummy
1814	aw: WINDOW/libWINDOW.dummy
1815	awt: AWT/libAWT.dummy
1816	awtc: AWTC/AWTC.dummy
1817	awti: AWTI/AWTI.dummy
1818
1819	mp: MULTI_PROBE/MULTI_PROBE.dummy
1820	mg: MERGE/MERGE.dummy
1821	ge: GENOM/GENOM.dummy
1822	prd: PRIMER_DESIGN/PRIMER_DESIGN.dummy
1823
1824	nt: menus $(NTREE)
1825
1826	nal: $(NALIGNER)
1827
1828	di: $(DIST)
1829	ph: $(PHYLO)
1830	pa: $(PARSIMONY)
1831	tg: $(TREEGEN)
1832
1833	ifeq ($(OPENGL),1)
1834	3d: RNA3D/RNA3D.dummy
1835	gl: GL/GL.dummy
1836	else
1837	noopengl:
1838	@echo "invalid target for OPENGL=0"
1839	3d: noopengl
1840	gl: noopengl
1841	endif
1842
1843	SL/SL.dummy: com
1844
1845	ds: $(DBSERVER)
1846	pt: $(PROBE)
1847	pst: PROBE_SET/PROBE_SET.dummy
1848	pd: PROBE_DESIGN/PROBE_DESIGN.dummy
1849	na: $(NAMES)
1850	sq: SEQ_QUALITY/SEQ_QUALITY.dummy
1851	cma: $(RNACMA)
1852
1853	sec: SECEDIT/SECEDIT.dummy
1854
1855	e4: $(EDIT4) readseq menus
1856
1857	gi: GENOM_IMPORT/GENOM_IMPORT.dummy
1858	wetc: $(WETC)
1859
1860	xml: XML/XML.dummy
1861	xmlin: XML_IMPORT/XML_IMPORT.dummy# broken
1862	stat: STAT/STAT.dummy $(NTREE) $(EDIT4)
1863	fa: SL/FAST_ALIGNER/FAST_ALIGNER.dummy
1864
1865	#********************************************************************************
1866
1867	up_by_remake: depends proto vectorize_checks
1868
1869	up: up_by_remake tags valgrind_update
1870
1871	#********************************************************************************
1872
1873	touch:
1874	SOURCE_TOOLS/touch_modified.pl
1875
1876	modified: touch
1877	$(MAKE) all
1878
1879	#********************************************************************************
1880
1881	libdepends:
1882	$(MAKE) -C "SOURCE_TOOLS" \
1883	"RNA3D_LIB=$(RNA3D_LIB_4_DEPENDS)" \
1884	libdepends
1885
1886	#********************************************************************************
1887
1888	# create generated headers:
1889	genheaders: TEMPLATES/TEMPLATES.dummy
1890
1891	clrdotdepends:
1892	rm PROBE_COM/.depends \|\| true
1893	rm NAMES_COM/.depends \|\| true
1894	rm PERL2ARB/.depends \|\| true
1895
1896	comdepends: comtools clrdotdepends
1897	@echo "$(SEP) Partially build com interface"
1898	$(MAKE) PROBE_COM/PROBE_COM.depends NAMES_COM/NAMES_COM.depends
1899	$(MAKE) PROBE_COM/server.depends NAMES_COM/server.depends
1900
1901	depends: genheaders comdepends vectorize_checks
1902	@echo "$(SEP) Updating other dependencies"
1903	$(MAKE) $(subst NAMES_COM/server.depends,,$(subst PROBE_COM/server.depends,,$(ARCHS:.a=.depends))) \
1904	HELP_SOURCE/HELP_SOURCE.depends \
1905	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.depends \
1906
1907	$(MAKE) libdepends
1908
1909	depend: depends
1910
1911	# ------------------------------------------------------------
1912	# dependency generation tests for AISC code
1913	#(all should work w/o creating wrong dependencies;
1914	# neither in XXX_COM/Makefile nor in code using AISC interface)
1915	dependstest1: silent_clean
1916	$(MAKE) depends
1917	dependstest2: silent_clean
1918	$(MAKE) com
1919	dependstest3: silent_clean
1920	$(MAKE) aw
1921	dependstest4: silent_clean
1922	$(MAKE) pt
1923	dependstest5: silent_clean
1924	$(MAKE) na
1925	dependstest6: silent_clean
1926	$(MAKE) nt
1927	dependstest7: silent_clean
1928	$(MAKE) all
1929	# ------------------------------------------------------------
1930
1931	vectorize_checks:
1932	$(MAKE) -C SOURCE_TOOLS -r vectorize_checks
1933
1934	clean_checked_vect: lib/lib.clean
1935	SOURCE_TOOLS/clean_checked_vectorizations.sh
1936
1937	# ------------------------------------------------------------
1938
1939	AISC_MKPTPS/AISC_MKPTPS.dummy: links
1940
1941	proto_tools: AISC_MKPTPS/AISC_MKPTPS.dummy
1942
1943	proto: proto_tools
1944	@echo $(SEP) Updating prototypes
1945	$(MAKE) \
1946	ARBDB/ARBDB.proto \
1947	AISC_COM/AISC_COM.proto \
1948	ARB_GDE/ARB_GDE.proto \
1949	CORE/CORE.proto \
1950	CONVERTALN/CONVERTALN.proto \
1951	NTREE/NTREE.proto \
1952	MERGE/MERGE.proto \
1953	$(ARCHS_PT_SERVER:.a=.proto) \
1954	SERVERCNTRL/SERVERCNTRL.proto \
1955	SL/SL.proto \
1956
1957	#********************************************************************************
1958
1959	valgrind_update: links
1960	@echo $(SEP) Updating for valgrind
1961	$(MAKE) -C SOURCE_TOOLS valgrind_update
1962
1963	#********************************************************************************
1964
1965	TAGFILE=TAGS
1966	TAGFILE_TMP=TAGS.tmp
1967
1968	TAG_SOURCE_HEADERS=TAGS.headers
1969	TAG_SOURCE_CODE=TAGS.codefiles
1970	TAG_SOURCE_LISTS=$(TAG_SOURCE_HEADERS) $(TAG_SOURCE_CODE)
1971
1972	ETAGS_IGNORE_LIST=SOURCE_TOOLS/etags_ignore.lst
1973
1974	ETAGS=ctags -e -I @$(ETAGS_IGNORE_LIST) --sort=no --if0=no --extra=q
1975	ETAGS_TYPES=--C-kinds=cgnsut --C++-kinds=cgnsut
1976	ETAGS_FUN =--C-kinds=fm --C++-kinds=fm
1977	ETAGS_REST =--C-kinds=dev --C++-kinds=dev
1978
1979	FILTER_TAGS_SOURCES= \
1980	$(SED) -e 's/^.\///g' \| \
1981	grep -vi '^HEADERLIBS\\|^GDE/\\|/GEN[CH]/'
1982
1983	$(TAG_SOURCE_HEADERS): links
1984	find . \( -name '.hxx' -o -name ".h" \) -type f \| $(FILTER_TAGS_SOURCES) > $@
1985
1986	$(TAG_SOURCE_CODE): links
1987	find . \( -name '.cxx' -o -name ".c" \) -type f \| $(FILTER_TAGS_SOURCES) > $@
1988
1989	TAGS.1.tmp: $(TAG_SOURCE_HEADERS)
1990	$(ETAGS) -f $@ $(ETAGS_TYPES) -L $<
1991	TAGS.2.tmp: $(TAG_SOURCE_HEADERS)
1992	$(ETAGS) -f $@ $(ETAGS_FUN) -L $<
1993	TAGS.3.tmp: $(TAG_SOURCE_HEADERS)
1994	$(ETAGS) -f $@ $(ETAGS_REST) -L $<
1995	TAGS.4.tmp: $(TAG_SOURCE_CODE)
1996	$(ETAGS) -f $@ $(ETAGS_TYPES) -L $<
1997	TAGS.5.tmp: $(TAG_SOURCE_CODE)
1998	$(ETAGS) -f $@ $(ETAGS_FUN) -L $<
1999	TAGS.6.tmp: $(TAG_SOURCE_CODE)
2000	$(ETAGS) -f $@ $(ETAGS_REST) -L $<
2001
2002	TAGS_ALL_PARTS=TAGS.1.tmp TAGS.2.tmp TAGS.3.tmp TAGS.4.tmp TAGS.5.tmp TAGS.6.tmp
2003
2004	$(TAGFILE_TMP) : $(TAGS_ALL_PARTS)
2005	cat $(TAGS_ALL_PARTS) > $@
2006	rm $(TAGS_ALL_PARTS) $(TAG_SOURCE_LISTS)
2007
2008	tags: $(TAGFILE_TMP)
2009	mv_if_diff $(TAGFILE_TMP) $(TAGFILE)
2010
2011	#********************************************************************************
2012
2013	LINKSTAMP=SOURCE_TOOLS/stamp.generate_all_links
2014
2015	links: checks $(LINKSTAMP) arbmainwrapper
2016	links_no_checks: $(LINKSTAMP) arbmainwrapper
2017
2018	forcelinks:
2019	-rm $(LINKSTAMP)
2020	$(MAKE) links
2021
2022	$(LINKSTAMP): SOURCE_TOOLS/generate_all_links.sh genheaders
2023	+SOURCE_TOOLS/generate_all_links.sh
2024	touch $(LINKSTAMP)
2025
2026	clean_links:
2027	# avoid to delete linked pts, nas or arb_tcp.dat:
2028	find . -path './lib' -prune -o -type l -exec rm {} \;
2029	# removed obsolete file - refuses to disappear due to 'prune' above
2030	@rm -f lib/help/GDEHELP
2031	@rm -f $(LINKSTAMP) lib/inputMasks/format.readme
2032
2033	redo_links: clean_links
2034	$(MAKE) links_no_checks
2035
2036	#********************************************************************************
2037
2038	header_libs:
2039	@(( \
2040	echo "$(SEP) Make HEADERLIBS"; \
2041	$(MAKE) -C HEADERLIBS all && \
2042	echo "$(SEP) Make HEADERLIBS [done]"; \
2043	) > HEADERLIBS.log 2>&1 && (cat HEADERLIBS.log;rm HEADERLIBS.log)) \|\| (cat HEADERLIBS.log;rm HEADERLIBS.log;false)
2044
2045	#********************************************************************************
2046
2047	gde: GDE/GDE.dummy
2048	GDE: gde
2049	agde: ARB_GDE/ARB_GDE.dummy
2050	tools: TOOLS/TOOLS.dummy
2051	convert: $(CONVERT_ALN)
2052	readseq: READSEQ/READSEQ.dummy
2053
2054	#***************************************************************************************
2055	# Some user commands
2056	#***************************************************************************************
2057
2058	menus: binlink links
2059	@(( \
2060	echo "$(SEP) Make GDEHELP"; \
2061	$(MAKE) -C GDEHELP -r all && \
2062	echo "$(SEP) Make GDEHELP [done]"; \
2063	) > GDEHELP.log 2>&1 && (cat GDEHELP.log;rm GDEHELP.log)) \|\| (cat GDEHELP.log;rm GDEHELP.log;false)
2064
2065	ifeq ($(DEBUG),1)
2066	BIN_TARGET=develall
2067	else
2068	BIN_TARGET=all
2069	endif
2070
2071
2072	binlink:
2073	$(MAKE) -C bin $(BIN_TARGET)
2074
2075	check_bin_dep: binlink
2076	SOURCE_TOOLS/check_bin_dependencies.pl
2077
2078	preplib:
2079	(cd lib;$(MAKE) all)
2080
2081	# --------------------------------------------------------------------------------
2082	# This section is quite tricky:
2083	#
2084	# make 'perl' is a BIG target, so when it has to be made, it has to be started
2085	# as early as possible to reduce overall compile time. Since 'make' does not
2086	# provide any priotities, i force it to build all 'perl'-prerequisites early, by
2087	# adding artificial dependencies to these prerequisites
2088	#
2089	# That behavior is likely to be system-dependent.
2090	# My goal was only to make it work on my current development system,
2091	# where this saves about 20% of overall build time.
2092
2093	ifeq ($(WITHPERL),1)
2094	links_non_perl: PERLTOOLS/PERLTOOLS.dummy
2095	perltools: links_non_perl
2096	perl: realperl
2097	else
2098	links_non_perl: links
2099	perl:
2100	$(MAKE) "WITHPERL=1" perl
2101	endif
2102
2103	# ---------------------------------------- perl
2104
2105	ifeq ($(ARB_64),$(BUILDHOST_64))
2106	TEST_PERL_SCRIPTS=$(MAKE) -C PERL_SCRIPTS/test test
2107	else
2108	TEST_PERL_SCRIPTS=echo "skipping perl script compilation (when cross-compiling)"
2109	endif
2110
2111	realperl: perltools
2112	(( \
2113	echo "$(SEP) Make PERL2ARB" ; \
2114	$(TIME) $(MAKE) -C PERL2ARB -r -f Makefile.main \
2115	"AUTODEPENDS=1" \
2116	"dflags=$(dflags)" \
2117	"cflags4perl=$(cflags) $(cxxflags) $(dflags)" \
2118	"lflags4perl=$(lflags4perl)" \
2119	"COMPILER_VERSION=$(COMPILER_VERSION)" \
2120	all && \
2121	$(TEST_PERL_SCRIPTS) && \
2122	echo "$(SEP) Make PERL2ARB [done]" ; \
2123	) > PERL2ARB.log 2>&1 && (cat PERL2ARB.log;rm PERL2ARB.log)) \|\| (cat PERL2ARB.log;rm PERL2ARB.log;false)
2124
2125	perl_clean:
2126	@$(MAKE) -C PERL2ARB -r -f Makefile.main \
2127	"AUTODEPENDS=0" \
2128	clean
2129
2130	PERL2ARB/PERL2ARB.clean:
2131	$(MAKE) perl_clean
2132	$(MAKE) -C PERL_SCRIPTS/test clean
2133
2134	# ---------------------------------------- bindings to script languages
2135
2136	bindings: lib/libCORE.so lib/libARBDB.so
2137	$(MAKE) -C BINDINGS all ARBDEPENDS="$(^:%=../%)" DFLAGS="$(dflags)"
2138
2139	bindings_clean:
2140	$(MAKE) -C BINDINGS clean
2141
2142	# ----------------------------------------
2143
2144	CLOC=cloc-1.08.pl
2145	CLOCFLAGS=--no3 --quiet --progress-rate=0
2146	CLOCARB=--exclude-dir=GDE .
2147	CLOCEXT=GDE
2148	CLOCCODE=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.code.def
2149	CLOCREST=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.rest.def
2150	CLOCFILT=tail --lines=+4
2151
2152	cloc:
2153	@echo 'Arb code:'
2154	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCARB) \| $(CLOCFILT)
2155	@echo 'Arb rest:'
2156	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCARB) \| $(CLOCFILT)
2157	@echo 'External code:'
2158	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCEXT) \| $(CLOCFILT)
2159	@echo 'External rest:'
2160	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCEXT) \| $(CLOCFILT)
2161
2162	# ---------------------------------------- check resources
2163
2164	check_res:
2165	$(ARBHOME)/SOURCE_TOOLS/check_resources.pl
2166
2167	# ---------------------------------------- cleaning
2168
2169	rmbak:
2170	@echo "[cleanup backup/core files]"
2171	@find . \( -name '*%' \
2172	-o -name '*.bak' \
2173	-o -name '*~' \) \
2174	-o \( -name 'core' -a \! -type d \) \
2175	-exec rm -v {} \; \|\| \
2176	echo "Warning: target 'rmbak' reported problems when removing misc. backup files (ignored)"
2177	@echo "[cleanup done]"
2178
2179	bin_reinit:
2180	$(MAKE) bin/bin.clean
2181	$(MAKE) -C "bin" all
2182
2183	clean_directories:
2184	-rm -rf \
2185	$(ARBHOME)/PROBE_SET/bin \
2186	$(ARBHOME)/INCLUDE \
2187
2188	libclean:
2189	-find $(ARBHOME) -type f \( -name '*.a' ! -type l \) -exec rm -f {} \;
2190
2191	objclean:
2192	-find $(ARBHOME) -type f \( -name '*.o' ! -type l \) -exec rm -f {} \;
2193
2194	# bin.clean and HELP_SOURCE.clean interfere
2195	clean3:
2196	$(MAKE) bin/bin.clean
2197	$(MAKE) HELP_SOURCE/HELP_SOURCE.clean
2198
2199	clean2: $(ARCHS:.a=.clean) \
2200	clean3 \
2201	rmbak \
2202	libclean \
2203	objclean \
2204	lib/lib.clean \
2205	GDEHELP/GDEHELP.clean \
2206	HEADERLIBS/HEADERLIBS.clean \
2207	SOURCE_TOOLS/SOURCE_TOOLS.clean \
2208	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.clean \
2209	UNIT_TESTER/UNIT_TESTER.clean \
2210	TEMPLATES/TEMPLATES.clean \
2211	perl_clean \
2212	clean_directories \
2213
2214	rm -f .last_gcc .last_compiler config.makefile.bak
2215
2216	# links are needed for cleanup
2217	clean: redo_links motif_xpm_hack_clean
2218	$(MAKE) clean2
2219	$(MAKE) clean_cov_all clean_links
2220
2221	silent_clean:
2222	$(MAKE) clean >/dev/null
2223
2224	# 'relocated' is about 50% faster than 'rebuild'
2225	reloc_clean: links
2226	@echo "---------------------------------------- Relocation cleanup"
2227	$(MAKE) \
2228	perl_clean \
2229	GDEHELP/GDEHELP.clean \
2230	HELP_SOURCE/genhelp/genhelp.clean \
2231	bin/bin.clean \
2232	libclean \
2233	objclean
2234
2235	relocated: links
2236	$(MAKE) reloc_clean
2237	@echo "---------------------------------------- and remake"
2238	$(MAKE) build
2239
2240	# -----------------------------------
2241	# some stress tests
2242	# (helpful to reveal race conditions with -j)
2243
2244	rebuild4ever: rebuild
2245	$(MAKE) rebuild4ever
2246
2247	build4ever: build
2248	$(MAKE) build4ever
2249
2250	clean4ever: clean
2251	$(MAKE) clean4ever
2252
2253	test4ever: ut
2254	$(MAKE) test4ever
2255
2256	perl4ever: clean
2257	$(MAKE) links
2258	$(MAKE) perl
2259	$(MAKE) perl4ever
2260
2261	help4ever: clean
2262	$(MAKE) help
2263	$(MAKE) help4ever
2264
2265	# -----------------------------------
2266
2267	rebuild: clean
2268	$(MAKE) all
2269
2270	cleanlinked: bin/bin.clean libclean
2271
2272	relink: cleanlinked
2273	$(MAKE) all
2274
2275	tarfile: rebuild
2276	$(MAKE) prepare_libdir
2277	util/arb_compress
2278
2279	tarfile_quick: build
2280	$(MAKE) prepare_libdir
2281	util/arb_compress
2282
2283	save: sourcetarfile
2284
2285	patch:
2286	SOURCE_TOOLS/arb_create_patch.sh arbPatch
2287
2288	# test early whether save will work
2289	savetest:
2290	@util/arb_srclst.pl >/dev/null
2291
2292	testsave: savetest
2293
2294	sourcetarfile: rmbak
2295	util/arb_save
2296
2297	save2: rmbak
2298	util/arb_save ignore
2299
2300	save_test: rmbak
2301	@echo "Testing source list.."
2302	@util/arb_srclst.pl > /dev/null
2303
2304	save_test_no_error:
2305	@-$(MAKE) save_test
2306
2307	inc_candi:
2308	touch SOURCE_TOOLS/inc_candi.stamp
2309	$(MAKE) do_version_update
2310
2311	inc_patch:
2312	touch SOURCE_TOOLS/inc_patch.stamp
2313	$(MAKE) do_version_update
2314
2315	inc_minor:
2316	touch SOURCE_TOOLS/inc_minor.stamp
2317	$(MAKE) do_version_update
2318
2319	inc_major:
2320	touch SOURCE_TOOLS/inc_major.stamp
2321	$(MAKE) do_version_update
2322
2323	do_version_update:
2324	@echo Incrementing version information
2325	$(MAKE) savetest
2326	$(MAKE) genheaders # auto upgrades version early
2327
2328	show_version:
2329	$(MAKE) genheaders # updates version info
2330	@echo "$(SEP) ARB version info"
2331	@grep ARB_VERSION TEMPLATES/arb_build.h
2332	@echo "$(SEP)"
2333
2334	release_quick:
2335	-rm arb.tgz arbsrc.tgz
2336	$(MAKE) tarfile_quick
2337	$(MAKE) sourcetarfile
2338
2339	# --------------------------------------------------------------------------------
2340	# special cleanups
2341
2342	clean_opengl_changed: RNA3D/RNA3D.clean EDIT4/EDIT4.clean WINDOW/WINDOW.clean GL/GL.clean
2343
2344	# --------------------------------------------------------------------------------
2345
2346	MAKE_IF_COMMITTED=$(MAKE) -C SOURCE_TOOLS -f Makefile.commitbuild
2347
2348	build_CTARGET:
2349	+$(MAKE_IF_COMMITTED) "CTARGET=$(CTARGET)" build_CTARGET
2350
2351	reset_committed_build:
2352	+$(MAKE_IF_COMMITTED) reset
2353
2354	# --------------------------------------------------------------------------------
2355
2356	arbapplications: nt pa e4 wetc pt na nal di ph ds wetc cma
2357
2358	arb_external: convert tools gde readseq tg pst xmlin
2359
2360	arb_no_perl: arbapplications help arb_external
2361
2362	arb: motif_xpm_hack
2363	$(MAKE) "WITHPERL=1" perl arb_no_perl
2364
2365	motif_xpm_hack:
2366	$(MAKE) -r -C "lib/motifHack" all
2367
2368	motif_xpm_hack_clean:
2369	$(MAKE) -r -C "lib/motifHack" clean
2370
2371	# --------------------------------------------------------------------------------
2372	# special targets for SOURCE_TOOLS/remake_after_change.pl
2373
2374	rac_arb_dist: di
2375	rac_arb_edit4: e4
2376	rac_arb_ntree: nt
2377	rac_arb_pars: pa
2378	rac_arb_phylo: ph
2379	rac_arb_wetc: wetc
2380	rac_arb_naligner: nal
2381	rac_arb_pt_server: pt
2382	rac_arb_db_server: ds
2383	rac_arb_name_server: na
2384	rac_arb_convert_aln: convert
2385	rac_arb_treegen: tg
2386	rac_arb_rnacma: cma
2387	rac_arb_help2xml: help
2388
2389	rac_arb_a2ps: tools
2390	rac_arb_consensus_tree: tools
2391	rac_arb_dnarates: tools
2392	rac_arb_export_rates: tools
2393	rac_arb_export_tree: tools
2394	rac_arb_gene_probe: tools
2395	rac_arb_message: tools
2396	rac_arb_primer: tools
2397	rac_arb_probe: tools
2398	rac_arb_read_tree: tools
2399
2400	# --------------------------------------------------------------------------------
2401	# unit testing
2402	# @@@ work in progress
2403	#
2404	# goal is to automatically test all libraries/executables using TESTED_UNITS_AUTO
2405	#
2406	# currently not all test executables link w/o error
2407	# (see UNITS_WORKING, UNITS_UNTESTABLE_ATM and UNITS_NEED_FIX)
2408
2409	# define RNA3D/RNA3D.test
2410	RNA3D_TEST := $(subst .a,.test,$(RNA3D_LIB))
2411
2412	TESTED_UNITS_AUTO = $(ARCHS:.a=.test)
2413
2414	UNITS_WORKING = \
2415	$(RNA3D_TEST) \
2416	EISPACK/EISPACK.test \
2417	GENOM/GENOM.test \
2418	GL/glAW/libglAW.test \
2419	GL/glpng/libglpng_arb.test \
2420	ISLAND_HOPPING/ISLAND_HOPPING.test \
2421	NALIGNER/NALIGNER.test \
2422	NAMES/NAMES.test \
2423	PHYLO/PHYLO.test \
2424	PRIMER_DESIGN/PRIMER_DESIGN.test \
2425	PROBE_DESIGN/PROBE_DESIGN.test \
2426	SECEDIT/SECEDIT.test \
2427	SEQ_QUALITY/SEQ_QUALITY.test \
2428	SERVERCNTRL/SERVERCNTRL.test \
2429	SL/ALIVIEW/ALIVIEW.test \
2430	SL/AP_TREE/AP_TREE.test \
2431	SL/ARB_TREE/ARB_TREE.test \
2432	SL/AW_HELIX/AW_HELIX.test \
2433	SL/AW_NAME/AW_NAME.test \
2434	SL/DB_SCANNER/DB_SCANNER.test \
2435	SL/GUI_ALIVIEW/GUI_ALIVIEW.test \
2436	SL/HELIX/HELIX.test \
2437	SL/LOCATION/LOCATION.test \
2438	SL/MATRIX/MATRIX.test \
2439	SL/QUERY/QUERY.test \
2440	SL/REFENTRIES/REFENTRIES.test \
2441	SL/SEQUENCE/SEQUENCE.test \
2442	SL/TRANSLATE/TRANSLATE.test \
2443	SL/TREE_ADMIN/TREE_ADMIN.test \
2444	SL/TREE_WRITE/TREE_WRITE.test \
2445	STAT/STAT.test \
2446	TREEGEN/TREEGEN.test \
2447	WETC/WETC.test \
2448	XML/XML.test \
2449
2450	# untestable units
2451
2452	UNITS_NEED_FIX = \
2453	ptpan/PROBE.test \
2454
2455	UNITS_UNTESTABLE_ATM = \
2456	XML_IMPORT/XML_IMPORT.test \
2457
2458	# for the moment, put all units containing tests into the following 4 sections (see also TESTED_UNITS below)
2459
2460	# recent development
2461	UNITS_TESTED_FIRST = \
2462	SL/PVP/PVP.test \
2463	AWTI/AWTI.test \
2464	SL/FILTSEQEXP/FILTSEQEXP.test \
2465	SL/GROUP_SEARCH/GROUP_SEARCH.test \
2466
2467	# start units with long duration early
2468	UNITS_RUNNING_LONG = \
2469	ARBDB/libARBDB.test \
2470	AWTC/AWTC.test \
2471	TOOLS/arb_test.test \
2472
2473	# plain test-libaries that are not linked anywhere
2474	TEST_SANDBOXES = \
2475	SL/CB/CB.test \
2476
2477	UNITS_TESTED = \
2478	AISC_MKPTPS/mkptypes.test \
2479	ARB_GDE/ARB_GDE.test \
2480	AWT/libAWT.test \
2481	CONSENSUS_TREE/CONSENSUS_TREE.test \
2482	CONVERTALN/CONVERTALN.test \
2483	CORE/libCORE.test \
2484	DBSERVER/DBSERVER.test \
2485	DIST/DIST.test \
2486	EDIT4/EDIT4.test \
2487	GENOM_IMPORT/GENOM_IMPORT.test \
2488	HELP_SOURCE/arb_help2xml.test \
2489	MERGE/MERGE.test \
2490	MULTI_PROBE/MULTI_PROBE.test \
2491	NTREE/NTREE.test \
2492	PARSIMONY/PARSIMONY.test \
2493	PERLTOOLS/arb_proto_2_xsub.test \
2494	PROBE/PROBE.test \
2495	PROBE_SET/fb_test.test \
2496	SERVERCNTRL/SERVERCNTRL.test \
2497	SL/ALILINK/ALILINK.test \
2498	SL/CONSENSUS/CONSENSUS.test \
2499	SL/DB_QUERY/DB_QUERY.test \
2500	SL/FAST_ALIGNER/FAST_ALIGNER.test \
2501	SL/FILTER/FILTER.test \
2502	SL/INSDEL/INSDEL.test \
2503	SL/ITEM_SHADER/ITEM_SHADER.test \
2504	SL/ITEMS/ITEMS.test \
2505	SL/MACROS/MACROS.test \
2506	SL/NDS/NDS.test \
2507	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.test \
2508	SL/PRONUC/PRONUC.test \
2509	SL/PTCLEAN/PTCLEAN.test \
2510	SL/REGEXPR/REGEXPR.test \
2511	SL/SEQIO/SEQIO.test \
2512	SL/TREE_READ/TREE_READ.test \
2513	SL/TREEDISP/TREEDISP.test \
2514	TOOLS/arb_consensus_tree.test \
2515	TOOLS/arb_probe.test \
2516	WINDOW/libWINDOW.test \
2517
2518	TESTED_UNITS = \
2519	$(UNITS_TESTED_FIRST) \
2520	$(UNITS_RUNNING_LONG) \
2521	$(TEST_SANDBOXES) \
2522	$(UNITS_TESTED) \
2523
2524	# see UNIT_TESTER/sym2testcode.pl@disableErrorOnUnitsWithoutTests
2525
2526	# ----------------------------------------
2527
2528	TEST_LOG_DIR = UNIT_TESTER/logs
2529	TEST_RUN_SUITE=$(MAKE) $(NODIR) -C UNIT_TESTER -f Makefile.suite -r
2530	TEST_MAKE_FLAGS=
2531	TEST_POST_CLEAN=
2532	ifeq ($(COVERAGE),1)
2533	TEST_POST_CLEAN=$(MAKE) clean_cov
2534	TEST_MAKE_FLAGS+=-j1
2535	endif
2536
2537
2538	%.test:
2539	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
2540	( \
2541	echo "fake[1]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
2542	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
2543	"UNITDIR=$(@D)" \
2544	"UNITLIBNAME=$(@F:.test=)" \
2545	"COVERAGE=$(COVERAGE)" \
2546	"ARB_PID=$(ARB_PID)_$(@F)" \
2547	runtest; \
2548	echo "fake[1]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"; \
2549	$(TEST_POST_CLEAN) \
2550	) >$(TEST_LOG_DIR)/$(@F).log 2>&1; \
2551	UNIT_TESTER/log_result.pl $(TEST_LOG_DIR)/$(@F).log )
2552
2553
2554	test_base: $(UNIT_TESTER_LIB:.a=.dummy) $(subst .test,.dummy,$(TEST_SANDBOXES))
2555
2556	clean_cov:
2557	find . \( -name ".gcda" -o -name ".gcov" -o -name "*.cov" \) -exec rm {} \;
2558
2559	clean_cov_all: clean_cov
2560	find . \( -name "*.gcno" \) -exec rm {} \;
2561
2562	run_tests: test_base clean_cov
2563	$(MAKE) "ARB_PID=UT_$$$$" run_tests_faked_arbpid
2564
2565	cleanup_faked_arbpids:
2566	@rm ~/.arb_tmp/tmp/arb_pids_${USER}_${ARB_PID}_* \|\| true
2567
2568	cleanup_faked_arbpids_and_fail: cleanup_faked_arbpids
2569	@false
2570
2571	run_tests_faked_arbpid:
2572	+@$(TEST_RUN_SUITE) init
2573	@echo "fake[2]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2574	$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(TESTED_UNITS) \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2575	@echo "fake[2]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2576	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2577	@$(MAKE) clean_cov >/dev/null
2578	@$(MAKE) cleanup_faked_arbpids
2579
2580	ut:
2581	ifeq ($(UNIT_TESTS),1)
2582	@echo $(MAKE) run_tests
2583	@$(MAKE) run_tests
2584	else
2585	@echo "Not compiled with unit tests"
2586	endif
2587
2588
2589	aut:
2590	+@$(TEST_RUN_SUITE) unskip
2591	$(MAKE) ut
2592
2593	# --------------------------------------------------------------------------------
2594
2595	TIMELOG=$(ARBHOME)/arb_time.log
2596	TIMEARGS=--append --output=$(TIMELOG) --format=" %E(%S+%U) %P [%C]"
2597	TIMECMD=$(TIME) $(TIMEARGS)
2598
2599	time_one:
2600	ifeq ($(ONE_TIMED_TARGET),)
2601	@echo "Error: You have to pass ONE_TIMED_TARGET to $@"
2602	false
2603	else
2604	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET)"
2605	@$(TIMECMD) $(MAKE) $(ONE_TIMED_TARGET)
2606	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET) [done]"
2607	endif
2608
2609	timed_target:
2610	ifeq ($(TIMED_TARGET),)
2611	@echo "Error: You have to pass TIMED_TARGET to $@"
2612	false
2613	else
2614	@echo "Build time:" > $(TIMELOG)
2615	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2616	@cat $(TIMELOG)
2617	@rm $(TIMELOG)
2618	endif
2619
2620	timed_target_tested:
2621	ifeq ($(TIMED_TARGET),)
2622	@echo "Error: You have to pass TIMED_TARGET to $@"
2623	false
2624	else
2625	@echo "Build time:" > $(TIMELOG)
2626	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2627	$(MAKE) "ONE_TIMED_TARGET=ut" time_one
2628	@cat $(TIMELOG)
2629	@rm $(TIMELOG)
2630	endif
2631
2632	clean_timed_target:
2633	ifeq ($(TIMED_TARGET),)
2634	@echo "Error: You have to pass TIMED_TARGET to $@"
2635	false
2636	else
2637	@echo "Build time:" > $(TIMELOG)
2638	$(MAKE) "ONE_TIMED_TARGET=clean" time_one
2639	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2640	@cat $(TIMELOG)
2641	@rm $(TIMELOG)
2642	endif
2643
2644	# --------------------------------------------------------------------------------
2645
2646	CHECKOUT_MODIFIED=0# set to 1 to temporarily skip test for modifications (do not check in if set to 1)
2647
2648	check_svn_does_not_contain_generated:
2649	ifeq ($(CHECKOUT_MODIFIED),0)
2650	@echo "Testing that build does not modify files in SVN"
2651	@test 0 = `svn status \| wc -l` \|\| ( \
2652	echo "The checkout is not/no longer clean:"; \
2653	svn status; \
2654	echo "- if this fails instantly, your checkout is not clean"; \
2655	echo "- if this fails after other targets, these targets modify checked in data"; \
2656	echo " (a common cause may be that depends are not up to date)"; \
2657	false)
2658	else
2659	grep -Hn 'CHECKOUT_MODIFIED' Makefile
2660	endif
2661
2662	check_svn_ignores_generated:
2663	@test 0 = `svn status \| grep '^\?' \| wc -l` \|\| ( \
2664	echo "There are svn-unignored files:"; \
2665	svn status \| grep '^\?'; \
2666	echo "(all generated files should be svn-ignored)"; \
2667	false)
2668
2669	check_svn_state: check_svn_does_not_contain_generated
2670	$(MAKE) check_svn_ignores_generated
2671	$(MAKE) savetest
2672
2673	things_that_always_should_work: depends proto
2674
2675	post_commit_check:
2676	@echo "---------------------------------------- [Initial]"
2677	$(MAKE) check_svn_state
2678
2679	$(MAKE) clean
2680	@echo "---------------------------------------- [After 'make clean']"
2681	$(MAKE) check_svn_state
2682
2683	$(MAKE) things_that_always_should_work
2684	@echo "---------------------------------------- [After 'make things_that_always_should_work']"
2685	$(MAKE) check_svn_state
2686
2687	$(MAKE) all
2688	@echo "---------------------------------------- [After 'make all']"
2689	$(MAKE) check_svn_state
2690
2691	$(MAKE) things_that_always_should_work
2692	@echo "---------------------------------------- [Final]"
2693	$(MAKE) check_svn_state
2694
2695	# --------------------------------------------------------------------------------
2696	# sanitize arb_ntree; also works for clients (arb_edit4, ...) started from there.
2697
2698	sanitize: all
2699	( \
2700	export "LSAN_OPTIONS=max_leaks=30:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp"; \
2701	echo "sake[1]: Entering directory \`$(ARBHOME)'"; \
2702	$(ARBHOME)/bin/arb_ntree --execute _logged ~/data/test.arb 2>&1 ; \
2703	echo "sake[1]: Leaving directory \`$(ARBHOME)'" \
2704	) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
2705
2706	# --------------------------------------------------------------------------------
2707	# build and test one unit:
2708
2709	make_oneunit:
2710	$(MAKE) "WITHPERL=1" $(UNIT).dummy
2711
2712	oneunit:
2713	ifndef UNIT
2714	@echo "Please define UNIT, e.g. using"
2715	@echo " make \"UNIT=ARBDB/libARBDB\" oneunit"
2716	@echo " make \"UNIT=SL/TREEDISP/TREEDISP\" oneunit"
2717	@echo "(Note: 1st is a shared library, 2nd isn't)"
2718	false
2719	else
2720	@echo "Build time" > $(TIMELOG)
2721	@echo "$(SEP) $(MAKE) make_oneunit"
2722	@$(TIMECMD) $(MAKE) make_oneunit
2723	ifeq ($(UNIT_TESTS),1)
2724	@echo $(MAKE) run_tests
2725	@$(TIMECMD) $(MAKE) run_tests
2726	endif
2727	@cat $(TIMELOG)
2728	@rm $(TIMELOG)
2729	endif
2730
2731	# --------------------------------------------------------------------------------
2732
2733	build: arb
2734	$(MAKE) check_bin_dep preplib compile_compatibility
2735
2736	all:
2737	@echo "Build time" > $(TIMELOG)
2738	# $(MAKE) clean_checked_vect # uncomment to rebuild sources where expected vectorization gets tested
2739	@echo "$(SEP) $(MAKE) build"
2740	@$(TIMECMD) $(MAKE) build
2741	@echo $(SEP)
2742	@echo "made 'all' with success."
2743	@echo "to start arb enter 'arb'"
2744	ifeq ($(UNIT_TESTS),1)
2745	@echo $(MAKE) run_tests
2746	@$(TIMECMD) $(MAKE) run_tests
2747	endif
2748	@echo "$(SEP) $(MAKE) build [done]"
2749	ifeq ($(DEBUG),1)
2750	@$(MAKE) save_test_no_error >/dev/null # just show hints
2751	endif
2752	@cat $(TIMELOG)
2753	@rm $(TIMELOG)
2754

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