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Last change on this file was 18092, checked in by westram, 5 years ago
full update from child 'fts' into 'trunk' implements #562 adds: [18091/branches/fts] log:branches/gui@17754:17924,17926:18090
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 80.5 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:=$(ARBHOME)/SH/arb_readlink
128
129	# ---------------------- compiler version detection
130
131	# supported gcc versions:
132	ALLOWED_gcc_VERSIONS=\
133	4.4.3 4.4.5 4.4.6 4.4.7 \
134	4.5.2 \
135	4.6.1 4.6.2 4.6.3 4.6.4 \
136	4.7.1 4.7.2 4.7.3 4.7.4 \
137	4.8.0 4.8.1 4.8.2 4.8.3 4.8.4 4.8.5 \
138	4.9.0 4.9.1 4.9.2 4.9.3 4.9.4 \
139	5.1.0 5.2.0 5.3.0 5.4.0 5.5.0 \
140	6.1.0 6.2.0 6.3.0 6.4.0 6.5.0 \
141	7.1.0 7.2.0 7.3.0 7.4.0 \
142	8.1.0 8.2.0 8.3.0 \
143	9.1.0 9.2.0 \
144
145	# Note: starting with version 5, arb silently accepts any subversion number
146	# above zero. See SOURCE_TOOLS/arb_compiler_version.pl@acceptSubVersions
147	#
148	# This may cause problems when manually checking for compiler versions in code
149	# (GCC_VERSION_CODE is not affected, GCC_PATCHLEVEL_CODE may cause problems!)
150	# ----------------------
151
152	COMPILER_INFO:=$(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	$(warning note that LeakSanitizer does not work with gcc $(COMPILER_VERSION))
528	endif
529	endif
530	endif
531
532	ifeq ($(SANITIZE_UNDEFINED),1)
533	ifneq ('$(USE_GCC_49_OR_HIGHER)','yes')
534	$(info UndefinedBehaviorSanitizer not usable with gcc $(COMPILER_VERSION) - disabled)
535	SANITIZE_UNDEFINED:=0
536	endif
537	endif
538
539	SANITIZE_ANY:=0
540	ifeq ($(SANITIZE_ADDRESS),1)
541	SANITIZE_ANY:=1
542	endif
543	ifeq ($(SANITIZE_UNDEFINED),1)
544	SANITIZE_ANY:=1
545	endif
546
547	# vectorization fails if sanitizer active where it normally succeeds -> disable check
548	ifeq ($(SANITIZE_ANY),1)
549	DISABLE_VECTORIZE_CHECK:=1
550	endif
551
552	# deactivate some bogus warnings occurring when sanitizing NDEBUG version
553	# (do not disable for future gcc-version >= 8.x -> test again when available)
554	ifeq ($(SANITIZE_ANY),1)
555	ifeq ($(DEBUG),0)
556	ifneq ('$(USE_GCC_80_OR_HIGHER)','yes')
557	extended_cpp_warnings += -Wno-format-overflow
558	extended_cpp_warnings += -Wno-maybe-uninitialized
559	endif
560	endif
561	endif
562
563	#---------------------- 32 or 64 bit
564
565	cross_cflags:=
566	cross_lflags:=
567	cross_clflags:=
568
569	ifeq ($(ARB_64),1)
570	dflags += -DARB_64
571	shared_cflags += -fPIC
572	CROSS_LIB:=# empty => autodetect below
573	ifeq ($(DARWIN),1)
574	cross_cflags += -arch x86_64
575	cross_lflags += -arch x86_64
576	cross_clflags += -arch x86_64
577	endif
578	else
579	CROSS_LIB:=/lib
580	endif
581
582	cflags += $(cross_cflags)
583	clflags += $(cross_clflags)
584
585	ifeq ('$(CROSS_LIB)','')
586	# autodetect libdir
587	ifeq ($(ARB_64),1)
588	CROSS_LIB:=$(shell (test -d /lib64 && echo lib64) \|\| echo lib)
589	else
590	CROSS_LIB:=$(shell (test -d /lib32 && echo lib32) \|\| echo lib)
591	endif
592	endif
593
594	#---------------------- unit tests
595
596	ifndef UNIT_TESTS
597	UNIT_TESTS=0#default is "no tests"
598	endif
599	ifeq ($(UNIT_TESTS),1)
600	dflags += -DUNIT_TESTS
601	UNIT_TESTER_LIB=UNIT_TESTER/UNIT_TESTER.a
602	else
603	UNIT_TESTER_LIB=
604	endif
605
606	#---------------------- use gcov
607
608	ifndef COVERAGE
609	COVERAGE=0#default is "no"
610	endif
611	ifneq ($(COVERAGE),0)
612	GCOV_FLAGS=--coverage
613	else
614	GCOV_FLAGS=
615	endif
616
617	cflags += $(GCOV_FLAGS)
618	clflags += $(GCOV_FLAGS)
619	cross_lflags += $(GCOV_FLAGS)
620
621	#---------------------- other flags
622
623	dflags += -D$(MACH) # define machine
624
625	ifeq ($(DARWIN),1)
626	shared_cflags += -fno-common
627	else
628	dflags += $(shell getconf LFS_CFLAGS)
629	endif
630
631	cflags += -pipe
632	cflags += -fmessage-length=0# dont wrap compiler output
633	cflags += -fshow-column# show columns
634	cflags += -funit-at-a-time
635	cflags += -fPIC
636	cflags += -fno-common# link all global data into one namespace
637	cflags += -fstrict-aliasing# gcc 3.4
638
639
640	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
641	cflags += -fno-diagnostics-show-caret#gcc 4.8 (4.7.?)
642	endif
643	#cflags += -save-temps# uncomment to see preprocessor output
644
645	#---------------------- various sanitizers
646	# There are some disabled tests in CORE/arb_misc.cxx@sanitizers
647	# which trigger sanitizer reports.
648
649	ifeq ($(SANITIZE_ANY),1)
650	cflags += -ggdb3 -fno-omit-frame-pointer
651	endif
652
653	# activate AddressSanitizer+LeakSanitizer?
654	ifeq ($(SANITIZE_ADDRESS),1)
655	cflags += -fsanitize=address
656	clflags += -fsanitize=address
657	dflags += -DLEAKS_SANITIZED
658	endif
659
660	# activate UndefinedBehaviorSanitizer?
661	ifeq ($(SANITIZE_UNDEFINED),1)
662	cflags += -fsanitize=undefined
663	clflags += -fsanitize=undefined
664	dflags += -DUNDEF_SANITIZED
665	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
666	# abort on runtime errors
667	cflags += -fno-sanitize-recover=all
668	endif
669	#
670	# Note: alignment-sanitizer is deactivated for ARBDB and PROBE!
671	ifeq ('$(DEBUG)','1')
672	ifeq ($(USE_GCC_MAJOR),4)
673	ifeq ($(USE_GCC_MINOR),9)
674	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),01)','')
675	# workaround https://gcc.gnu.org/bugzilla/show_bug.cgi?id=63531 for 4.9.0 + 4.9.1
676	# (problem is fixed in 4.9.2 release)
677	extended_cpp_warnings:=$(subst -Weffc++,,$(extended_cpp_warnings))
678	endif
679	endif
680	endif
681	endif
682	endif
683
684	#---------------------- X11 location
685
686	ifeq ($(DARWIN),1)
687	XHOME:=$(PREFIX)
688	else
689	ifeq ($(DEBIAN),1)
690	XHOME:=$(PREFIX)
691	else
692	XHOME:=/usr/X11R6
693	endif
694	endif
695
696	XINCLUDES ?= -I$(XHOME)/include
697	XLIBS ?= -L$(XHOME)/$(CROSS_LIB)
698	ifeq ($(DARWIN),1)
699	XINCLUDES += -I$(OSX_FW)/GLUT.framework/Headers -I$(OSX_FW)/OpenGL.framework/Headers -I$(OSX_SDK)/usr/include/krb5
700
701	XLIBS += -lXm -lpng -lz -lXt -lX11 -lXext -lXp -lXmu -lXi
702	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGL.dylib:$(OSX_FW_OPENGL)/libGL.dylib
703	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGLU.dylib:$(OSX_FW_OPENGL)/libGLU.dylib
704	else
705	XLIBS += -lXm -lXpm -lXt -lXext -lX11
706	endif
707
708	#---------------------- open GL
709
710	ifeq ($(OPENGL),1)
711	cflags += -DARB_OPENGL # activate OPENGL code
712	GL := gl # this is the name of the OPENGL base target
713	GL_LIB_SYS := -lGL -lGLU
714	GL_LIB_ARB := -L$(ARBHOME)/GL/glAW -lglAW
715
716	ifeq ($(DARWIN),1)
717	GL_LIB_SYS += -lpthread
718	endif
719
720	GL_PNGLIBS_ARB := -L$(ARBHOME)/GL/glpng -lglpng_arb
721	GL_PNGLIBS_SYS := -lpng
722
723	GLEWLIB := -lGLEW -lGLw
724	ifeq ($(DARWIN),1)
725	GLUTLIB := -glut
726	else
727	GLUTLIB := -lglut
728	endif
729
730	GL_LIBS_SYS := $(GL_LIB_SYS) $(GL_PNGLIBS_SYS) $(GLEWLIB) $(GLUTLIB)
731	GL_LIBS_ARB := $(GL_LIB_ARB) $(GL_PNGLIBS_ARB)
732
733	RNA3D_LIB := RNA3D/RNA3D.a
734	else
735	GL_LIBS_ARB:=# no opengl -> no libs
736	GL_LIBS_SYS:=# no opengl -> no libs
737	GL:=# dont build ARB openGL libs
738
739	RNA3D_LIB :=
740	endif
741
742	RNA3D_LIB_4_DEPENDS := RNA3D/RNA3D.a
743
744	GL_LIBS:=$(GL_LIBS_ARB) $(GL_LIBS_SYS)
745
746	#---------------------- tiff lib:
747
748	TIFFLIBS := -ltiff
749
750	#---------------------- XML lib:
751
752	XMLLIBS := -lxerces-c
753
754	#---------------------- glib:
755
756	ARB_NEEDED_GLIB=glib-2.0
757
758	ARB_GLIB_INCLUDE:=$(strip $(shell pkg-config --cflags $(ARB_NEEDED_GLIB)))
759	ARB_GLIB_LIBS:=$(strip $(shell pkg-config --libs $(ARB_NEEDED_GLIB)))
760
761	#---------------------- basic libs:
762
763	SYSLIBS:=
764	ifeq ($(DARWIN),1)
765	SYSLIBS += -lstdc++
766	else
767	SYSLIBS += -lm $(ARB_GLIB_LIBS)
768	endif
769
770	#---------------------- include symbols?
771
772	ifeq ($(TRACESYM),1)
773	ifeq ($(USE_CLANG),0)
774	cflags += -rdynamic
775	clflags += -rdynamic -Wl,--export-dynamic
776	endif
777	endif
778
779	#---------------------- system dependent commands
780
781	ifeq ($(DARWIN),1)
782	TIME:=gtime
783	else
784	TIME:=/usr/bin/time
785	endif
786
787	#---------------------- SSE vectorizer
788	# for details see SOURCE_TOOLS/vectorize.README
789
790	ifeq ($(DEBUG),0)
791	ifeq ($(USE_GCC_49_OR_HIGHER),yes)
792	ifeq ($(DISABLE_VECTORIZE_CHECK),0)
793	cflags += -fopt-info-vec
794	cflags += -fopt-info-vec-missed
795	ifeq ($(TRACE_MISSED_VECTORIZATIONS),1)
796	# Shows reasons for unsuccessful vectorization:
797	cflags += -ftree-vectorizer-verbose=10
798	POST_COMPILE += --dump-loop-optimization
799	ifeq ($(VECTORIZATION_CHECK_CANDIDATES),1)
800	$(error TRACE_MISSED_VECTORIZATIONS and VECTORIZATION_CHECK_CANDIDATES may not be used together!)
801	endif
802	endif
803	ifeq ($(VECTORIZATION_CHECK_CANDIDATES),1)
804	POST_COMPILE += --loop-optimization-candi
805	endif
806	POST_COMPILE += --check-loop-optimization
807	endif
808	else
809	ifeq ($(USE_GCC_48_OR_HIGHER),yes)
810	# no automatic vectorization-check for gcc<4.9.0
811	# -> uncomment the next 2 lines and grep the spam it will produce for 'vectorized.*loops'
812	# cflags += -fopt-info -fopt-info-vec-missed
813	# POST_COMPILE += --original
814	endif
815	endif
816	endif
817
818	#---------------------- stop early on broken flags/compiler combination
819
820	ifeq ($(DEBUG),0)
821	ifeq ($(SANITIZE_ANY),1)
822	ifeq ('$(COMPILER_VERSION)','4.9.1')
823	$(error compiling DEBUG=0 + SANITIZE!=0 crashes with gcc $(COMPILER_VERSION) (gcc 4.9.2 works))
824	endif
825	endif
826	endif
827
828	#---------------------- differences between linking executables and shared libs:
829
830	# executables:
831	ifeq ($(DARWIN),1)
832	blflags:=$(clflags)
833	else
834	blflags:=$(clflags) -Wl,--no-undefined
835	endif
836
837	# shared libraries
838	llflags:=$(clflags)
839
840	# dont use clflags below
841	clflags:=
842
843	# -------------------------------------------------------------------------
844	# Don't put any machine/version/etc conditionals below!
845	# (instead define variables above)
846	# -------------------------------------------------------------------------
847
848	cflags += -W -Wall $(dflags) $(extended_warnings)
849	cxxflags := $(extended_cpp_warnings)
850
851	# add CFLAGS + CPPFLAGS from environment for DEBIAN build
852	ifeq ($(DEBIAN),1)
853	cflags := $(CFLAGS) $(cflags)
854	cxxflags += $(CPPFLAGS)
855	endif
856
857	ifeq ('$(USE_CLANG)','1')
858	# none of the following standards works with clang3.3 (under linux) => dont use standard (as done before r15516)
859	# cxxflags += -std=gnu++11
860	# cxxflags += -std=gnu++0x
861	else
862	ifeq ('$(USE_GCC_60_OR_HIGHER)','yes')
863	cxxflags += -std=gnu++14# see also TEMPLATES/cxxforward.h@USE_Cxx14
864	else
865	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
866	cxxflags += -std=gnu++11# see also TEMPLATES/cxxforward.h@USE_Cxx11
867	else
868	# gcc versions between 4.3 (lowest supported) and <4.7
869	cxxflags += -std=gnu++0x
870	endif
871	endif
872	endif
873
874	LINK_STATIC_LIB := $(AR) -csq# link static lib
875	LINK_EXECUTABLE := $(A_CXX) $(blflags) -o# link executable (c++)
876
877	ifeq ($(LINK_STATIC),1)
878	SHARED_LIB_SUFFIX = a# static lib suffix
879	LINK_SHARED_LIB := $(LINK_STATIC_LIB)
880	else
881	SHARED_LIB_SUFFIX = so# shared lib suffix
882	LINK_SHARED_LIB := $(A_CXX) $(llflags) -shared -o# link shared lib
883	endif
884
885	ifeq ($(DARWIN),1)
886	lflags4perl:=
887	else
888	lflags4perl:=$(cross_lflags) -shared
889	endif
890
891	# delete variables unused below
892	blflags:=
893	llflags:=
894
895	# other used tools
896	MAKEDEPEND_PLAIN = makedepend
897	MAKEDEPEND = $(FORCEMASK);$(MAKEDEPEND_PLAIN)
898
899	#SEP:=--------------------------------------------------------------------------------
900	SEP=[`date +%M:%S.%N`] ------------------------------------------------
901	# to analyse timings run
902	# make -j9 clean; make -j9 all \| grep '^\[' \| sort
903	# make -j9 "TIMED_TARGET=perl" clean_timed_target \| grep '^\[' \| sort
904
905	# ------------------------------------------------------------ DYNLIBDEFS
906	# various dynamic library definitions for linking executables:
907	#
908	# SYSLIBS: system libraries needed by database lib
909	# ARBDB_LIB: database lib
910	# DBSYS_LIBS: executable using database (but no GUI)
911	# GUI_LIBS: executable using database and GUI (arb gui uses database)
912	#
913	# Note: definitions exported to sub-makefiles are described in SOURCE_TOOLS/parent_make.txt
914
915	CORE_LIB=-lCORE
916	ARBDB_LIB=-lARBDB $(CORE_LIB)
917	DBSYS_LIBS = $(ARBDB_LIB) $(SYSLIBS)
918
919	GUI_LIBS_PREFIX:=
920	ifeq ($(DARWIN),1)
921	# this seem to be added at wrong place, since opengl is only needed to link EDIT4
922	GUI_LIBS_PREFIX:=-framework GLUT -framework OpenGL
923	endif
924
925	GUI_LIBS=$(GUI_LIBS_PREFIX) $(DBSYS_LIBS) -lAWT -lWINDOW $(XLIBS)
926
927	LIBPATH = -L$(ARBHOME)/lib
928
929	DEST_LIB = lib
930	DEST_BIN = bin
931
932	CC_INCLUDES := -I. -I$(ARBHOME)/INCLUDE $(XINCLUDES) $(ARB_GLIB_INCLUDE)
933	CXX_INCLUDES := $(CC_INCLUDES)
934	MAKEDEPENDFLAGS := -- -DARB_OPENGL -DUNIT_TESTS -D__cplusplus -I. -Y$(ARBHOME)/INCLUDE
935
936	# ---------------------------------------
937	# wrap main()
938
939	use_ARB_main=$(ARBHOME)/SOURCE_TOOLS/arb_main_cpp.o
940	use_ARB_main_C=$(ARBHOME)/SOURCE_TOOLS/arb_main_c.o
941
942	# -----------------------------------------
943	# unique build-id
944	# - different for different calls of make
945	# - constant in recursive calls
946
947	ifndef ARBBID
948	ARBBID:=$(shell SOURCE_TOOLS/uniqueID.sh)
949	endif
950
951	# -----------------------------------------
952	# export variables to submakefiles
953
954	include SOURCE_TOOLS/export2sub
955
956	# do not define (exported) variables below this point
957
958	# -------------------------
959	# Main arb targets:
960	# -------------------------
961
962	first_target:
963	$(MAKE) checks
964	@echo $(SEP)
965	@echo 'Main targets:'
966	@echo ''
967	@echo ' all - Compile ARB + TOOLs + and copy shared libs + link foreign software'
968	@echo ' (That is most likely the target you want)'
969	@echo ''
970	@echo ' clean - remove generated files ("SUBDIR/SUBDIR.clean" to clean only SUBDIR)'
971	@echo ' rebuild - clean + all'
972	@echo ' cleanlinked - remove all binaries'
973	@echo ' relink - cleanlinked + all (=relink all from objects)'
974	@echo ''
975	@echo 'Some often used sub targets (make all makes them all):'
976	@echo ''
977	@echo ' arb - Just compile ARB (but none of the integrated tools)'
978	@echo ' menus - create lib/gde/arb.menu from GDEHELP/ARB_GDEmenus.source'
979	@echo ' perl - Compile the PERL XSUBS into lib/ARB.so and create links in lib to perl'
980	@echo ' binlink - Create all links in the bin directory'
981	@echo ''
982	@echo 'Development targets:'
983	@echo ''
984	@echo ' depends - create or update dependencies ("SUBDIR/SUBDIR.depends" to update only SUBDIR)'
985	@echo ' proto - create or update prototypes ("SUBDIR/SUBDIR.proto" to update only SUBDIR)'
986	@echo ' tags - create tags for xemacs'
987	@echo ' show - show available shortcuts (AKA subtargets)'
988	@echo ' up - shortcut for depends+proto+tags'
989	ifeq ($(UNIT_TESTS),1)
990	@echo ' ut - only run tests'
991	@echo ' "UNIT=..." oneunit - build one unit and run tests (see also UNIT_TESTER/Makefile.setup.local)'
992	endif
993	ifneq ($(SANITIZE),0)
994	@echo ' sanitize - all + run arb_ntree with sanitizer (test.arb + execute _logged)'
995	endif
996	@echo ' modified - rebuild files modified in svn checkout (does touch)'
997	@echo ' touch - touch files modified in svn checkout'
998	@echo ''
999	@echo 'Internal maintenance:'
1000	@echo ''
1001	@echo ' relinfo - show help on release targets'
1002	@echo ' tarfile - make rebuild and create arb version tarfile ("tarfile_quick" to skip rebuild)'
1003	@echo ' save - save all basic ARB sources into arbsrc_DATE ("savetest" to check filelist)'
1004	@echo ' patch - save svn diff to patchfile'
1005	@echo ' source_doc - create doxygen documentation'
1006	@echo ' relocated - rebuild partly (use when you have relocated ARBHOME)'
1007	@echo ' check_res - check resource usage'
1008	@echo ' dep_graph - Build dependency graphs'
1009	@echo ' clean_cov - Clean coverage results'
1010	@echo ''
1011	@echo ' clean_opengl_changed - clean after changing OPENGL setting in config.Makefile'
1012	@echo ' clean_checked_vect - clean units containing vectorization checks'
1013	@echo ''
1014	@echo ' post_commit_check - Checks whether'
1015	@echo ' * main make targets work,'
1016	@echo ' * dependencies and prototypes are up to date,'
1017	@echo ' * SVN-controlled files remain unaffected by called targets and'
1018	@echo ' * all generated files are ignored.'
1019	@echo ' (has to be called in a clean SVN checkout)'
1020	@echo $(SEP)
1021	@echo ''
1022
1023	relinfo:
1024	@echo ''
1025	@echo $(SEP)
1026	@echo 'Release targets:'
1027	@echo ''
1028	@echo ' inc_candi - increase RC candidate-number (only possible in "rc" branch, not needed for RC1)'
1029	@echo ' inc_patch - increase release patchlevel (only possible in "stable" branch)'
1030	@echo ' inc_minor - increase minor version number (only possible in "trunk")'
1031	@echo ' inc_major - increase MAJOR version number (only possible in "trunk")'
1032	@echo ''
1033	@echo ' show_version - show version tag'
1034	@echo ''
1035	@echo $(SEP)
1036	@echo ''
1037
1038	# auto-generate config.makefile:
1039
1040	config.makefile : config.makefile.template
1041	@echo --------------------------------------------------------------------------------
1042	ifeq ($(CONFIG_MAKEFILE_FOUND),)
1043	@cp $< $@
1044	@echo '$(ARBHOME)/$@:1: has been generated.'
1045	@echo 'Please edit $@ to configure your system!'
1046	@echo --------------------------------------------------------------------------------
1047	@false
1048	else
1049	@echo '$(ARBHOME)/$<:1: is more recent than'
1050	@echo '$(ARBHOME)/$@:1:'
1051	@ls -al config.makefile*
1052	@echo --------------------------------------------------------------------------------
1053	@echo "Updating $@ (if this fails, check manually)"
1054	SOURCE_TOOLS/update_config_makefile.pl
1055	@echo "Sucessfully updated $@"
1056	@echo --------------------------------------------------------------------------------
1057	@ls -al config.makefile*
1058	@echo --------------------------------------------------------------------------------
1059	@echo "Diff to your old config.makefile:"
1060	@echo --------------------------------------------------------------------------------
1061	-diff $@.bak $@
1062	@echo --------------------------------------------------------------------------------
1063	endif
1064
1065	# check if everything is configured correctly
1066
1067	check_DEVELOPER:
1068	ifndef DEVELOPER
1069	@echo 'config.makefile:1: DEVELOPER not defined'
1070	@false
1071	endif
1072
1073	check_DEBUG:
1074	ifndef dflags
1075	@echo 'config.makefile:1: DEBUG has to be defined. Valid values are 0 and 1'
1076	@false
1077	endif
1078
1079	check_ARB_64:
1080	ifndef ARB_64
1081	@echo 'config.makefile:1: ARB_64 has to be defined. Valid values are 0 and 1'
1082	@false
1083	endif
1084
1085	# ---------------------------------------- check gcc version
1086
1087	COMPILER_BROKEN:=0
1088
1089	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.6.4')
1090	COMPILER_BROKEN:=1
1091	endif
1092	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.8.0')
1093	COMPILER_BROKEN:=1
1094	endif
1095
1096	check_same_GCC_VERSION:
1097	$(ARBHOME)/SOURCE_TOOLS/check_same_compiler_version.pl $(COMPILER_NAME) $(COMPILER_VERSION_ALLOWED)
1098
1099	check_GCC_VERSION:
1100	@echo 'Compiler version check:'
1101	# see .@ALLOWED_gcc_VERSIONS
1102	ifeq ('$(COMPILER_VERSION_ALLOWED)', '')
1103	@echo " - Your compiler is '$(COMPILER_NAME)' version '$(COMPILER_VERSION)'"
1104	@echo ' This version is not in the list of supported $(COMPILER_NAME)-versions:'
1105	@$(foreach version,$(ALLOWED_COMPILER_VERSIONS),echo ' * $(version)';)
1106	@echo ' - You may either ..'
1107	@echo ' - add your version to ALLOWED_$(COMPILER_NAME)_VERSIONS in the Makefile and try it out or'
1108	@echo ' - switch to one of the allowed versions (see arb_README_gcc.txt for installing'
1109	@echo ' a different version of gcc)'
1110	$(error Unsupported compiler '$(COMPILER_NAME)' version '$(COMPILER_VERSION)')
1111	else
1112	ifeq ($(COMPILER_BROKEN),1)
1113	$(error compilation refused for $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)'. Refer to http://bugs.arb-home.de/wiki/GccVersionInfo for details.)
1114	else
1115	@echo " - Supported $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)' detected - fine!"
1116	@echo ''
1117	ifeq ($(USE_CLANG),1)
1118	@echo "Dump clang version:"
1119	$(A_CXX) -v
1120	endif
1121	$(MAKE) check_same_GCC_VERSION
1122	endif
1123	endif
1124
1125	#---------------------- check ARBHOME
1126
1127	# use arb_INSTALL.txt to determine whether ARBHOME points to correct directory
1128	ARB_INSTALL_FOUND=$(wildcard $(ARBHOME)/arb_INSTALL.txt)
1129
1130	check_ARBHOME:
1131	ifeq ($(strip $(ARB_INSTALL_FOUND)),)
1132	@echo ------------------------------------------------------------
1133	@echo "ARBHOME is set to '$(ARBHOME)'"
1134	@echo "The environment variable ARBHOME has to point to the top arb source directory."
1135	@echo "If you use bash enter:"
1136	@echo " export ARBHOME='`pwd`'"
1137	@echo ------------------------------------------------------------
1138	@false
1139	endif
1140
1141	ARB_PATH_SET=$(findstring $(ARBHOME)/bin,$(PATH))
1142
1143	check_PATH: check_ARBHOME
1144	ifeq ($(strip $(ARB_PATH_SET)),)
1145	@echo ------------------------------------------------------------
1146	@echo "The environment variable PATH has to contain $(ARBHOME)/bin"
1147	@echo "If you use bash enter:"
1148	@echo ' export PATH=$$ARBHOME/bin:$$PATH'
1149	@echo ------------------------------------------------------------
1150	@false
1151	endif
1152
1153	check_TOOLS:
1154	@util/arb_check_build_env.pl \
1155	"$(A_CC)" \
1156	"$(A_CXX)" \
1157	"$(MAKEDEPEND_PLAIN)" \
1158	"$(LINK_SHARED_LIB)" \
1159	"$(LINK_SHARED_LIB)" \
1160
1161	check_ENVIRONMENT : check_PATH check_TOOLS
1162	@echo "-------------------- Environment [start]"
1163	@echo "ARBHOME='$(ARBHOME)'"
1164	@echo "PATH='$(PATH)'"
1165	@echo "LD_LIBRARY_PATH='$(LD_LIBRARY_PATH)'"
1166	@echo "-------------------- Environment [end]"
1167
1168	check_tabs: check_setup
1169	ifeq ($(DEBUG),1)
1170	@SOURCE_TOOLS/tabBrake.pl
1171	endif
1172
1173	force_tab_check:
1174	@touch -t 198001010000 SOURCE_TOOLS/stamp.tabBrake
1175	@$(MAKE) check_tabs
1176
1177
1178	# ---------------------
1179
1180	check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION
1181	@echo Your setup seems to be ok.
1182
1183	checks: check_setup check_tabs
1184	@rm -f SOURCE_TOOLS/postcompile.sav
1185
1186
1187	# end test section ------------------------------
1188
1189	# ---------------------------------------
1190	# List of standard top level directories
1191	#
1192	# sub-makefiles have to define the targets
1193	# - 'depends' and
1194	# - 'clean'
1195	#
1196	# when adding new libs here, also add a dependency vs 'links' or 'links_non_perl' in .@DD_links_non_perl
1197
1198	ARCHS = \
1199	AISC/AISC.a \
1200	AISC_MKPTPS/AISC_MKPTPS.a \
1201	ARBDB/libARBDB.a \
1202	CORE/libCORE.a \
1203	ARB_GDE/ARB_GDE.a \
1204	AWT/libAWT.a \
1205	AWTC/AWTC.a \
1206	AWTI/AWTI.a \
1207	CONSENSUS_TREE/CONSENSUS_TREE.a \
1208	CONVERTALN/CONVERTALN.a \
1209	DBSERVER/DBSERVER.a \
1210	DIST/DIST.a \
1211	EDIT4/EDIT4.a \
1212	EISPACK/EISPACK.a \
1213	GDE/GDE.a \
1214	GENOM/GENOM.a \
1215	GENOM_IMPORT/GENOM_IMPORT.a \
1216	GL/GL.a \
1217	ISLAND_HOPPING/ISLAND_HOPPING.a \
1218	MERGE/MERGE.a \
1219	MULTI_PROBE/MULTI_PROBE.a \
1220	NALIGNER/NALIGNER.a \
1221	NAMES/NAMES.a \
1222	NAMES_COM/server.a \
1223	NTREE/NTREE.a \
1224	PARSIMONY/PARSIMONY.a \
1225	PERLTOOLS/PERLTOOLS.a \
1226	PHYLO/PHYLO.a \
1227	PRIMER_DESIGN/PRIMER_DESIGN.a \
1228	PROBE/PROBE.a \
1229	PROBE_COM/server.a \
1230	PROBE_DESIGN/PROBE_DESIGN.a \
1231	PROBE_SET/PROBE_SET.a \
1232	READSEQ/READSEQ.a \
1233	RNA3D/RNA3D.a \
1234	RNACMA/RNACMA.a \
1235	SECEDIT/SECEDIT.a \
1236	SEQ_QUALITY/SEQ_QUALITY.a \
1237	SERVERCNTRL/SERVERCNTRL.a \
1238	SL/SL.a \
1239	STAT/STAT.a \
1240	TOOLS/TOOLS.a \
1241	TREEGEN/TREEGEN.a \
1242	UNIT_TESTER/UNIT_TESTER.a \
1243	WETC/WETC.a \
1244	WINDOW/libWINDOW.a \
1245	XML/XML.a \
1246
1247	# -----------------------
1248	# library packets
1249
1250	ARCHS_CLIENT_PROBE = PROBE_COM/client.a
1251	ARCHS_CLIENT_NAMES = NAMES_COM/client.a
1252
1253	ARCHS_MAKEBIN = AISC_MKPTPS/AISC_MKPTPS.a AISC/AISC.a
1254
1255	# communication libs need aisc and aisc_mkpts:
1256
1257	AISC/AISC.dummy: proto_tools
1258
1259	comtools: AISC/AISC.dummy
1260
1261	ARCHS_SEQUENCE = \
1262	SL/SEQUENCE/SEQUENCE.a \
1263	SL/ALIVIEW/ALIVIEW.a \
1264	SL/PRONUC/PRONUC.a \
1265
1266	ARCHS_TREE = \
1267	SL/ARB_TREE/ARB_TREE.a \
1268	SL/FILTER/FILTER.a \
1269	$(ARCHS_SEQUENCE) \
1270
1271	# parsimony tree (used by NTREE, PARSIMONY, STAT(->EDIT4), DIST(obsolete!))
1272	ARCHS_AP_TREE = \
1273	SL/AP_TREE/AP_TREE.a \
1274	$(ARCHS_TREE) \
1275
1276	# --------------------------------------------------------------------------------
1277	# dependencies for linking shared libs
1278
1279	link_core: core
1280	link_db: db link_core
1281	link_aw: aw link_db
1282	link_awt: awt link_aw
1283
1284	#***************************************************************************************
1285	# Individual_Programs_Section
1286	#***************************************************************************************
1287
1288	arbmainwrapper:
1289	$(MAKE) -C SOURCE_TOOLS -r mainwrapper
1290
1291
1292	#********************************* arb_ntree ************************************
1293	NTREE = bin/arb_ntree
1294	ARCHS_NTREE = \
1295	NTREE/NTREE.a \
1296	ARB_GDE/ARB_GDE.a \
1297	SL/GROUP_SEARCH/GROUP_SEARCH.a \
1298	SL/DB_UI/DB_UI.a \
1299	AWTC/AWTC.a \
1300	AWTI/AWTI.a \
1301	CONSENSUS_TREE/CONSENSUS_TREE.a \
1302	GENOM_IMPORT/GENOM_IMPORT.a \
1303	GENOM/GENOM.a \
1304	MERGE/MERGE.a \
1305	MULTI_PROBE/MULTI_PROBE.a \
1306	PRIMER_DESIGN/PRIMER_DESIGN.a \
1307	PROBE_DESIGN/PROBE_DESIGN.a \
1308	SEQ_QUALITY/SEQ_QUALITY.a \
1309	SERVERCNTRL/SERVERCNTRL.a \
1310	SL/ALILINK/ALILINK.a \
1311	SL/AW_NAME/AW_NAME.a \
1312	SL/CONSENSUS/CONSENSUS.a \
1313	SL/DB_SCANNER/DB_SCANNER.a \
1314	SL/DB_QUERY/DB_QUERY.a \
1315	SL/QUERY/QUERY.a \
1316	SL/SEQIO/SEQIO.a \
1317	STAT/STAT.a \
1318	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1319	SL/HELIX/HELIX.a \
1320	SL/REGEXPR/REGEXPR.a \
1321	SL/REFENTRIES/REFENTRIES.a \
1322	SL/NDS/NDS.a \
1323	SL/ITEM_SHADER/ITEM_SHADER.a \
1324	SL/ITEMS/ITEMS.a \
1325	SL/INSDEL/INSDEL.a \
1326	SL/LOCATION/LOCATION.a \
1327	SL/MACROS/MACROS.a \
1328	SL/PVP/PVP.a \
1329	SL/TRANSLATE/TRANSLATE.a \
1330	SL/TREEDISP/TREEDISP.a \
1331	SL/TREE_ADMIN/TREE_ADMIN.a \
1332	SL/TREE_READ/TREE_READ.a \
1333	SL/TREE_WRITE/TREE_WRITE.a \
1334	SL/XFERGUI/XFERGUI.a \
1335	SL/XFERSET/XFERSET.a \
1336	XML/XML.a \
1337	$(ARCHS_AP_TREE) \
1338
1339	ARCHS_NTREE_ALL = $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(XMLLIBS)
1340
1341	$(NTREE): $(ARCHS_NTREE:.a=.dummy) link_awt
1342	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NTREE_ALL) \|\| ( \
1343	echo "$(SEP) Link $@"; \
1344	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE_ALL)" ; \
1345	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE_ALL) && \
1346	echo "$(SEP) Link $@ [done]"; \
1347	)
1348
1349	#********************************* arb_edit4 ************************************
1350	EDIT4 = bin/arb_edit4
1351
1352	ARCHS_EDIT4 := \
1353	EDIT4/EDIT4.a \
1354	ARB_GDE/ARB_GDE.a \
1355	SL/FAST_ALIGNER/FAST_ALIGNER.a \
1356	AWTC/AWTC.a \
1357	ISLAND_HOPPING/ISLAND_HOPPING.a \
1358	SECEDIT/SECEDIT.a \
1359	SERVERCNTRL/SERVERCNTRL.a \
1360	SL/AW_HELIX/AW_HELIX.a \
1361	SL/AW_NAME/AW_NAME.a \
1362	SL/CONSENSUS/CONSENSUS.a \
1363	SL/ITEMS/ITEMS.a \
1364	STAT/STAT.a \
1365	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1366	SL/HELIX/HELIX.a \
1367	SL/TRANSLATE/TRANSLATE.a \
1368	SL/MACROS/MACROS.a \
1369	SL/NDS/NDS.a \
1370	$(ARCHS_AP_TREE) \
1371	XML/XML.a \
1372
1373	ifeq ($(OPENGL),1)
1374	ARCHS_EDIT4 += RNA3D/RNA3D.a
1375	endif
1376
1377	ARCHS_EDIT4_ALL = $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4)
1378
1379	LIBS_EDIT4 := $(GL_LIBS)
1380
1381	$(EDIT4): $(ARCHS_EDIT4:.a=.dummy) link_awt
1382	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_EDIT4_ALL) \|\| ( \
1383	echo "$(SEP) Link $@"; \
1384	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4_ALL)" ; \
1385	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4_ALL) && \
1386	echo "$(SEP) Link $@ [done]"; \
1387	)
1388
1389	#********************************* arb_rnacma ************************************
1390	RNACMA = bin/arb_rnacma
1391	ARCHS_RNACMA = \
1392	RNACMA/RNACMA.a \
1393
1394	ARCHS_RNACMA_ALL = $(ARCHS_RNACMA) $(DBSYS_LIBS)
1395
1396	$(RNACMA) : $(ARCHS_RNACMA:.a=.dummy) link_db
1397	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_RNACMA_ALL) \|\| ( \
1398	echo "$(SEP) Link $@"; \
1399	echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_RNACMA_ALL)"; \
1400	$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_RNACMA_ALL) && \
1401	echo "$(SEP) Link $@ [done]"; \
1402	)
1403
1404	#********************************* arb_wetc ************************************
1405	WETC = bin/arb_wetc
1406	ARCHS_WETC = \
1407	WETC/WETC.a \
1408	SL/HELIX/HELIX.a \
1409	SL/FILTER/FILTER.a \
1410	XML/XML.a \
1411
1412	ARCHS_WETC_ALL = $(ARCHS_WETC) $(GUI_LIBS)
1413
1414	$(WETC): $(ARCHS_WETC:.a=.dummy) link_awt
1415	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_WETC_ALL) \|\| ( \
1416	echo "$(SEP) Link $@"; \
1417	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC_ALL)" ; \
1418	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC_ALL) && \
1419	echo "$(SEP) Link $@ [done]"; \
1420	)
1421
1422	#********************************* arb_dist ************************************
1423	DIST = bin/arb_dist
1424	ARCHS_DIST = \
1425	DIST/DIST.a \
1426	CONSENSUS_TREE/CONSENSUS_TREE.a \
1427	EISPACK/EISPACK.a \
1428	SERVERCNTRL/SERVERCNTRL.a \
1429	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1430	SL/HELIX/HELIX.a \
1431	SL/MATRIX/MATRIX.a \
1432	SL/MACROS/MACROS.a \
1433	SL/NDS/NDS.a \
1434	SL/ITEMS/ITEMS.a \
1435	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.a \
1436	XML/XML.a \
1437	$(ARCHS_AP_TREE) \
1438
1439	ARCHS_DIST_ALL = $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS)
1440
1441	$(DIST): $(ARCHS_DIST:.a=.dummy) link_awt
1442	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_DIST_ALL) \|\| ( \
1443	echo "$(SEP) Link $@"; \
1444	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST_ALL)" ; \
1445	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST_ALL) && \
1446	echo "$(SEP) Link $@ [done]"; \
1447	)
1448
1449	#********************************* arb_pars ************************************
1450	PARSIMONY = bin/arb_pars
1451	ARCHS_PARSIMONY = \
1452	PARSIMONY/PARSIMONY.a \
1453	SERVERCNTRL/SERVERCNTRL.a \
1454	SL/AW_NAME/AW_NAME.a \
1455	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1456	SL/HELIX/HELIX.a \
1457	SL/MACROS/MACROS.a \
1458	SL/NDS/NDS.a \
1459	SL/ITEMS/ITEMS.a \
1460	SL/TRANSLATE/TRANSLATE.a \
1461	SL/TREEDISP/TREEDISP.a \
1462	XML/XML.a \
1463	$(ARCHS_AP_TREE) \
1464
1465	ARCHS_PARSIMONY_ALL = $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS)
1466
1467	$(PARSIMONY): $(ARCHS_PARSIMONY:.a=.dummy) link_awt
1468	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_PARSIMONY_ALL) \|\| ( \
1469	echo "$(SEP) Link $@"; \
1470	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY_ALL)" ; \
1471	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY_ALL) && \
1472	echo "$(SEP) Link $@ [done]"; \
1473	)
1474
1475	#********************************* arb_convert_aln ************************************
1476	CONVERT_ALN = bin/arb_convert_aln
1477	ARCHS_CONVERT_ALN = \
1478	CONVERTALN/CONVERTALN.a \
1479
1480	ARCHS_CONVERT_ALN_ALL = $(ARCHS_CONVERT_ALN) $(DBSYS_LIBS)
1481
1482	$(CONVERT_ALN) : $(ARCHS_CONVERT_ALN:.a=.dummy) link_db
1483	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_CONVERT_ALN_ALL) \|\| ( \
1484	echo "$(SEP) Link $@"; \
1485	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN_ALL)"; \
1486	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN_ALL) && \
1487	echo "$(SEP) Link $@ [done]"; \
1488	)
1489
1490	#********************************* arb_treegen ************************************
1491
1492	TREEGEN = bin/arb_treegen
1493	ARCHS_TREEGEN = \
1494	TREEGEN/TREEGEN.a \
1495
1496	ARCHS_TREEGEN_ALL = $(ARCHS_TREEGEN)
1497
1498	$(TREEGEN) : $(ARCHS_TREEGEN:.a=.dummy)
1499	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main_C) $(ARCHS_TREEGEN_ALL) \|\| ( \
1500	echo "$(SEP) Link $@"; \
1501	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN_ALL)" ; \
1502	$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN_ALL) && \
1503	echo "$(SEP) Link $@ [done]"; \
1504	)
1505
1506	#********************************* arb_naligner ************************************
1507	NALIGNER = bin/arb_naligner
1508	ARCHS_NALIGNER = \
1509	NALIGNER/NALIGNER.a \
1510	SERVERCNTRL/SERVERCNTRL.a \
1511	SL/HELIX/HELIX.a \
1512
1513	ARCHS_NALIGNER_ALL = $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(DBSYS_LIBS)
1514
1515	$(NALIGNER): $(ARCHS_NALIGNER:.a=.dummy) link_db
1516	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NALIGNER_ALL) \|\| ( \
1517	echo "$(SEP) Link $@"; \
1518	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER_ALL)" ; \
1519	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER_ALL) && \
1520	echo "$(SEP) Link $@ [done]"; \
1521	)
1522
1523	#********************************* arb_phylo ************************************
1524	PHYLO = bin/arb_phylo
1525	ARCHS_PHYLO = \
1526	PHYLO/PHYLO.a \
1527	SL/HELIX/HELIX.a \
1528	SL/FILTER/FILTER.a \
1529	SL/MACROS/MACROS.a \
1530	XML/XML.a \
1531
1532	ARCHS_PHYLO_ALL = $(ARCHS_PHYLO) $(GUI_LIBS)
1533
1534	$(PHYLO): $(ARCHS_PHYLO:.a=.dummy) link_awt
1535	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_PHYLO_ALL) \|\| ( \
1536	echo "$(SEP) Link $@"; \
1537	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO_ALL)" ; \
1538	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO_ALL) && \
1539	echo "$(SEP) Link $@ [done]"; \
1540	)
1541
1542	#***************************************************************************************
1543	# SERVER SECTION
1544	#***************************************************************************************
1545
1546	#********************************* arb_db_server ************************************
1547	DBSERVER = bin/arb_db_server
1548	ARCHS_DBSERVER = \
1549	DBSERVER/DBSERVER.a \
1550	SERVERCNTRL/SERVERCNTRL.a \
1551
1552	ARCHS_DBSERVER_ALL = $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS)
1553
1554	$(DBSERVER): $(ARCHS_DBSERVER:.a=.dummy) link_db
1555	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_DBSERVER_ALL) \|\| ( \
1556	echo "$(SEP) Link $@"; \
1557	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER_ALL)" ; \
1558	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER_ALL) && \
1559	echo "$(SEP) Link $@ [done]"; \
1560	)
1561
1562	#********************************* arb_pt_server ************************************
1563	PROBE = bin/arb_pt_server
1564
1565	ARCHS_PROBE_DEPEND = \
1566	PROBE/PROBE.a \
1567	SL/PTCLEAN/PTCLEAN.a \
1568	SERVERCNTRL/SERVERCNTRL.a \
1569	SL/HELIX/HELIX.a \
1570
1571	ARCHS_PROBE_ALL = $(ARCHS_PROBE_DEPEND) $(ARCHS_CLIENT_PROBE) $(ARBDB_LIB) $(SYSLIBS)
1572
1573	$(PROBE): $(ARCHS_PROBE_DEPEND:.a=.dummy) link_db
1574	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) config.makefile $(ARCHS_PROBE_ALL) \|\| ( \
1575	echo "$(SEP) Link $@"; \
1576	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_ALL)" ; \
1577	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_ALL) && \
1578	echo "$(SEP) Link $@ [done]"; \
1579	)
1580
1581	#********************************* arb_name_server ************************************
1582	NAMES = bin/arb_name_server
1583	ARCHS_NAMES = \
1584	NAMES/NAMES.a \
1585	SERVERCNTRL/SERVERCNTRL.a \
1586
1587	ARCHS_NAMES_ALL = $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS)
1588
1589	$(NAMES): $(ARCHS_NAMES:.a=.dummy) link_db
1590	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NAMES_ALL) \|\| ( \
1591	echo "$(SEP) Link $@"; \
1592	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES_ALL)" ; \
1593	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES_ALL) && \
1594	echo "$(SEP) Link $@ [done]"; \
1595	)
1596
1597	#********************************* SHARED LIBRARIES SECTION ************************************
1598
1599	prepare_libdir: addlibs
1600
1601	addlibs:
1602	(perl $(ARBHOME)/SOURCE_TOOLS/provide_libs.pl \
1603	"arbhome=$(ARBHOME)" \
1604	"opengl=$(OPENGL)" \
1605	"link_static=$(LINK_STATIC)" \
1606	)
1607
1608	#***************************************************************************************
1609	# Recursive calls to sub-makefiles
1610	#***************************************************************************************
1611
1612	%.depends:
1613	@cp -p $(@D)/Makefile $(@D)/Makefile.old # save old Makefile
1614	@$(MAKE) -C $(@D) -r \
1615	"AUTODEPENDS=1" \
1616	"MAIN=nothing" \
1617	"cflags=noCflagsHere_use_MAKEDEPENDFLAGS" \
1618	"cxxflags=noCxxflagsHere_use_MAKEDEPENDFLAGS" \
1619	depends
1620	@grep "^# DO NOT DELETE" $(@D)/Makefile >/dev/null
1621	@cat $(@D)/Makefile \
1622	\| SOURCE_TOOLS/fix_depends.pl "(from main)" \
1623	>$(@D)/Makefile.2
1624	@mv $(@D)/Makefile.old $(@D)/Makefile # restore old Makefile
1625	@$(ARBHOME)/SOURCE_TOOLS/mv_if_diff $(@D)/Makefile.2 $(@D)/Makefile # update Makefile if changed
1626
1627	%.proto:
1628	@($(MAKE) -C $(@D) \
1629	"AUTODEPENDS=0" \
1630	"MAIN=nothing" \
1631	"cflags=noCflags" \
1632	"cxxflags=noCxxflags" \
1633	proto 2>&1 ) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
1634
1635	%.clean:
1636	@$(MAKE) -C $(@D) \
1637	"AUTODEPENDS=0" \
1638	"MAIN=nothing" \
1639	"cflags=noCflags" \
1640	"cxxflags=noCxxflags" \
1641	clean
1642
1643
1644	# stop wrong targets
1645	target_is_missing_lib_prefix:
1646	@echo "Error: Denied to build shared library target with missing 'lib'-prefix"
1647	false
1648
1649	ARBDB/ARBDB.dummy: target_is_missing_lib_prefix
1650	CORE/CORE.dummy: target_is_missing_lib_prefix
1651	AWT/AWT.dummy: target_is_missing_lib_prefix
1652	WINDOW/WINDOW.dummy: target_is_missing_lib_prefix
1653
1654	# rule to generate main target (normally a library):
1655	# @@@ check effect of setting LANG=C below
1656	%.dummy:
1657	@( export ID=$$$$; LANG=C; \
1658	(( \
1659	echo "$(SEP) Make $(@D)"; \
1660	$(MAKE) -C $(@D) -r \
1661	"AUTODEPENDS=1" \
1662	"MAIN=$(@F:.dummy=.a)" \
1663	"cflags=$(cflags) -DIN_ARB_$(subst /,_,$(@D))" \
1664	&& \
1665	echo "$(SEP) Make $(@D) [done]"; \
1666	) >$(@D).$$ID.log 2>&1 && (cat $(@D).$$ID.log;rm $(@D).$$ID.log)) \|\| (cat $(@D).$$ID.log;rm $(@D).$$ID.log;false))
1667
1668	# Additional dependencies for subtargets:
1669
1670	PROBE_COM/PROBE_COM.dummy : comtools
1671	NAMES_COM/NAMES_COM.dummy : comtools
1672
1673	com: PROBE_COM/PROBE_COM.dummy NAMES_COM/NAMES_COM.dummy
1674
1675	PROBE_COM/server.dummy:
1676	@echo Unwanted request to make target $<
1677	false
1678
1679	PROBE_COM/client.dummy:
1680	@echo Unwanted request to make target $<
1681	false
1682
1683	NAMES_COM/server.dummy:
1684	@echo Unwanted request to make target $<
1685	false
1686
1687	NAMES_COM/client.dummy:
1688	@echo Unwanted request to make target $<
1689	false
1690
1691
1692	ARBDB/libARBDB.dummy: links
1693	CORE/libCORE.dummy: links
1694
1695	PERLTOOLS/PERLTOOLS.dummy: core db
1696
1697	# all subdirs perl not depends on go here (ADD_links_non_perl)
1698	AWT/libAWT.dummy: links_non_perl
1699	AWTI/AWTI.dummy: links_non_perl
1700	CONSENSUS_TREE/CONSENSUS_TREE.dummy: links_non_perl
1701	CONVERTALN/CONVERTALN.dummy: links_non_perl
1702	DBSERVER/DBSERVER.dummy: links_non_perl
1703	DIST/DIST.dummy: links_non_perl
1704	EDIT4/EDIT4.dummy: links_non_perl com
1705	EISPACK/EISPACK.dummy: links_non_perl
1706	GDE/GDE.dummy: links_non_perl
1707	GENOM/GENOM.dummy: links_non_perl
1708	GENOM_IMPORT/GENOM_IMPORT.dummy: links_non_perl
1709	ISLAND_HOPPING/ISLAND_HOPPING.dummy: links_non_perl
1710	MERGE/MERGE.dummy: links_non_perl
1711	NTREE/NTREE.dummy: links_non_perl
1712	PARSIMONY/PARSIMONY.dummy: links_non_perl
1713	PHYLO/PHYLO.dummy: links_non_perl
1714	PRIMER_DESIGN/PRIMER_DESIGN.dummy: links_non_perl
1715	PROBE_SET/PROBE_SET.dummy: links_non_perl link_db
1716	READSEQ/READSEQ.dummy: links_non_perl
1717	RNACMA/RNACMA.dummy: links_non_perl header_libs
1718	SECEDIT/SECEDIT.dummy: links_non_perl
1719	SEQ_QUALITY/SEQ_QUALITY.dummy: links_non_perl
1720	SERVERCNTRL/SERVERCNTRL.dummy: links_non_perl com
1721	SL/ALILINK/ALILINK.dummy: links_non_perl
1722	SL/ALIVIEW/ALIVIEW.dummy: links_non_perl
1723	SL/AP_TREE/AP_TREE.dummy: links_non_perl
1724	SL/ARB_TREE/ARB_TREE.dummy: links_non_perl
1725	SL/AW_HELIX/AW_HELIX.dummy: links_non_perl
1726	SL/CONSENSUS/CONSENSUS.dummy: links_non_perl
1727	SL/DB_QUERY/DB_QUERY.dummy: links_non_perl
1728	SL/DB_SCANNER/DB_SCANNER.dummy: links_non_perl
1729	SL/DB_UI/DB_UI.dummy: links_non_perl
1730	SL/FAST_ALIGNER/FAST_ALIGNER.dummy: links_non_perl
1731	SL/FILTER/FILTER.dummy: links_non_perl
1732	SL/FILTSEQEXP/FILTSEQEXP.dummy: links_non_perl
1733	SL/GROUP_SEARCH/GROUP_SEARCH.dummy: links_non_perl
1734	SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy: links_non_perl
1735	SL/HELIX/HELIX.dummy: links_non_perl
1736	SL/INSDEL/INSDEL.dummy: links_non_perl
1737	SL/ITEM_SHADER/ITEM_SHADER.dummy: links_non_perl
1738	SL/ITEMS/ITEMS.dummy: links_non_perl
1739	SL/LOCATION/LOCATION.dummy: links_non_perl
1740	SL/MACROS/MACROS.dummy: links_non_perl
1741	SL/MATRIX/MATRIX.dummy: links_non_perl
1742	SL/NDS/NDS.dummy: links_non_perl
1743	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.dummy: links_non_perl
1744	SL/PRONUC/PRONUC.dummy: links_non_perl
1745	SL/PTCLEAN/PTCLEAN.dummy: links_non_perl link_db
1746	SL/PVP/PVP.dummy: links_non_perl
1747	SL/QUERY/QUERY.dummy: links_non_perl link_db
1748	SL/REFENTRIES/REFENTRIES.dummy: links_non_perl
1749	SL/REGEXPR/REGEXPR.dummy: links_non_perl
1750	SL/SEQIO/SEQIO.dummy: links_non_perl
1751	SL/SEQUENCE/SEQUENCE.dummy: links_non_perl
1752	SL/TRANSLATE/TRANSLATE.dummy: links_non_perl
1753	SL/TREE_ADMIN/TREE_ADMIN.dummy: links_non_perl
1754	SL/TREE_READ/TREE_READ.dummy: links_non_perl
1755	SL/TREE_WRITE/TREE_WRITE.dummy: links_non_perl
1756	SL/TREEDISP/TREEDISP.dummy: links_non_perl
1757	SL/XFERGUI/XFERGUI.dummy: links_non_perl
1758	SL/XFERSET/XFERSET.dummy: links_non_perl
1759	STAT/STAT.dummy: links_non_perl
1760	TREEGEN/TREEGEN.dummy: links_non_perl
1761	WETC/WETC.dummy: links_non_perl
1762	WINDOW/libWINDOW.dummy: links_non_perl
1763	XML/XML.dummy: links_non_perl
1764
1765	ifeq ($(OPENGL),1)
1766	GL/glAW/glAW.dummy: links_non_perl
1767	GL/glpng/glpng.dummy: links_non_perl
1768	GL/GL.dummy: GL/glAW/glAW.dummy GL/glpng/glpng.dummy
1769	RNA3D/RNA3D.dummy: links_non_perl gl
1770	endif
1771
1772	UNIT_TESTER/UNIT_TESTER.dummy: link_db \
1773	SERVERCNTRL/SERVERCNTRL.dummy \
1774
1775	# see also TOOLS/Makefile@TOOLSLIBDEPENDS
1776	TOOLS/TOOLS.dummy : links_non_perl link_db \
1777	CONSENSUS_TREE/CONSENSUS_TREE.dummy \
1778	SERVERCNTRL/SERVERCNTRL.dummy \
1779	SL/FILTER/FILTER.dummy \
1780	SL/FILTSEQEXP/FILTSEQEXP.dummy \
1781	SL/INSDEL/INSDEL.dummy \
1782	SL/REGEXPR/REGEXPR.dummy \
1783	SL/SEQIO/SEQIO.dummy \
1784	SL/TREE_READ/TREE_READ.dummy \
1785	SL/TREE_WRITE/TREE_WRITE.dummy \
1786	XML/XML.dummy \
1787
1788	AWTC/AWTC.dummy : com
1789
1790	NAMES/NAMES.dummy : com
1791	SL/AW_NAME/AW_NAME.dummy : com
1792
1793	PROBE/PROBE.dummy : com
1794	ptpan/PROBE.dummy : com
1795	MULTI_PROBE/MULTI_PROBE.dummy : com
1796	PROBE_DESIGN/PROBE_DESIGN.dummy : com
1797	NALIGNER/NALIGNER.dummy : com
1798
1799	ARB_GDE/ARB_GDE.dummy : proto_tools
1800
1801	compile_compatibility: SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.dummy
1802
1803	#***************************************************************************************
1804	# Short aliases to make targets
1805	#***************************************************************************************
1806
1807	show:
1808	@echo $(SEP)
1809	@echo 'Aliases for often needed targets:'
1810	@echo ''
1811	@echo ' executables:'
1812	@echo ''
1813	@echo ' nt arb_ntree'
1814	@echo ' e4 arb_edit4 (includes secedit)'
1815	@echo ' di arb_dist'
1816	@echo ' ph arb_phylo'
1817	@echo ' pa arb_parsimony'
1818	@echo ' tg arb_treegen'
1819	@echo ' ds arb_dbserver'
1820	@echo ' pt arb_pt_server'
1821	@echo ' na arb_name_server'
1822	@echo ''
1823	@echo ' libraries:'
1824	@echo ''
1825	@echo ' com communication libraries'
1826	@echo ' db ARB database'
1827	@echo ' aw GUI lib'
1828	@echo ' awt GUI toolkit'
1829	@echo ' awtc general purpose library'
1830	@echo ' awti import/export library'
1831	@echo ' mp multi probe library'
1832	@echo ' ge genome library'
1833	@echo ' pd probe design lib'
1834	@echo ' prd primer design lib'
1835	@echo ''
1836	@echo ' other targets:'
1837	@echo ''
1838	@echo ' help recompile help files'
1839	@echo ' tools make small tools used by arb'
1840	@echo ''
1841	@echo ' foreign targets:'
1842	@echo ''
1843	@echo ' gde GDE'
1844	@echo ' agde ARB_GDE'
1845	@echo ''
1846	@echo 'for other targets inspect $(ARBHOME)/Makefile'
1847	@echo ''
1848	@echo $(SEP)
1849
1850	source_doc:
1851	@echo "Remove some links (doxygen crashes otherwise):"
1852	find . \( -name "AISC" -o -name "C" -o -name "GDEHELP" \) -type l -exec rm {} \;
1853	doxygen 2>&1 1>/dev/null
1854	$(MAKE) forcelinks
1855
1856	dep_graph:
1857	@echo "Building some dependency graphs"
1858	SOURCE_TOOLS/dependency_graphs.pl
1859
1860	help: HELP_SOURCE/HELP_SOURCE.dummy
1861
1862	HELP_SOURCE/HELP_SOURCE.dummy: link_core xml menus
1863
1864	db: ARBDB/libARBDB.dummy
1865	core: CORE/libCORE.dummy
1866	aw: WINDOW/libWINDOW.dummy
1867	awt: AWT/libAWT.dummy
1868	awtc: AWTC/AWTC.dummy
1869	awti: AWTI/AWTI.dummy
1870
1871	mp: MULTI_PROBE/MULTI_PROBE.dummy
1872	mg: MERGE/MERGE.dummy
1873	ge: GENOM/GENOM.dummy
1874	prd: PRIMER_DESIGN/PRIMER_DESIGN.dummy
1875
1876	nt: menus $(NTREE)
1877
1878	nal: $(NALIGNER)
1879
1880	di: $(DIST)
1881	ph: $(PHYLO)
1882	pa: $(PARSIMONY)
1883	tg: $(TREEGEN)
1884
1885	ifeq ($(OPENGL),1)
1886	3d: RNA3D/RNA3D.dummy
1887	gl: GL/GL.dummy
1888	else
1889	noopengl:
1890	@echo "invalid target for OPENGL=0"
1891	3d: noopengl
1892	gl: noopengl
1893	endif
1894
1895	SL/SL.dummy: com
1896
1897	ds: $(DBSERVER)
1898	pt: $(PROBE)
1899	pst: PROBE_SET/PROBE_SET.dummy
1900	pd: PROBE_DESIGN/PROBE_DESIGN.dummy
1901	na: $(NAMES)
1902	sq: SEQ_QUALITY/SEQ_QUALITY.dummy
1903	cma: $(RNACMA)
1904
1905	sec: SECEDIT/SECEDIT.dummy
1906
1907	e4: $(EDIT4) readseq menus
1908
1909	gi: GENOM_IMPORT/GENOM_IMPORT.dummy
1910	wetc: $(WETC)
1911
1912	xml: XML/XML.dummy
1913	xmlin: XML_IMPORT/XML_IMPORT.dummy# broken
1914	stat: STAT/STAT.dummy $(NTREE) $(EDIT4)
1915	fa: SL/FAST_ALIGNER/FAST_ALIGNER.dummy
1916
1917	#********************************************************************************
1918
1919	up_by_remake: depends proto vectorize_checks
1920
1921	up: up_by_remake tags valgrind_update
1922
1923	#********************************************************************************
1924
1925	touch:
1926	SOURCE_TOOLS/touch_modified.pl
1927
1928	modified: touch
1929	$(MAKE) all
1930
1931	#********************************************************************************
1932
1933	libdepends:
1934	$(MAKE) -C "SOURCE_TOOLS" \
1935	"RNA3D_LIB=$(RNA3D_LIB_4_DEPENDS)" \
1936	libdepends
1937
1938	#********************************************************************************
1939
1940	# create generated headers:
1941	genheaders: TEMPLATES/TEMPLATES.dummy
1942
1943	clrdotdepends:
1944	rm PROBE_COM/.depends \|\| true
1945	rm NAMES_COM/.depends \|\| true
1946	rm PERL2ARB/.depends \|\| true
1947
1948	comdepends: comtools clrdotdepends
1949	@echo "$(SEP) Partially build com interface"
1950	$(MAKE) PROBE_COM/PROBE_COM.depends NAMES_COM/NAMES_COM.depends
1951	$(MAKE) PROBE_COM/server.depends NAMES_COM/server.depends
1952
1953	depends: genheaders comdepends vectorize_checks
1954	@echo "$(SEP) Updating other dependencies"
1955	$(MAKE) $(subst NAMES_COM/server.depends,,$(subst PROBE_COM/server.depends,,$(ARCHS:.a=.depends))) \
1956	HELP_SOURCE/HELP_SOURCE.depends \
1957	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.depends \
1958
1959	$(MAKE) libdepends
1960
1961	depend: depends
1962
1963	# ------------------------------------------------------------
1964	# dependency generation tests for AISC code
1965	#(all should work w/o creating wrong dependencies;
1966	# neither in XXX_COM/Makefile nor in code using AISC interface)
1967	dependstest1: silent_clean
1968	$(MAKE) depends
1969	dependstest2: silent_clean
1970	$(MAKE) com
1971	dependstest3: silent_clean
1972	$(MAKE) aw
1973	dependstest4: silent_clean
1974	$(MAKE) pt
1975	dependstest5: silent_clean
1976	$(MAKE) na
1977	dependstest6: silent_clean
1978	$(MAKE) nt
1979	dependstest7: silent_clean
1980	$(MAKE) all
1981	# ------------------------------------------------------------
1982
1983	vectorize_checks:
1984	$(MAKE) -C SOURCE_TOOLS -r vectorize_checks
1985
1986	clean_checked_vect: lib/lib.clean
1987	SOURCE_TOOLS/clean_checked_vectorizations.sh
1988
1989	# ------------------------------------------------------------
1990
1991	AISC_MKPTPS/AISC_MKPTPS.dummy: links
1992
1993	proto_tools: AISC_MKPTPS/AISC_MKPTPS.dummy
1994
1995	proto: proto_tools
1996	@echo $(SEP) Updating prototypes
1997	$(MAKE) \
1998	ARBDB/ARBDB.proto \
1999	AISC_COM/AISC_COM.proto \
2000	ARB_GDE/ARB_GDE.proto \
2001	CORE/CORE.proto \
2002	CONVERTALN/CONVERTALN.proto \
2003	NTREE/NTREE.proto \
2004	MERGE/MERGE.proto \
2005	PROBE/PROBE.proto \
2006	SERVERCNTRL/SERVERCNTRL.proto \
2007	SL/SL.proto \
2008
2009	#********************************************************************************
2010
2011	valgrind_update: links
2012	@echo $(SEP) Updating for valgrind
2013	$(MAKE) -C SOURCE_TOOLS valgrind_update
2014
2015	#********************************************************************************
2016
2017	TAGFILE=TAGS
2018	UTAGS=TAGS.$(ARBBID)
2019	TAGFILE_TMP=$(UTAGS).tmp
2020
2021	TAG_SOURCE_HEADERS=$(UTAGS).headers.tmp
2022	TAG_SOURCE_CODE=$(UTAGS).codefiles.tmp
2023	TAG_SOURCE_LISTS=$(TAG_SOURCE_HEADERS) $(TAG_SOURCE_CODE)
2024
2025	ETAGS_IGNORE_LIST=SOURCE_TOOLS/etags_ignore.lst
2026
2027	ETAGS=ctags -e -I @$(ETAGS_IGNORE_LIST) --sort=no --if0=no --extra=q
2028	ETAGS_TYPES=--C-kinds=cgnsut --C++-kinds=cgnsut
2029	ETAGS_FUN =--C-kinds=fm --C++-kinds=fm
2030	ETAGS_REST =--C-kinds=dev --C++-kinds=dev
2031
2032	FILTER_TAGS_SOURCES= \
2033	$(SED) -e 's/^.\///g' \| \
2034	grep -vi '^HEADERLIBS\\|^GDE/\\|/GEN[CH]/'
2035
2036	$(TAG_SOURCE_HEADERS): links
2037	@find . \( -name '.hxx' -o -name ".h" \) -type f \| $(FILTER_TAGS_SOURCES) > $@
2038
2039	$(TAG_SOURCE_CODE): links
2040	@find . \( -name '.cxx' -o -name ".c" \) -type f \| $(FILTER_TAGS_SOURCES) > $@
2041
2042	$(UTAGS).1.tmp: $(TAG_SOURCE_HEADERS)
2043	@$(ETAGS) -f $@ $(ETAGS_TYPES) -L $<
2044	$(UTAGS).2.tmp: $(TAG_SOURCE_HEADERS)
2045	@$(ETAGS) -f $@ $(ETAGS_FUN) -L $<
2046	$(UTAGS).3.tmp: $(TAG_SOURCE_HEADERS)
2047	@$(ETAGS) -f $@ $(ETAGS_REST) -L $<
2048	$(UTAGS).4.tmp: $(TAG_SOURCE_CODE)
2049	@$(ETAGS) -f $@ $(ETAGS_TYPES) -L $<
2050	$(UTAGS).5.tmp: $(TAG_SOURCE_CODE)
2051	@$(ETAGS) -f $@ $(ETAGS_FUN) -L $<
2052	$(UTAGS).6.tmp: $(TAG_SOURCE_CODE)
2053	@$(ETAGS) -f $@ $(ETAGS_REST) -L $<
2054
2055	TAGS_ALL_PARTS=$(UTAGS).1.tmp $(UTAGS).2.tmp $(UTAGS).3.tmp $(UTAGS).4.tmp $(UTAGS).5.tmp $(UTAGS).6.tmp
2056
2057	$(TAGFILE_TMP) : $(TAGS_ALL_PARTS)
2058	@cat $(TAGS_ALL_PARTS) > $@
2059	@rm $(TAGS_ALL_PARTS) $(TAG_SOURCE_LISTS)
2060
2061	cleanOldTags:
2062	@find $(ARBHOME) -name 'TAGS.*.tmp' -ctime +2 -exec rm {} \;
2063
2064	tags: $(TAGFILE_TMP) cleanOldTags
2065	@mv_if_diff $(TAGFILE_TMP) $(TAGFILE)
2066
2067	#********************************************************************************
2068
2069	LINKSTAMP=SOURCE_TOOLS/stamp.generate_all_links
2070
2071	links: checks $(LINKSTAMP) arbmainwrapper
2072	links_no_checks: $(LINKSTAMP) arbmainwrapper
2073
2074	forcelinks:
2075	-rm $(LINKSTAMP)
2076	$(MAKE) links
2077
2078	$(LINKSTAMP): SOURCE_TOOLS/generate_all_links.sh genheaders
2079	+SOURCE_TOOLS/generate_all_links.sh
2080	touch $(LINKSTAMP)
2081
2082	clean_links:
2083	# avoid to delete linked pts, nas or arb_tcp.dat:
2084	find . -path './lib' -prune -o -type l -exec rm {} \;
2085	# removed obsolete file - refuses to disappear due to 'prune' above
2086	@rm -f lib/help/GDEHELP
2087	@rm -f $(LINKSTAMP) lib/inputMasks/format.readme
2088
2089	redo_links: clean_links
2090	$(MAKE) links_no_checks
2091
2092	#********************************************************************************
2093
2094	header_libs:
2095	@(( \
2096	echo "$(SEP) Make HEADERLIBS"; \
2097	$(MAKE) -C HEADERLIBS all && \
2098	echo "$(SEP) Make HEADERLIBS [done]"; \
2099	) > HEADERLIBS.log 2>&1 && (cat HEADERLIBS.log;rm HEADERLIBS.log)) \|\| (cat HEADERLIBS.log;rm HEADERLIBS.log;false)
2100
2101	#********************************************************************************
2102
2103	gde: GDE/GDE.dummy
2104	GDE: gde
2105	agde: ARB_GDE/ARB_GDE.dummy
2106	tools: TOOLS/TOOLS.dummy
2107	convert: $(CONVERT_ALN)
2108	readseq: READSEQ/READSEQ.dummy
2109
2110	#***************************************************************************************
2111	# Some user commands
2112	#***************************************************************************************
2113
2114	menus: binlink links
2115	@(( \
2116	echo "$(SEP) Make GDEHELP"; \
2117	$(MAKE) -C GDEHELP -r all && \
2118	echo "$(SEP) Make GDEHELP [done]"; \
2119	) > GDEHELP.log 2>&1 && (cat GDEHELP.log;rm GDEHELP.log)) \|\| (cat GDEHELP.log;rm GDEHELP.log;false)
2120
2121	ifeq ($(DEBUG),1)
2122	BIN_TARGET=develall
2123	else
2124	BIN_TARGET=all
2125	endif
2126
2127
2128	binlink:
2129	$(MAKE) -C bin $(BIN_TARGET)
2130
2131	check_bin_dep: binlink
2132	SOURCE_TOOLS/check_bin_dependencies.pl
2133
2134	preplib:
2135	(cd lib;$(MAKE) all)
2136
2137	# --------------------------------------------------------------------------------
2138	# This section is quite tricky:
2139	#
2140	# make 'perl' is a BIG target, so when it has to be made, it has to be started
2141	# as early as possible to reduce overall compile time. Since 'make' does not
2142	# provide any priorities, i force it to build all 'perl'-prerequisites early, by
2143	# adding artificial dependencies to these prerequisites
2144	#
2145	# That behavior is likely to be system-dependent.
2146	# My goal was only to make it work on my current development system,
2147	# where this saves about 20% of overall build time.
2148
2149	ifeq ($(WITHPERL),1)
2150	links_non_perl: PERLTOOLS/PERLTOOLS.dummy
2151	perltools: links_non_perl
2152	perl: realperl
2153	else
2154	links_non_perl: links
2155	perl:
2156	$(MAKE) "WITHPERL=1" perl
2157	endif
2158
2159	# ---------------------------------------- perl
2160
2161	realperl: perltools
2162	(( \
2163	echo "$(SEP) Make PERL2ARB" ; \
2164	$(TIME) $(MAKE) -C PERL2ARB -r -f Makefile.main \
2165	"AUTODEPENDS=1" \
2166	"dflags=$(dflags)" \
2167	"cflags4perl=$(cflags) $(cxxflags) $(dflags)" \
2168	"lflags4perl=$(lflags4perl)" \
2169	"COMPILER_VERSION=$(COMPILER_VERSION)" \
2170	all && \
2171	$(MAKE) -C PERL_SCRIPTS/test test && \
2172	echo "$(SEP) Make PERL2ARB [done]" ; \
2173	) > PERL2ARB.log 2>&1 && (cat PERL2ARB.log;rm PERL2ARB.log)) \|\| (cat PERL2ARB.log;rm PERL2ARB.log;false)
2174
2175	perl_clean:
2176	@$(MAKE) -C PERL2ARB -r -f Makefile.main \
2177	"AUTODEPENDS=0" \
2178	clean
2179
2180	PERL2ARB/PERL2ARB.clean:
2181	$(MAKE) perl_clean
2182	$(MAKE) -C PERL_SCRIPTS/test clean
2183
2184	# ---------------------------------------- bindings to script languages
2185
2186	bindings: lib/libCORE.so lib/libARBDB.so
2187	$(MAKE) -C BINDINGS all ARBDEPENDS="$(^:%=../%)" DFLAGS="$(dflags)"
2188
2189	bindings_clean:
2190	$(MAKE) -C BINDINGS clean
2191
2192	# ----------------------------------------
2193
2194	CLOC=cloc-1.08.pl
2195	CLOCFLAGS=--no3 --quiet --progress-rate=0
2196	CLOCARB=--exclude-dir=GDE .
2197	CLOCEXT=GDE
2198	CLOCCODE=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.code.def
2199	CLOCREST=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.rest.def
2200	CLOCFILT=tail --lines=+4
2201
2202	cloc:
2203	@echo 'Arb code:'
2204	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCARB) \| $(CLOCFILT)
2205	@echo 'Arb rest:'
2206	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCARB) \| $(CLOCFILT)
2207	@echo 'External code:'
2208	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCEXT) \| $(CLOCFILT)
2209	@echo 'External rest:'
2210	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCEXT) \| $(CLOCFILT)
2211
2212	# ---------------------------------------- check resources
2213
2214	check_res:
2215	$(ARBHOME)/SOURCE_TOOLS/check_resources.pl
2216
2217	# ---------------------------------------- cleaning
2218
2219	rmbak:
2220	@echo "[cleanup backup/core files]"
2221	@find . \( -name '*%' \
2222	-o -name '*.bak' \
2223	-o -name '*~' \) \
2224	-o \( -name 'core' -a \! -type d \) \
2225	-exec rm -v {} \; \|\| \
2226	echo "Warning: target 'rmbak' reported problems when removing misc. backup files (ignored)"
2227	@echo "[cleanup done]"
2228
2229	bin_reinit:
2230	$(MAKE) bin/bin.clean
2231	$(MAKE) -C "bin" all
2232
2233	clean_directories:
2234	-rm -rf \
2235	$(ARBHOME)/PROBE_SET/bin \
2236	$(ARBHOME)/INCLUDE \
2237
2238	libclean:
2239	-find $(ARBHOME) -type f \( -name '*.a' ! -type l \) -exec rm -f {} \;
2240
2241	objclean:
2242	-find $(ARBHOME) -type f \( -name '*.o' ! -type l \) -exec rm -f {} \;
2243
2244	# bin.clean and HELP_SOURCE.clean interfere
2245	clean3:
2246	$(MAKE) bin/bin.clean
2247	$(MAKE) HELP_SOURCE/HELP_SOURCE.clean
2248
2249	clean2: $(ARCHS:.a=.clean) \
2250	clean3 \
2251	rmbak \
2252	libclean \
2253	objclean \
2254	lib/lib.clean \
2255	GDEHELP/GDEHELP.clean \
2256	HEADERLIBS/HEADERLIBS.clean \
2257	SOURCE_TOOLS/SOURCE_TOOLS.clean \
2258	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.clean \
2259	UNIT_TESTER/UNIT_TESTER.clean \
2260	TEMPLATES/TEMPLATES.clean \
2261	perl_clean \
2262	clean_directories \
2263
2264	rm -f .last_gcc .last_compiler config.makefile.bak
2265
2266	# links are needed for cleanup
2267	clean: redo_links motif_xpm_hack_clean
2268	$(MAKE) clean2
2269	$(MAKE) clean_cov_all clean_links
2270
2271	silent_clean:
2272	$(MAKE) clean >/dev/null
2273
2274	# 'relocated' is about 50% faster than 'rebuild'
2275	reloc_clean: links
2276	@echo "---------------------------------------- Relocation cleanup"
2277	$(MAKE) \
2278	perl_clean \
2279	GDEHELP/GDEHELP.clean \
2280	HELP_SOURCE/genhelp/genhelp.clean \
2281	bin/bin.clean \
2282	libclean \
2283	objclean
2284
2285	relocated: links
2286	$(MAKE) reloc_clean
2287	@echo "---------------------------------------- and remake"
2288	$(MAKE) build
2289
2290	# -----------------------------------
2291	# some stress tests
2292	# (helpful to reveal race conditions with -j)
2293
2294	rebuild4ever: rebuild
2295	$(MAKE) rebuild4ever
2296
2297	build4ever: build
2298	$(MAKE) build4ever
2299
2300	clean4ever: clean
2301	$(MAKE) clean4ever
2302
2303	test4ever: ut
2304	$(MAKE) test4ever
2305
2306	perl4ever: clean
2307	$(MAKE) links
2308	$(MAKE) perl
2309	$(MAKE) perl4ever
2310
2311	help4ever: clean
2312	$(MAKE) help
2313	$(MAKE) help4ever
2314
2315	# -----------------------------------
2316
2317	rebuild: clean
2318	$(MAKE) all
2319
2320	cleanlinked: bin/bin.clean libclean
2321
2322	relink: cleanlinked
2323	$(MAKE) all
2324
2325	tarfile: rebuild
2326	$(MAKE) prepare_libdir
2327	util/arb_compress
2328
2329	tarfile_quick: build
2330	$(MAKE) prepare_libdir
2331	util/arb_compress
2332
2333	save: sourcetarfile
2334
2335	patch:
2336	SOURCE_TOOLS/arb_create_patch.sh arbPatch
2337
2338	# test early whether save will work
2339	savetest:
2340	@util/arb_srclst.pl >/dev/null
2341
2342	testsave: savetest
2343
2344	sourcetarfile: rmbak
2345	util/arb_save
2346
2347	save2: rmbak
2348	util/arb_save ignore
2349
2350	save_test: rmbak
2351	@echo "Testing source list.."
2352	@util/arb_srclst.pl > /dev/null
2353
2354	save_test_no_error:
2355	@-$(MAKE) save_test
2356
2357	inc_candi:
2358	touch SOURCE_TOOLS/inc_candi.stamp
2359	$(MAKE) do_version_update
2360
2361	inc_patch:
2362	touch SOURCE_TOOLS/inc_patch.stamp
2363	$(MAKE) do_version_update
2364
2365	inc_minor:
2366	touch SOURCE_TOOLS/inc_minor.stamp
2367	$(MAKE) do_version_update
2368
2369	inc_major:
2370	touch SOURCE_TOOLS/inc_major.stamp
2371	$(MAKE) do_version_update
2372
2373	do_version_update:
2374	@echo Incrementing version information
2375	$(MAKE) savetest
2376	$(MAKE) genheaders # auto upgrades version early
2377
2378	show_version:
2379	$(MAKE) genheaders # updates version info
2380	@echo "$(SEP) ARB version info"
2381	@grep ARB_VERSION TEMPLATES/arb_build.h
2382	@echo "$(SEP)"
2383
2384	release_quick:
2385	-rm arb.tgz arbsrc.tgz
2386	$(MAKE) tarfile_quick
2387	$(MAKE) sourcetarfile
2388
2389	# --------------------------------------------------------------------------------
2390	# special cleanups
2391
2392	clean_opengl_changed: RNA3D/RNA3D.clean EDIT4/EDIT4.clean WINDOW/WINDOW.clean GL/GL.clean
2393
2394	# --------------------------------------------------------------------------------
2395
2396	MAKE_IF_COMMITTED=$(MAKE) -C SOURCE_TOOLS -f Makefile.commitbuild
2397
2398	build_CTARGET:
2399	+$(MAKE_IF_COMMITTED) "CTARGET=$(CTARGET)" build_CTARGET
2400
2401	reset_committed_build:
2402	+$(MAKE_IF_COMMITTED) reset
2403
2404	# --------------------------------------------------------------------------------
2405
2406	arbapplications: nt pa e4 wetc pt na nal di ph ds wetc cma
2407
2408	arb_external: convert tools gde readseq tg pst xmlin
2409
2410	arb_no_perl: arbapplications help arb_external
2411
2412	arb: motif_xpm_hack
2413	$(MAKE) "WITHPERL=1" perl arb_no_perl
2414
2415	motif_xpm_hack:
2416	$(MAKE) -r -C "lib/motifHack" all
2417
2418	motif_xpm_hack_clean:
2419	$(MAKE) -r -C "lib/motifHack" clean
2420
2421	# --------------------------------------------------------------------------------
2422	# special targets for SOURCE_TOOLS/remake_after_change.pl
2423
2424	rac_arb_dist: di
2425	rac_arb_edit4: e4
2426	rac_arb_ntree: nt
2427	rac_arb_pars: pa
2428	rac_arb_phylo: ph
2429	rac_arb_wetc: wetc
2430	rac_arb_naligner: nal
2431	rac_arb_pt_server: pt
2432	rac_arb_db_server: ds
2433	rac_arb_name_server: na
2434	rac_arb_convert_aln: convert
2435	rac_arb_treegen: tg
2436	rac_arb_rnacma: cma
2437	rac_arb_help2xml: help
2438
2439	rac_arb_a2ps: tools
2440	rac_arb_consensus_tree: tools
2441	rac_arb_dnarates: tools
2442	rac_arb_export_rates: tools
2443	rac_arb_export_tree: tools
2444	rac_arb_gene_probe: tools
2445	rac_arb_message: tools
2446	rac_arb_primer: tools
2447	rac_arb_probe: tools
2448	rac_arb_read_tree: tools
2449
2450	# --------------------------------------------------------------------------------
2451	# unit testing
2452	# @@@ work in progress
2453	#
2454	# goal is to automatically test all libraries/executables using TESTED_UNITS_AUTO
2455	#
2456	# currently not all test executables link w/o error
2457	# (see UNITS_WORKING, UNITS_UNTESTABLE_ATM and UNITS_NEED_FIX)
2458
2459	# define RNA3D/RNA3D.test
2460	RNA3D_TEST := $(subst .a,.test,$(RNA3D_LIB))
2461
2462	TESTED_UNITS_AUTO = $(ARCHS:.a=.test)
2463
2464	UNITS_WORKING = \
2465	$(RNA3D_TEST) \
2466	EISPACK/EISPACK.test \
2467	GENOM/GENOM.test \
2468	GL/glAW/libglAW.test \
2469	GL/glpng/libglpng_arb.test \
2470	ISLAND_HOPPING/ISLAND_HOPPING.test \
2471	NALIGNER/NALIGNER.test \
2472	NAMES/NAMES.test \
2473	PHYLO/PHYLO.test \
2474	PRIMER_DESIGN/PRIMER_DESIGN.test \
2475	PROBE_DESIGN/PROBE_DESIGN.test \
2476	SECEDIT/SECEDIT.test \
2477	SEQ_QUALITY/SEQ_QUALITY.test \
2478	SERVERCNTRL/SERVERCNTRL.test \
2479	SL/ALIVIEW/ALIVIEW.test \
2480	SL/AP_TREE/AP_TREE.test \
2481	SL/ARB_TREE/ARB_TREE.test \
2482	SL/AW_HELIX/AW_HELIX.test \
2483	SL/AW_NAME/AW_NAME.test \
2484	SL/DB_SCANNER/DB_SCANNER.test \
2485	SL/GUI_ALIVIEW/GUI_ALIVIEW.test \
2486	SL/HELIX/HELIX.test \
2487	SL/LOCATION/LOCATION.test \
2488	SL/MATRIX/MATRIX.test \
2489	SL/QUERY/QUERY.test \
2490	SL/REFENTRIES/REFENTRIES.test \
2491	SL/SEQUENCE/SEQUENCE.test \
2492	SL/TREE_ADMIN/TREE_ADMIN.test \
2493	SL/TREE_WRITE/TREE_WRITE.test \
2494	STAT/STAT.test \
2495	TREEGEN/TREEGEN.test \
2496	WETC/WETC.test \
2497	XML/XML.test \
2498
2499	# untestable units
2500
2501	UNITS_NEED_FIX = \
2502	ptpan/PROBE.test \
2503
2504	UNITS_UNTESTABLE_ATM = \
2505	XML_IMPORT/XML_IMPORT.test \
2506
2507	# for the moment, put all units containing tests into the following 4 sections (see also TESTED_UNITS below)
2508
2509	# recent development
2510	UNITS_TESTED_FIRST = \
2511	SL/XFERGUI/XFERGUI.test \
2512	SL/XFERSET/XFERSET.test \
2513	SL/TRANSLATE/TRANSLATE.test \
2514	SL/PVP/PVP.test \
2515	AWTI/AWTI.test \
2516	SL/FILTSEQEXP/FILTSEQEXP.test \
2517	SL/GROUP_SEARCH/GROUP_SEARCH.test \
2518
2519	# start units with long duration early
2520	UNITS_RUNNING_LONG = \
2521	ARBDB/libARBDB.test \
2522	AWTC/AWTC.test \
2523	TOOLS/arb_test.test \
2524
2525	# plain test-libaries that are not linked anywhere
2526	TEST_SANDBOXES = \
2527	SL/CB/CB.test \
2528
2529	UNITS_TESTED = \
2530	AISC_MKPTPS/mkptypes.test \
2531	ARB_GDE/ARB_GDE.test \
2532	AWT/libAWT.test \
2533	CONSENSUS_TREE/CONSENSUS_TREE.test \
2534	CONVERTALN/CONVERTALN.test \
2535	CORE/libCORE.test \
2536	DBSERVER/DBSERVER.test \
2537	DIST/DIST.test \
2538	EDIT4/EDIT4.test \
2539	GENOM_IMPORT/GENOM_IMPORT.test \
2540	HELP_SOURCE/arb_help2xml.test \
2541	MERGE/MERGE.test \
2542	MULTI_PROBE/MULTI_PROBE.test \
2543	NTREE/NTREE.test \
2544	PARSIMONY/PARSIMONY.test \
2545	PERLTOOLS/arb_proto_2_xsub.test \
2546	PROBE/PROBE.test \
2547	PROBE_SET/fb_test.test \
2548	SERVERCNTRL/SERVERCNTRL.test \
2549	SL/ALILINK/ALILINK.test \
2550	SL/CONSENSUS/CONSENSUS.test \
2551	SL/DB_QUERY/DB_QUERY.test \
2552	SL/FAST_ALIGNER/FAST_ALIGNER.test \
2553	SL/FILTER/FILTER.test \
2554	SL/INSDEL/INSDEL.test \
2555	SL/ITEM_SHADER/ITEM_SHADER.test \
2556	SL/ITEMS/ITEMS.test \
2557	SL/MACROS/MACROS.test \
2558	SL/NDS/NDS.test \
2559	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.test \
2560	SL/PRONUC/PRONUC.test \
2561	SL/PTCLEAN/PTCLEAN.test \
2562	SL/REGEXPR/REGEXPR.test \
2563	SL/SEQIO/SEQIO.test \
2564	SL/TREE_READ/TREE_READ.test \
2565	SL/TREEDISP/TREEDISP.test \
2566	TOOLS/arb_consensus_tree.test \
2567	TOOLS/arb_probe.test \
2568	WINDOW/libWINDOW.test \
2569
2570	TESTED_UNITS = \
2571	$(UNITS_TESTED_FIRST) \
2572	$(UNITS_RUNNING_LONG) \
2573	$(TEST_SANDBOXES) \
2574	$(UNITS_TESTED) \
2575
2576	# see UNIT_TESTER/sym2testcode.pl@disableErrorOnUnitsWithoutTests
2577
2578	# ----------------------------------------
2579
2580	TEST_LOG_DIR = UNIT_TESTER/logs
2581	TEST_RUN_SUITE=$(MAKE) $(NODIR) -C UNIT_TESTER -f Makefile.suite -r
2582	TEST_MAKE_FLAGS=
2583	TEST_POST_CLEAN=
2584	ifeq ($(COVERAGE),1)
2585	TEST_POST_CLEAN=$(MAKE) clean_cov
2586	TEST_MAKE_FLAGS+=-j1
2587	endif
2588
2589
2590	%.test:
2591	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
2592	( \
2593	echo "fake[1]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
2594	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
2595	"UNITDIR=$(@D)" \
2596	"UNITLIBNAME=$(@F:.test=)" \
2597	"COVERAGE=$(COVERAGE)" \
2598	"ARB_PID=$(ARB_PID)_$(@F)" \
2599	runtest; \
2600	echo "fake[1]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"; \
2601	$(TEST_POST_CLEAN) \
2602	) >$(TEST_LOG_DIR)/$(@F).log 2>&1; \
2603	UNIT_TESTER/log_result.pl $(TEST_LOG_DIR)/$(@F).log )
2604
2605
2606	test_base: $(UNIT_TESTER_LIB:.a=.dummy) $(subst .test,.dummy,$(TEST_SANDBOXES))
2607
2608	clean_cov:
2609	find . \( -name ".gcda" -o -name ".gcov" -o -name "*.cov" \) -exec rm {} \;
2610
2611	clean_cov_all: clean_cov
2612	find . \( -name "*.gcno" \) -exec rm {} \;
2613
2614	cleanup_faked_arbpids:
2615	@rm ~/.arb_tmp/tmp/arb_pids_${USER}_${ARB_PID}_* \|\| true
2616
2617	cleanup_faked_arbpids_and_fail: cleanup_faked_arbpids
2618	@false
2619
2620
2621	run_tests_faked_arbpid:
2622	+@$(TEST_RUN_SUITE) init
2623	@echo "fake[2]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2624	$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(TESTED_UNITS) \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2625	@echo "fake[2]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2626	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2627	@$(MAKE) clean_cov >/dev/null
2628	@$(MAKE) cleanup_faked_arbpids
2629
2630	# @@@ instead of only running UNIT, this should as well run all tests this unit depends on? according to 'needs_libs'
2631	# @@@ 'run_tests_faked_arbpid' does not work for UNIT=ARBDB/libARBDB or UNIT=PARS/PARS -> could be solved via extra suffix, e.g. ARBDB/libARBDB.unit
2632
2633	run_onetest_faked_arbpid:
2634	+@$(TEST_RUN_SUITE) init
2635	@echo "fake[2]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2636	test -n "$(UNIT)" \|\| (echo "Error: UNIT has to be defined for target 'run_onetest_faked_arbpid'!"; false)
2637	$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(UNIT).test \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2638	@echo "fake[2]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2639	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2640	@$(MAKE) clean_cov >/dev/null
2641	@$(MAKE) cleanup_faked_arbpids
2642
2643
2644	run_tests: test_base clean_cov
2645	$(MAKE) "ARB_PID=UT_$$$$" run_tests_faked_arbpid
2646
2647	run_oneunitstests: test_base
2648	$(MAKE) "ARB_PID=UT_$$$$" run_onetest_faked_arbpid
2649
2650
2651	ut:
2652	ifeq ($(UNIT_TESTS),1)
2653	@echo $(MAKE) run_tests
2654	@$(MAKE) run_tests
2655	else
2656	@echo "Not compiled with unit tests"
2657	endif
2658
2659
2660	aut:
2661	+@$(TEST_RUN_SUITE) unskip
2662	$(MAKE) ut
2663
2664	# --------------------------------------------------------------------------------
2665
2666	TIMELOG=$(ARBHOME)/arb_time.log
2667	TIMEARGS=--append --output=$(TIMELOG) --format=" * %E(%S+%U) %P [%C]"
2668	TIMECMD=$(TIME) $(TIMEARGS)
2669
2670	time_one:
2671	ifeq ($(ONE_TIMED_TARGET),)
2672	@echo "Error: You have to pass ONE_TIMED_TARGET to $@"
2673	false
2674	else
2675	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET)"
2676	@$(TIMECMD) $(MAKE) $(ONE_TIMED_TARGET)
2677	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET) [done]"
2678	endif
2679
2680	timed_target:
2681	ifeq ($(TIMED_TARGET),)
2682	@echo "Error: You have to pass TIMED_TARGET to $@"
2683	false
2684	else
2685	@echo "Build time:" > $(TIMELOG)
2686	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2687	@cat $(TIMELOG)
2688	@rm $(TIMELOG)
2689	endif
2690
2691	timed_target_tested:
2692	ifeq ($(TIMED_TARGET),)
2693	@echo "Error: You have to pass TIMED_TARGET to $@"
2694	false
2695	else
2696	@echo "Build time:" > $(TIMELOG)
2697	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2698	$(MAKE) "ONE_TIMED_TARGET=ut" time_one
2699	@cat $(TIMELOG)
2700	@rm $(TIMELOG)
2701	endif
2702
2703	clean_timed_target:
2704	ifeq ($(TIMED_TARGET),)
2705	@echo "Error: You have to pass TIMED_TARGET to $@"
2706	false
2707	else
2708	@echo "Build time:" > $(TIMELOG)
2709	$(MAKE) "ONE_TIMED_TARGET=clean" time_one
2710	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2711	@cat $(TIMELOG)
2712	@rm $(TIMELOG)
2713	endif
2714
2715	# --------------------------------------------------------------------------------
2716
2717	CHECKOUT_MODIFIED=0# set to 1 to temporarily skip test for modifications (do not check in if set to 1)
2718
2719	check_svn_does_not_contain_generated:
2720	ifeq ($(CHECKOUT_MODIFIED),0)
2721	@echo "Testing that build does not modify files in SVN"
2722	@test 0 = `svn status \| wc -l` \|\| ( \
2723	echo "The checkout is not/no longer clean:"; \
2724	svn status; \
2725	echo "- if this fails instantly, your checkout is not clean"; \
2726	echo "- if this fails after other targets, these targets modify checked in data"; \
2727	echo " (a common cause may be that depends are not up to date)"; \
2728	false)
2729	else
2730	grep -Hn 'CHECKOUT_MODIFIED' Makefile
2731	endif
2732
2733	check_svn_ignores_generated:
2734	@test 0 = `svn status \| grep '^\?' \| wc -l` \|\| ( \
2735	echo "There are svn-unignored files:"; \
2736	svn status \| grep '^\?'; \
2737	echo "(all generated files should be svn-ignored)"; \
2738	false)
2739
2740	check_svn_state: check_svn_does_not_contain_generated
2741	$(MAKE) check_svn_ignores_generated
2742	$(MAKE) savetest
2743
2744	things_that_always_should_work: depends proto
2745
2746	post_commit_check:
2747	@echo "---------------------------------------- [Initial]"
2748	$(MAKE) check_svn_state
2749
2750	$(MAKE) clean
2751	@echo "---------------------------------------- [After 'make clean']"
2752	$(MAKE) check_svn_state
2753
2754	$(MAKE) things_that_always_should_work
2755	@echo "---------------------------------------- [After 'make things_that_always_should_work']"
2756	$(MAKE) check_svn_state
2757
2758	$(MAKE) all
2759	@echo "---------------------------------------- [After 'make all']"
2760	$(MAKE) check_svn_state
2761
2762	$(MAKE) things_that_always_should_work
2763	@echo "---------------------------------------- [Final]"
2764	$(MAKE) check_svn_state
2765
2766	# --------------------------------------------------------------------------------
2767	# sanitize arb_ntree; also works for clients (arb_edit4, ...) started from there.
2768
2769	sanitize: all
2770	( \
2771	export "LSAN_OPTIONS=max_leaks=30:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp"; \
2772	echo "sake[1]: Entering directory \`$(ARBHOME)'"; \
2773	$(ARBHOME)/bin/arb_ntree --execute _logged ~/data/test.arb 2>&1 ; \
2774	echo "sake[1]: Leaving directory \`$(ARBHOME)'" \
2775	) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
2776
2777	# --------------------------------------------------------------------------------
2778	# build and test one unit:
2779
2780	build_oneunit:
2781	$(MAKE) "WITHPERL=1" $(UNIT).dummy
2782
2783	oneunit:
2784	ifndef UNIT
2785	@echo "Please define UNIT, e.g. using"
2786	@echo " make \"UNIT=ARBDB/libARBDB\" oneunit"
2787	@echo " make \"UNIT=SL/TREEDISP/TREEDISP\" oneunit"
2788	@echo "(Note: 1st is a shared library, 2nd isn't)"
2789	false
2790	else
2791	@echo "Build time" > $(TIMELOG)
2792	@echo "$(SEP) $(MAKE) build_oneunit"
2793	@$(TIMECMD) $(MAKE) build_oneunit
2794	ifeq ($(UNIT_TESTS),1)
2795	@echo "$(SEP) $(MAKE) run_oneunitstests"
2796	@$(TIMECMD) $(MAKE) run_oneunitstests
2797	endif
2798	@cat $(TIMELOG)
2799	@rm $(TIMELOG)
2800	endif
2801
2802	# --------------------------------------------------------------------------------
2803
2804	build: arb
2805	$(MAKE) check_bin_dep preplib compile_compatibility
2806
2807	all:
2808	@echo "Build time" > $(TIMELOG)
2809	# $(MAKE) clean_checked_vect # uncomment to rebuild sources where expected vectorization gets tested
2810	@echo "$(SEP) $(MAKE) all"
2811	@$(TIMECMD) $(MAKE) build
2812	@echo $(SEP)
2813	@echo "made 'all' with success."
2814	@echo "to start arb enter 'arb'"
2815	ifeq ($(UNIT_TESTS),1)
2816	@echo "$(SEP) $(MAKE) run_tests"
2817	@$(TIMECMD) $(MAKE) run_tests
2818	endif
2819	@echo "$(SEP) $(MAKE) all [done]"
2820	ifeq ($(DEBUG),1)
2821	@$(MAKE) save_test_no_error >/dev/null # just show hints
2822	endif
2823	@cat $(TIMELOG)
2824	@rm $(TIMELOG)
2825

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