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Last change on this file was 18126, checked in by westram, 5 years ago
full update from 'trunk' into 'alilink' adds: log:branches/cleanup@17627:17650,18105:18112 log:branches/clone@17813:17835 log:branches/config@17733:17737 log:branches/dbui@17881:17889 log:branches/fix@17380:17395,17480:17592,17597:17617 log:branches/fts@17653:18088,18090:18094 log:branches/gcc@17850:17876 log:branches/group@17162:17341 log:branches/gui@17754:18092 log:branches/mix@17631:17633,17637:17640 log:branches/optional@17481:17568 log:branches/progress@17195:17259 log:branches/svalues@17357:17477 log:trunk@17179:18123
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 81.0 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	$(info LeakSanitizer does not work with gcc $(COMPILER_VERSION) - disabled)
528	# need to disable AddressSanitizer (otherwise build fails; only affects gcc 4.8.x series)
529	SANITIZE_ADDRESS:=0
530	endif
531	endif
532	endif
533
534	ifeq ($(SANITIZE_UNDEFINED),1)
535	ifneq ('$(USE_GCC_49_OR_HIGHER)','yes')
536	$(info UndefinedBehaviorSanitizer not usable with gcc $(COMPILER_VERSION) - disabled)
537	SANITIZE_UNDEFINED:=0
538	endif
539	endif
540
541	SANITIZE_ANY:=0
542	ifeq ($(SANITIZE_ADDRESS),1)
543	SANITIZE_ANY:=1
544	endif
545	ifeq ($(SANITIZE_UNDEFINED),1)
546	SANITIZE_ANY:=1
547	endif
548
549	# vectorization fails if sanitizer active where it normally succeeds -> disable check
550	ifeq ($(SANITIZE_ANY),1)
551	$(info disabling vectorize checks. would fail with sanitized code)
552	DISABLE_VECTORIZE_CHECK:=1
553	else
554	$(info no sanitizer enabled. reset: SANITIZE=0)
555	SANITIZE:=0
556	endif
557
558	# deactivate some bogus warnings occurring when sanitizing NDEBUG version
559	# (do not disable for future gcc-version >= 8.x -> test again when available)
560	ifeq ($(SANITIZE_ANY),1)
561	ifeq ($(DEBUG),0)
562	ifneq ('$(USE_GCC_80_OR_HIGHER)','yes')
563	extended_cpp_warnings += -Wno-format-overflow
564	extended_cpp_warnings += -Wno-maybe-uninitialized
565	endif
566	endif
567	endif
568
569	#---------------------- 32 or 64 bit
570
571	cross_cflags:=
572	cross_lflags:=
573	cross_clflags:=
574
575	ifeq ($(ARB_64),1)
576	dflags += -DARB_64
577	shared_cflags += -fPIC
578	CROSS_LIB:=# empty => autodetect below
579	ifeq ($(DARWIN),1)
580	cross_cflags += -arch x86_64
581	cross_lflags += -arch x86_64
582	cross_clflags += -arch x86_64
583	endif
584	else
585	CROSS_LIB:=/lib
586	endif
587
588	cflags += $(cross_cflags)
589	clflags += $(cross_clflags)
590
591	ifeq ('$(CROSS_LIB)','')
592	# autodetect libdir
593	ifeq ($(ARB_64),1)
594	CROSS_LIB:=$(shell (test -d /lib64 && echo lib64) \|\| echo lib)
595	else
596	CROSS_LIB:=$(shell (test -d /lib32 && echo lib32) \|\| echo lib)
597	endif
598	endif
599
600	#---------------------- unit tests
601
602	ifndef UNIT_TESTS
603	UNIT_TESTS=0#default is "no tests"
604	endif
605	ifeq ($(UNIT_TESTS),1)
606	dflags += -DUNIT_TESTS
607	UNIT_TESTER_LIB=UNIT_TESTER/UNIT_TESTER.a
608	else
609	UNIT_TESTER_LIB=
610	endif
611
612	#---------------------- use gcov
613
614	ifndef COVERAGE
615	COVERAGE=0#default is "no"
616	endif
617	ifneq ($(COVERAGE),0)
618	GCOV_FLAGS=--coverage
619	else
620	GCOV_FLAGS=
621	endif
622
623	cflags += $(GCOV_FLAGS)
624	clflags += $(GCOV_FLAGS)
625	cross_lflags += $(GCOV_FLAGS)
626
627	#---------------------- other flags
628
629	dflags += -D$(MACH) # define machine
630
631	ifeq ($(DARWIN),1)
632	shared_cflags += -fno-common
633	else
634	dflags += $(shell getconf LFS_CFLAGS)
635	endif
636
637	cflags += -pipe
638	cflags += -fmessage-length=0# dont wrap compiler output
639	cflags += -fshow-column# show columns
640	cflags += -funit-at-a-time
641	cflags += -fPIC
642	cflags += -fno-common# link all global data into one namespace
643	cflags += -fstrict-aliasing# gcc 3.4
644
645
646	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
647	cflags += -fno-diagnostics-show-caret#gcc 4.8 (4.7.?)
648	endif
649	#cflags += -save-temps# uncomment to see preprocessor output
650
651	#---------------------- various sanitizers
652	# There are some disabled tests in CORE/arb_misc.cxx@sanitizers
653	# which trigger sanitizer reports.
654
655	ifeq ($(SANITIZE_ANY),1)
656	cflags += -ggdb3 -fno-omit-frame-pointer
657	endif
658
659	# activate AddressSanitizer+LeakSanitizer?
660	ifeq ($(SANITIZE_ADDRESS),1)
661	cflags += -fsanitize=address
662	clflags += -fsanitize=address
663	dflags += -DLEAKS_SANITIZED
664	endif
665
666	# activate UndefinedBehaviorSanitizer?
667	ifeq ($(SANITIZE_UNDEFINED),1)
668	cflags += -fsanitize=undefined
669	clflags += -fsanitize=undefined
670	dflags += -DUNDEF_SANITIZED
671	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
672	# abort on runtime errors
673	cflags += -fno-sanitize-recover=all
674	endif
675	#
676	# Note: alignment-sanitizer is deactivated for ARBDB and PROBE!
677	ifeq ('$(DEBUG)','1')
678	ifeq ($(USE_GCC_MAJOR),4)
679	ifeq ($(USE_GCC_MINOR),9)
680	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),01)','')
681	# workaround https://gcc.gnu.org/bugzilla/show_bug.cgi?id=63531 for 4.9.0 + 4.9.1
682	# (problem is fixed in 4.9.2 release)
683	extended_cpp_warnings:=$(subst -Weffc++,,$(extended_cpp_warnings))
684	endif
685	endif
686	endif
687	endif
688	endif
689
690	#---------------------- X11 location
691
692	ifeq ($(DARWIN),1)
693	XHOME:=$(PREFIX)
694	else
695	ifeq ($(DEBIAN),1)
696	XHOME:=$(PREFIX)
697	else
698	XHOME:=/usr/X11R6
699	endif
700	endif
701
702	XINCLUDES ?= -I$(XHOME)/include
703	XLIBS ?= -L$(XHOME)/$(CROSS_LIB)
704	ifeq ($(DARWIN),1)
705	XINCLUDES += -I$(OSX_FW)/GLUT.framework/Headers -I$(OSX_FW)/OpenGL.framework/Headers -I$(OSX_SDK)/usr/include/krb5
706
707	XLIBS += -lXm -lpng -lz -lXt -lX11 -lXext -lXp -lXmu -lXi
708	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGL.dylib:$(OSX_FW_OPENGL)/libGL.dylib
709	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGLU.dylib:$(OSX_FW_OPENGL)/libGLU.dylib
710	else
711	XLIBS += -lXm -lXpm -lXt -lXext -lX11
712	endif
713
714	#---------------------- open GL
715
716	ifeq ($(OPENGL),1)
717	cflags += -DARB_OPENGL # activate OPENGL code
718	GL := gl # this is the name of the OPENGL base target
719	GL_LIB_SYS := -lGL -lGLU
720	GL_LIB_ARB := -L$(ARBHOME)/GL/glAW -lglAW
721
722	ifeq ($(DARWIN),1)
723	GL_LIB_SYS += -lpthread
724	endif
725
726	GL_PNGLIBS_ARB := -L$(ARBHOME)/GL/glpng -lglpng_arb
727	GL_PNGLIBS_SYS := -lpng
728
729	GLEWLIB := -lGLEW -lGLw
730	ifeq ($(DARWIN),1)
731	GLUTLIB := -glut
732	else
733	GLUTLIB := -lglut
734	endif
735
736	GL_LIBS_SYS := $(GL_LIB_SYS) $(GL_PNGLIBS_SYS) $(GLEWLIB) $(GLUTLIB)
737	GL_LIBS_ARB := $(GL_LIB_ARB) $(GL_PNGLIBS_ARB)
738
739	RNA3D_LIB := RNA3D/RNA3D.a
740	else
741	GL_LIBS_ARB:=# no opengl -> no libs
742	GL_LIBS_SYS:=# no opengl -> no libs
743	GL:=# dont build ARB openGL libs
744
745	RNA3D_LIB :=
746	endif
747
748	RNA3D_LIB_4_DEPENDS := RNA3D/RNA3D.a
749
750	GL_LIBS:=$(GL_LIBS_ARB) $(GL_LIBS_SYS)
751
752	#---------------------- tiff lib:
753
754	TIFFLIBS := -ltiff
755
756	#---------------------- XML lib:
757
758	XMLLIBS := -lxerces-c
759
760	#---------------------- glib:
761
762	ARB_NEEDED_GLIB=glib-2.0
763
764	ARB_GLIB_INCLUDE:=$(strip $(shell pkg-config --cflags $(ARB_NEEDED_GLIB)))
765	ARB_GLIB_LIBS:=$(strip $(shell pkg-config --libs $(ARB_NEEDED_GLIB)))
766
767	#---------------------- basic libs:
768
769	SYSLIBS:=
770	ifeq ($(DARWIN),1)
771	SYSLIBS += -lstdc++
772	else
773	SYSLIBS += -lm $(ARB_GLIB_LIBS)
774	endif
775
776	#---------------------- include symbols?
777
778	ifeq ($(TRACESYM),1)
779	ifeq ($(USE_CLANG),0)
780	cflags += -rdynamic
781	clflags += -rdynamic -Wl,--export-dynamic
782	endif
783	endif
784
785	#---------------------- system dependent commands
786
787	ifeq ($(DARWIN),1)
788	TIME:=gtime
789	else
790	TIME:=/usr/bin/time
791	endif
792
793	#---------------------- SSE vectorizer
794	# for details see SOURCE_TOOLS/vectorize.README
795
796	ifeq ($(DEBUG),0)
797	ifeq ($(USE_GCC_49_OR_HIGHER),yes)
798	ifeq ($(DISABLE_VECTORIZE_CHECK),0)
799	cflags += -fopt-info-vec
800	cflags += -fopt-info-vec-missed
801	ifeq ($(TRACE_MISSED_VECTORIZATIONS),1)
802	# Shows reasons for unsuccessful vectorization:
803	cflags += -ftree-vectorizer-verbose=10
804	POST_COMPILE += --dump-loop-optimization
805	ifeq ($(VECTORIZATION_CHECK_CANDIDATES),1)
806	$(error TRACE_MISSED_VECTORIZATIONS and VECTORIZATION_CHECK_CANDIDATES may not be used together!)
807	endif
808	endif
809	ifeq ($(VECTORIZATION_CHECK_CANDIDATES),1)
810	POST_COMPILE += --loop-optimization-candi
811	endif
812	POST_COMPILE += --check-loop-optimization
813	endif
814	else
815	ifeq ($(USE_GCC_48_OR_HIGHER),yes)
816	# no automatic vectorization-check for gcc<4.9.0
817	# -> uncomment the next 2 lines and grep the spam it will produce for 'vectorized.*loops'
818	# cflags += -fopt-info -fopt-info-vec-missed
819	# POST_COMPILE += --original
820	endif
821	endif
822	endif
823
824	#---------------------- stop early on broken flags/compiler combination
825
826	ifeq ($(DEBUG),0)
827	ifeq ($(SANITIZE_ANY),1)
828	ifeq ('$(COMPILER_VERSION)','4.9.1')
829	$(error compiling DEBUG=0 + SANITIZE!=0 crashes with gcc $(COMPILER_VERSION) (gcc 4.9.2 works))
830	endif
831	endif
832	endif
833
834	#---------------------- differences between linking executables and shared libs:
835
836	# executables:
837	ifeq ($(DARWIN),1)
838	blflags:=$(clflags)
839	else
840	blflags:=$(clflags) -Wl,--no-undefined
841	endif
842
843	# shared libraries
844	llflags:=$(clflags)
845
846	# dont use clflags below
847	clflags:=
848
849	# -------------------------------------------------------------------------
850	# Don't put any machine/version/etc conditionals below!
851	# (instead define variables above)
852	# -------------------------------------------------------------------------
853
854	cflags += -W -Wall $(dflags) $(extended_warnings)
855	cxxflags := $(extended_cpp_warnings)
856
857	# add CFLAGS + CPPFLAGS from environment for DEBIAN build
858	ifeq ($(DEBIAN),1)
859	cflags := $(CFLAGS) $(cflags)
860	cxxflags += $(CPPFLAGS)
861	endif
862
863	ifeq ('$(USE_CLANG)','1')
864	# none of the following standards works with clang3.3 (under linux) => dont use standard (as done before r15516)
865	# cxxflags += -std=gnu++11
866	# cxxflags += -std=gnu++0x
867	else
868	ifeq ('$(USE_GCC_60_OR_HIGHER)','yes')
869	cxxflags += -std=gnu++14# see also TEMPLATES/cxxforward.h@USE_Cxx14
870	else
871	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
872	cxxflags += -std=gnu++11# see also TEMPLATES/cxxforward.h@USE_Cxx11
873	else
874	# gcc versions between 4.3 (lowest supported) and <4.7
875	cxxflags += -std=gnu++0x
876	endif
877	endif
878	endif
879
880	LINK_STATIC_LIB := $(AR) -csq# link static lib
881	LINK_EXECUTABLE := $(A_CXX) $(blflags) -o# link executable (c++)
882
883	ifeq ($(LINK_STATIC),1)
884	SHARED_LIB_SUFFIX = a# static lib suffix
885	LINK_SHARED_LIB := $(LINK_STATIC_LIB)
886	else
887	SHARED_LIB_SUFFIX = so# shared lib suffix
888	LINK_SHARED_LIB := $(A_CXX) $(llflags) -shared -o# link shared lib
889	endif
890
891	ifeq ($(DARWIN),1)
892	lflags4perl:=
893	else
894	lflags4perl:=$(cross_lflags) -shared
895	endif
896
897	# delete variables unused below
898	blflags:=
899	llflags:=
900
901	# other used tools
902	MAKEDEPEND_PLAIN = makedepend
903	MAKEDEPEND = $(FORCEMASK);$(MAKEDEPEND_PLAIN)
904
905	#SEP:=--------------------------------------------------------------------------------
906	SEP=[`date +%M:%S.%N`] ------------------------------------------------
907	# to analyse timings run
908	# make -j9 clean; make -j9 all \| grep '^\[' \| sort
909	# make -j9 "TIMED_TARGET=perl" clean_timed_target \| grep '^\[' \| sort
910
911	# ------------------------------------------------------------ DYNLIBDEFS
912	# various dynamic library definitions for linking executables:
913	#
914	# SYSLIBS: system libraries needed by database lib
915	# ARBDB_LIB: database lib
916	# DBSYS_LIBS: executable using database (but no GUI)
917	# GUI_LIBS: executable using database and GUI (arb gui uses database)
918	#
919	# Note: definitions exported to sub-makefiles are described in SOURCE_TOOLS/parent_make.txt
920
921	CORE_LIB=-lCORE
922	ARBDB_LIB=-lARBDB $(CORE_LIB)
923	DBSYS_LIBS = $(ARBDB_LIB) $(SYSLIBS)
924
925	GUI_LIBS_PREFIX:=
926	ifeq ($(DARWIN),1)
927	# this seem to be added at wrong place, since opengl is only needed to link EDIT4
928	GUI_LIBS_PREFIX:=-framework GLUT -framework OpenGL
929	endif
930
931	GUI_LIBS=$(GUI_LIBS_PREFIX) $(DBSYS_LIBS) -lAWT -lWINDOW $(XLIBS)
932
933	LIBPATH = -L$(ARBHOME)/lib
934
935	DEST_LIB = lib
936	DEST_BIN = bin
937
938	CC_INCLUDES := -I. -I$(ARBHOME)/INCLUDE $(XINCLUDES) $(ARB_GLIB_INCLUDE)
939	CXX_INCLUDES := $(CC_INCLUDES)
940	MAKEDEPENDFLAGS := -- -DARB_OPENGL -DUNIT_TESTS -D__cplusplus -I. -Y$(ARBHOME)/INCLUDE
941
942	# ---------------------------------------
943	# wrap main()
944
945	use_ARB_main=$(ARBHOME)/SOURCE_TOOLS/arb_main_cpp.o
946	use_ARB_main_C=$(ARBHOME)/SOURCE_TOOLS/arb_main_c.o
947
948	# -----------------------------------------
949	# unique build-id
950	# - different for different calls of make
951	# - constant in recursive calls
952
953	ifndef ARBBID
954	ARBBID:=$(shell SOURCE_TOOLS/uniqueID.sh)
955	endif
956
957	# -----------------------------------------
958	# export variables to submakefiles
959
960	include SOURCE_TOOLS/export2sub
961
962	# do not define (exported) variables below this point
963
964	# -------------------------
965	# Main arb targets:
966	# -------------------------
967
968	first_target:
969	$(MAKE) checks
970	@echo $(SEP)
971	@echo 'Main targets:'
972	@echo ''
973	@echo ' all - Compile ARB + TOOLs + and copy shared libs + link foreign software'
974	@echo ' (That is most likely the target you want)'
975	@echo ''
976	@echo ' clean - remove generated files ("SUBDIR/SUBDIR.clean" to clean only SUBDIR)'
977	@echo ' rebuild - clean + all'
978	@echo ' cleanlinked - remove all binaries'
979	@echo ' relink - cleanlinked + all (=relink all from objects)'
980	@echo ''
981	@echo 'Some often used sub targets (make all makes them all):'
982	@echo ''
983	@echo ' arb - Just compile ARB (but none of the integrated tools)'
984	@echo ' menus - create lib/gde/arb.menu from GDEHELP/ARB_GDEmenus.source'
985	@echo ' perl - Compile the PERL XSUBS into lib/ARB.so and create links in lib to perl'
986	@echo ' binlink - Create all links in the bin directory'
987	@echo ''
988	@echo 'Development targets:'
989	@echo ''
990	@echo ' depends - create or update dependencies ("SUBDIR/SUBDIR.depends" to update only SUBDIR)'
991	@echo ' proto - create or update prototypes ("SUBDIR/SUBDIR.proto" to update only SUBDIR)'
992	@echo ' tags - create tags for xemacs'
993	@echo ' show - show available shortcuts (AKA subtargets)'
994	@echo ' up - shortcut for depends+proto+tags'
995	ifeq ($(UNIT_TESTS),1)
996	@echo ' ut - only run tests'
997	@echo ' "UNIT=..." oneunit - build one unit and run tests (see also UNIT_TESTER/Makefile.setup.local)'
998	endif
999	ifneq ($(SANITIZE),0)
1000	@echo ' sanitize - all + run arb_ntree with sanitizer (test.arb + execute _logged)'
1001	endif
1002	@echo ' modified - rebuild files modified in svn checkout (does touch)'
1003	@echo ' touch - touch files modified in svn checkout'
1004	@echo ''
1005	@echo 'Internal maintenance:'
1006	@echo ''
1007	@echo ' relinfo - show help on release targets'
1008	@echo ' tarfile - make rebuild and create arb version tarfile ("tarfile_quick" to skip rebuild)'
1009	@echo ' save - save all basic ARB sources into arbsrc_DATE ("savetest" to check filelist)'
1010	@echo ' patch - save svn diff to patchfile'
1011	@echo ' source_doc - create doxygen documentation'
1012	@echo ' relocated - rebuild partly (use when you have relocated ARBHOME)'
1013	@echo ' check_res - check resource usage'
1014	@echo ' dep_graph - Build dependency graphs'
1015	@echo ' clean_cov - Clean coverage results'
1016	@echo ''
1017	@echo ' clean_opengl_changed - clean after changing OPENGL setting in config.Makefile'
1018	@echo ' clean_checked_vect - clean units containing vectorization checks'
1019	@echo ' cleanRelinkable - similar to cleanlinked (but skips raxml8 to avoid rebuild)'
1020	@echo ''
1021	@echo ' post_commit_check - Checks whether'
1022	@echo ' * main make targets work,'
1023	@echo ' * dependencies and prototypes are up to date,'
1024	@echo ' * SVN-controlled files remain unaffected by called targets and'
1025	@echo ' * all generated files are ignored.'
1026	@echo ' (has to be called in a clean SVN checkout)'
1027	@echo $(SEP)
1028	@echo ''
1029
1030	relinfo:
1031	@echo ''
1032	@echo $(SEP)
1033	@echo 'Release targets:'
1034	@echo ''
1035	@echo ' inc_candi - increase RC candidate-number (only possible in "rc" branch, not needed for RC1)'
1036	@echo ' inc_patch - increase release patchlevel (only possible in "stable" branch)'
1037	@echo ' inc_minor - increase minor version number (only possible in "trunk")'
1038	@echo ' inc_major - increase MAJOR version number (only possible in "trunk")'
1039	@echo ''
1040	@echo ' show_version - show version tag'
1041	@echo ''
1042	@echo $(SEP)
1043	@echo ''
1044
1045	# auto-generate config.makefile:
1046
1047	config.makefile : config.makefile.template
1048	@echo --------------------------------------------------------------------------------
1049	ifeq ($(CONFIG_MAKEFILE_FOUND),)
1050	@cp $< $@
1051	@echo '$(ARBHOME)/$@:1: has been generated.'
1052	@echo 'Please edit $@ to configure your system!'
1053	@echo --------------------------------------------------------------------------------
1054	@false
1055	else
1056	@echo '$(ARBHOME)/$<:1: is more recent than'
1057	@echo '$(ARBHOME)/$@:1:'
1058	@ls -al config.makefile*
1059	@echo --------------------------------------------------------------------------------
1060	@echo "Updating $@ (if this fails, check manually)"
1061	SOURCE_TOOLS/update_config_makefile.pl
1062	@echo "Sucessfully updated $@"
1063	@echo --------------------------------------------------------------------------------
1064	@ls -al config.makefile*
1065	@echo --------------------------------------------------------------------------------
1066	@echo "Diff to your old config.makefile:"
1067	@echo --------------------------------------------------------------------------------
1068	-diff $@.bak $@
1069	@echo --------------------------------------------------------------------------------
1070	endif
1071
1072	# check if everything is configured correctly
1073
1074	check_DEVELOPER:
1075	ifndef DEVELOPER
1076	@echo 'config.makefile:1: DEVELOPER not defined'
1077	@false
1078	endif
1079
1080	check_DEBUG:
1081	ifndef dflags
1082	@echo 'config.makefile:1: DEBUG has to be defined. Valid values are 0 and 1'
1083	@false
1084	endif
1085
1086	check_ARB_64:
1087	ifndef ARB_64
1088	@echo 'config.makefile:1: ARB_64 has to be defined. Valid values are 0 and 1'
1089	@false
1090	endif
1091
1092	# ---------------------------------------- check gcc version
1093
1094	COMPILER_BROKEN:=0
1095
1096	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.6.4')
1097	COMPILER_BROKEN:=1
1098	endif
1099	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.8.0')
1100	COMPILER_BROKEN:=1
1101	endif
1102
1103	check_same_GCC_VERSION:
1104	$(ARBHOME)/SOURCE_TOOLS/check_same_compiler_version.pl $(COMPILER_NAME) $(COMPILER_VERSION_ALLOWED)
1105
1106	check_GCC_VERSION:
1107	@echo 'Compiler version check:'
1108	# see .@ALLOWED_gcc_VERSIONS
1109	ifeq ('$(COMPILER_VERSION_ALLOWED)', '')
1110	@echo " - Your compiler is '$(COMPILER_NAME)' version '$(COMPILER_VERSION)'"
1111	@echo ' This version is not in the list of supported $(COMPILER_NAME)-versions:'
1112	@$(foreach version,$(ALLOWED_COMPILER_VERSIONS),echo ' * $(version)';)
1113	@echo ' - You may either ..'
1114	@echo ' - add your version to ALLOWED_$(COMPILER_NAME)_VERSIONS in the Makefile and try it out or'
1115	@echo ' - switch to one of the allowed versions (see arb_README_gcc.txt for installing'
1116	@echo ' a different version of gcc)'
1117	$(error Unsupported compiler '$(COMPILER_NAME)' version '$(COMPILER_VERSION)')
1118	else
1119	ifeq ($(COMPILER_BROKEN),1)
1120	$(error compilation refused for $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)'. Refer to http://bugs.arb-home.de/wiki/GccVersionInfo for details.)
1121	else
1122	@echo " - Supported $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)' detected - fine!"
1123	@echo ''
1124	ifeq ($(USE_CLANG),1)
1125	@echo "Dump clang version:"
1126	$(A_CXX) -v
1127	endif
1128	$(MAKE) check_same_GCC_VERSION
1129	endif
1130	endif
1131
1132	#---------------------- check ARBHOME
1133
1134	# use arb_INSTALL.txt to determine whether ARBHOME points to correct directory
1135	ARB_INSTALL_FOUND=$(wildcard $(ARBHOME)/arb_INSTALL.txt)
1136
1137	check_ARBHOME:
1138	ifeq ($(strip $(ARB_INSTALL_FOUND)),)
1139	@echo ------------------------------------------------------------
1140	@echo "ARBHOME is set to '$(ARBHOME)'"
1141	@echo "The environment variable ARBHOME has to point to the top arb source directory."
1142	@echo "If you use bash enter:"
1143	@echo " export ARBHOME='`pwd`'"
1144	@echo ------------------------------------------------------------
1145	@false
1146	endif
1147
1148	ARB_PATH_SET=$(findstring $(ARBHOME)/bin,$(PATH))
1149
1150	check_PATH: check_ARBHOME
1151	ifeq ($(strip $(ARB_PATH_SET)),)
1152	@echo ------------------------------------------------------------
1153	@echo "The environment variable PATH has to contain $(ARBHOME)/bin"
1154	@echo "If you use bash enter:"
1155	@echo ' export PATH=$$ARBHOME/bin:$$PATH'
1156	@echo ------------------------------------------------------------
1157	@false
1158	endif
1159
1160	check_TOOLS:
1161	@util/arb_check_build_env.pl \
1162	"$(A_CC)" \
1163	"$(A_CXX)" \
1164	"$(MAKEDEPEND_PLAIN)" \
1165	"$(LINK_SHARED_LIB)" \
1166	"$(LINK_SHARED_LIB)" \
1167
1168	check_ENVIRONMENT : check_PATH check_TOOLS
1169	@echo "-------------------- Environment [start]"
1170	@echo "ARBHOME='$(ARBHOME)'"
1171	@echo "PATH='$(PATH)'"
1172	@echo "LD_LIBRARY_PATH='$(LD_LIBRARY_PATH)'"
1173	@echo "-------------------- Environment [end]"
1174
1175	check_tabs: check_setup
1176	ifeq ($(DEBUG),1)
1177	@SOURCE_TOOLS/tabBrake.pl
1178	endif
1179
1180	force_tab_check:
1181	@touch -t 198001010000 SOURCE_TOOLS/stamp.tabBrake
1182	@$(MAKE) check_tabs
1183
1184
1185	# ---------------------
1186
1187	check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION
1188	@echo Your setup seems to be ok.
1189
1190	checks: check_setup check_tabs
1191	@rm -f SOURCE_TOOLS/postcompile.sav
1192
1193
1194	# end test section ------------------------------
1195
1196	# ---------------------------------------
1197	# List of standard top level directories
1198	#
1199	# sub-makefiles have to define the targets
1200	# - 'depends' and
1201	# - 'clean'
1202	#
1203	# when adding new libs here, also add a dependency vs 'links' or 'links_non_perl' in .@DD_links_non_perl
1204
1205	ARCHS = \
1206	AISC/AISC.a \
1207	AISC_MKPTPS/AISC_MKPTPS.a \
1208	ARBDB/libARBDB.a \
1209	CORE/libCORE.a \
1210	ARB_GDE/ARB_GDE.a \
1211	AWT/libAWT.a \
1212	AWTC/AWTC.a \
1213	AWTI/AWTI.a \
1214	CONSENSUS_TREE/CONSENSUS_TREE.a \
1215	CONVERTALN/CONVERTALN.a \
1216	DBSERVER/DBSERVER.a \
1217	DIST/DIST.a \
1218	EDIT4/EDIT4.a \
1219	EISPACK/EISPACK.a \
1220	GDE/GDE.a \
1221	GENOM/GENOM.a \
1222	GENOM_IMPORT/GENOM_IMPORT.a \
1223	GL/GL.a \
1224	ISLAND_HOPPING/ISLAND_HOPPING.a \
1225	MERGE/MERGE.a \
1226	MULTI_PROBE/MULTI_PROBE.a \
1227	NALIGNER/NALIGNER.a \
1228	NAMES/NAMES.a \
1229	NAMES_COM/server.a \
1230	NTREE/NTREE.a \
1231	PARSIMONY/PARSIMONY.a \
1232	PERLTOOLS/PERLTOOLS.a \
1233	PHYLO/PHYLO.a \
1234	PRIMER_DESIGN/PRIMER_DESIGN.a \
1235	PROBE/PROBE.a \
1236	PROBE_COM/server.a \
1237	PROBE_DESIGN/PROBE_DESIGN.a \
1238	PROBE_SET/PROBE_SET.a \
1239	READSEQ/READSEQ.a \
1240	RNA3D/RNA3D.a \
1241	RNACMA/RNACMA.a \
1242	SECEDIT/SECEDIT.a \
1243	SEQ_QUALITY/SEQ_QUALITY.a \
1244	SERVERCNTRL/SERVERCNTRL.a \
1245	SL/SL.a \
1246	STAT/STAT.a \
1247	TOOLS/TOOLS.a \
1248	TREEGEN/TREEGEN.a \
1249	UNIT_TESTER/UNIT_TESTER.a \
1250	WETC/WETC.a \
1251	WINDOW/libWINDOW.a \
1252	XML/XML.a \
1253
1254	# -----------------------
1255	# library packets
1256
1257	ARCHS_CLIENT_PROBE = PROBE_COM/client.a
1258	ARCHS_CLIENT_NAMES = NAMES_COM/client.a
1259
1260	ARCHS_MAKEBIN = AISC_MKPTPS/AISC_MKPTPS.a AISC/AISC.a
1261
1262	# communication libs need aisc and aisc_mkpts:
1263
1264	AISC/AISC.dummy: proto_tools
1265
1266	comtools: AISC/AISC.dummy
1267
1268	ARCHS_SEQUENCE = \
1269	SL/SEQUENCE/SEQUENCE.a \
1270	SL/ALIVIEW/ALIVIEW.a \
1271	SL/PRONUC/PRONUC.a \
1272
1273	ARCHS_TREE = \
1274	SL/ARB_TREE/ARB_TREE.a \
1275	SL/FILTER/FILTER.a \
1276	$(ARCHS_SEQUENCE) \
1277
1278	# parsimony tree (used by NTREE, PARSIMONY, STAT(->EDIT4), DIST(obsolete!))
1279	ARCHS_AP_TREE = \
1280	SL/AP_TREE/AP_TREE.a \
1281	$(ARCHS_TREE) \
1282
1283	# --------------------------------------------------------------------------------
1284	# dependencies for linking shared libs
1285
1286	link_core: core
1287	link_db: db link_core
1288	link_aw: aw link_db
1289	link_awt: awt link_aw
1290
1291	#***************************************************************************************
1292	# Individual_Programs_Section
1293	#***************************************************************************************
1294
1295	arbmainwrapper:
1296	$(MAKE) -C SOURCE_TOOLS -r mainwrapper
1297
1298
1299	#********************************* arb_ntree ************************************
1300	NTREE = bin/arb_ntree
1301	ARCHS_NTREE = \
1302	NTREE/NTREE.a \
1303	ARB_GDE/ARB_GDE.a \
1304	SL/GROUP_SEARCH/GROUP_SEARCH.a \
1305	SL/DB_UI/DB_UI.a \
1306	AWTC/AWTC.a \
1307	AWTI/AWTI.a \
1308	CONSENSUS_TREE/CONSENSUS_TREE.a \
1309	GENOM_IMPORT/GENOM_IMPORT.a \
1310	GENOM/GENOM.a \
1311	MERGE/MERGE.a \
1312	MULTI_PROBE/MULTI_PROBE.a \
1313	PRIMER_DESIGN/PRIMER_DESIGN.a \
1314	PROBE_DESIGN/PROBE_DESIGN.a \
1315	SEQ_QUALITY/SEQ_QUALITY.a \
1316	SERVERCNTRL/SERVERCNTRL.a \
1317	SL/ALILINK/ALILINK.a \
1318	SL/AW_NAME/AW_NAME.a \
1319	SL/CONSENSUS/CONSENSUS.a \
1320	SL/DB_SCANNER/DB_SCANNER.a \
1321	SL/DB_QUERY/DB_QUERY.a \
1322	SL/QUERY/QUERY.a \
1323	SL/SEQIO/SEQIO.a \
1324	STAT/STAT.a \
1325	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1326	SL/HELIX/HELIX.a \
1327	SL/REGEXPR/REGEXPR.a \
1328	SL/REFENTRIES/REFENTRIES.a \
1329	SL/NDS/NDS.a \
1330	SL/ITEM_SHADER/ITEM_SHADER.a \
1331	SL/ITEMS/ITEMS.a \
1332	SL/INSDEL/INSDEL.a \
1333	SL/LOCATION/LOCATION.a \
1334	SL/MACROS/MACROS.a \
1335	SL/PVP/PVP.a \
1336	SL/TRANSLATE/TRANSLATE.a \
1337	SL/TREEDISP/TREEDISP.a \
1338	SL/TREE_ADMIN/TREE_ADMIN.a \
1339	SL/TREE_READ/TREE_READ.a \
1340	SL/TREE_WRITE/TREE_WRITE.a \
1341	SL/XFERGUI/XFERGUI.a \
1342	SL/XFERSET/XFERSET.a \
1343	XML/XML.a \
1344	$(ARCHS_AP_TREE) \
1345
1346	ARCHS_NTREE_ALL = $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(XMLLIBS)
1347
1348	$(NTREE): $(ARCHS_NTREE:.a=.dummy) link_awt
1349	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NTREE_ALL) \|\| ( \
1350	echo "$(SEP) Link $@"; \
1351	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE_ALL)" ; \
1352	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE_ALL) && \
1353	echo "$(SEP) Link $@ [done]"; \
1354	)
1355
1356	#********************************* arb_edit4 ************************************
1357	EDIT4 = bin/arb_edit4
1358
1359	ARCHS_EDIT4 := \
1360	EDIT4/EDIT4.a \
1361	ARB_GDE/ARB_GDE.a \
1362	SL/FAST_ALIGNER/FAST_ALIGNER.a \
1363	AWTC/AWTC.a \
1364	ISLAND_HOPPING/ISLAND_HOPPING.a \
1365	SECEDIT/SECEDIT.a \
1366	SERVERCNTRL/SERVERCNTRL.a \
1367	SL/AW_HELIX/AW_HELIX.a \
1368	SL/AW_NAME/AW_NAME.a \
1369	SL/CONSENSUS/CONSENSUS.a \
1370	SL/ITEMS/ITEMS.a \
1371	STAT/STAT.a \
1372	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1373	SL/HELIX/HELIX.a \
1374	SL/TRANSLATE/TRANSLATE.a \
1375	SL/MACROS/MACROS.a \
1376	SL/NDS/NDS.a \
1377	$(ARCHS_AP_TREE) \
1378	XML/XML.a \
1379
1380	ifeq ($(OPENGL),1)
1381	ARCHS_EDIT4 += RNA3D/RNA3D.a
1382	endif
1383
1384	ARCHS_EDIT4_ALL = $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4)
1385
1386	LIBS_EDIT4 := $(GL_LIBS)
1387
1388	$(EDIT4): $(ARCHS_EDIT4:.a=.dummy) link_awt
1389	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_EDIT4_ALL) \|\| ( \
1390	echo "$(SEP) Link $@"; \
1391	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4_ALL)" ; \
1392	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4_ALL) && \
1393	echo "$(SEP) Link $@ [done]"; \
1394	)
1395
1396	#********************************* arb_rnacma ************************************
1397	RNACMA = bin/arb_rnacma
1398	ARCHS_RNACMA = \
1399	RNACMA/RNACMA.a \
1400
1401	ARCHS_RNACMA_ALL = $(ARCHS_RNACMA) $(DBSYS_LIBS)
1402
1403	$(RNACMA) : $(ARCHS_RNACMA:.a=.dummy) link_db
1404	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_RNACMA_ALL) \|\| ( \
1405	echo "$(SEP) Link $@"; \
1406	echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_RNACMA_ALL)"; \
1407	$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_RNACMA_ALL) && \
1408	echo "$(SEP) Link $@ [done]"; \
1409	)
1410
1411	#********************************* arb_wetc ************************************
1412	WETC = bin/arb_wetc
1413	ARCHS_WETC = \
1414	WETC/WETC.a \
1415	SL/HELIX/HELIX.a \
1416	SL/FILTER/FILTER.a \
1417	XML/XML.a \
1418
1419	ARCHS_WETC_ALL = $(ARCHS_WETC) $(GUI_LIBS)
1420
1421	$(WETC): $(ARCHS_WETC:.a=.dummy) link_awt
1422	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_WETC_ALL) \|\| ( \
1423	echo "$(SEP) Link $@"; \
1424	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC_ALL)" ; \
1425	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC_ALL) && \
1426	echo "$(SEP) Link $@ [done]"; \
1427	)
1428
1429	#********************************* arb_dist ************************************
1430	DIST = bin/arb_dist
1431	ARCHS_DIST = \
1432	DIST/DIST.a \
1433	CONSENSUS_TREE/CONSENSUS_TREE.a \
1434	EISPACK/EISPACK.a \
1435	SERVERCNTRL/SERVERCNTRL.a \
1436	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1437	SL/HELIX/HELIX.a \
1438	SL/MATRIX/MATRIX.a \
1439	SL/MACROS/MACROS.a \
1440	SL/NDS/NDS.a \
1441	SL/ITEMS/ITEMS.a \
1442	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.a \
1443	XML/XML.a \
1444	$(ARCHS_AP_TREE) \
1445
1446	ARCHS_DIST_ALL = $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS)
1447
1448	$(DIST): $(ARCHS_DIST:.a=.dummy) link_awt
1449	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_DIST_ALL) \|\| ( \
1450	echo "$(SEP) Link $@"; \
1451	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST_ALL)" ; \
1452	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST_ALL) && \
1453	echo "$(SEP) Link $@ [done]"; \
1454	)
1455
1456	#********************************* arb_pars ************************************
1457	PARSIMONY = bin/arb_pars
1458	ARCHS_PARSIMONY = \
1459	PARSIMONY/PARSIMONY.a \
1460	SERVERCNTRL/SERVERCNTRL.a \
1461	SL/AW_NAME/AW_NAME.a \
1462	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1463	SL/HELIX/HELIX.a \
1464	SL/MACROS/MACROS.a \
1465	SL/NDS/NDS.a \
1466	SL/ITEMS/ITEMS.a \
1467	SL/TRANSLATE/TRANSLATE.a \
1468	SL/TREEDISP/TREEDISP.a \
1469	XML/XML.a \
1470	$(ARCHS_AP_TREE) \
1471
1472	ARCHS_PARSIMONY_ALL = $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS)
1473
1474	$(PARSIMONY): $(ARCHS_PARSIMONY:.a=.dummy) link_awt
1475	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_PARSIMONY_ALL) \|\| ( \
1476	echo "$(SEP) Link $@"; \
1477	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY_ALL)" ; \
1478	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY_ALL) && \
1479	echo "$(SEP) Link $@ [done]"; \
1480	)
1481
1482	#********************************* arb_convert_aln ************************************
1483	CONVERT_ALN = bin/arb_convert_aln
1484	ARCHS_CONVERT_ALN = \
1485	CONVERTALN/CONVERTALN.a \
1486
1487	ARCHS_CONVERT_ALN_ALL = $(ARCHS_CONVERT_ALN) $(DBSYS_LIBS)
1488
1489	$(CONVERT_ALN) : $(ARCHS_CONVERT_ALN:.a=.dummy) link_db
1490	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_CONVERT_ALN_ALL) \|\| ( \
1491	echo "$(SEP) Link $@"; \
1492	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN_ALL)"; \
1493	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN_ALL) && \
1494	echo "$(SEP) Link $@ [done]"; \
1495	)
1496
1497	#********************************* arb_treegen ************************************
1498
1499	TREEGEN = bin/arb_treegen
1500	ARCHS_TREEGEN = \
1501	TREEGEN/TREEGEN.a \
1502
1503	ARCHS_TREEGEN_ALL = $(ARCHS_TREEGEN)
1504
1505	$(TREEGEN) : $(ARCHS_TREEGEN:.a=.dummy)
1506	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main_C) $(ARCHS_TREEGEN_ALL) \|\| ( \
1507	echo "$(SEP) Link $@"; \
1508	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN_ALL)" ; \
1509	$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN_ALL) && \
1510	echo "$(SEP) Link $@ [done]"; \
1511	)
1512
1513	#********************************* arb_naligner ************************************
1514	NALIGNER = bin/arb_naligner
1515	ARCHS_NALIGNER = \
1516	NALIGNER/NALIGNER.a \
1517	SERVERCNTRL/SERVERCNTRL.a \
1518	SL/HELIX/HELIX.a \
1519
1520	ARCHS_NALIGNER_ALL = $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(DBSYS_LIBS)
1521
1522	$(NALIGNER): $(ARCHS_NALIGNER:.a=.dummy) link_db
1523	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NALIGNER_ALL) \|\| ( \
1524	echo "$(SEP) Link $@"; \
1525	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER_ALL)" ; \
1526	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER_ALL) && \
1527	echo "$(SEP) Link $@ [done]"; \
1528	)
1529
1530	#********************************* arb_phylo ************************************
1531	PHYLO = bin/arb_phylo
1532	ARCHS_PHYLO = \
1533	PHYLO/PHYLO.a \
1534	SL/HELIX/HELIX.a \
1535	SL/FILTER/FILTER.a \
1536	SL/MACROS/MACROS.a \
1537	XML/XML.a \
1538
1539	ARCHS_PHYLO_ALL = $(ARCHS_PHYLO) $(GUI_LIBS)
1540
1541	$(PHYLO): $(ARCHS_PHYLO:.a=.dummy) link_awt
1542	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_PHYLO_ALL) \|\| ( \
1543	echo "$(SEP) Link $@"; \
1544	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO_ALL)" ; \
1545	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO_ALL) && \
1546	echo "$(SEP) Link $@ [done]"; \
1547	)
1548
1549	#***************************************************************************************
1550	# SERVER SECTION
1551	#***************************************************************************************
1552
1553	#********************************* arb_db_server ************************************
1554	DBSERVER = bin/arb_db_server
1555	ARCHS_DBSERVER = \
1556	DBSERVER/DBSERVER.a \
1557	SERVERCNTRL/SERVERCNTRL.a \
1558
1559	ARCHS_DBSERVER_ALL = $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS)
1560
1561	$(DBSERVER): $(ARCHS_DBSERVER:.a=.dummy) link_db
1562	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_DBSERVER_ALL) \|\| ( \
1563	echo "$(SEP) Link $@"; \
1564	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER_ALL)" ; \
1565	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER_ALL) && \
1566	echo "$(SEP) Link $@ [done]"; \
1567	)
1568
1569	#********************************* arb_pt_server ************************************
1570	PROBE = bin/arb_pt_server
1571
1572	ARCHS_PROBE_DEPEND = \
1573	PROBE/PROBE.a \
1574	SL/PTCLEAN/PTCLEAN.a \
1575	SERVERCNTRL/SERVERCNTRL.a \
1576	SL/HELIX/HELIX.a \
1577
1578	ARCHS_PROBE_ALL = $(ARCHS_PROBE_DEPEND) $(ARCHS_CLIENT_PROBE) $(ARBDB_LIB) $(SYSLIBS)
1579
1580	$(PROBE): $(ARCHS_PROBE_DEPEND:.a=.dummy) link_db
1581	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) config.makefile $(ARCHS_PROBE_ALL) \|\| ( \
1582	echo "$(SEP) Link $@"; \
1583	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_ALL)" ; \
1584	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_ALL) && \
1585	echo "$(SEP) Link $@ [done]"; \
1586	)
1587
1588	#********************************* arb_name_server ************************************
1589	NAMES = bin/arb_name_server
1590	ARCHS_NAMES = \
1591	NAMES/NAMES.a \
1592	SERVERCNTRL/SERVERCNTRL.a \
1593
1594	ARCHS_NAMES_ALL = $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS)
1595
1596	$(NAMES): $(ARCHS_NAMES:.a=.dummy) link_db
1597	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NAMES_ALL) \|\| ( \
1598	echo "$(SEP) Link $@"; \
1599	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES_ALL)" ; \
1600	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES_ALL) && \
1601	echo "$(SEP) Link $@ [done]"; \
1602	)
1603
1604	#********************************* SHARED LIBRARIES SECTION ************************************
1605
1606	prepare_libdir: addlibs
1607
1608	addlibs:
1609	(perl $(ARBHOME)/SOURCE_TOOLS/provide_libs.pl \
1610	"arbhome=$(ARBHOME)" \
1611	"opengl=$(OPENGL)" \
1612	"link_static=$(LINK_STATIC)" \
1613	)
1614
1615	#***************************************************************************************
1616	# Recursive calls to sub-makefiles
1617	#***************************************************************************************
1618
1619	%.depends:
1620	@cp -p $(@D)/Makefile $(@D)/Makefile.old # save old Makefile
1621	@$(MAKE) -C $(@D) -r \
1622	"AUTODEPENDS=1" \
1623	"MAIN=nothing" \
1624	"cflags=noCflagsHere_use_MAKEDEPENDFLAGS" \
1625	"cxxflags=noCxxflagsHere_use_MAKEDEPENDFLAGS" \
1626	depends
1627	@grep "^# DO NOT DELETE" $(@D)/Makefile >/dev/null
1628	@cat $(@D)/Makefile \
1629	\| SOURCE_TOOLS/fix_depends.pl "(from main)" \
1630	>$(@D)/Makefile.2
1631	@mv $(@D)/Makefile.old $(@D)/Makefile # restore old Makefile
1632	@$(ARBHOME)/SOURCE_TOOLS/mv_if_diff $(@D)/Makefile.2 $(@D)/Makefile # update Makefile if changed
1633
1634	%.proto:
1635	@($(MAKE) -C $(@D) \
1636	"AUTODEPENDS=0" \
1637	"MAIN=nothing" \
1638	"cflags=noCflags" \
1639	"cxxflags=noCxxflags" \
1640	proto 2>&1 ) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
1641
1642	%.clean:
1643	@$(MAKE) -C $(@D) \
1644	"AUTODEPENDS=0" \
1645	"MAIN=nothing" \
1646	"cflags=noCflags" \
1647	"cxxflags=noCxxflags" \
1648	clean
1649
1650
1651	# stop wrong targets
1652	target_is_missing_lib_prefix:
1653	@echo "Error: Denied to build shared library target with missing 'lib'-prefix"
1654	false
1655
1656	ARBDB/ARBDB.dummy: target_is_missing_lib_prefix
1657	CORE/CORE.dummy: target_is_missing_lib_prefix
1658	AWT/AWT.dummy: target_is_missing_lib_prefix
1659	WINDOW/WINDOW.dummy: target_is_missing_lib_prefix
1660
1661	# rule to generate main target (normally a library):
1662	# @@@ check effect of setting LANG=C below
1663	%.dummy:
1664	@( export ID=$$$$; LANG=C; \
1665	(( \
1666	echo "$(SEP) Make $(@D)"; \
1667	$(MAKE) -C $(@D) -r \
1668	"AUTODEPENDS=1" \
1669	"MAIN=$(@F:.dummy=.a)" \
1670	"cflags=$(cflags) -DIN_ARB_$(subst /,_,$(@D))" \
1671	&& \
1672	echo "$(SEP) Make $(@D) [done]"; \
1673	) >$(@D).$$ID.log 2>&1 && (cat $(@D).$$ID.log;rm $(@D).$$ID.log)) \|\| (cat $(@D).$$ID.log;rm $(@D).$$ID.log;false))
1674
1675	# Additional dependencies for subtargets:
1676
1677	PROBE_COM/PROBE_COM.dummy : comtools
1678	NAMES_COM/NAMES_COM.dummy : comtools
1679
1680	com: PROBE_COM/PROBE_COM.dummy NAMES_COM/NAMES_COM.dummy
1681
1682	PROBE_COM/server.dummy:
1683	@echo Unwanted request to make target $<
1684	false
1685
1686	PROBE_COM/client.dummy:
1687	@echo Unwanted request to make target $<
1688	false
1689
1690	NAMES_COM/server.dummy:
1691	@echo Unwanted request to make target $<
1692	false
1693
1694	NAMES_COM/client.dummy:
1695	@echo Unwanted request to make target $<
1696	false
1697
1698
1699	ARBDB/libARBDB.dummy: links
1700	CORE/libCORE.dummy: links
1701
1702	PERLTOOLS/PERLTOOLS.dummy: core db
1703
1704	# all subdirs perl not depends on go here (ADD_links_non_perl)
1705	AWT/libAWT.dummy: links_non_perl
1706	AWTI/AWTI.dummy: links_non_perl
1707	CONSENSUS_TREE/CONSENSUS_TREE.dummy: links_non_perl
1708	CONVERTALN/CONVERTALN.dummy: links_non_perl
1709	DBSERVER/DBSERVER.dummy: links_non_perl
1710	DIST/DIST.dummy: links_non_perl
1711	EDIT4/EDIT4.dummy: links_non_perl com
1712	EISPACK/EISPACK.dummy: links_non_perl
1713	GDE/GDE.dummy: links_non_perl
1714	GENOM/GENOM.dummy: links_non_perl
1715	GENOM_IMPORT/GENOM_IMPORT.dummy: links_non_perl
1716	ISLAND_HOPPING/ISLAND_HOPPING.dummy: links_non_perl
1717	MERGE/MERGE.dummy: links_non_perl
1718	NTREE/NTREE.dummy: links_non_perl
1719	PARSIMONY/PARSIMONY.dummy: links_non_perl
1720	PHYLO/PHYLO.dummy: links_non_perl
1721	PRIMER_DESIGN/PRIMER_DESIGN.dummy: links_non_perl
1722	PROBE_SET/PROBE_SET.dummy: links_non_perl link_db
1723	READSEQ/READSEQ.dummy: links_non_perl
1724	RNACMA/RNACMA.dummy: links_non_perl header_libs
1725	SECEDIT/SECEDIT.dummy: links_non_perl
1726	SEQ_QUALITY/SEQ_QUALITY.dummy: links_non_perl
1727	SERVERCNTRL/SERVERCNTRL.dummy: links_non_perl com
1728	SL/ALILINK/ALILINK.dummy: links_non_perl
1729	SL/ALIVIEW/ALIVIEW.dummy: links_non_perl
1730	SL/AP_TREE/AP_TREE.dummy: links_non_perl
1731	SL/ARB_TREE/ARB_TREE.dummy: links_non_perl
1732	SL/AW_HELIX/AW_HELIX.dummy: links_non_perl
1733	SL/CONSENSUS/CONSENSUS.dummy: links_non_perl
1734	SL/DB_QUERY/DB_QUERY.dummy: links_non_perl
1735	SL/DB_SCANNER/DB_SCANNER.dummy: links_non_perl
1736	SL/DB_UI/DB_UI.dummy: links_non_perl
1737	SL/FAST_ALIGNER/FAST_ALIGNER.dummy: links_non_perl
1738	SL/FILTER/FILTER.dummy: links_non_perl
1739	SL/FILTSEQEXP/FILTSEQEXP.dummy: links_non_perl
1740	SL/GROUP_SEARCH/GROUP_SEARCH.dummy: links_non_perl
1741	SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy: links_non_perl
1742	SL/HELIX/HELIX.dummy: links_non_perl
1743	SL/INSDEL/INSDEL.dummy: links_non_perl
1744	SL/ITEM_SHADER/ITEM_SHADER.dummy: links_non_perl
1745	SL/ITEMS/ITEMS.dummy: links_non_perl
1746	SL/LOCATION/LOCATION.dummy: links_non_perl
1747	SL/MACROS/MACROS.dummy: links_non_perl
1748	SL/MATRIX/MATRIX.dummy: links_non_perl
1749	SL/NDS/NDS.dummy: links_non_perl
1750	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.dummy: links_non_perl
1751	SL/PRONUC/PRONUC.dummy: links_non_perl
1752	SL/PTCLEAN/PTCLEAN.dummy: links_non_perl link_db
1753	SL/PVP/PVP.dummy: links_non_perl
1754	SL/QUERY/QUERY.dummy: links_non_perl link_db
1755	SL/REFENTRIES/REFENTRIES.dummy: links_non_perl
1756	SL/REGEXPR/REGEXPR.dummy: links_non_perl
1757	SL/SEQIO/SEQIO.dummy: links_non_perl
1758	SL/SEQUENCE/SEQUENCE.dummy: links_non_perl
1759	SL/TRANSLATE/TRANSLATE.dummy: links_non_perl
1760	SL/TREE_ADMIN/TREE_ADMIN.dummy: links_non_perl
1761	SL/TREE_READ/TREE_READ.dummy: links_non_perl
1762	SL/TREE_WRITE/TREE_WRITE.dummy: links_non_perl
1763	SL/TREEDISP/TREEDISP.dummy: links_non_perl
1764	SL/XFERGUI/XFERGUI.dummy: links_non_perl
1765	SL/XFERSET/XFERSET.dummy: links_non_perl
1766	STAT/STAT.dummy: links_non_perl
1767	TREEGEN/TREEGEN.dummy: links_non_perl
1768	WETC/WETC.dummy: links_non_perl
1769	WINDOW/libWINDOW.dummy: links_non_perl
1770	XML/XML.dummy: links_non_perl
1771
1772	ifeq ($(OPENGL),1)
1773	GL/glAW/glAW.dummy: links_non_perl
1774	GL/glpng/glpng.dummy: links_non_perl
1775	GL/GL.dummy: GL/glAW/glAW.dummy GL/glpng/glpng.dummy
1776	RNA3D/RNA3D.dummy: links_non_perl gl
1777	endif
1778
1779	UNIT_TESTER/UNIT_TESTER.dummy: link_db \
1780	SERVERCNTRL/SERVERCNTRL.dummy \
1781
1782	# see also TOOLS/Makefile@TOOLSLIBDEPENDS
1783	TOOLS/TOOLS.dummy : links_non_perl link_db \
1784	CONSENSUS_TREE/CONSENSUS_TREE.dummy \
1785	SERVERCNTRL/SERVERCNTRL.dummy \
1786	SL/FILTER/FILTER.dummy \
1787	SL/FILTSEQEXP/FILTSEQEXP.dummy \
1788	SL/INSDEL/INSDEL.dummy \
1789	SL/REGEXPR/REGEXPR.dummy \
1790	SL/SEQIO/SEQIO.dummy \
1791	SL/TREE_READ/TREE_READ.dummy \
1792	SL/TREE_WRITE/TREE_WRITE.dummy \
1793	XML/XML.dummy \
1794
1795	AWTC/AWTC.dummy : com
1796
1797	NAMES/NAMES.dummy : com
1798	SL/AW_NAME/AW_NAME.dummy : com
1799
1800	PROBE/PROBE.dummy : com
1801	ptpan/PROBE.dummy : com
1802	MULTI_PROBE/MULTI_PROBE.dummy : com
1803	PROBE_DESIGN/PROBE_DESIGN.dummy : com
1804	NALIGNER/NALIGNER.dummy : com
1805
1806	ARB_GDE/ARB_GDE.dummy : proto_tools
1807
1808	compile_compatibility: SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.dummy
1809
1810	#***************************************************************************************
1811	# Short aliases to make targets
1812	#***************************************************************************************
1813
1814	show:
1815	@echo $(SEP)
1816	@echo 'Aliases for often needed targets:'
1817	@echo ''
1818	@echo ' executables:'
1819	@echo ''
1820	@echo ' nt arb_ntree'
1821	@echo ' e4 arb_edit4 (includes secedit)'
1822	@echo ' di arb_dist'
1823	@echo ' ph arb_phylo'
1824	@echo ' pa arb_parsimony'
1825	@echo ' tg arb_treegen'
1826	@echo ' ds arb_dbserver'
1827	@echo ' pt arb_pt_server'
1828	@echo ' na arb_name_server'
1829	@echo ''
1830	@echo ' libraries:'
1831	@echo ''
1832	@echo ' com communication libraries'
1833	@echo ' db ARB database'
1834	@echo ' aw GUI lib'
1835	@echo ' awt GUI toolkit'
1836	@echo ' awtc general purpose library'
1837	@echo ' awti import/export library'
1838	@echo ' mp multi probe library'
1839	@echo ' ge genome library'
1840	@echo ' pd probe design lib'
1841	@echo ' prd primer design lib'
1842	@echo ''
1843	@echo ' other targets:'
1844	@echo ''
1845	@echo ' help recompile help files'
1846	@echo ' tools make small tools used by arb'
1847	@echo ''
1848	@echo ' foreign targets:'
1849	@echo ''
1850	@echo ' gde GDE'
1851	@echo ' agde ARB_GDE'
1852	@echo ''
1853	@echo 'for other targets inspect $(ARBHOME)/Makefile'
1854	@echo ''
1855	@echo $(SEP)
1856
1857	source_doc:
1858	@echo "Remove some links (doxygen crashes otherwise):"
1859	find . $ -name "AISC" -o -name "C" -o -name "GDEHELP" $ -type l -exec rm {} \;
1860	doxygen 2>&1 1>/dev/null
1861	$(MAKE) forcelinks
1862
1863	dep_graph:
1864	@echo "Building some dependency graphs"
1865	SOURCE_TOOLS/dependency_graphs.pl
1866
1867	help: HELP_SOURCE/HELP_SOURCE.dummy
1868
1869	HELP_SOURCE/HELP_SOURCE.dummy: link_core xml menus
1870
1871	db: ARBDB/libARBDB.dummy
1872	core: CORE/libCORE.dummy
1873	aw: WINDOW/libWINDOW.dummy
1874	awt: AWT/libAWT.dummy
1875	awtc: AWTC/AWTC.dummy
1876	awti: AWTI/AWTI.dummy
1877
1878	mp: MULTI_PROBE/MULTI_PROBE.dummy
1879	mg: MERGE/MERGE.dummy
1880	ge: GENOM/GENOM.dummy
1881	prd: PRIMER_DESIGN/PRIMER_DESIGN.dummy
1882
1883	nt: menus $(NTREE)
1884
1885	nal: $(NALIGNER)
1886
1887	di: $(DIST)
1888	ph: $(PHYLO)
1889	pa: $(PARSIMONY)
1890	tg: $(TREEGEN)
1891
1892	ifeq ($(OPENGL),1)
1893	3d: RNA3D/RNA3D.dummy
1894	gl: GL/GL.dummy
1895	else
1896	noopengl:
1897	@echo "invalid target for OPENGL=0"
1898	3d: noopengl
1899	gl: noopengl
1900	endif
1901
1902	SL/SL.dummy: com
1903
1904	ds: $(DBSERVER)
1905	pt: $(PROBE)
1906	pst: PROBE_SET/PROBE_SET.dummy
1907	pd: PROBE_DESIGN/PROBE_DESIGN.dummy
1908	na: $(NAMES)
1909	sq: SEQ_QUALITY/SEQ_QUALITY.dummy
1910	cma: $(RNACMA)
1911
1912	sec: SECEDIT/SECEDIT.dummy
1913
1914	e4: $(EDIT4) readseq menus
1915
1916	gi: GENOM_IMPORT/GENOM_IMPORT.dummy
1917	wetc: $(WETC)
1918
1919	xml: XML/XML.dummy
1920	xmlin: XML_IMPORT/XML_IMPORT.dummy# broken
1921	stat: STAT/STAT.dummy $(NTREE) $(EDIT4)
1922	fa: SL/FAST_ALIGNER/FAST_ALIGNER.dummy
1923
1924	#********************************************************************************
1925
1926	up_by_remake: depends proto vectorize_checks
1927
1928	up: up_by_remake tags valgrind_update
1929
1930	#********************************************************************************
1931
1932	touch:
1933	SOURCE_TOOLS/touch_modified.pl
1934
1935	modified: touch
1936	$(MAKE) all
1937
1938	#********************************************************************************
1939
1940	libdepends:
1941	$(MAKE) -C "SOURCE_TOOLS" \
1942	"RNA3D_LIB=$(RNA3D_LIB_4_DEPENDS)" \
1943	libdepends
1944
1945	#********************************************************************************
1946
1947	# create generated headers:
1948	genheaders: TEMPLATES/TEMPLATES.dummy
1949
1950	clrdotdepends:
1951	rm PROBE_COM/.depends \|\| true
1952	rm NAMES_COM/.depends \|\| true
1953	rm PERL2ARB/.depends \|\| true
1954
1955	comdepends: comtools clrdotdepends
1956	@echo "$(SEP) Partially build com interface"
1957	$(MAKE) PROBE_COM/PROBE_COM.depends NAMES_COM/NAMES_COM.depends
1958	$(MAKE) PROBE_COM/server.depends NAMES_COM/server.depends
1959
1960	depends: genheaders comdepends vectorize_checks
1961	@echo "$(SEP) Updating other dependencies"
1962	$(MAKE) $(subst NAMES_COM/server.depends,,$(subst PROBE_COM/server.depends,,$(ARCHS:.a=.depends))) \
1963	HELP_SOURCE/HELP_SOURCE.depends \
1964	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.depends \
1965
1966	$(MAKE) libdepends
1967
1968	depend: depends
1969
1970	# ------------------------------------------------------------
1971	# dependency generation tests for AISC code
1972	#(all should work w/o creating wrong dependencies;
1973	# neither in XXX_COM/Makefile nor in code using AISC interface)
1974	dependstest1: silent_clean
1975	$(MAKE) depends
1976	dependstest2: silent_clean
1977	$(MAKE) com
1978	dependstest3: silent_clean
1979	$(MAKE) aw
1980	dependstest4: silent_clean
1981	$(MAKE) pt
1982	dependstest5: silent_clean
1983	$(MAKE) na
1984	dependstest6: silent_clean
1985	$(MAKE) nt
1986	dependstest7: silent_clean
1987	$(MAKE) all
1988	# ------------------------------------------------------------
1989
1990	vectorize_checks:
1991	$(MAKE) -C SOURCE_TOOLS -r vectorize_checks
1992
1993	clean_checked_vect: lib/lib.clean
1994	SOURCE_TOOLS/clean_checked_vectorizations.sh
1995
1996	# ------------------------------------------------------------
1997
1998	AISC_MKPTPS/AISC_MKPTPS.dummy: links
1999
2000	proto_tools: AISC_MKPTPS/AISC_MKPTPS.dummy
2001
2002	proto: proto_tools
2003	@echo $(SEP) Updating prototypes
2004	$(MAKE) \
2005	ARBDB/ARBDB.proto \
2006	AISC_COM/AISC_COM.proto \
2007	ARB_GDE/ARB_GDE.proto \
2008	CORE/CORE.proto \
2009	CONVERTALN/CONVERTALN.proto \
2010	NTREE/NTREE.proto \
2011	MERGE/MERGE.proto \
2012	PROBE/PROBE.proto \
2013	SERVERCNTRL/SERVERCNTRL.proto \
2014	SL/SL.proto \
2015
2016	#********************************************************************************
2017
2018	valgrind_update: links
2019	@echo $(SEP) Updating for valgrind
2020	$(MAKE) -C SOURCE_TOOLS valgrind_update
2021
2022	#********************************************************************************
2023
2024	TAGFILE=TAGS
2025	UTAGS=TAGS.$(ARBBID)
2026	TAGFILE_TMP=$(UTAGS).tmp
2027
2028	TAG_SOURCE_HEADERS=$(UTAGS).headers.tmp
2029	TAG_SOURCE_CODE=$(UTAGS).codefiles.tmp
2030	TAG_SOURCE_LISTS=$(TAG_SOURCE_HEADERS) $(TAG_SOURCE_CODE)
2031
2032	ETAGS_IGNORE_LIST=SOURCE_TOOLS/etags_ignore.lst
2033
2034	ETAGS=ctags -e -I @$(ETAGS_IGNORE_LIST) --sort=no --if0=no --extra=q
2035	ETAGS_TYPES=--C-kinds=cgnsut --C++-kinds=cgnsut
2036	ETAGS_FUN =--C-kinds=fm --C++-kinds=fm
2037	ETAGS_REST =--C-kinds=dev --C++-kinds=dev
2038
2039	FILTER_TAGS_SOURCES= \
2040	$(SED) -e 's/^.\///g' \| \
2041	grep -vi '^HEADERLIBS\\|^GDE/\\|/GEN[CH]/'
2042
2043	$(TAG_SOURCE_HEADERS): links
2044	@find . $ -name '.hxx' -o -name ".h" $ -type f \| $(FILTER_TAGS_SOURCES) > $@
2045
2046	$(TAG_SOURCE_CODE): links
2047	@find . $ -name '.cxx' -o -name ".c" $ -type f \| $(FILTER_TAGS_SOURCES) > $@
2048
2049	$(UTAGS).1.tmp: $(TAG_SOURCE_HEADERS)
2050	@$(ETAGS) -f $@ $(ETAGS_TYPES) -L $<
2051	$(UTAGS).2.tmp: $(TAG_SOURCE_HEADERS)
2052	@$(ETAGS) -f $@ $(ETAGS_FUN) -L $<
2053	$(UTAGS).3.tmp: $(TAG_SOURCE_HEADERS)
2054	@$(ETAGS) -f $@ $(ETAGS_REST) -L $<
2055	$(UTAGS).4.tmp: $(TAG_SOURCE_CODE)
2056	@$(ETAGS) -f $@ $(ETAGS_TYPES) -L $<
2057	$(UTAGS).5.tmp: $(TAG_SOURCE_CODE)
2058	@$(ETAGS) -f $@ $(ETAGS_FUN) -L $<
2059	$(UTAGS).6.tmp: $(TAG_SOURCE_CODE)
2060	@$(ETAGS) -f $@ $(ETAGS_REST) -L $<
2061
2062	TAGS_ALL_PARTS=$(UTAGS).1.tmp $(UTAGS).2.tmp $(UTAGS).3.tmp $(UTAGS).4.tmp $(UTAGS).5.tmp $(UTAGS).6.tmp
2063
2064	$(TAGFILE_TMP) : $(TAGS_ALL_PARTS)
2065	@cat $(TAGS_ALL_PARTS) > $@
2066	@rm $(TAGS_ALL_PARTS) $(TAG_SOURCE_LISTS)
2067
2068	cleanOldTags:
2069	@find $(ARBHOME) -name 'TAGS.*.tmp' -ctime +2 -exec rm {} \;
2070
2071	tags: $(TAGFILE_TMP) cleanOldTags
2072	@mv_if_diff $(TAGFILE_TMP) $(TAGFILE)
2073
2074	#********************************************************************************
2075
2076	LINKSTAMP=SOURCE_TOOLS/stamp.generate_all_links
2077
2078	links: checks $(LINKSTAMP) arbmainwrapper
2079	links_no_checks: $(LINKSTAMP) arbmainwrapper
2080
2081	forcelinks:
2082	-rm $(LINKSTAMP)
2083	$(MAKE) links
2084
2085	$(LINKSTAMP): SOURCE_TOOLS/generate_all_links.sh genheaders
2086	+SOURCE_TOOLS/generate_all_links.sh
2087	touch $(LINKSTAMP)
2088
2089	clean_links:
2090	# avoid to delete linked pts, nas or arb_tcp.dat:
2091	find . -path './lib' -prune -o -type l -exec rm {} \;
2092	# removed obsolete file - refuses to disappear due to 'prune' above
2093	@rm -f lib/help/GDEHELP
2094	@rm -f $(LINKSTAMP) lib/inputMasks/format.readme
2095
2096	redo_links: clean_links
2097	$(MAKE) links_no_checks
2098
2099	#********************************************************************************
2100
2101	header_libs:
2102	@(( \
2103	echo "$(SEP) Make HEADERLIBS"; \
2104	$(MAKE) -C HEADERLIBS all && \
2105	echo "$(SEP) Make HEADERLIBS [done]"; \
2106	) > HEADERLIBS.log 2>&1 && (cat HEADERLIBS.log;rm HEADERLIBS.log)) \|\| (cat HEADERLIBS.log;rm HEADERLIBS.log;false)
2107
2108	#********************************************************************************
2109
2110	gde: GDE/GDE.dummy
2111	GDE: gde
2112	agde: ARB_GDE/ARB_GDE.dummy
2113	tools: TOOLS/TOOLS.dummy
2114	convert: $(CONVERT_ALN)
2115	readseq: READSEQ/READSEQ.dummy
2116
2117	#***************************************************************************************
2118	# Some user commands
2119	#***************************************************************************************
2120
2121	menus: binlink links
2122	@(( \
2123	echo "$(SEP) Make GDEHELP"; \
2124	$(MAKE) -C GDEHELP -r all && \
2125	echo "$(SEP) Make GDEHELP [done]"; \
2126	) > GDEHELP.log 2>&1 && (cat GDEHELP.log;rm GDEHELP.log)) \|\| (cat GDEHELP.log;rm GDEHELP.log;false)
2127
2128	ifeq ($(DEBUG),1)
2129	BIN_TARGET=develall
2130	else
2131	BIN_TARGET=all
2132	endif
2133
2134
2135	binlink:
2136	$(MAKE) -C bin $(BIN_TARGET)
2137
2138	check_bin_dep: binlink
2139	SOURCE_TOOLS/check_bin_dependencies.pl
2140
2141	preplib:
2142	(cd lib;$(MAKE) all)
2143
2144	# --------------------------------------------------------------------------------
2145	# This section is quite tricky:
2146	#
2147	# make 'perl' is a BIG target, so when it has to be made, it has to be started
2148	# as early as possible to reduce overall compile time. Since 'make' does not
2149	# provide any priorities, i force it to build all 'perl'-prerequisites early, by
2150	# adding artificial dependencies to these prerequisites
2151	#
2152	# That behavior is likely to be system-dependent.
2153	# My goal was only to make it work on my current development system,
2154	# where this saves about 20% of overall build time.
2155
2156	ifeq ($(WITHPERL),1)
2157	links_non_perl: PERLTOOLS/PERLTOOLS.dummy
2158	perltools: links_non_perl
2159	perl: realperl
2160	else
2161	links_non_perl: links
2162	perl:
2163	$(MAKE) "WITHPERL=1" perl
2164	endif
2165
2166	# ---------------------------------------- perl
2167
2168	realperl: perltools
2169	(( \
2170	echo "$(SEP) Make PERL2ARB" ; \
2171	$(TIME) $(MAKE) -C PERL2ARB -r -f Makefile.main \
2172	"AUTODEPENDS=1" \
2173	"dflags=$(dflags)" \
2174	"cflags4perl=$(cflags) $(cxxflags) $(dflags)" \
2175	"lflags4perl=$(lflags4perl)" \
2176	"COMPILER_VERSION=$(COMPILER_VERSION)" \
2177	all && \
2178	$(MAKE) -C PERL_SCRIPTS/test test && \
2179	echo "$(SEP) Make PERL2ARB [done]" ; \
2180	) > PERL2ARB.log 2>&1 && (cat PERL2ARB.log;rm PERL2ARB.log)) \|\| (cat PERL2ARB.log;rm PERL2ARB.log;false)
2181
2182	perl_clean:
2183	@$(MAKE) -C PERL2ARB -r -f Makefile.main \
2184	"AUTODEPENDS=0" \
2185	clean
2186
2187	PERL2ARB/PERL2ARB.clean:
2188	$(MAKE) perl_clean
2189	$(MAKE) -C PERL_SCRIPTS/test clean
2190
2191	# ---------------------------------------- bindings to script languages
2192
2193	bindings: lib/libCORE.so lib/libARBDB.so
2194	$(MAKE) -C BINDINGS all ARBDEPENDS="$(^:%=../%)" DFLAGS="$(dflags)"
2195
2196	bindings_clean:
2197	$(MAKE) -C BINDINGS clean
2198
2199	# ----------------------------------------
2200
2201	CLOC=cloc-1.08.pl
2202	CLOCFLAGS=--no3 --quiet --progress-rate=0
2203	CLOCARB=--exclude-dir=GDE .
2204	CLOCEXT=GDE
2205	CLOCCODE=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.code.def
2206	CLOCREST=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.rest.def
2207	CLOCFILT=tail --lines=+4
2208
2209	cloc:
2210	@echo 'Arb code:'
2211	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCARB) \| $(CLOCFILT)
2212	@echo 'Arb rest:'
2213	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCARB) \| $(CLOCFILT)
2214	@echo 'External code:'
2215	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCEXT) \| $(CLOCFILT)
2216	@echo 'External rest:'
2217	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCEXT) \| $(CLOCFILT)
2218
2219	# ---------------------------------------- check resources
2220
2221	check_res:
2222	$(ARBHOME)/SOURCE_TOOLS/check_resources.pl
2223
2224	# ---------------------------------------- cleaning
2225
2226	rmbak:
2227	@echo "[cleanup backup/core files]"
2228	@find . \( -name '*%' \
2229	-o -name '*.bak' \
2230	-o -name '*~' \) \
2231	-o $ -name 'core' -a \! -type d $ \
2232	-exec rm -v {} \; \|\| \
2233	echo "Warning: target 'rmbak' reported problems when removing misc. backup files (ignored)"
2234	@echo "[cleanup done]"
2235
2236	bin_reinit:
2237	$(MAKE) bin/bin.clean
2238	$(MAKE) -C "bin" all
2239
2240	clean_directories:
2241	-rm -rf \
2242	$(ARBHOME)/PROBE_SET/bin \
2243	$(ARBHOME)/INCLUDE \
2244
2245	libclean:
2246	-find $(ARBHOME) -type f $ -name '*.a' ! -type l $ -exec rm -f {} \;
2247
2248	objclean:
2249	-find $(ARBHOME) -type f $ -name '*.o' ! -type l $ -exec rm -f {} \;
2250
2251	# bin.clean and HELP_SOURCE.clean interfere
2252	clean3:
2253	$(MAKE) bin/bin.clean
2254	$(MAKE) HELP_SOURCE/HELP_SOURCE.clean
2255
2256
2257	# delete all binaries (similar to 'cleanlinked')
2258	cleanRelinkable: libclean UNIT_TESTER/UNIT_TESTER.clean
2259	$(MAKE) -C bin cleanbinariesRelinkable
2260
2261
2262	clean2: $(ARCHS:.a=.clean) \
2263	clean3 \
2264	rmbak \
2265	libclean \
2266	objclean \
2267	lib/lib.clean \
2268	GDEHELP/GDEHELP.clean \
2269	HEADERLIBS/HEADERLIBS.clean \
2270	SOURCE_TOOLS/SOURCE_TOOLS.clean \
2271	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.clean \
2272	UNIT_TESTER/UNIT_TESTER.clean \
2273	TEMPLATES/TEMPLATES.clean \
2274	perl_clean \
2275	clean_directories \
2276
2277	rm -f .last_gcc .last_compiler config.makefile.bak
2278
2279	# links are needed for cleanup
2280	clean: redo_links motif_xpm_hack_clean
2281	$(MAKE) clean2
2282	$(MAKE) clean_cov_all clean_links
2283
2284	silent_clean:
2285	$(MAKE) clean >/dev/null
2286
2287	# 'relocated' is about 50% faster than 'rebuild'
2288	reloc_clean: links
2289	@echo "---------------------------------------- Relocation cleanup"
2290	$(MAKE) \
2291	perl_clean \
2292	GDEHELP/GDEHELP.clean \
2293	HELP_SOURCE/genhelp/genhelp.clean \
2294	bin/bin.clean \
2295	libclean \
2296	objclean
2297
2298	relocated: links
2299	$(MAKE) reloc_clean
2300	@echo "---------------------------------------- and remake"
2301	$(MAKE) build
2302
2303	# -----------------------------------
2304	# some stress tests
2305	# (helpful to reveal race conditions with -j)
2306
2307	rebuild4ever: rebuild
2308	$(MAKE) rebuild4ever
2309
2310	build4ever: build
2311	$(MAKE) build4ever
2312
2313	clean4ever: clean
2314	$(MAKE) clean4ever
2315
2316	test4ever: ut
2317	$(MAKE) test4ever
2318
2319	perl4ever: clean
2320	$(MAKE) links
2321	$(MAKE) perl
2322	$(MAKE) perl4ever
2323
2324	help4ever: clean
2325	$(MAKE) help
2326	$(MAKE) help4ever
2327
2328	# -----------------------------------
2329
2330	rebuild: clean
2331	$(MAKE) all
2332
2333	cleanlinked: bin/bin.clean libclean
2334
2335	relink: cleanlinked
2336	$(MAKE) all
2337
2338	tarfile: rebuild
2339	$(MAKE) prepare_libdir
2340	util/arb_compress
2341
2342	tarfile_quick: build
2343	$(MAKE) prepare_libdir
2344	util/arb_compress
2345
2346	save: sourcetarfile
2347
2348	patch:
2349	SOURCE_TOOLS/arb_create_patch.sh arbPatch
2350
2351	# test early whether save will work
2352	savetest:
2353	@util/arb_srclst.pl >/dev/null
2354
2355	testsave: savetest
2356
2357	sourcetarfile: rmbak
2358	util/arb_save
2359
2360	save2: rmbak
2361	util/arb_save ignore
2362
2363	save_test: rmbak
2364	@echo "Testing source list.."
2365	@util/arb_srclst.pl > /dev/null
2366
2367	save_test_no_error:
2368	@-$(MAKE) save_test
2369
2370	inc_candi:
2371	touch SOURCE_TOOLS/inc_candi.stamp
2372	$(MAKE) do_version_update
2373
2374	inc_patch:
2375	touch SOURCE_TOOLS/inc_patch.stamp
2376	$(MAKE) do_version_update
2377
2378	inc_minor:
2379	touch SOURCE_TOOLS/inc_minor.stamp
2380	$(MAKE) do_version_update
2381
2382	inc_major:
2383	touch SOURCE_TOOLS/inc_major.stamp
2384	$(MAKE) do_version_update
2385
2386	do_version_update:
2387	@echo Incrementing version information
2388	$(MAKE) savetest
2389	$(MAKE) genheaders # auto upgrades version early
2390
2391	show_version:
2392	$(MAKE) genheaders # updates version info
2393	@echo "$(SEP) ARB version info"
2394	@grep ARB_VERSION TEMPLATES/arb_build.h
2395	@echo "$(SEP)"
2396
2397	release_quick:
2398	-rm arb.tgz arbsrc.tgz
2399	$(MAKE) tarfile_quick
2400	$(MAKE) sourcetarfile
2401
2402	# --------------------------------------------------------------------------------
2403	# special cleanups
2404
2405	clean_opengl_changed: RNA3D/RNA3D.clean EDIT4/EDIT4.clean WINDOW/WINDOW.clean GL/GL.clean
2406
2407	# --------------------------------------------------------------------------------
2408
2409	MAKE_IF_COMMITTED=$(MAKE) -C SOURCE_TOOLS -f Makefile.commitbuild
2410
2411	build_CTARGET:
2412	+$(MAKE_IF_COMMITTED) "CTARGET=$(CTARGET)" build_CTARGET
2413
2414	reset_committed_build:
2415	+$(MAKE_IF_COMMITTED) reset
2416
2417	# --------------------------------------------------------------------------------
2418
2419	arbapplications: nt pa e4 wetc pt na nal di ph ds wetc cma
2420
2421	arb_external: convert tools gde readseq tg pst xmlin
2422
2423	arb_no_perl: arbapplications help arb_external
2424
2425	arb: motif_xpm_hack
2426	$(MAKE) "WITHPERL=1" perl arb_no_perl
2427
2428	motif_xpm_hack:
2429	$(MAKE) -r -C "lib/motifHack" all
2430
2431	motif_xpm_hack_clean:
2432	$(MAKE) -r -C "lib/motifHack" clean
2433
2434	# --------------------------------------------------------------------------------
2435	# special targets for SOURCE_TOOLS/remake_after_change.pl
2436
2437	rac_arb_dist: di
2438	rac_arb_edit4: e4
2439	rac_arb_ntree: nt
2440	rac_arb_pars: pa
2441	rac_arb_phylo: ph
2442	rac_arb_wetc: wetc
2443	rac_arb_naligner: nal
2444	rac_arb_pt_server: pt
2445	rac_arb_db_server: ds
2446	rac_arb_name_server: na
2447	rac_arb_convert_aln: convert
2448	rac_arb_treegen: tg
2449	rac_arb_rnacma: cma
2450	rac_arb_help2xml: help
2451
2452	rac_arb_a2ps: tools
2453	rac_arb_consensus_tree: tools
2454	rac_arb_dnarates: tools
2455	rac_arb_export_rates: tools
2456	rac_arb_export_tree: tools
2457	rac_arb_gene_probe: tools
2458	rac_arb_message: tools
2459	rac_arb_primer: tools
2460	rac_arb_probe: tools
2461	rac_arb_read_tree: tools
2462
2463	# --------------------------------------------------------------------------------
2464	# unit testing
2465	# @@@ work in progress
2466	#
2467	# goal is to automatically test all libraries/executables using TESTED_UNITS_AUTO
2468	#
2469	# currently not all test executables link w/o error
2470	# (see UNITS_WORKING, UNITS_UNTESTABLE_ATM and UNITS_NEED_FIX)
2471
2472	# define RNA3D/RNA3D.test
2473	RNA3D_TEST := $(subst .a,.test,$(RNA3D_LIB))
2474
2475	TESTED_UNITS_AUTO = $(ARCHS:.a=.test)
2476
2477	UNITS_WORKING = \
2478	$(RNA3D_TEST) \
2479	EISPACK/EISPACK.test \
2480	GENOM/GENOM.test \
2481	GL/glAW/libglAW.test \
2482	GL/glpng/libglpng_arb.test \
2483	ISLAND_HOPPING/ISLAND_HOPPING.test \
2484	NALIGNER/NALIGNER.test \
2485	NAMES/NAMES.test \
2486	PHYLO/PHYLO.test \
2487	PRIMER_DESIGN/PRIMER_DESIGN.test \
2488	PROBE_DESIGN/PROBE_DESIGN.test \
2489	SECEDIT/SECEDIT.test \
2490	SEQ_QUALITY/SEQ_QUALITY.test \
2491	SERVERCNTRL/SERVERCNTRL.test \
2492	SL/ALIVIEW/ALIVIEW.test \
2493	SL/AP_TREE/AP_TREE.test \
2494	SL/ARB_TREE/ARB_TREE.test \
2495	SL/AW_HELIX/AW_HELIX.test \
2496	SL/AW_NAME/AW_NAME.test \
2497	SL/DB_SCANNER/DB_SCANNER.test \
2498	SL/GUI_ALIVIEW/GUI_ALIVIEW.test \
2499	SL/HELIX/HELIX.test \
2500	SL/LOCATION/LOCATION.test \
2501	SL/MATRIX/MATRIX.test \
2502	SL/QUERY/QUERY.test \
2503	SL/REFENTRIES/REFENTRIES.test \
2504	SL/SEQUENCE/SEQUENCE.test \
2505	SL/TREE_ADMIN/TREE_ADMIN.test \
2506	SL/TREE_WRITE/TREE_WRITE.test \
2507	STAT/STAT.test \
2508	TREEGEN/TREEGEN.test \
2509	WETC/WETC.test \
2510	XML/XML.test \
2511
2512	# untestable units
2513
2514	UNITS_NEED_FIX = \
2515	ptpan/PROBE.test \
2516
2517	UNITS_UNTESTABLE_ATM = \
2518	XML_IMPORT/XML_IMPORT.test \
2519
2520	# for the moment, put all units containing tests into the following 4 sections (see also TESTED_UNITS below)
2521
2522	# recent development
2523	UNITS_TESTED_FIRST = \
2524	SL/XFERGUI/XFERGUI.test \
2525	SL/XFERSET/XFERSET.test \
2526	SL/TRANSLATE/TRANSLATE.test \
2527	SL/PVP/PVP.test \
2528	AWTI/AWTI.test \
2529	SL/FILTSEQEXP/FILTSEQEXP.test \
2530	SL/GROUP_SEARCH/GROUP_SEARCH.test \
2531
2532	# start units with long duration early
2533	UNITS_RUNNING_LONG = \
2534	ARBDB/libARBDB.test \
2535	AWTC/AWTC.test \
2536	TOOLS/arb_test.test \
2537
2538	# plain test-libaries that are not linked anywhere
2539	TEST_SANDBOXES = \
2540	SL/CB/CB.test \
2541
2542	UNITS_TESTED = \
2543	AISC_MKPTPS/mkptypes.test \
2544	ARB_GDE/ARB_GDE.test \
2545	AWT/libAWT.test \
2546	CONSENSUS_TREE/CONSENSUS_TREE.test \
2547	CONVERTALN/CONVERTALN.test \
2548	CORE/libCORE.test \
2549	DBSERVER/DBSERVER.test \
2550	DIST/DIST.test \
2551	EDIT4/EDIT4.test \
2552	GENOM_IMPORT/GENOM_IMPORT.test \
2553	HELP_SOURCE/arb_help2xml.test \
2554	MERGE/MERGE.test \
2555	MULTI_PROBE/MULTI_PROBE.test \
2556	NTREE/NTREE.test \
2557	PARSIMONY/PARSIMONY.test \
2558	PERLTOOLS/arb_proto_2_xsub.test \
2559	PROBE/PROBE.test \
2560	PROBE_SET/fb_test.test \
2561	SERVERCNTRL/SERVERCNTRL.test \
2562	SL/ALILINK/ALILINK.test \
2563	SL/CONSENSUS/CONSENSUS.test \
2564	SL/DB_QUERY/DB_QUERY.test \
2565	SL/FAST_ALIGNER/FAST_ALIGNER.test \
2566	SL/FILTER/FILTER.test \
2567	SL/INSDEL/INSDEL.test \
2568	SL/ITEM_SHADER/ITEM_SHADER.test \
2569	SL/ITEMS/ITEMS.test \
2570	SL/MACROS/MACROS.test \
2571	SL/NDS/NDS.test \
2572	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.test \
2573	SL/PRONUC/PRONUC.test \
2574	SL/PTCLEAN/PTCLEAN.test \
2575	SL/REGEXPR/REGEXPR.test \
2576	SL/SEQIO/SEQIO.test \
2577	SL/TREE_READ/TREE_READ.test \
2578	SL/TREEDISP/TREEDISP.test \
2579	TOOLS/arb_consensus_tree.test \
2580	TOOLS/arb_probe.test \
2581	WINDOW/libWINDOW.test \
2582
2583	TESTED_UNITS = \
2584	$(UNITS_TESTED_FIRST) \
2585	$(UNITS_RUNNING_LONG) \
2586	$(TEST_SANDBOXES) \
2587	$(UNITS_TESTED) \
2588
2589	# see UNIT_TESTER/sym2testcode.pl@disableErrorOnUnitsWithoutTests
2590
2591	# ----------------------------------------
2592
2593	TEST_LOG_DIR = UNIT_TESTER/logs
2594	TEST_RUN_SUITE=$(MAKE) $(NODIR) -C UNIT_TESTER -f Makefile.suite -r
2595	TEST_MAKE_FLAGS=
2596	TEST_POST_CLEAN=
2597	ifeq ($(COVERAGE),1)
2598	TEST_POST_CLEAN=$(MAKE) clean_cov
2599	TEST_MAKE_FLAGS+=-j1
2600	endif
2601
2602
2603	%.test:
2604	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
2605	( \
2606	echo "fake[1]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
2607	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
2608	"UNITDIR=$(@D)" \
2609	"UNITLIBNAME=$(@F:.test=)" \
2610	"COVERAGE=$(COVERAGE)" \
2611	"ARB_PID=$(ARB_PID)_$(@F)" \
2612	runtest; \
2613	echo "fake[1]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"; \
2614	$(TEST_POST_CLEAN) \
2615	) >$(TEST_LOG_DIR)/$(@F).log 2>&1; \
2616	UNIT_TESTER/log_result.pl $(TEST_LOG_DIR)/$(@F).log )
2617
2618
2619	test_base: $(UNIT_TESTER_LIB:.a=.dummy) $(subst .test,.dummy,$(TEST_SANDBOXES))
2620
2621	clean_cov:
2622	find . $ -name ".gcda" -o -name ".gcov" -o -name "*.cov" $ -exec rm {} \;
2623
2624	clean_cov_all: clean_cov
2625	find . $ -name "*.gcno" $ -exec rm {} \;
2626
2627	cleanup_faked_arbpids:
2628	@rm ~/.arb_tmp/tmp/arb_pids_${USER}_${ARB_PID}_* \|\| true
2629
2630	cleanup_faked_arbpids_and_fail: cleanup_faked_arbpids
2631	@false
2632
2633
2634	run_tests_faked_arbpid:
2635	+@$(TEST_RUN_SUITE) init
2636	@echo "fake[2]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2637	$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(TESTED_UNITS) \|\| $(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	# @@@ instead of only running UNIT, this should as well run all tests this unit depends on? according to 'needs_libs'
2644	# @@@ '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
2645
2646	run_onetest_faked_arbpid:
2647	+@$(TEST_RUN_SUITE) init
2648	@echo "fake[2]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2649	test -n "$(UNIT)" \|\| (echo "Error: UNIT has to be defined for target 'run_onetest_faked_arbpid'!"; false)
2650	$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(UNIT).test \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2651	@echo "fake[2]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2652	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2653	@$(MAKE) clean_cov >/dev/null
2654	@$(MAKE) cleanup_faked_arbpids
2655
2656
2657	run_tests: test_base clean_cov
2658	$(MAKE) "ARB_PID=UT_$$$$" run_tests_faked_arbpid
2659
2660	run_oneunitstests: test_base
2661	$(MAKE) "ARB_PID=UT_$$$$" run_onetest_faked_arbpid
2662
2663
2664	ut:
2665	ifeq ($(UNIT_TESTS),1)
2666	@echo $(MAKE) run_tests
2667	@$(MAKE) run_tests
2668	else
2669	@echo "Not compiled with unit tests"
2670	endif
2671
2672
2673	aut:
2674	+@$(TEST_RUN_SUITE) unskip
2675	$(MAKE) ut
2676
2677	# --------------------------------------------------------------------------------
2678
2679	TIMELOG=$(ARBHOME)/arb_time.log
2680	TIMEARGS=--append --output=$(TIMELOG) --format=" * %E(%S+%U) %P [%C]"
2681	TIMECMD=$(TIME) $(TIMEARGS)
2682
2683	time_one:
2684	ifeq ($(ONE_TIMED_TARGET),)
2685	@echo "Error: You have to pass ONE_TIMED_TARGET to $@"
2686	false
2687	else
2688	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET)"
2689	@$(TIMECMD) $(MAKE) $(ONE_TIMED_TARGET)
2690	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET) [done]"
2691	endif
2692
2693	timed_target:
2694	ifeq ($(TIMED_TARGET),)
2695	@echo "Error: You have to pass TIMED_TARGET to $@"
2696	false
2697	else
2698	@echo "Build time:" > $(TIMELOG)
2699	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2700	@cat $(TIMELOG)
2701	@rm $(TIMELOG)
2702	endif
2703
2704	timed_target_tested:
2705	ifeq ($(TIMED_TARGET),)
2706	@echo "Error: You have to pass TIMED_TARGET to $@"
2707	false
2708	else
2709	@echo "Build time:" > $(TIMELOG)
2710	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2711	$(MAKE) "ONE_TIMED_TARGET=ut" time_one
2712	@cat $(TIMELOG)
2713	@rm $(TIMELOG)
2714	endif
2715
2716	clean_timed_target:
2717	ifeq ($(TIMED_TARGET),)
2718	@echo "Error: You have to pass TIMED_TARGET to $@"
2719	false
2720	else
2721	@echo "Build time:" > $(TIMELOG)
2722	$(MAKE) "ONE_TIMED_TARGET=clean" time_one
2723	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2724	@cat $(TIMELOG)
2725	@rm $(TIMELOG)
2726	endif
2727
2728	# --------------------------------------------------------------------------------
2729
2730	CHECKOUT_MODIFIED=0# set to 1 to temporarily skip test for modifications (do not check in if set to 1)
2731
2732	check_svn_does_not_contain_generated:
2733	ifeq ($(CHECKOUT_MODIFIED),0)
2734	@echo "Testing that build does not modify files in SVN"
2735	@test 0 = `svn status \| wc -l` \|\| ( \
2736	echo "The checkout is not/no longer clean:"; \
2737	svn status; \
2738	echo "- if this fails instantly, your checkout is not clean"; \
2739	echo "- if this fails after other targets, these targets modify checked in data"; \
2740	echo " (a common cause may be that depends are not up to date)"; \
2741	false)
2742	else
2743	grep -Hn 'CHECKOUT_MODIFIED' Makefile
2744	endif
2745
2746	check_svn_ignores_generated:
2747	@test 0 = `svn status \| grep '^\?' \| wc -l` \|\| ( \
2748	echo "There are svn-unignored files:"; \
2749	svn status \| grep '^\?'; \
2750	echo "(all generated files should be svn-ignored)"; \
2751	false)
2752
2753	check_svn_state: check_svn_does_not_contain_generated
2754	$(MAKE) check_svn_ignores_generated
2755	$(MAKE) savetest
2756
2757	things_that_always_should_work: depends proto
2758
2759	post_commit_check:
2760	@echo "---------------------------------------- [Initial]"
2761	$(MAKE) check_svn_state
2762
2763	$(MAKE) clean
2764	@echo "---------------------------------------- [After 'make clean']"
2765	$(MAKE) check_svn_state
2766
2767	$(MAKE) things_that_always_should_work
2768	@echo "---------------------------------------- [After 'make things_that_always_should_work']"
2769	$(MAKE) check_svn_state
2770
2771	$(MAKE) all
2772	@echo "---------------------------------------- [After 'make all']"
2773	$(MAKE) check_svn_state
2774
2775	$(MAKE) things_that_always_should_work
2776	@echo "---------------------------------------- [Final]"
2777	$(MAKE) check_svn_state
2778
2779	# --------------------------------------------------------------------------------
2780	# sanitize arb_ntree; also works for clients (arb_edit4, ...) started from there.
2781
2782	sanitize: all
2783	( \
2784	export "LSAN_OPTIONS=max_leaks=30:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp"; \
2785	echo "sake[1]: Entering directory \`$(ARBHOME)'"; \
2786	$(ARBHOME)/bin/arb_ntree --execute _logged ~/data/test.arb 2>&1 ; \
2787	echo "sake[1]: Leaving directory \`$(ARBHOME)'" \
2788	) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
2789
2790	# --------------------------------------------------------------------------------
2791	# build and test one unit:
2792
2793	build_oneunit:
2794	$(MAKE) "WITHPERL=1" $(UNIT).dummy
2795
2796	oneunit:
2797	ifndef UNIT
2798	@echo "Please define UNIT, e.g. using"
2799	@echo " make \"UNIT=ARBDB/libARBDB\" oneunit"
2800	@echo " make \"UNIT=SL/TREEDISP/TREEDISP\" oneunit"
2801	@echo "(Note: 1st is a shared library, 2nd isn't)"
2802	false
2803	else
2804	@echo "Build time" > $(TIMELOG)
2805	@echo "$(SEP) $(MAKE) build_oneunit"
2806	@$(TIMECMD) $(MAKE) build_oneunit
2807	ifeq ($(UNIT_TESTS),1)
2808	@echo "$(SEP) $(MAKE) run_oneunitstests"
2809	@$(TIMECMD) $(MAKE) run_oneunitstests
2810	endif
2811	@cat $(TIMELOG)
2812	@rm $(TIMELOG)
2813	endif
2814
2815	# --------------------------------------------------------------------------------
2816
2817	build: arb
2818	$(MAKE) check_bin_dep preplib compile_compatibility
2819
2820	all:
2821	@echo "Build time" > $(TIMELOG)
2822	# $(MAKE) clean_checked_vect # uncomment to rebuild sources where expected vectorization gets tested
2823	@echo "$(SEP) $(MAKE) all"
2824	@$(TIMECMD) $(MAKE) build
2825	@echo $(SEP)
2826	@echo "made 'all' with success."
2827	@echo "to start arb enter 'arb'"
2828	ifeq ($(UNIT_TESTS),1)
2829	@echo "$(SEP) $(MAKE) run_tests"
2830	@$(TIMECMD) $(MAKE) run_tests
2831	endif
2832	@echo "$(SEP) $(MAKE) all [done]"
2833	ifeq ($(DEBUG),1)
2834	@$(MAKE) save_test_no_error >/dev/null # just show hints
2835	endif
2836	@cat $(TIMELOG)
2837	@rm $(TIMELOG)
2838

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