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Last change on this file was 19040, checked in by westram, 2 years ago
partial merge from 'trunk' into 'stable' fixes build for systems where Sun/rpc moved from glib→libtirpc. adds: log:trunk@18981:18983
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 84.8 KB

Line
1	# =============================================================== #
2	# #
3	# File : Makefile #
4	# #
5	# Institute of Microbiology (Technical University Munich) #
6	# http://www.arb-home.de/ #
7	# #
8	# =============================================================== #
9
10	# -----------------------------------------------------
11	# The ARB Makefile is aware of the following defines:
12	#
13	# CC C compiler (should be defined by OS)
14	# CXX C++ compiler (should be defined by OS)
15	#
16	# DEVELOPER=name special compilation (values: ANY,RELEASE,your name)
17	# OPENGL=0/1 whether OPENGL is available
18	#
19	# -----------------------------------------------------
20	# Paths for several libraries may be set from config.makefile by using:
21	#
22	# export XLIBS=$(shell pkg-config --libs xpm xerces-c)
23	# export XINCLUDES=$(shell pkg-config --cflags x11)
24	# export XAW_LIBS=$(shell pkg-config --libs xaw7)
25	# export XML_INCLUDES=$(shell pkg-config --cflags xerces-c)
26	#
27	# You make have to explicitely point pkg-config to the *.pc files needed.
28	# For example, Xquartz X11 libraries on macOS can be located by adding
29	# the following line before those given above:
30	#
31	# export PKG_CONFIG_PATH=/usr/X11/lib/pkgconfig
32	#
33	# If you introduce a new variable that is handled as described above,
34	# please add to section .@InjectedEnvironment
35	#
36	# -----------------------------------------------------
37	# ARB Makefile and ARB source code are aware of the following defines:
38	#
39	# $(MACH) name of the machine (LINUX or DARWIN; see config.makefile)
40	# DEBUG compiles the DEBUG sections
41	# DEBUG_GRAPHICS all X-graphics are flushed immediately (for debugging)
42	# ARB_64=0/1 1=>compile 64 bit version
43	# UNIT_TESTS=0/1 1=>compile in unit tests and call them after build
44	# COVERAGE=0/1/2 compile in gcov support (useful together with UNIT_TESTS=1)
45	# 0=no, 1+2=compile in, 1=show
46	# STABS=0/1 force stabs format? (0 = "use default format")
47	# SANITIZE=0/#/all use Sanitizer? (defaults to 0,
48	# 1=AddressSanitizer+LeakSanitizer,
49	# 2=UndefinedBehaviorSanitizer,
50	# combine bit-values to activate multiple Sanitizers,
51	# specify 'all' to activate all)
52	# IGNORE_LEAKS=1 does not abort when leaks are detected (while using SANITIZE=1/all)
53	# SHOWTODO=0/1 activate TODO-warnings? (defaults to 0, except for ralf)
54	#
55	# -----------------------------------------------------
56	# The ARB source code is aware of the following defines:
57	#
58	# NDEBUG doesn't compile the DEBUG sections
59	# DEVEL_$(DEVELOPER) developer-dependent flag (enables you to have private sections in code)
60	# DEVELOPER='ANY' (default setting) will be ignored
61	# configurable in config.makefile
62	#
63	# -----------------------------------------------------
64	# Read configuration
65	include config.makefile
66	CONFIG_MAKEFILE_FOUND=$(strip $(wildcard config.makefile))
67
68	# set defaults for variables commented out in config.makefile:
69	ifndef DARWIN
70	DARWIN:=0
71	endif
72	ifndef LINUX
73	LINUX:=0
74	endif
75	ifndef DEBIAN
76	DEBIAN:=0
77	endif
78	ifndef ARB_64
79	ARB_64=1#default to 64bit
80	endif
81
82	# Variables allowed for injection [InjectedEnvironment]
83	# (alternatively initialize them with '?=', e.g. done for XLIBS and XINCLUDES)
84	# In both cases add them to SOURCE_TOOLS/export2sub
85	ifndef XML_INCLUDES
86	XML_INCLUDES=
87	endif
88	ifndef XAW_LIBS
89	XAW_LIBS=
90	endif
91
92
93	ifneq ($(CONFIG_MAKEFILE_FOUND),)
94	ifneq ($(DARWIN)$(LINUX),10)
95	ifneq ($(DARWIN)$(LINUX),01)
96	$(error exactly one of DARWIN=1 or LINUX=1 has to be defined (got:$(DARWIN)$(LINUX)))
97	endif
98	endif
99	endif
100
101	# compiler settings:
102	ifneq ($(CC),use__A_CC__instead_of__CC)
103	A_CC:=$(CC)# compile C
104	A_CXX:=$(CXX)# compile C++
105
106	# uncomment to ensure no submakefile uses CC and CXX directly
107	override CC:=use__A_CC__instead_of__CC
108	override CXX:=use__A_CXX__instead_of__CXX
109	endif
110
111	export CC CXX A_CC A_CXX
112
113	# unconditionally prepend $(ARBHOME)/lib to LD_LIBRARY_PATH if not found
114	ifeq ($(findstring $(ARBHOME)/lib,$(LD_LIBRARY_PATH)),)
115	LD_LIBRARY_PATH:=${ARBHOME}/lib:$(LD_LIBRARY_PATH)
116	endif
117
118	# store LD_LIBRARY_PATH to circumvent SIP restrictions:
119	ARBBUILD_LIBRARY_PATH:=$(LD_LIBRARY_PATH)
120
121	FORCEMASK = umask 002
122	NODIR=--no-print-directory
123
124	SED:=$(ARBHOME)/SH/arb_sed
125	READLINK:=$(ARBHOME)/SH/arb_readlink
126
127	# ---------------------- compiler version detection
128
129	# supported gcc versions:
130	ALLOWED_gcc_VERSIONS=\
131	4.4.3 4.4.5 4.4.6 4.4.7 \
132	4.5.2 \
133	4.6.1 4.6.2 4.6.3 4.6.4 \
134	4.7.1 4.7.2 4.7.3 4.7.4 \
135	4.8.0 4.8.1 4.8.2 4.8.3 4.8.4 4.8.5 \
136	4.9.0 4.9.1 4.9.2 4.9.3 4.9.4 \
137	5.1.0 5.2.0 5.3.0 5.4.0 5.5.0 \
138	6.1.0 6.2.0 6.3.0 6.4.0 6.5.0 \
139	7.1.0 7.2.0 7.3.0 7.4.0 7.5.0 \
140	8.1.0 8.2.0 8.3.0 8.4.0 \
141	9.1.0 9.2.0 9.3.0 \
142
143	# Note: starting with version 5, arb silently accepts any subversion number
144	# above zero. See SOURCE_TOOLS/arb_compiler_version.pl@acceptSubVersions
145	#
146	# This may cause problems when manually checking for compiler versions in code
147	# (GCC_VERSION_CODE is not affected, GCC_PATCHLEVEL_CODE may cause problems!)
148	# ----------------------
149
150	COMPILER_INFO:=$(shell SOURCE_TOOLS/arb_compiler_version.pl $(A_CXX))
151	COMPILER_NAME:=$(word 1,$(COMPILER_INFO))
152	COMPILER_VERSION:=$(word 2,$(COMPILER_INFO))
153
154	USE_CLANG:=0
155	ifneq ($(COMPILER_NAME),gcc)
156	ifeq ($(COMPILER_NAME),clang)
157	USE_CLANG:=1
158	else
159	ifeq ($(COMPILER_VERSION),4.6.4)
160	# gcc version 4.6.4 segfaults when dumping symbols for detection (silently accept as gcc)
161	COMPILER_NAME:=gcc
162	else
163	$(error failed to detect COMPILER_NAME (got '$(COMPILER_NAME)', expected 'clang' or 'gcc'))
164	endif
165	endif
166	endif
167
168	ifeq ($(USE_CLANG),1)
169	# accept all clang versions:
170	ALLOWED_COMPILER_VERSIONS=$(COMPILER_VERSION)
171	else
172	ALLOWED_COMPILER_VERSIONS=$(ALLOWED_gcc_VERSIONS)
173	endif
174
175	COMPILER_VERSION_ALLOWED=$(strip $(subst ___,,$(foreach version,$(ALLOWED_COMPILER_VERSIONS),$(findstring ___$(version)___,___$(COMPILER_VERSION)___))))
176
177	#---------------------- split gcc version
178
179	SPLITTED_VERSION:=$(subst ., ,$(COMPILER_VERSION))
180
181	USE_GCC_MAJOR:=$(word 1,$(SPLITTED_VERSION))
182	USE_GCC_MINOR:=$(word 2,$(SPLITTED_VERSION))
183	USE_GCC_PATCHLEVEL:=$(word 3,$(SPLITTED_VERSION))
184
185	USE_GCC_452_OR_HIGHER:=
186	USE_GCC_46_OR_HIGHER:=
187	USE_GCC_47_OR_HIGHER:=
188	USE_GCC_48_OR_HIGHER:=
189	USE_GCC_49_OR_HIGHER:=
190	USE_GCC_50_OR_HIGHER:=
191	USE_GCC_60_OR_HIGHER:=
192	USE_GCC_70_OR_HIGHER:=
193	USE_GCC_80_OR_HIGHER:=
194	USE_GCC_90_OR_HIGHER:=
195
196	ifeq ($(USE_CLANG),0)
197	ifeq ($(USE_GCC_MAJOR),4)
198	ifeq ($(USE_GCC_MINOR),5)
199	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),23456789)','')
200	USE_GCC_452_OR_HIGHER:=yes
201	endif
202	else
203	ifneq ('$(findstring $(USE_GCC_MINOR),6789)','')
204	USE_GCC_452_OR_HIGHER:=yes
205	USE_GCC_46_OR_HIGHER:=yes
206	ifneq ($(USE_GCC_MINOR),6)
207	USE_GCC_47_OR_HIGHER:=yes
208	ifneq ($(USE_GCC_MINOR),7)
209	USE_GCC_48_OR_HIGHER:=yes
210	ifneq ($(USE_GCC_MINOR),8)
211	USE_GCC_49_OR_HIGHER:=yes
212	endif
213	endif
214	endif
215	endif
216	endif
217	else
218	# gcc 5.x or higher
219	USE_GCC_452_OR_HIGHER:=yes
220	USE_GCC_46_OR_HIGHER:=yes
221	USE_GCC_47_OR_HIGHER:=yes
222	USE_GCC_48_OR_HIGHER:=yes
223	USE_GCC_49_OR_HIGHER:=yes
224	USE_GCC_50_OR_HIGHER:=yes
225	ifneq ($(USE_GCC_MAJOR),5)
226	# gcc 6.x or higher
227	USE_GCC_60_OR_HIGHER:=yes
228	ifneq ($(USE_GCC_MAJOR),6)
229	# gcc 7.x or higher
230	USE_GCC_70_OR_HIGHER:=yes
231	ifneq ($(USE_GCC_MAJOR),7)
232	# gcc 8.x or higher
233	USE_GCC_80_OR_HIGHER:=yes
234	ifneq ($(USE_GCC_MAJOR),8)
235	# gcc 9.x or higher
236	USE_GCC_90_OR_HIGHER:=yes
237	endif
238	endif
239	endif
240	endif
241	endif
242	endif
243
244	#---------------------- define special directories for non standard builds
245
246	ifeq ($(DARWIN),1)
247	OSX_FW:=/System/Library/Frameworks
248	OSX_FW_OPENGL:=$(OSX_FW)/OpenGL.framework/Versions/A/Libraries
249	OSX_FW_GLUT:=$(OSX_FW)/GLUT.framework/Versions/A/Libraries
250	OSX_FW_IMAGEIO:=$(OSX_FW)/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources
251	endif
252
253	#---------------------- SSE vectorization
254	# for details about vectorization checks see SOURCE_TOOLS/vectorize.README
255
256	DISABLE_VECTORIZE_CHECK:=0# set to 1 to completely disable vectorization checks
257	TRACE_MISSED_VECTORIZATIONS:=0# set to 1 to activate detailed output about failed vectorizations
258	# (does also show details about successful vectorized loops, which are not optimal)
259	VECTORIZATION_CHECK_CANDIDATES:=0# set to 1 to show vectorizations that may be checked
260	# (for yet unchecked files)
261	# Note: TRACE_MISSED_VECTORIZATIONS and VECTORIZATION_CHECK_CANDIDATES cannot be used together!
262
263	#----------------------
264
265	ifeq ($(DARWIN),1)
266	LINK_STATIC=1# link static
267	else
268	LINK_STATIC=0# link dynamically
269	# LINK_STATIC=1# link static (testing only)
270	endif
271
272	shared_cflags :=# flags for shared lib compilation
273	clflags :=# linker flags (when passed through gcc)
274	extended_warnings :=# warning flags for C and C++-compiler
275	extended_cpp_warnings :=# warning flags for C++-compiler only
276
277	ifeq ($(DEBUG),0)
278	dflags := -DNDEBUG# defines
279	ifeq ($(USE_CLANG),1)
280	cflags := -O3# compiler flags (C and C++)
281	else
282	clflags += -Wl,-O2# passthrough linker flags
283	# ------- standard optimization:
284	cflags := -O3# compiler flags (C and C++)
285	# ------- test changed optimization (DISABLE_VECTORIZE_CHECK for -O2 or lower):
286	# cflags := -O2# do not commit uncommented!
287	# DISABLE_VECTORIZE_CHECK:=1
288	endif
289	endif
290
291	ifeq ($(DEBIAN),1)
292	clflags += -Wl,-rpath=/usr/lib/arb/lib -Wl,-z,relro
293	endif
294
295	ifeq ($(DEBUG),1)
296	dflags := -DDEBUG
297
298	gdb_common := -g -g3 -ggdb -ggdb3
299
300	DBGOPTI:=-O0
301	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
302	DBGOPTI:=-Og
303	endif
304
305	ifeq ($(STABS),1)
306	cflags := $(DBGOPTI) $(gdb_common) -gstabs+ # using stabs+ (enable this for bigger debug session: debugs inlines, quick var inspect, BUT valgrind stops working :/)
307	else
308	cflags := $(DBGOPTI) $(gdb_common) # (using dwarf - cant debug inlines here, incredible slow on showing variable content)
309	endif
310
311	# cflags := $(DBGOPTI) $(gdb_common) -gdwarf-3 # (specify explicit dwarf format)
312	# cflags := $(DBGOPTI) $(gdb_common) -gstabs # using stabs (same here IIRC)
313	# cflags := -O2 $(gdb_common) # use this for callgrind (force inlining)
314
315	ifeq ($(DARWIN),0)
316	clflags += -Wl,-g
317	# Note:
318	# Previously '-Wl,-noinhibit-exec' was added to 'clflags' here,
319	# to fix some issues with launchpad binutils (see [12972]).
320	# But that change also caused 'undefined symbols' NOT to be reported as errors
321	# at link time, producing executables that fail at runtime :/
322	endif
323
324	ifeq ($(DEBUG_GRAPHICS),1)
325	dflags += -DDEBUG_GRAPHICS
326	endif
327
328	endif # DEBUG only
329
330	# ------------------------------ POST_COMPILE - control how much you get spammed
331	# (please do not change default in SVN)
332	POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl
333
334	# POST_COMPILE += --original # dont modify compiler output
335	# POST_COMPILE += --hide-Noncopyable-advices
336	# POST_COMPILE += --show-useless-Weff++
337	# POST_COMPILE += --no-warnings
338	# POST_COMPILE += --only-first-error
339	# POST_COMPILE += --no-warnings --only-first-error
340
341	# always pass used compiler version to postcompile:
342	POST_COMPILE += --compiler=$(COMPILER_VERSION)
343
344	# ------------------------------
345
346	# Enable extra warnings
347	extended_warnings :=
348	extended_cpp_warnings :=
349
350	# C and C++
351	extended_warnings += -Wwrite-strings -Wunused -Wno-aggregate-return
352
353	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
354	# disable shadow warnings for gcc 4.8 (and lower)
355	# (does e.g. warn if a method-name is used as parameter in another method - even for derived classes. unusable!)
356	extended_warnings += -Wshadow
357	endif
358
359	# C++ only
360	extended_cpp_warnings += -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute
361	extended_cpp_warnings += -Wctor-dtor-privacy
362	# extended_cpp_warnings += -Wfloat-equal
363
364	extended_cpp_warnings += -Wmissing-noreturn
365	# extended_cpp_warnings += -Wold-style-cast# (warns about 28405 old-style casts)
366	extended_cpp_warnings += -Winit-self
367	extended_cpp_warnings += -Wstrict-aliasing
368	extended_cpp_warnings += -Wextra
369
370	# ------- above only warning-options already available in gcc 4.4.3
371
372	# -Weffc++ broken in 4.7.x series
373	# gcc 4.7.3 crashes on GenomeImport.cxx when -Weffc++ is active
374	# (bug reported https://gcc.gnu.org/bugzilla/show_bug.cgi?id=56923; apparently wont be fixed for 4.7-series)
375	# gcc 4.7.4 crashes on DBwriter.cxx when -Weffc++ is active
376	WEFFC_BROKEN:=0
377	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
378	ifneq ('$(USE_GCC_48_OR_HIGHER)','yes')
379	WEFFC_BROKEN:=1
380	endif
381	endif
382	ifeq ('$(WEFFC_BROKEN)','0')
383	extended_cpp_warnings += -Weffc++
384	endif
385
386	# turn off -Wmaybe-uninitialized in debug mode (gets activated with -Wextra). too many bogus warnings
387	ifeq ($(DEBUG),1)
388	ifeq ($(USE_CLANG),0)
389	extended_cpp_warnings += -Wno-maybe-uninitialized
390	endif
391	endif
392
393	SUGGEST_FINAL:=
394
395	ifeq ('$(USE_GCC_452_OR_HIGHER)','yes')
396	extended_cpp_warnings += -Wlogical-op# gcc 4.5.2
397	endif
398	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
399	extended_cpp_warnings += -Wzero-as-null-pointer-constant# gcc 4.7
400	endif
401	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
402	extended_cpp_warnings += -Wunused-local-typedefs# available since gcc 4.7 (but fails for each STATIC_ASSERT, so enable only for Cxx11)
403	endif
404	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
405	extended_cpp_warnings += -Wswitch-bool
406	extended_cpp_warnings += -Wlogical-not-parentheses
407	extended_cpp_warnings += -Wsizeof-array-argument
408	extended_cpp_warnings += -Wbool-compare
409
410	SUGGEST_FINAL:=yes
411	endif
412	ifeq ('$(USE_GCC_60_OR_HIGHER)','yes')
413	extended_cpp_warnings += -Wduplicated-cond
414	endif
415	ifeq ('$(USE_GCC_80_OR_HIGHER)','yes')
416	extended_cpp_warnings += -Wmultistatement-macros
417	endif
418
419	# switch off final suggestions for 8.3.0 and 8.4.0:
420	ifeq ('$(COMPILER_VERSION)','8.3.0')
421	SUGGEST_FINAL:=no
422	endif
423	ifeq ('$(COMPILER_VERSION)','8.4.0')
424	SUGGEST_FINAL:=no
425	endif
426
427	ifeq ($(DEVELOPER),RELEASE)
428	# switch off final suggestions in RELEASE:
429	SUGGEST_FINAL:=no
430	endif
431	# suggest final:
432	ifeq ('$(SUGGEST_FINAL)','yes')
433	extended_cpp_warnings += -Wsuggest-final-types
434	extended_cpp_warnings += -Wsuggest-final-methods
435	dflags += -DSUGGESTS_FINAL
436	endif
437
438	#---------------------- turn off clang bogus warnings
439
440	ifeq ($(USE_CLANG),1)
441	# -Wmismatched-tags warns about struct/class mismatch in forward declarations (which is explicitely allowed)
442	# -Wchar-subscripts reports too many bogus warnings for "array['x']" (when 'x' is known to be in range [0..128])
443	# -Wunused-private-field report too many false positives (currently ~ 2 of 3)
444	# -Wstring-plus-int warns about common ARB coding practice
445	# -Wgnu-static-float-init warns about accepted GNU extension
446	extended_cpp_warnings += -Wno-mismatched-tags -Wno-char-subscripts -Wno-unused-private-field -Wno-string-plus-int
447	ifeq ('$(COMPILER_VERSION)','4.2.1')
448	# jenkins build (doesn't know switch -Wno-gnu-static-float-init)
449	extended_cpp_warnings += -Wno-gnu
450	else
451	extended_cpp_warnings += -Wno-gnu-static-float-init
452	endif
453	endif
454
455	#---------------------- developer
456
457	ifneq ($(DEVELOPER),ANY) # ANY=default setting (skip all developer specific code)
458	dflags += -DDEVEL_$(DEVELOPER)# activate developer/release specific code
459	endif
460
461	#---------------------- activate TODO warnings?
462
463	ifndef SHOWTODO
464	ifeq ($(DEVELOPER),RALF)
465	SHOWTODO:=1
466	else
467	SHOWTODO:=0
468	endif
469	endif
470	ifeq ($(SHOWTODO),1)
471	dflags += -DWARN_TODO# activate "TODO" warnings
472	endif
473
474	#---------------------- activate threads?
475	# only useful if compiler is able to compile Cxx11 or better
476
477	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
478	# see also ./TEMPLATES/cxxforward.h@USE_Cxx11
479	cflags += -pthread
480	clflags += -pthread
481	endif
482
483	#---------------------- activate Sanitizers?
484
485	ifndef IGNORE_LEAKS
486	IGNORE_LEAKS:=0
487	endif
488
489	ASAN_OPTIONS:=handle_segv=0:color=0
490	ifeq ($(IGNORE_LEAKS),1)
491	ASAN_OPTIONS+=:detect_leaks=0 # disable leak-detection
492	else
493	ASAN_OPTIONS+=:detect_leaks=1 # detect leaks (normal setting)
494	endif
495	ASAN_OPTIONS+=:check_initialization_order=1
496	# ASAN_OPTIONS+=:abort_on_error=1
497
498	# suppressions: SOURCE_TOOLS/arb.leaksan.supp
499	LSAN_OPTIONS:=max_leaks=3:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp
500
501	UBSAN_OPTIONS:=print_stacktrace=1
502
503	ifndef SANITIZE
504	SANITIZE:=0
505	endif
506
507	SANITIZE_ADDRESS:=0
508	SANITIZE_UNDEFINED:=0
509
510	ifneq ($(SANITIZE),0)
511	ifeq ($(SANITIZE),all)
512	SANITIZE:=3
513	endif
514
515	ifeq ($(SANITIZE),1)
516	SANITIZE_ADDRESS:=1
517	else
518	ifeq ($(SANITIZE),2)
519	SANITIZE_UNDEFINED:=1
520	else
521	ifeq ($(SANITIZE),3)
522	SANITIZE_ADDRESS:=1
523	SANITIZE_UNDEFINED:=1
524	else
525	$(error Unknown value '$(SANITIZE)' specified for SANITIZE in config.makefile)
526	endif
527	endif
528	endif
529	endif
530
531	ifeq ($(SANITIZE_ADDRESS),1)
532	ifneq ('$(USE_GCC_48_OR_HIGHER)','yes')
533	$(info AddressSanitizer not usable with gcc $(COMPILER_VERSION) - disabled)
534	SANITIZE_ADDRESS:=0
535	else
536	ifneq ('$(USE_GCC_49_OR_HIGHER)','yes')
537	$(info LeakSanitizer does not work with gcc $(COMPILER_VERSION) - disabled)
538	# need to disable AddressSanitizer (otherwise build fails; only affects gcc 4.8.x series)
539	SANITIZE_ADDRESS:=0
540	endif
541	endif
542	endif
543
544	ifeq ($(SANITIZE_UNDEFINED),1)
545	ifneq ('$(USE_GCC_49_OR_HIGHER)','yes')
546	$(info UndefinedBehaviorSanitizer not usable with gcc $(COMPILER_VERSION) - disabled)
547	SANITIZE_UNDEFINED:=0
548	endif
549	endif
550
551	SANITIZE_ANY:=0
552	ifeq ($(SANITIZE_ADDRESS),1)
553	SANITIZE_ANY:=1
554	endif
555	ifeq ($(SANITIZE_UNDEFINED),1)
556	SANITIZE_ANY:=1
557	endif
558
559	# vectorization fails if sanitizer active where it normally succeeds -> disable check
560	ifeq ($(SANITIZE_ANY),1)
561	$(info disabling vectorize checks. would fail with sanitized code)
562	DISABLE_VECTORIZE_CHECK:=1
563	else
564	$(info no sanitizer enabled. reset: SANITIZE=0)
565	SANITIZE:=0
566	endif
567
568	# deactivate some bogus warnings occurring when sanitizing NDEBUG version
569	# (do not disable for future gcc-version >= 8.x -> test again when available)
570	ifeq ($(SANITIZE_ANY),1)
571	ifeq ($(DEBUG),0)
572	ifneq ('$(USE_GCC_80_OR_HIGHER)','yes')
573	extended_cpp_warnings += -Wno-format-overflow
574	extended_cpp_warnings += -Wno-maybe-uninitialized
575	endif
576	endif
577	endif
578
579	#---------------------- 32 or 64 bit
580
581	cross_cflags:=
582	cross_lflags:=
583	cross_clflags:=
584
585	ifeq ($(ARB_64),1)
586	dflags += -DARB_64
587	shared_cflags += -fPIC
588	CROSS_LIB:=# empty => autodetect below
589	ifeq ($(DARWIN),1)
590	cross_cflags += -arch x86_64
591	cross_lflags += -arch x86_64
592	cross_clflags += -arch x86_64
593	endif
594	else
595	CROSS_LIB:=/lib
596	endif
597
598	cflags += $(cross_cflags)
599	clflags += $(cross_clflags)
600
601	ifeq ('$(CROSS_LIB)','')
602	# autodetect libdir
603	ifeq ($(ARB_64),1)
604	CROSS_LIB:=$(shell (test -d /lib64 && echo lib64) \|\| echo lib)
605	else
606	CROSS_LIB:=$(shell (test -d /lib32 && echo lib32) \|\| echo lib)
607	endif
608	endif
609
610	#---------------------- unit tests
611
612	ifndef UNIT_TESTS
613	UNIT_TESTS=0#default is "no tests"
614	endif
615	ifeq ($(UNIT_TESTS),1)
616	dflags += -DUNIT_TESTS
617	UNIT_TESTER_LIB=UNIT_TESTER/UNIT_TESTER.a
618	else
619	UNIT_TESTER_LIB=
620	endif
621
622	#---------------------- use gcov
623
624	ifndef COVERAGE
625	COVERAGE=0#default is "no"
626	endif
627	ifneq ($(COVERAGE),0)
628	GCOV_FLAGS=--coverage
629	$(info disabling vectorize checks. would fail with COVERAGE on)
630	DISABLE_VECTORIZE_CHECK:=1
631	else
632	GCOV_FLAGS=
633	endif
634
635	cflags += $(GCOV_FLAGS)
636	clflags += $(GCOV_FLAGS)
637	cross_lflags += $(GCOV_FLAGS)
638
639	#---------------------- other flags
640
641	dflags += -D$(MACH) # define machine
642
643	ifeq ($(DARWIN),1)
644	shared_cflags += -fno-common
645	else
646	dflags += $(shell getconf LFS_CFLAGS)
647	endif
648
649	cflags += -pipe
650	cflags += -fmessage-length=0# dont wrap compiler output
651	cflags += -fshow-column# show columns
652	cflags += -funit-at-a-time
653	cflags += -fPIC
654	cflags += -fno-common# link all global data into one namespace
655	cflags += -fstrict-aliasing# gcc 3.4
656
657
658	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
659	cflags += -fno-diagnostics-show-caret#gcc 4.8 (4.7.?)
660	endif
661	#cflags += -save-temps# uncomment to see preprocessor output
662
663	#---------------------- various sanitizers
664	# There are some disabled tests in CORE/arb_misc.cxx@sanitizers
665	# which trigger sanitizer reports.
666
667	ifeq ($(SANITIZE_ANY),1)
668	cflags += -ggdb3 -fno-omit-frame-pointer
669	endif
670
671	# activate AddressSanitizer+LeakSanitizer?
672	ifeq ($(SANITIZE_ADDRESS),1)
673	cflags += -fsanitize=address
674	clflags += -fsanitize=address
675	dflags += -DLEAKS_SANITIZED
676	endif
677
678	# activate UndefinedBehaviorSanitizer?
679	ifeq ($(SANITIZE_UNDEFINED),1)
680	cflags += -fsanitize=undefined
681	clflags += -fsanitize=undefined
682	dflags += -DUNDEF_SANITIZED
683	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
684	# abort on runtime errors
685	cflags += -fno-sanitize-recover=all
686	endif
687	#
688	# Note: alignment-sanitizer is deactivated for ARBDB and PROBE!
689	ifeq ('$(DEBUG)','1')
690	ifeq ($(USE_GCC_MAJOR),4)
691	ifeq ($(USE_GCC_MINOR),9)
692	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),01)','')
693	# workaround https://gcc.gnu.org/bugzilla/show_bug.cgi?id=63531 for 4.9.0 + 4.9.1
694	# (problem is fixed in 4.9.2 release)
695	extended_cpp_warnings:=$(subst -Weffc++,,$(extended_cpp_warnings))
696	endif
697	endif
698	endif
699	endif
700	endif
701
702	#---------------------- X11 location
703
704	ifeq ($(DARWIN),1)
705	XHOME:=$(PREFIX)
706	else
707	ifeq ($(DEBIAN),1)
708	XHOME:=$(PREFIX)
709	else
710	XHOME:=/usr/X11R6
711	endif
712	endif
713
714	XINCLUDES ?= -I$(XHOME)/include
715	XLIBS ?= -L$(XHOME)/$(CROSS_LIB)
716	ifeq ($(DARWIN),1)
717	XINCLUDES += -I$(OSX_FW)/GLUT.framework/Headers -I$(OSX_FW)/OpenGL.framework/Headers -I$(OSX_SDK)/usr/include/krb5
718
719	XLIBS += -lXm -lpng -lz -lXt -lX11 -lXext -lXp -lXmu -lXi
720	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGL.dylib:$(OSX_FW_OPENGL)/libGL.dylib
721	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGLU.dylib:$(OSX_FW_OPENGL)/libGLU.dylib
722	else
723	XLIBS += -lXm -lXpm -lXt -lXext -lX11
724	endif
725
726	#---------------------- open GL
727
728	ifeq ($(OPENGL),1)
729	cflags += -DARB_OPENGL # activate OPENGL code
730	GL := gl # this is the name of the OPENGL base target
731	GL_LIB_SYS := -lGL -lGLU
732	GL_LIB_ARB := -L$(ARBHOME)/GL/glAW -lglAW
733
734	ifeq ($(DARWIN),1)
735	GL_LIB_SYS += -lpthread
736	endif
737
738	GL_PNGLIBS_ARB := -L$(ARBHOME)/GL/glpng -lglpng_arb
739	GL_PNGLIBS_SYS := -lpng
740
741	GLEWLIB := -lGLEW -lGLw
742	GLUTLIB := -lglut
743
744	GL_LIBS_SYS := $(GL_LIB_SYS) $(GL_PNGLIBS_SYS) $(GLEWLIB) $(GLUTLIB)
745	GL_LIBS_ARB := $(GL_LIB_ARB) $(GL_PNGLIBS_ARB)
746
747	RNA3D_LIB := RNA3D/RNA3D.a
748	else
749	GL_LIBS_SYS:=# no opengl -> no libs
750	GL_LIBS_ARB:=# no opengl -> no libs
751	GL:=# dont build ARB openGL libs
752
753	RNA3D_LIB :=
754	endif
755
756	RNA3D_LIB_4_DEPENDS := RNA3D/RNA3D.a
757
758	GL_LIBS:=$(GL_LIBS_ARB) $(GL_LIBS_SYS)
759
760	#---------------------- tiff lib:
761
762	TIFFLIBS := -ltiff
763
764	#---------------------- XML lib:
765
766	XMLLIBS := -lxerces-c
767
768	#---------------------- glib:
769
770	ARB_NEEDED_GLIB=glib-2.0
771
772	ARB_GLIB_INCLUDE:=$(strip $(shell pkg-config --cflags $(ARB_NEEDED_GLIB)))
773	ARB_GLIB_LIBS:=$(strip $(shell pkg-config --libs $(ARB_NEEDED_GLIB)))
774
775	#---------------------- sunrpc lib:
776	# Note: sunrpc has been removed from glibc
777	# (e.g. in SuSE Leap 15.3 and Fedora 28)
778	# see https://fedoraproject.org/wiki/Changes/SunRPCRemoval
779	#
780	HAVE_LIBTIRPC=$(strip $(shell pkg-config --exists libtirpc && echo libtirpc))
781	ifeq ($(HAVE_LIBTIRPC),)
782	ARB_RPC_INCLUDE:=
783	ARB_RPC_LIBS:=
784	else
785	ARB_RPC_INCLUDE:=$(strip $(shell pkg-config --cflags $(HAVE_LIBTIRPC)))
786	ARB_RPC_LIBS:=$(strip $(shell pkg-config --libs $(HAVE_LIBTIRPC)))
787	endif
788
789	#---------------------- basic libs:
790
791	ARB_CORE_LIBS:=$(ARB_GLIB_LIBS) $(ARB_RPC_LIBS)
792
793	SYSLIBS:=
794	ifeq ($(DARWIN),1)
795	SYSLIBS += -lstdc++
796	else
797	SYSLIBS += -lm $(ARB_CORE_LIBS)
798	endif
799
800	#---------------------- system dependent commands
801
802	ifeq ($(DARWIN),1)
803	TIME:=gtime
804	else
805	TIME:=/usr/bin/time
806	endif
807
808	#---------------------- SSE vectorizer
809	# for details see SOURCE_TOOLS/vectorize.README
810
811	ifeq ($(DEBUG),0)
812	ifeq ($(USE_GCC_49_OR_HIGHER),yes)
813	ifeq ($(DISABLE_VECTORIZE_CHECK),0)
814	cflags += -fopt-info-vec
815	cflags += -fopt-info-vec-missed
816	ifeq ($(TRACE_MISSED_VECTORIZATIONS),1)
817	# Shows reasons for unsuccessful vectorization:
818	cflags += -ftree-vectorizer-verbose=10
819	POST_COMPILE += --dump-loop-optimization
820	ifeq ($(VECTORIZATION_CHECK_CANDIDATES),1)
821	$(error TRACE_MISSED_VECTORIZATIONS and VECTORIZATION_CHECK_CANDIDATES may not be used together!)
822	endif
823	endif
824	ifeq ($(VECTORIZATION_CHECK_CANDIDATES),1)
825	POST_COMPILE += --loop-optimization-candi
826	endif
827	POST_COMPILE += --check-loop-optimization
828	endif
829	else
830	ifeq ($(USE_GCC_48_OR_HIGHER),yes)
831	# no automatic vectorization-check for gcc<4.9.0
832	# -> uncomment the next 2 lines and grep the spam it will produce for 'vectorized.*loops'
833	# cflags += -fopt-info -fopt-info-vec-missed
834	# POST_COMPILE += --original
835	endif
836	endif
837	endif
838
839	#---------------------- stop early on broken flags/compiler combination
840
841	ifeq ($(DEBUG),0)
842	ifeq ($(SANITIZE_ANY),1)
843	ifeq ('$(COMPILER_VERSION)','4.9.1')
844	$(error compiling DEBUG=0 + SANITIZE!=0 crashes with gcc $(COMPILER_VERSION) (gcc 4.9.2 works))
845	endif
846	endif
847	endif
848
849	#---------------------- include symbols?
850
851	ifeq ($(TRACESYM),1)
852	ifeq ($(USE_CLANG),0)
853	cflags += -rdynamic
854	clflags += -rdynamic -Wl,--export-dynamic
855	endif
856	endif
857
858	#---------------------- warn about duplicate variable definitions
859
860	ifeq ($(DARWIN),1)
861	clflags += -Wl,-warn_commons
862	else
863	clflags += -Wl,--warn-common
864	endif
865
866	#---------------------- differences between linking executables and shared libs:
867
868	# executables:
869	ifeq ($(DARWIN),1)
870	blflags:=$(clflags)
871	else
872	blflags:=$(clflags) -Wl,--no-undefined
873	endif
874
875	# shared libraries
876	llflags:=$(clflags)
877
878	# dont use clflags below
879	clflags:=
880
881	# -------------------------------------------------------------------------
882	# Don't put any machine/version/etc conditionals below!
883	# (instead define variables above)
884	# -------------------------------------------------------------------------
885
886	cflags += -W -Wall $(dflags) $(extended_warnings)
887	cxxflags := $(extended_cpp_warnings)
888
889	# add CFLAGS + CPPFLAGS from environment for DEBIAN build
890	ifeq ($(DEBIAN),1)
891	cflags := $(CFLAGS) $(cflags)
892	cxxflags += $(CPPFLAGS)
893	endif
894
895	ifeq ('$(USE_CLANG)','1')
896	# none of the following standards works with clang3.3 (under linux) => dont use standard (as done before r15516)
897	# cxxflags += -std=gnu++11
898	# cxxflags += -std=gnu++0x
899	else
900	ifeq ('$(USE_GCC_60_OR_HIGHER)','yes')
901	cxxflags += -std=gnu++14# see also TEMPLATES/cxxforward.h@USE_Cxx14
902	else
903	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
904	cxxflags += -std=gnu++11# see also TEMPLATES/cxxforward.h@USE_Cxx11
905	else
906	# gcc versions between 4.3 (lowest supported) and <4.7
907	cxxflags += -std=gnu++0x
908	endif
909	endif
910	endif
911
912	LINK_STATIC_LIB := $(AR) -csq# link static lib
913	LINK_EXECUTABLE := $(A_CXX) $(blflags) -o# link executable (c++)
914
915	ifeq ($(LINK_STATIC),1)
916	SHARED_LIB_SUFFIX = a# static lib suffix
917	LINK_SHARED_LIB := $(LINK_STATIC_LIB)
918	else
919	SHARED_LIB_SUFFIX = so# shared lib suffix
920	LINK_SHARED_LIB := $(A_CXX) $(llflags) -shared -o# link shared lib
921	endif
922
923	ifeq ($(DARWIN),1)
924	lflags4perl:=
925	else
926	lflags4perl:=$(cross_lflags) -shared
927	endif
928
929	# delete variables unused below
930	blflags:=
931	llflags:=
932
933	# other used tools
934	MAKEDEPEND_PLAIN = makedepend
935	MAKEDEPEND = $(FORCEMASK);$(MAKEDEPEND_PLAIN)
936
937	#SEP:=--------------------------------------------------------------------------------
938	SEP=[`date +%M:%S.%N`] ------------------------------------------------
939	# to analyse timings run
940	# make -j9 clean; make -j9 all \| grep '^\[' \| sort
941	# make -j9 "TIMED_TARGET=perl" clean_timed_target \| grep '^\[' \| sort
942
943	# ------------------------------------------------------------ DYNLIBDEFS
944	# various dynamic library definitions for linking executables:
945	#
946	# SYSLIBS: system libraries needed by database lib
947	# ARBDB_LIB: database lib
948	# DBSYS_LIBS: executable using database (but no GUI)
949	# GUI_LIBS: executable using database and GUI (arb gui uses database)
950	#
951	# Note: definitions exported to sub-makefiles are described in SOURCE_TOOLS/parent_make.txt
952
953	CORE_LIB=-lCORE
954	ARBDB_LIB=-lARBDB $(CORE_LIB)
955	DBSYS_LIBS = $(ARBDB_LIB) $(SYSLIBS)
956
957	GUI_LIBS_PREFIX:=
958	ifeq ($(DARWIN),1)
959	# this seem to be added at wrong place, since opengl is only needed to link EDIT4
960	GUI_LIBS_PREFIX:=-framework GLUT -framework OpenGL
961	endif
962
963	GUI_LIBS=$(GUI_LIBS_PREFIX) $(DBSYS_LIBS) -lAWT -lWINDOW $(XLIBS)
964
965	LIBPATH = -L$(ARBHOME)/lib
966
967	DEST_LIB = lib
968	DEST_BIN = bin
969
970	CC_INCLUDES := -I. -I$(ARBHOME)/INCLUDE $(XINCLUDES) $(ARB_GLIB_INCLUDE) $(ARB_RPC_INCLUDE)
971	CXX_INCLUDES := $(CC_INCLUDES)
972	MAKEDEPENDFLAGS := -- -DARB_OPENGL -DUNIT_TESTS -D__cplusplus -I. -Y$(ARBHOME)/INCLUDE
973
974	# ---------------------------------------
975	# wrap main()
976
977	use_ARB_main=$(ARBHOME)/SOURCE_TOOLS/arb_main_cpp.o
978	use_ARB_main_C=$(ARBHOME)/SOURCE_TOOLS/arb_main_c.o
979
980	# -----------------------------------------
981	# unique build-id
982	# - different for different calls of make
983	# - constant in recursive calls
984
985	ifndef ARBBID
986	ARBBID:=$(shell SOURCE_TOOLS/uniqueID.sh)
987	endif
988
989	# -----------------------------------------
990	# export variables to submakefiles
991
992	include SOURCE_TOOLS/export2sub
993
994	# do not define (exported) variables below this point
995
996	# -------------------------
997	# Main arb targets:
998	# -------------------------
999
1000	first_target:
1001	$(MAKE) checks
1002	@echo $(SEP)
1003	@echo 'Main targets:'
1004	@echo ''
1005	@echo ' all - Compile ARB + TOOLs + and copy shared libs + link foreign software'
1006	@echo ' (That is most likely the target you want)'
1007	@echo ''
1008	@echo ' clean - remove generated files ("SUBDIR/SUBDIR.clean" to clean only SUBDIR)'
1009	@echo ' rebuild - clean + all'
1010	@echo ' cleanlinked - remove all binaries'
1011	@echo ' relink - cleanlinked + all (=relink all from objects)'
1012	@echo ''
1013	@echo 'Some often used sub targets (make all makes them all):'
1014	@echo ''
1015	@echo ' arb - Just compile ARB (but none of the integrated tools)'
1016	@echo ' menus - create lib/gde/arb.menu from GDEHELP/ARB_GDEmenus.source'
1017	@echo ' perl - Compile the PERL XSUBS into lib/ARB.so and create links in lib to perl'
1018	@echo ' binlink - Create all links in the bin directory'
1019	@echo ''
1020	@echo 'Development targets:'
1021	@echo ''
1022	@echo ' depends - create or update dependencies ("SUBDIR/SUBDIR.depends" to update only SUBDIR)'
1023	@echo ' proto - create or update prototypes ("SUBDIR/SUBDIR.proto" to update only SUBDIR)'
1024	@echo ' tags - create tags for xemacs'
1025	@echo ' show - show available shortcuts (AKA subtargets)'
1026	@echo ' up - shortcut for depends+proto+tags'
1027	ifeq ($(UNIT_TESTS),1)
1028	@echo ' ut - only run tests'
1029	@echo ' "UNIT=..." oneunit - build one unit and run tests (see also UNIT_TESTER/Makefile.setup.local)'
1030	endif
1031	ifneq ($(SANITIZE),0)
1032	@echo ' sanitize - all + run arb_ntree with sanitizer (test.arb + execute _logged)'
1033	endif
1034	@echo ' modified - rebuild files modified in svn checkout (does touch)'
1035	@echo ' touch - touch files modified in svn checkout'
1036	@echo ''
1037	@echo 'Internal maintenance:'
1038	@echo ''
1039	@echo ' relinfo - show help on release targets'
1040	@echo ' tarfile - make rebuild and create arb version tarfile ("tarfile_quick" to skip rebuild)'
1041	@echo ' save - save all basic ARB sources into arbsrc_DATE ("savetest" to check filelist)'
1042	@echo ' patch - save svn diff to patchfile'
1043	@echo ' source_doc - create doxygen documentation'
1044	@echo ' relocated - rebuild partly (use when you have relocated ARBHOME)'
1045	@echo ' check_res - check resource usage'
1046	@echo ' dep_graph - Build dependency graphs'
1047	@echo ' clean_cov - Clean coverage results'
1048	@echo ''
1049	@echo ' clean_opengl_changed - clean after changing OPENGL setting in config.Makefile'
1050	@echo ' clean_checked_vect - clean units containing vectorization checks'
1051	@echo ' cleanRelinkable - similar to cleanlinked (but skips raxml8 to avoid rebuild)'
1052	@echo ''
1053	@echo ' post_commit_check - Checks whether'
1054	@echo ' * main make targets work,'
1055	@echo ' * dependencies and prototypes are up to date,'
1056	@echo ' * SVN-controlled files remain unaffected by called targets and'
1057	@echo ' * all generated files are ignored.'
1058	@echo ' (has to be called in a clean SVN checkout)'
1059	@echo $(SEP)
1060	@echo ''
1061
1062	relinfo:
1063	@echo ''
1064	@echo $(SEP)
1065	@echo 'Release targets:'
1066	@echo ''
1067	@echo ' inc_candi - increase RC candidate-number (only possible in "rc" branch, not needed for RC1)'
1068	@echo ' inc_patch - increase release patchlevel (only possible in "stable" branch)'
1069	@echo ' inc_minor - increase minor version number (only possible in "trunk")'
1070	@echo ' inc_major - increase MAJOR version number (only possible in "trunk")'
1071	@echo ''
1072	@echo ' show_version - show version tag'
1073	@echo ''
1074	@echo $(SEP)
1075	@echo ''
1076
1077	# auto-generate config.makefile:
1078
1079	config.makefile : config.makefile.template
1080	@echo --------------------------------------------------------------------------------
1081	ifeq ($(CONFIG_MAKEFILE_FOUND),)
1082	@cp $< $@
1083	@echo '$(ARBHOME)/$@:1: has been generated.'
1084	@echo 'Please edit $@ to configure your system!'
1085	@echo --------------------------------------------------------------------------------
1086	@false
1087	else
1088	@echo '$(ARBHOME)/$<:1: is more recent than'
1089	@echo '$(ARBHOME)/$@:1:'
1090	@ls -al config.makefile*
1091	@echo --------------------------------------------------------------------------------
1092	@echo "Updating $@ (if this fails, check manually)"
1093	SOURCE_TOOLS/update_config_makefile.pl
1094	@echo "Sucessfully updated $@"
1095	@echo --------------------------------------------------------------------------------
1096	@ls -al config.makefile*
1097	@echo --------------------------------------------------------------------------------
1098	@echo "Diff to your old config.makefile:"
1099	@echo --------------------------------------------------------------------------------
1100	-diff $@.bak $@
1101	@echo --------------------------------------------------------------------------------
1102	endif
1103
1104	# check if everything is configured correctly
1105
1106	check_DEVELOPER:
1107	ifndef DEVELOPER
1108	@echo 'config.makefile:1: DEVELOPER not defined'
1109	@false
1110	endif
1111
1112	check_DEBUG:
1113	ifndef dflags
1114	@echo 'config.makefile:1: DEBUG has to be defined. Valid values are 0 and 1'
1115	@false
1116	endif
1117
1118	check_ARB_64:
1119	ifndef ARB_64
1120	@echo 'config.makefile:1: ARB_64 has to be defined. Valid values are 0 and 1'
1121	@false
1122	endif
1123
1124	# ---------------------------------------- check gcc version
1125
1126	COMPILER_BROKEN:=0
1127
1128	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.6.4')
1129	COMPILER_BROKEN:=1
1130	endif
1131	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.8.0')
1132	COMPILER_BROKEN:=1
1133	endif
1134
1135	check_same_GCC_VERSION:
1136	$(ARBHOME)/SOURCE_TOOLS/check_same_compiler_version.pl $(COMPILER_NAME) $(COMPILER_VERSION_ALLOWED)
1137
1138	check_GCC_VERSION:
1139	@echo 'Compiler version check:'
1140	# see .@ALLOWED_gcc_VERSIONS
1141	ifeq ('$(COMPILER_VERSION_ALLOWED)', '')
1142	@echo " - Your compiler is '$(COMPILER_NAME)' version '$(COMPILER_VERSION)'"
1143	@echo ' This version is not in the list of supported $(COMPILER_NAME)-versions:'
1144	@$(foreach version,$(ALLOWED_COMPILER_VERSIONS),echo ' * $(version)';)
1145	@echo ' - You may either ..'
1146	@echo ' - add your version to ALLOWED_$(COMPILER_NAME)_VERSIONS in the Makefile and try it out or'
1147	@echo ' - switch to one of the allowed versions (see arb_README_gcc.txt for installing'
1148	@echo ' a different version of gcc)'
1149	$(error Unsupported compiler '$(COMPILER_NAME)' version '$(COMPILER_VERSION)')
1150	else
1151	ifeq ($(COMPILER_BROKEN),1)
1152	$(error compilation refused for $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)'. Refer to http://bugs.arb-home.de/wiki/GccVersionInfo for details.)
1153	else
1154	@echo " - Supported $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)' detected - fine!"
1155	@echo ''
1156	ifeq ($(USE_CLANG),1)
1157	@echo "Dump clang version:"
1158	$(A_CXX) -v
1159	endif
1160	$(MAKE) check_same_GCC_VERSION
1161	endif
1162	endif
1163
1164	#---------------------- check ARBHOME
1165
1166	# use arb_INSTALL.txt to determine whether ARBHOME points to correct directory
1167	ARB_INSTALL_FOUND=$(wildcard $(ARBHOME)/arb_INSTALL.txt)
1168
1169	check_ARBHOME:
1170	ifeq ($(strip $(ARB_INSTALL_FOUND)),)
1171	@echo ------------------------------------------------------------
1172	@echo "ARBHOME is set to '$(ARBHOME)'"
1173	@echo "The environment variable ARBHOME has to point to the top arb source directory."
1174	@echo "If you use bash enter:"
1175	@echo " export ARBHOME='`pwd`'"
1176	@echo ------------------------------------------------------------
1177	@false
1178	endif
1179
1180	ARB_PATH_SET=$(findstring $(ARBHOME)/bin,$(PATH))
1181
1182	check_PATH: check_ARBHOME
1183	ifeq ($(strip $(ARB_PATH_SET)),)
1184	@echo ------------------------------------------------------------
1185	@echo "The environment variable PATH has to contain $(ARBHOME)/bin"
1186	@echo "If you use bash enter:"
1187	@echo ' export PATH=$$ARBHOME/bin:$$PATH'
1188	@echo ------------------------------------------------------------
1189	@false
1190	endif
1191
1192	check_TOOLS:
1193	@util/arb_check_build_env.pl \
1194	"$(A_CC)" \
1195	"$(A_CXX)" \
1196	"$(MAKEDEPEND_PLAIN)" \
1197	"$(LINK_SHARED_LIB)" \
1198	"$(LINK_SHARED_LIB)" \
1199
1200	check_ENVIRONMENT : check_PATH check_TOOLS
1201	@echo "-------------------- Environment [start]"
1202	@echo "ARBHOME='$(ARBHOME)'"
1203	@echo "PATH='$(PATH)'"
1204	@echo "LD_LIBRARY_PATH='$(LD_LIBRARY_PATH)'"
1205	@echo "-------------------- Environment [end]"
1206
1207	check_tabs: check_setup
1208	ifeq ($(DEBUG),1)
1209	@SOURCE_TOOLS/tabBrake.pl
1210	endif
1211
1212	force_tab_check:
1213	@touch -t 198001010000 SOURCE_TOOLS/stamp.tabBrake
1214	@$(MAKE) check_tabs
1215
1216
1217	# ---------------------
1218
1219	check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION
1220	@echo Your setup seems to be ok.
1221
1222	checks: check_setup check_tabs
1223	@rm -f SOURCE_TOOLS/postcompile.sav
1224
1225
1226	# end test section ------------------------------
1227
1228	# ---------------------------------------
1229	# List of standard top level directories
1230	#
1231	# sub-makefiles have to define the targets
1232	# - 'depends' and
1233	# - 'clean'
1234	#
1235	# when adding new libraries/subdirs here, also add a dependency vs 'links' or 'links_non_perl' in .@DD_links_non_perl
1236
1237	TL_ARCHIVES = \
1238	AISC/AISC.a \
1239	ARB_GDE/ARB_GDE.a \
1240	AWTC/AWTC.a \
1241	AWTI/AWTI.a \
1242	CONSENSUS_TREE/CONSENSUS_TREE.a \
1243	CONVERTALN/CONVERTALN.a \
1244	DBSERVER/DBSERVER.a \
1245	DIST/DIST.a \
1246	EDIT4/EDIT4.a \
1247	EISPACK/EISPACK.a \
1248	GENOM/GENOM.a \
1249	GENOM_IMPORT/GENOM_IMPORT.a \
1250	ISLAND_HOPPING/ISLAND_HOPPING.a \
1251	MERGE/MERGE.a \
1252	MULTI_PROBE/MULTI_PROBE.a \
1253	NALIGNER/NALIGNER.a \
1254	NAMES/NAMES.a \
1255	NAMES_COM/server.a \
1256	NTREE/NTREE.a \
1257	PARSIMONY/PARSIMONY.a \
1258	PHYLO/PHYLO.a \
1259	PRIMER_DESIGN/PRIMER_DESIGN.a \
1260	PROBE/PROBE.a \
1261	PROBE_COM/server.a \
1262	PROBE_DESIGN/PROBE_DESIGN.a \
1263	$(RNA3D_LIB) \
1264	RNACMA/RNACMA.a \
1265	SECEDIT/SECEDIT.a \
1266	SEQ_QUALITY/SEQ_QUALITY.a \
1267	SERVERCNTRL/SERVERCNTRL.a \
1268	STAT/STAT.a \
1269	TREEGEN/TREEGEN.a \
1270	WETC/WETC.a \
1271	XML/XML.a \
1272
1273	TL_SHARED_ARCHIVES = \
1274	ARBDB/libARBDB.so \
1275	CORE/libCORE.so \
1276	AWT/libAWT.so \
1277	WINDOW/libWINDOW.so \
1278
1279	TL_ARCHIV_COLLECTIONS = \
1280	SL/SL.archColl \
1281
1282	TL_TOOLS_COLLECTIONS = \
1283	AISC_MKPTPS/AISC_MKPTPS.toolColl \
1284	TOOLS/TOOLS.toolColl \
1285	PERLTOOLS/PERLTOOLS.toolColl \
1286	PROBE_SET/PROBE_SET.toolColl \
1287	READSEQ/READSEQ.toolColl \
1288
1289	RECURSIVE_SUBS = \
1290	GDE/GDE.sub \
1291	UNIT_TESTER/UNIT_TESTER.sub \
1292
1293	SUBDIRS = \
1294	$(RECURSIVE_SUBS) \
1295	$(TL_ARCHIVES:.a=.sub) \
1296	$(TL_SHARED_ARCHIVES:.so=.sub) \
1297	$(TL_ARCHIV_COLLECTIONS:.archColl=.sub) \
1298	$(TL_TOOLS_COLLECTIONS:.toolColl=.sub) \
1299
1300	# sub directories inside TL_ARCHIV_COLLECTIONS
1301	CL_ARCH_DIRS = $(foreach coll,$(TL_ARCHIV_COLLECTIONS),$(shell find $(dir $(coll)) -maxdepth 1 -mindepth 1 -type d))
1302
1303	# archives inside CL_ARCH_DIRS:
1304	CL_ARCHIVES = $(foreach adir,$(CL_ARCH_DIRS),$(dir $(adir))$(notdir $(adir))/$(notdir $(adir)).a)
1305
1306	# -----------------------
1307	# library packets
1308
1309	ARCHS_CLIENT_PROBE = PROBE_COM/client.a
1310	ARCHS_CLIENT_NAMES = NAMES_COM/client.a
1311
1312	ARCHS_MAKEBIN = AISC_MKPTPS/AISC_MKPTPS.a AISC/AISC.a
1313
1314	# communication libs need aisc and aisc_mkpts:
1315
1316	AISC/AISC.dummy: proto_tools
1317
1318	comtools: AISC/AISC.dummy
1319
1320	ARCHS_SEQUENCE = \
1321	SL/SEQUENCE/SEQUENCE.a \
1322	SL/ALIVIEW/ALIVIEW.a \
1323	SL/PRONUC/PRONUC.a \
1324
1325	ARCHS_TREE = \
1326	SL/ARB_TREE/ARB_TREE.a \
1327	SL/FILTER/FILTER.a \
1328	$(ARCHS_SEQUENCE) \
1329
1330	# parsimony tree (used by NTREE, PARSIMONY, STAT(->EDIT4), DIST(obsolete!))
1331	ARCHS_AP_TREE = \
1332	SL/AP_TREE/AP_TREE.a \
1333	$(ARCHS_TREE) \
1334
1335	# --------------------------------------------------------------------------------
1336	# dependencies for linking shared libs
1337
1338	link_core: core
1339	link_db: db link_core
1340	link_aw: aw link_db
1341	link_awt: awt link_aw
1342
1343	#***************************************************************************************
1344	# Individual_Programs_Section
1345	#***************************************************************************************
1346
1347	arbmainwrapper:
1348	$(MAKE) -C SOURCE_TOOLS -r mainwrapper
1349
1350
1351	#********************************* arb_ntree ************************************
1352	NTREE = bin/arb_ntree
1353	ARCHS_NTREE = \
1354	NTREE/NTREE.a \
1355	ARB_GDE/ARB_GDE.a \
1356	SL/GROUP_SEARCH/GROUP_SEARCH.a \
1357	SL/SAICALC/SAICALC.a \
1358	SL/DB_UI/DB_UI.a \
1359	AWTC/AWTC.a \
1360	AWTI/AWTI.a \
1361	CONSENSUS_TREE/CONSENSUS_TREE.a \
1362	GENOM_IMPORT/GENOM_IMPORT.a \
1363	GENOM/GENOM.a \
1364	MERGE/MERGE.a \
1365	MULTI_PROBE/MULTI_PROBE.a \
1366	PRIMER_DESIGN/PRIMER_DESIGN.a \
1367	PROBE_DESIGN/PROBE_DESIGN.a \
1368	SEQ_QUALITY/SEQ_QUALITY.a \
1369	SERVERCNTRL/SERVERCNTRL.a \
1370	SL/ALILINK/ALILINK.a \
1371	SL/AW_NAME/AW_NAME.a \
1372	SL/CONSENSUS/CONSENSUS.a \
1373	SL/DB_SCANNER/DB_SCANNER.a \
1374	SL/DB_QUERY/DB_QUERY.a \
1375	SL/QUERY/QUERY.a \
1376	SL/SEQIO/SEQIO.a \
1377	STAT/STAT.a \
1378	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1379	SL/HELIX/HELIX.a \
1380	SL/REGEXPR/REGEXPR.a \
1381	SL/REFENTRIES/REFENTRIES.a \
1382	SL/NDS/NDS.a \
1383	SL/ITEM_SHADER/ITEM_SHADER.a \
1384	SL/ITEMS/ITEMS.a \
1385	SL/INSDEL/INSDEL.a \
1386	SL/LOCATION/LOCATION.a \
1387	SL/MACROS/MACROS.a \
1388	SL/PVP/PVP.a \
1389	SL/TRANSLATE/TRANSLATE.a \
1390	SL/TREEDISP/TREEDISP.a \
1391	SL/TREE_ADMIN/TREE_ADMIN.a \
1392	SL/TREE_READ/TREE_READ.a \
1393	SL/TREE_WRITE/TREE_WRITE.a \
1394	SL/XFERGUI/XFERGUI.a \
1395	SL/XFERSET/XFERSET.a \
1396	XML/XML.a \
1397	$(ARCHS_AP_TREE) \
1398
1399	ARCHS_NTREE_ALL = $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(XMLLIBS)
1400
1401	$(NTREE): $(ARCHS_NTREE:.a=.dummy) link_awt
1402	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NTREE_ALL) \|\| ( \
1403	echo "$(SEP) Link $@"; \
1404	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE_ALL)" ; \
1405	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE_ALL) && \
1406	echo "$(SEP) Link $@ [done]"; \
1407	)
1408
1409	#********************************* arb_edit4 ************************************
1410	EDIT4 = bin/arb_edit4
1411
1412	ARCHS_EDIT4 := \
1413	EDIT4/EDIT4.a \
1414	ARB_GDE/ARB_GDE.a \
1415	SL/FAST_ALIGNER/FAST_ALIGNER.a \
1416	AWTC/AWTC.a \
1417	ISLAND_HOPPING/ISLAND_HOPPING.a \
1418	SECEDIT/SECEDIT.a \
1419	SERVERCNTRL/SERVERCNTRL.a \
1420	SL/AW_HELIX/AW_HELIX.a \
1421	SL/AW_NAME/AW_NAME.a \
1422	SL/CONSENSUS/CONSENSUS.a \
1423	SL/ITEMS/ITEMS.a \
1424	STAT/STAT.a \
1425	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1426	SL/HELIX/HELIX.a \
1427	SL/TRANSLATE/TRANSLATE.a \
1428	SL/MACROS/MACROS.a \
1429	SL/NDS/NDS.a \
1430	$(ARCHS_AP_TREE) \
1431	XML/XML.a \
1432
1433	ifeq ($(OPENGL),1)
1434	ARCHS_EDIT4 += RNA3D/RNA3D.a
1435	endif
1436
1437	ARCHS_EDIT4_ALL = $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4)
1438
1439	LIBS_EDIT4 := $(GL_LIBS)
1440
1441	$(EDIT4): $(ARCHS_EDIT4:.a=.dummy) link_awt
1442	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_EDIT4_ALL) \|\| ( \
1443	echo "$(SEP) Link $@"; \
1444	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4_ALL)" ; \
1445	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4_ALL) && \
1446	echo "$(SEP) Link $@ [done]"; \
1447	)
1448
1449	#********************************* arb_rnacma ************************************
1450	RNACMA = bin/arb_rnacma
1451	ARCHS_RNACMA = \
1452	RNACMA/RNACMA.a \
1453
1454	ARCHS_RNACMA_ALL = $(ARCHS_RNACMA) $(DBSYS_LIBS)
1455
1456	$(RNACMA) : $(ARCHS_RNACMA:.a=.dummy) link_db
1457	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_RNACMA_ALL) \|\| ( \
1458	echo "$(SEP) Link $@"; \
1459	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_RNACMA_ALL)"; \
1460	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_RNACMA_ALL) && \
1461	echo "$(SEP) Link $@ [done]"; \
1462	)
1463
1464	#********************************* arb_wetc ************************************
1465	WETC = bin/arb_wetc
1466	ARCHS_WETC = \
1467	WETC/WETC.a \
1468	SL/HELIX/HELIX.a \
1469	SL/FILTER/FILTER.a \
1470	XML/XML.a \
1471
1472	ARCHS_WETC_ALL = $(ARCHS_WETC) $(GUI_LIBS)
1473
1474	$(WETC): $(ARCHS_WETC:.a=.dummy) link_awt
1475	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_WETC_ALL) \|\| ( \
1476	echo "$(SEP) Link $@"; \
1477	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC_ALL)" ; \
1478	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC_ALL) && \
1479	echo "$(SEP) Link $@ [done]"; \
1480	)
1481
1482	#********************************* arb_dist ************************************
1483	DIST = bin/arb_dist
1484	ARCHS_DIST = \
1485	DIST/DIST.a \
1486	CONSENSUS_TREE/CONSENSUS_TREE.a \
1487	EISPACK/EISPACK.a \
1488	SERVERCNTRL/SERVERCNTRL.a \
1489	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1490	SL/HELIX/HELIX.a \
1491	SL/MATRIX/MATRIX.a \
1492	SL/MACROS/MACROS.a \
1493	SL/NDS/NDS.a \
1494	SL/ITEMS/ITEMS.a \
1495	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.a \
1496	XML/XML.a \
1497	$(ARCHS_AP_TREE) \
1498
1499	ARCHS_DIST_ALL = $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS)
1500
1501	$(DIST): $(ARCHS_DIST:.a=.dummy) link_awt
1502	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_DIST_ALL) \|\| ( \
1503	echo "$(SEP) Link $@"; \
1504	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST_ALL)" ; \
1505	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST_ALL) && \
1506	echo "$(SEP) Link $@ [done]"; \
1507	)
1508
1509	#********************************* arb_pars ************************************
1510	PARSIMONY = bin/arb_pars
1511	ARCHS_PARSIMONY = \
1512	PARSIMONY/PARSIMONY.a \
1513	SERVERCNTRL/SERVERCNTRL.a \
1514	SL/AW_NAME/AW_NAME.a \
1515	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1516	SL/HELIX/HELIX.a \
1517	SL/MACROS/MACROS.a \
1518	SL/NDS/NDS.a \
1519	SL/ITEMS/ITEMS.a \
1520	SL/TRANSLATE/TRANSLATE.a \
1521	SL/TREEDISP/TREEDISP.a \
1522	XML/XML.a \
1523	$(ARCHS_AP_TREE) \
1524
1525	ARCHS_PARSIMONY_ALL = $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS)
1526
1527	$(PARSIMONY): $(ARCHS_PARSIMONY:.a=.dummy) link_awt
1528	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_PARSIMONY_ALL) \|\| ( \
1529	echo "$(SEP) Link $@"; \
1530	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY_ALL)" ; \
1531	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY_ALL) && \
1532	echo "$(SEP) Link $@ [done]"; \
1533	)
1534
1535	#********************************* arb_convert_aln ************************************
1536	CONVERT_ALN = bin/arb_convert_aln
1537	ARCHS_CONVERT_ALN = \
1538	CONVERTALN/CONVERTALN.a \
1539
1540	ARCHS_CONVERT_ALN_ALL = $(ARCHS_CONVERT_ALN) $(DBSYS_LIBS)
1541
1542	$(CONVERT_ALN) : $(ARCHS_CONVERT_ALN:.a=.dummy) link_db
1543	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_CONVERT_ALN_ALL) \|\| ( \
1544	echo "$(SEP) Link $@"; \
1545	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN_ALL)"; \
1546	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN_ALL) && \
1547	echo "$(SEP) Link $@ [done]"; \
1548	)
1549
1550	#********************************* arb_treegen ************************************
1551
1552	TREEGEN = bin/arb_treegen
1553	ARCHS_TREEGEN = \
1554	TREEGEN/TREEGEN.a \
1555
1556	ARCHS_TREEGEN_ALL = $(ARCHS_TREEGEN)
1557
1558	$(TREEGEN) : $(ARCHS_TREEGEN:.a=.dummy)
1559	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main_C) $(ARCHS_TREEGEN_ALL) \|\| ( \
1560	echo "$(SEP) Link $@"; \
1561	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN_ALL)" ; \
1562	$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN_ALL) && \
1563	echo "$(SEP) Link $@ [done]"; \
1564	)
1565
1566	#********************************* arb_naligner ************************************
1567	NALIGNER = bin/arb_naligner
1568	ARCHS_NALIGNER = \
1569	NALIGNER/NALIGNER.a \
1570	SERVERCNTRL/SERVERCNTRL.a \
1571	SL/HELIX/HELIX.a \
1572
1573	ARCHS_NALIGNER_ALL = $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(DBSYS_LIBS)
1574
1575	$(NALIGNER): $(ARCHS_NALIGNER:.a=.dummy) link_db
1576	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NALIGNER_ALL) \|\| ( \
1577	echo "$(SEP) Link $@"; \
1578	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER_ALL)" ; \
1579	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER_ALL) && \
1580	echo "$(SEP) Link $@ [done]"; \
1581	)
1582
1583	#********************************* arb_phylo ************************************
1584	PHYLO = bin/arb_phylo
1585	ARCHS_PHYLO = \
1586	PHYLO/PHYLO.a \
1587	SL/HELIX/HELIX.a \
1588	SL/FILTER/FILTER.a \
1589	SL/MACROS/MACROS.a \
1590	XML/XML.a \
1591
1592	ARCHS_PHYLO_ALL = $(ARCHS_PHYLO) $(GUI_LIBS)
1593
1594	$(PHYLO): $(ARCHS_PHYLO:.a=.dummy) link_awt
1595	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_PHYLO_ALL) \|\| ( \
1596	echo "$(SEP) Link $@"; \
1597	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO_ALL)" ; \
1598	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO_ALL) && \
1599	echo "$(SEP) Link $@ [done]"; \
1600	)
1601
1602	#***************************************************************************************
1603	# SERVER SECTION
1604	#***************************************************************************************
1605
1606	#********************************* arb_db_server ************************************
1607	DBSERVER = bin/arb_db_server
1608	ARCHS_DBSERVER = \
1609	DBSERVER/DBSERVER.a \
1610	SERVERCNTRL/SERVERCNTRL.a \
1611
1612	ARCHS_DBSERVER_ALL = $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS)
1613
1614	$(DBSERVER): $(ARCHS_DBSERVER:.a=.dummy) link_db
1615	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_DBSERVER_ALL) \|\| ( \
1616	echo "$(SEP) Link $@"; \
1617	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER_ALL)" ; \
1618	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER_ALL) && \
1619	echo "$(SEP) Link $@ [done]"; \
1620	)
1621
1622	#********************************* arb_pt_server ************************************
1623	PROBE = bin/arb_pt_server
1624
1625	ARCHS_PROBE_DEPEND = \
1626	PROBE/PROBE.a \
1627	SL/PTCLEAN/PTCLEAN.a \
1628	SERVERCNTRL/SERVERCNTRL.a \
1629	SL/HELIX/HELIX.a \
1630
1631	ARCHS_PROBE_ALL = $(ARCHS_PROBE_DEPEND) $(ARCHS_CLIENT_PROBE) $(ARBDB_LIB) $(SYSLIBS)
1632
1633	$(PROBE): $(ARCHS_PROBE_DEPEND:.a=.dummy) link_db
1634	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) config.makefile $(ARCHS_PROBE_ALL) \|\| ( \
1635	echo "$(SEP) Link $@"; \
1636	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_ALL)" ; \
1637	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_ALL) && \
1638	echo "$(SEP) Link $@ [done]"; \
1639	)
1640
1641	#********************************* arb_name_server ************************************
1642	NAMES = bin/arb_name_server
1643	ARCHS_NAMES = \
1644	NAMES/NAMES.a \
1645	SERVERCNTRL/SERVERCNTRL.a \
1646
1647	ARCHS_NAMES_ALL = $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS)
1648
1649	$(NAMES): $(ARCHS_NAMES:.a=.dummy) link_db
1650	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NAMES_ALL) \|\| ( \
1651	echo "$(SEP) Link $@"; \
1652	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES_ALL)" ; \
1653	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES_ALL) && \
1654	echo "$(SEP) Link $@ [done]"; \
1655	)
1656
1657	#********************************* SHARED LIBRARIES SECTION ************************************
1658
1659	prepare_libdir: addlibs
1660
1661	addlibs:
1662	(perl $(ARBHOME)/SOURCE_TOOLS/provide_libs.pl \
1663	"arbhome=$(ARBHOME)" \
1664	"opengl=$(OPENGL)" \
1665	"link_static=$(LINK_STATIC)" \
1666	)
1667
1668	#***************************************************************************************
1669	# Recursive calls to sub-makefiles
1670	#***************************************************************************************
1671
1672	%.depends:
1673	@cp -p $(@D)/Makefile $(@D)/Makefile.old # save old Makefile
1674	@$(MAKE) -C $(@D) -r \
1675	"AUTODEPENDS=1" \
1676	"MAIN=nothing" \
1677	"cflags=noCflagsHere_use_MAKEDEPENDFLAGS" \
1678	"cxxflags=noCxxflagsHere_use_MAKEDEPENDFLAGS" \
1679	depends
1680	@grep "^# DO NOT DELETE" $(@D)/Makefile >/dev/null
1681	@cat $(@D)/Makefile \
1682	\| SOURCE_TOOLS/fix_depends.pl "(from main)" \
1683	>$(@D)/Makefile.2
1684	@mv $(@D)/Makefile.old $(@D)/Makefile # restore old Makefile
1685	@$(ARBHOME)/SOURCE_TOOLS/mv_if_diff $(@D)/Makefile.2 $(@D)/Makefile # update Makefile if changed
1686
1687	%.proto:
1688	@($(MAKE) -C $(@D) \
1689	"AUTODEPENDS=0" \
1690	"MAIN=nothing" \
1691	"cflags=noCflags" \
1692	"cxxflags=noCxxflags" \
1693	proto 2>&1 ) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
1694
1695	%.clean:
1696	@$(MAKE) -C $(@D) \
1697	"AUTODEPENDS=0" \
1698	"MAIN=nothing" \
1699	"cflags=noCflags" \
1700	"cxxflags=noCxxflags" \
1701	clean
1702
1703
1704	# stop wrong targets:
1705	target_is_missing_lib_prefix:
1706	@echo "Error: Denied to build shared library target with missing 'lib'-prefix"
1707	false
1708
1709	ARBDB/ARBDB.dummy: target_is_missing_lib_prefix
1710	CORE/CORE.dummy: target_is_missing_lib_prefix
1711	AWT/AWT.dummy: target_is_missing_lib_prefix
1712	WINDOW/WINDOW.dummy: target_is_missing_lib_prefix
1713
1714	# rule to generate main target (normally a library):
1715	# @@@ check effect of setting LANG=C below
1716	%.dummy:
1717	@( export ID=$$$$; LANG=C; \
1718	(( \
1719	echo "$(SEP) Make $(@D)"; \
1720	$(MAKE) -C $(@D) -r \
1721	"AUTODEPENDS=1" \
1722	"MAIN=$(@F:.dummy=.a)" \
1723	"cflags=$(cflags) -DIN_ARB_$(subst /,_,$(@D))" \
1724	&& \
1725	echo "$(SEP) Make $(@D) [done]"; \
1726	) >$(@D).$$ID.log 2>&1 && (cat $(@D).$$ID.log;rm $(@D).$$ID.log)) \|\| (cat $(@D).$$ID.log;rm $(@D).$$ID.log;false))
1727
1728	# Additional dependencies for subtargets:
1729
1730	PROBE_COM/PROBE_COM.dummy : comtools
1731	NAMES_COM/NAMES_COM.dummy : comtools
1732
1733	com: PROBE_COM/PROBE_COM.dummy NAMES_COM/NAMES_COM.dummy
1734
1735	# stop wrong more targets:
1736	PROBE_COM/server.dummy:
1737	@echo Unwanted request to make target $<
1738	false
1739
1740	PROBE_COM/client.dummy:
1741	@echo Unwanted request to make target $<
1742	false
1743
1744	NAMES_COM/server.dummy:
1745	@echo Unwanted request to make target $<
1746	false
1747
1748	NAMES_COM/client.dummy:
1749	@echo Unwanted request to make target $<
1750	false
1751
1752
1753	ARBDB/libARBDB.dummy: links
1754	CORE/libCORE.dummy: links
1755
1756	PERLTOOLS/PERLTOOLS.dummy: core db
1757
1758	# all subdirs perl not depends on go here (ADD_links_non_perl)
1759	AWT/libAWT.dummy: links_non_perl
1760	AWTI/AWTI.dummy: links_non_perl
1761	CONSENSUS_TREE/CONSENSUS_TREE.dummy: links_non_perl
1762	CONVERTALN/CONVERTALN.dummy: links_non_perl
1763	DBSERVER/DBSERVER.dummy: links_non_perl
1764	DIST/DIST.dummy: links_non_perl
1765	EDIT4/EDIT4.dummy: links_non_perl com
1766	EISPACK/EISPACK.dummy: links_non_perl
1767	GDE/GDE.dummy: links_non_perl
1768	GENOM/GENOM.dummy: links_non_perl
1769	GENOM_IMPORT/GENOM_IMPORT.dummy: links_non_perl
1770	ISLAND_HOPPING/ISLAND_HOPPING.dummy: links_non_perl
1771	MERGE/MERGE.dummy: links_non_perl
1772	NTREE/NTREE.dummy: links_non_perl
1773	PARSIMONY/PARSIMONY.dummy: links_non_perl
1774	PHYLO/PHYLO.dummy: links_non_perl
1775	PRIMER_DESIGN/PRIMER_DESIGN.dummy: links_non_perl
1776	PROBE_SET/PROBE_SET.dummy: links_non_perl link_db
1777	READSEQ/READSEQ.dummy: links_non_perl
1778	RNACMA/RNACMA.dummy: links_non_perl header_libs
1779	SECEDIT/SECEDIT.dummy: links_non_perl
1780	SEQ_QUALITY/SEQ_QUALITY.dummy: links_non_perl
1781	SERVERCNTRL/SERVERCNTRL.dummy: links_non_perl com
1782	SL/ALILINK/ALILINK.dummy: links_non_perl
1783	SL/ALIVIEW/ALIVIEW.dummy: links_non_perl
1784	SL/AP_TREE/AP_TREE.dummy: links_non_perl
1785	SL/ARB_TREE/ARB_TREE.dummy: links_non_perl
1786	SL/AW_HELIX/AW_HELIX.dummy: links_non_perl
1787	SL/CONSENSUS/CONSENSUS.dummy: links_non_perl
1788	SL/DB_QUERY/DB_QUERY.dummy: links_non_perl
1789	SL/DB_SCANNER/DB_SCANNER.dummy: links_non_perl
1790	SL/DB_UI/DB_UI.dummy: links_non_perl
1791	SL/FAST_ALIGNER/FAST_ALIGNER.dummy: links_non_perl
1792	SL/FILTER/FILTER.dummy: links_non_perl
1793	SL/FILTSEQEXP/FILTSEQEXP.dummy: links_non_perl
1794	SL/GROUP_SEARCH/GROUP_SEARCH.dummy: links_non_perl
1795	SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy: links_non_perl
1796	SL/HELIX/HELIX.dummy: links_non_perl
1797	SL/INSDEL/INSDEL.dummy: links_non_perl
1798	SL/ITEM_SHADER/ITEM_SHADER.dummy: links_non_perl
1799	SL/ITEMS/ITEMS.dummy: links_non_perl
1800	SL/LOCATION/LOCATION.dummy: links_non_perl
1801	SL/MACROS/MACROS.dummy: links_non_perl
1802	SL/MATRIX/MATRIX.dummy: links_non_perl
1803	SL/NDS/NDS.dummy: links_non_perl
1804	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.dummy: links_non_perl
1805	SL/PRONUC/PRONUC.dummy: links_non_perl
1806	SL/PTCLEAN/PTCLEAN.dummy: links_non_perl link_db
1807	SL/PVP/PVP.dummy: links_non_perl
1808	SL/QUERY/QUERY.dummy: links_non_perl link_db
1809	SL/REFENTRIES/REFENTRIES.dummy: links_non_perl
1810	SL/REGEXPR/REGEXPR.dummy: links_non_perl
1811	SL/SAICALC/SAICALC.dummy: links_non_perl
1812	SL/SEQIO/SEQIO.dummy: links_non_perl
1813	SL/SEQUENCE/SEQUENCE.dummy: links_non_perl
1814	SL/TRANSLATE/TRANSLATE.dummy: links_non_perl
1815	SL/TREE_ADMIN/TREE_ADMIN.dummy: links_non_perl
1816	SL/TREE_READ/TREE_READ.dummy: links_non_perl
1817	SL/TREE_WRITE/TREE_WRITE.dummy: links_non_perl
1818	SL/TREEDISP/TREEDISP.dummy: links_non_perl
1819	SL/XFERGUI/XFERGUI.dummy: links_non_perl
1820	SL/XFERSET/XFERSET.dummy: links_non_perl
1821	STAT/STAT.dummy: links_non_perl
1822	TREEGEN/TREEGEN.dummy: links_non_perl
1823	WETC/WETC.dummy: links_non_perl
1824	WINDOW/libWINDOW.dummy: links_non_perl
1825	XML/XML.dummy: links_non_perl
1826
1827	ifeq ($(OPENGL),1)
1828	GL/glAW/glAW.dummy: links_non_perl
1829	GL/glpng/glpng.dummy: links_non_perl
1830	GL/GL.dummy: GL/glAW/glAW.dummy GL/glpng/glpng.dummy
1831	RNA3D/RNA3D.dummy: links_non_perl gl
1832	endif
1833
1834	UNIT_TESTER/UNIT_TESTER.dummy: link_db \
1835	SERVERCNTRL/SERVERCNTRL.dummy \
1836
1837	# see also TOOLS/Makefile@TOOLSLIBDEPENDS
1838	TOOLS/TOOLS.dummy : links_non_perl link_db \
1839	CONSENSUS_TREE/CONSENSUS_TREE.dummy \
1840	SERVERCNTRL/SERVERCNTRL.dummy \
1841	SL/FILTER/FILTER.dummy \
1842	SL/FILTSEQEXP/FILTSEQEXP.dummy \
1843	SL/INSDEL/INSDEL.dummy \
1844	SL/REGEXPR/REGEXPR.dummy \
1845	SL/SEQIO/SEQIO.dummy \
1846	SL/TREE_READ/TREE_READ.dummy \
1847	SL/TREE_WRITE/TREE_WRITE.dummy \
1848	XML/XML.dummy \
1849
1850	AWTC/AWTC.dummy : com
1851
1852	NAMES/NAMES.dummy : com
1853	SL/AW_NAME/AW_NAME.dummy : com
1854
1855	PROBE/PROBE.dummy : com
1856	MULTI_PROBE/MULTI_PROBE.dummy : com
1857	PROBE_DESIGN/PROBE_DESIGN.dummy : com
1858	NALIGNER/NALIGNER.dummy : com
1859
1860	ARB_GDE/ARB_GDE.dummy : proto_tools
1861
1862	compile_compatibility: SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.dummy
1863
1864	#***************************************************************************************
1865	# Short aliases to make targets
1866	#***************************************************************************************
1867
1868	show:
1869	@echo $(SEP)
1870	@echo 'Aliases for often needed targets:'
1871	@echo ''
1872	@echo ' executables:'
1873	@echo ''
1874	@echo ' nt arb_ntree'
1875	@echo ' e4 arb_edit4 (includes secedit)'
1876	@echo ' di arb_dist'
1877	@echo ' ph arb_phylo'
1878	@echo ' pa arb_parsimony'
1879	@echo ' tg arb_treegen'
1880	@echo ' ds arb_dbserver'
1881	@echo ' pt arb_pt_server'
1882	@echo ' na arb_name_server'
1883	@echo ''
1884	@echo ' libraries:'
1885	@echo ''
1886	@echo ' com communication libraries'
1887	@echo ' db ARB database'
1888	@echo ' aw GUI lib'
1889	@echo ' awt GUI toolkit'
1890	@echo ' awtc general purpose library'
1891	@echo ' awti import/export library'
1892	@echo ' mp multi probe library'
1893	@echo ' ge genome library'
1894	@echo ' pd probe design lib'
1895	@echo ' prd primer design lib'
1896	@echo ''
1897	@echo ' other targets:'
1898	@echo ''
1899	@echo ' help recompile help files'
1900	@echo ' tools make small tools used by arb'
1901	@echo ''
1902	@echo ' foreign targets:'
1903	@echo ''
1904	@echo ' gde GDE'
1905	@echo ' agde ARB_GDE'
1906	@echo ''
1907	@echo 'for other targets inspect $(ARBHOME)/Makefile'
1908	@echo ''
1909	@echo $(SEP)
1910
1911	source_doc:
1912	@echo "Remove some links (doxygen crashes otherwise):"
1913	find . $ -name "AISC" -o -name "C" -o -name "GDEHELP" $ -type l -exec rm {} \;
1914	doxygen 2>&1 1>/dev/null
1915	$(MAKE) forcelinks
1916
1917	dep_graph:
1918	@echo "Building some dependency graphs"
1919	SOURCE_TOOLS/dependency_graphs.pl
1920
1921	help: HELP_SOURCE/HELP_SOURCE.dummy
1922
1923	HELP_SOURCE/HELP_SOURCE.dummy: link_core xml menus
1924
1925	db: ARBDB/libARBDB.dummy
1926	core: CORE/libCORE.dummy
1927	aw: WINDOW/libWINDOW.dummy
1928	awt: AWT/libAWT.dummy
1929	awtc: AWTC/AWTC.dummy
1930	awti: AWTI/AWTI.dummy
1931
1932	mp: MULTI_PROBE/MULTI_PROBE.dummy
1933	mg: MERGE/MERGE.dummy
1934	ge: GENOM/GENOM.dummy
1935	prd: PRIMER_DESIGN/PRIMER_DESIGN.dummy
1936
1937	nt: menus $(NTREE)
1938
1939	nal: $(NALIGNER)
1940
1941	di: $(DIST)
1942	ph: $(PHYLO)
1943	pa: $(PARSIMONY)
1944	tg: $(TREEGEN)
1945
1946	ifeq ($(OPENGL),1)
1947	3d: RNA3D/RNA3D.dummy
1948	gl: GL/GL.dummy
1949	else
1950	noopengl:
1951	@echo "invalid target for OPENGL=0"
1952	3d: noopengl
1953	gl: noopengl
1954	endif
1955
1956	SL/SL.dummy: com
1957
1958	ds: $(DBSERVER)
1959	pt: $(PROBE)
1960	pst: PROBE_SET/PROBE_SET.dummy
1961	pd: PROBE_DESIGN/PROBE_DESIGN.dummy
1962	na: $(NAMES)
1963	sq: SEQ_QUALITY/SEQ_QUALITY.dummy
1964	cma: $(RNACMA)
1965
1966	sec: SECEDIT/SECEDIT.dummy
1967
1968	e4: $(EDIT4) readseq menus
1969
1970	gi: GENOM_IMPORT/GENOM_IMPORT.dummy
1971	wetc: $(WETC)
1972
1973	xml: XML/XML.dummy
1974	stat: STAT/STAT.dummy $(NTREE) $(EDIT4)
1975	fa: SL/FAST_ALIGNER/FAST_ALIGNER.dummy
1976
1977	#********************************************************************************
1978
1979	up_by_remake: depends proto vectorize_checks
1980
1981	up: up_by_remake tags valgrind_update
1982
1983	#********************************************************************************
1984
1985	touch:
1986	SOURCE_TOOLS/touch_modified.pl
1987
1988	modified: touch
1989	$(MAKE) all
1990
1991	#********************************************************************************
1992
1993	libdepends:
1994	$(MAKE) -C "SOURCE_TOOLS" \
1995	"RNA3D_LIB=$(RNA3D_LIB_4_DEPENDS)" \
1996	libdepends
1997
1998	#********************************************************************************
1999
2000	# create generated headers:
2001	genheaders: TEMPLATES/TEMPLATES.dummy
2002
2003	clrdotdepends:
2004	rm PROBE_COM/.depends \|\| true
2005	rm NAMES_COM/.depends \|\| true
2006	rm PERL2ARB/.depends \|\| true
2007
2008	comdepends: comtools clrdotdepends
2009	@echo "$(SEP) Partially build com interface"
2010	$(MAKE) PROBE_COM/PROBE_COM.depends NAMES_COM/NAMES_COM.depends
2011	$(MAKE) PROBE_COM/server.depends NAMES_COM/server.depends
2012
2013	depends: genheaders comdepends vectorize_checks
2014	@echo "$(SEP) Updating other dependencies"
2015	$(MAKE) $(subst NAMES_COM/server.depends,,$(subst PROBE_COM/server.depends,,$(SUBDIRS:.sub=.depends))) \
2016	HELP_SOURCE/HELP_SOURCE.depends \
2017	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.depends \
2018
2019	$(MAKE) libdepends
2020
2021	depend: depends
2022
2023	# ------------------------------------------------------------
2024	# dependency generation tests for AISC code
2025	#(all should work w/o creating wrong dependencies;
2026	# neither in XXX_COM/Makefile nor in code using AISC interface)
2027	dependstest1: silent_clean
2028	$(MAKE) depends
2029	dependstest2: silent_clean
2030	$(MAKE) com
2031	dependstest3: silent_clean
2032	$(MAKE) aw
2033	dependstest4: silent_clean
2034	$(MAKE) pt
2035	dependstest5: silent_clean
2036	$(MAKE) na
2037	dependstest6: silent_clean
2038	$(MAKE) nt
2039	dependstest7: silent_clean
2040	$(MAKE) all
2041	# ------------------------------------------------------------
2042
2043	vectorize_checks:
2044	$(MAKE) -C SOURCE_TOOLS -r vectorize_checks
2045
2046	clean_checked_vect: lib/lib.clean
2047	SOURCE_TOOLS/clean_checked_vectorizations.sh
2048
2049	# ------------------------------------------------------------
2050
2051	AISC_MKPTPS/AISC_MKPTPS.dummy: links
2052
2053	proto_tools: AISC_MKPTPS/AISC_MKPTPS.dummy
2054
2055	proto: proto_tools
2056	@echo $(SEP) Updating prototypes
2057	$(MAKE) \
2058	ARBDB/ARBDB.proto \
2059	AISC_COM/AISC_COM.proto \
2060	ARB_GDE/ARB_GDE.proto \
2061	CORE/CORE.proto \
2062	CONVERTALN/CONVERTALN.proto \
2063	NTREE/NTREE.proto \
2064	MERGE/MERGE.proto \
2065	PROBE/PROBE.proto \
2066	SERVERCNTRL/SERVERCNTRL.proto \
2067	SL/SL.proto \
2068
2069	#********************************************************************************
2070
2071	valgrind_update: links
2072	@echo $(SEP) Updating for valgrind
2073	$(MAKE) -C SOURCE_TOOLS valgrind_update
2074
2075	#********************************************************************************
2076
2077	TAGFILE=TAGS
2078	UTAGS=TAGS.$(ARBBID)
2079	TAGFILE_TMP=$(UTAGS).tmp
2080
2081	TAG_SOURCE_HEADERS=$(UTAGS).headers.tmp
2082	TAG_SOURCE_CODE=$(UTAGS).codefiles.tmp
2083	TAG_SOURCE_LISTS=$(TAG_SOURCE_HEADERS) $(TAG_SOURCE_CODE)
2084
2085	ETAGS_IGNORE_LIST=SOURCE_TOOLS/etags_ignore.lst
2086
2087	ETAGS=ctags -e -I @$(ETAGS_IGNORE_LIST) --sort=no --if0=no --extra=q
2088	ETAGS_TYPES=--C-kinds=cgnsut --C++-kinds=cgnsut
2089	ETAGS_FUN =--C-kinds=fm --C++-kinds=fm
2090	ETAGS_REST =--C-kinds=dev --C++-kinds=dev
2091
2092	FILTER_TAGS_SOURCES= \
2093	$(SED) -e 's/^.\///g' \| \
2094	grep -vi '^HEADERLIBS\\|^GDE/\\|/GEN[CH]/'
2095
2096	$(TAG_SOURCE_HEADERS): links
2097	@find . $ -name '.hxx' -o -name ".h" $ -type f \| $(FILTER_TAGS_SOURCES) > $@
2098
2099	$(TAG_SOURCE_CODE): links
2100	@find . $ -name '.cxx' -o -name ".c" $ -type f \| $(FILTER_TAGS_SOURCES) > $@
2101
2102	$(UTAGS).1.tmp: $(TAG_SOURCE_HEADERS)
2103	@$(ETAGS) -f $@ $(ETAGS_TYPES) -L $<
2104	$(UTAGS).2.tmp: $(TAG_SOURCE_HEADERS)
2105	@$(ETAGS) -f $@ $(ETAGS_FUN) -L $<
2106	$(UTAGS).3.tmp: $(TAG_SOURCE_HEADERS)
2107	@$(ETAGS) -f $@ $(ETAGS_REST) -L $<
2108	$(UTAGS).4.tmp: $(TAG_SOURCE_CODE)
2109	@$(ETAGS) -f $@ $(ETAGS_TYPES) -L $<
2110	$(UTAGS).5.tmp: $(TAG_SOURCE_CODE)
2111	@$(ETAGS) -f $@ $(ETAGS_FUN) -L $<
2112	$(UTAGS).6.tmp: $(TAG_SOURCE_CODE)
2113	@$(ETAGS) -f $@ $(ETAGS_REST) -L $<
2114
2115	TAGS_ALL_PARTS=$(UTAGS).1.tmp $(UTAGS).2.tmp $(UTAGS).3.tmp $(UTAGS).4.tmp $(UTAGS).5.tmp $(UTAGS).6.tmp
2116
2117	$(TAGFILE_TMP) : $(TAGS_ALL_PARTS)
2118	@cat $(TAGS_ALL_PARTS) > $@
2119	@rm $(TAGS_ALL_PARTS) $(TAG_SOURCE_LISTS)
2120
2121	cleanOldTags:
2122	@find $(ARBHOME) -name 'TAGS.*.tmp' -ctime +2 -exec rm {} \;
2123
2124	tags: $(TAGFILE_TMP) cleanOldTags
2125	@mv_if_diff $(TAGFILE_TMP) $(TAGFILE)
2126
2127	#********************************************************************************
2128
2129	LINKSTAMP=SOURCE_TOOLS/stamp.generate_all_links
2130
2131	links: checks $(LINKSTAMP) arbmainwrapper
2132	links_no_checks: $(LINKSTAMP) arbmainwrapper
2133
2134	forcelinks:
2135	-rm $(LINKSTAMP)
2136	$(MAKE) links
2137
2138	$(LINKSTAMP): SOURCE_TOOLS/generate_all_links.sh genheaders
2139	+SOURCE_TOOLS/generate_all_links.sh
2140	touch $(LINKSTAMP)
2141
2142	clean_links:
2143	# avoid to delete linked pts, nas or arb_tcp.dat:
2144	find . -path './lib' -prune -o -type l -exec rm {} \;
2145	# removed obsolete file - refuses to disappear due to 'prune' above
2146	@rm -f lib/help/GDEHELP
2147	@rm -f $(LINKSTAMP) lib/inputMasks/format.readme
2148
2149	redo_links: clean_links
2150	$(MAKE) links_no_checks
2151
2152	#********************************************************************************
2153
2154	header_libs:
2155	@(( \
2156	echo "$(SEP) Make HEADERLIBS"; \
2157	$(MAKE) -C HEADERLIBS all && \
2158	echo "$(SEP) Make HEADERLIBS [done]"; \
2159	) > HEADERLIBS.log 2>&1 && (cat HEADERLIBS.log;rm HEADERLIBS.log)) \|\| (cat HEADERLIBS.log;rm HEADERLIBS.log;false)
2160
2161	#********************************************************************************
2162
2163	gde: GDE/GDE.dummy
2164	GDE: gde
2165	agde: ARB_GDE/ARB_GDE.dummy
2166	tools: TOOLS/TOOLS.dummy
2167	convert: $(CONVERT_ALN)
2168	readseq: READSEQ/READSEQ.dummy
2169
2170	#***************************************************************************************
2171	# Some user commands
2172	#***************************************************************************************
2173
2174	menus: binlink links
2175	@(( \
2176	echo "$(SEP) Make GDEHELP"; \
2177	$(MAKE) -C GDEHELP -r all && \
2178	echo "$(SEP) Make GDEHELP [done]"; \
2179	) > GDEHELP.log 2>&1 && (cat GDEHELP.log;rm GDEHELP.log)) \|\| (cat GDEHELP.log;rm GDEHELP.log;false)
2180
2181	ifeq ($(DEBUG),1)
2182	BIN_TARGET=develall
2183	else
2184	BIN_TARGET=all
2185	endif
2186
2187
2188	binlink:
2189	$(MAKE) -C bin $(BIN_TARGET)
2190
2191	check_bin_dep: binlink
2192	SOURCE_TOOLS/check_bin_dependencies.pl
2193
2194	fig_cure:
2195	SOURCE_TOOLS/sortfig.pl doit
2196
2197	preplib:
2198	(cd lib;$(MAKE) all)
2199
2200	# --------------------------------------------------------------------------------
2201	# This section is quite tricky:
2202	#
2203	# make 'perl' is a BIG target, so when it has to be made, it has to be started
2204	# as early as possible to reduce overall compile time. Since 'make' does not
2205	# provide any priorities, i force it to build all 'perl'-prerequisites early, by
2206	# adding artificial dependencies to these prerequisites
2207	#
2208	# That behavior is likely to be system-dependent.
2209	# My goal was only to make it work on my current development system,
2210	# where this saves about 20% of overall build time.
2211
2212	ifeq ($(WITHPERL),1)
2213	links_non_perl: PERLTOOLS/PERLTOOLS.dummy
2214	perltools: links_non_perl
2215	perl: realperl
2216	else
2217	links_non_perl: links
2218	perl: links
2219	$(MAKE) "WITHPERL=1" perl
2220	endif
2221
2222	# ---------------------------------------- perl
2223
2224	realperl: perltools
2225	(( \
2226	echo "$(SEP) Make PERL2ARB" ; \
2227	$(TIME) $(MAKE) -C PERL2ARB -r -f Makefile.main \
2228	"AUTODEPENDS=1" \
2229	"dflags=$(dflags)" \
2230	"cflags4perl=$(cflags) $(cxxflags) $(dflags)" \
2231	"lflags4perl=$(lflags4perl)" \
2232	"COMPILER_VERSION=$(COMPILER_VERSION)" \
2233	all && \
2234	$(MAKE) -C PERL_SCRIPTS/test test && \
2235	echo "$(SEP) Make PERL2ARB [done]" ; \
2236	) > PERL2ARB.log 2>&1 && (cat PERL2ARB.log;rm PERL2ARB.log)) \|\| (cat PERL2ARB.log;rm PERL2ARB.log;false)
2237
2238	perl_clean:
2239	@$(MAKE) -C PERL2ARB -r -f Makefile.main \
2240	"AUTODEPENDS=0" \
2241	clean
2242
2243	PERL2ARB/PERL2ARB.clean:
2244	$(MAKE) perl_clean
2245	$(MAKE) -C PERL_SCRIPTS/test clean
2246
2247	# ---------------------------------------- bindings to script languages
2248
2249	bindings: lib/libCORE.so lib/libARBDB.so
2250	$(MAKE) -C BINDINGS all ARBDEPENDS="$(^:%=../%)" DFLAGS="$(dflags)"
2251
2252	bindings_clean:
2253	$(MAKE) -C BINDINGS clean
2254
2255	# ----------------------------------------
2256
2257	CLOC=cloc-1.08.pl
2258	CLOCFLAGS=--no3 --quiet --progress-rate=0
2259	CLOCARB=--exclude-dir=GDE .
2260	CLOCEXT=GDE
2261	CLOCCODE=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.code.def
2262	CLOCREST=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.rest.def
2263	CLOCFILT=tail --lines=+4
2264
2265	cloc:
2266	@echo 'Arb code:'
2267	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCARB) \| $(CLOCFILT)
2268	@echo 'Arb rest:'
2269	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCARB) \| $(CLOCFILT)
2270	@echo 'External code:'
2271	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCEXT) \| $(CLOCFILT)
2272	@echo 'External rest:'
2273	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCEXT) \| $(CLOCFILT)
2274
2275	# ---------------------------------------- check resources
2276
2277	check_res:
2278	$(ARBHOME)/SOURCE_TOOLS/check_resources.pl
2279
2280	# ---------------------------------------- cleaning
2281
2282	rmbak:
2283	@echo "[cleanup backup/core files]"
2284	@find . \( -name '*%' \
2285	-o -name '*.bak' \
2286	-o -name '*~' \) \
2287	-o $ -name 'core' -a \! -type d $ \
2288	-exec rm -v {} \; \|\| \
2289	echo "Warning: target 'rmbak' reported problems when removing misc. backup files (ignored)"
2290	@echo "[cleanup done]"
2291
2292	bin_reinit:
2293	$(MAKE) bin/bin.clean
2294	$(MAKE) -C "bin" all
2295
2296	clean_directories:
2297	-rm -rf \
2298	$(ARBHOME)/PROBE_SET/bin \
2299	$(ARBHOME)/INCLUDE \
2300
2301	libclean:
2302	-find $(ARBHOME) -type f $ -name '*.a' ! -type l $ -exec rm -f {} \;
2303	-find $(ARBHOME) -type f $ -name 'lib*.so' ! -type l $ -exec rm -f {} \;
2304
2305	objclean:
2306	-find $(ARBHOME) -type f $ -name '*.o' ! -type l $ -exec rm -f {} \;
2307
2308	# bin.clean and HELP_SOURCE.clean interfere
2309	clean3:
2310	$(MAKE) bin/bin.clean
2311	$(MAKE) HELP_SOURCE/HELP_SOURCE.clean
2312
2313
2314	# delete all binaries (similar to 'cleanlinked')
2315	cleanRelinkable: libclean UNIT_TESTER/UNIT_TESTER.clean
2316	$(MAKE) -C bin cleanbinariesRelinkable
2317	$(MAKE) -C PROBE_SET cleanLinked
2318
2319
2320	clean2: $(SUBDIRS:.sub=.clean) \
2321	clean3 \
2322	rmbak \
2323	libclean \
2324	objclean \
2325	lib/lib.clean \
2326	GDEHELP/GDEHELP.clean \
2327	HEADERLIBS/HEADERLIBS.clean \
2328	SOURCE_TOOLS/SOURCE_TOOLS.clean \
2329	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.clean \
2330	UNIT_TESTER/UNIT_TESTER.clean \
2331	TEMPLATES/TEMPLATES.clean \
2332	perl_clean \
2333	clean_directories \
2334
2335	rm -f .last_gcc .last_compiler config.makefile.bak
2336
2337	# links are needed for cleanup
2338	clean: redo_links motif_xpm_hack_clean
2339	$(MAKE) clean2
2340	$(MAKE) clean_cov_all clean_links
2341
2342	silent_clean:
2343	$(MAKE) clean >/dev/null
2344
2345	# 'relocated' is about 50% faster than 'rebuild'
2346	reloc_clean: links
2347	@echo "---------------------------------------- Relocation cleanup"
2348	$(MAKE) \
2349	perl_clean \
2350	GDEHELP/GDEHELP.clean \
2351	HELP_SOURCE/genhelp/genhelp.clean \
2352	bin/bin.clean \
2353	libclean \
2354	objclean
2355
2356	relocated: links
2357	$(MAKE) reloc_clean
2358	@echo "---------------------------------------- and remake"
2359	$(MAKE) build
2360
2361	# -----------------------------------
2362	# some stress tests
2363	# (helpful to reveal race conditions with -j)
2364
2365	rebuild4ever: rebuild
2366	$(MAKE) rebuild4ever
2367
2368	build4ever: build
2369	$(MAKE) build4ever
2370
2371	clean4ever: clean
2372	$(MAKE) clean4ever
2373
2374	test4ever: ut
2375	$(MAKE) test4ever
2376
2377	perl4ever: clean
2378	$(MAKE) links
2379	$(MAKE) perl
2380	$(MAKE) perl4ever
2381
2382	help4ever: clean
2383	$(MAKE) help
2384	$(MAKE) help4ever
2385
2386	# -----------------------------------
2387
2388	rebuild: clean
2389	$(MAKE) all
2390
2391	cleanlinked: bin/bin.clean libclean
2392
2393	relink: cleanlinked
2394	$(MAKE) all
2395
2396	tarfile: rebuild
2397	$(MAKE) prepare_libdir
2398	util/arb_compress
2399
2400	tarfile_quick: build
2401	$(MAKE) prepare_libdir
2402	util/arb_compress
2403
2404	save: sourcetarfile
2405
2406	patch:
2407	SOURCE_TOOLS/arb_create_patch.sh arbPatch
2408
2409	# test early whether save will work
2410	savetest:
2411	@util/arb_srclst.pl >/dev/null
2412
2413	testsave: savetest
2414
2415	sourcetarfile: rmbak
2416	util/arb_save
2417
2418	save2: rmbak
2419	util/arb_save ignore
2420
2421	save_test: rmbak
2422	@echo "Testing source list.."
2423	@util/arb_srclst.pl > /dev/null
2424
2425	save_test_no_error:
2426	@-$(MAKE) save_test
2427
2428	inc_candi:
2429	touch SOURCE_TOOLS/inc_candi.stamp
2430	$(MAKE) do_version_update
2431
2432	inc_patch:
2433	touch SOURCE_TOOLS/inc_patch.stamp
2434	$(MAKE) do_version_update
2435
2436	inc_minor:
2437	touch SOURCE_TOOLS/inc_minor.stamp
2438	$(MAKE) do_version_update
2439
2440	inc_major:
2441	touch SOURCE_TOOLS/inc_major.stamp
2442	$(MAKE) do_version_update
2443
2444	do_version_update:
2445	@echo Incrementing version information
2446	$(MAKE) savetest
2447	$(MAKE) genheaders # auto upgrades version early
2448
2449	show_version:
2450	$(MAKE) genheaders # updates version info
2451	@echo "$(SEP) ARB version info"
2452	@grep ARB_VERSION TEMPLATES/arb_build.h
2453	@echo "$(SEP)"
2454
2455	release_quick:
2456	-rm arb.tgz arbsrc.tgz
2457	$(MAKE) tarfile_quick
2458	$(MAKE) sourcetarfile
2459
2460	# --------------------------------------------------------------------------------
2461	# special cleanups
2462
2463	clean_opengl_changed: RNA3D/RNA3D.clean EDIT4/EDIT4.clean WINDOW/WINDOW.clean GL/GL.clean
2464
2465	# --------------------------------------------------------------------------------
2466
2467	MAKE_IF_COMMITTED=$(MAKE) -C SOURCE_TOOLS -f Makefile.commitbuild
2468
2469	build_CTARGET:
2470	+$(MAKE_IF_COMMITTED) "CTARGET=$(CTARGET)" build_CTARGET
2471
2472	reset_committed_build:
2473	+$(MAKE_IF_COMMITTED) reset
2474
2475	# --------------------------------------------------------------------------------
2476
2477	arbapplications: nt pa e4 wetc pt na nal di ph ds wetc cma
2478
2479	arb_external: convert tools gde readseq tg pst
2480
2481	arb_no_perl: arbapplications help arb_external
2482
2483	arb: motif_xpm_hack
2484	$(MAKE) "WITHPERL=1" perl arb_no_perl
2485
2486	motif_xpm_hack:
2487	$(MAKE) -r -C "lib/motifHack" all
2488
2489	motif_xpm_hack_clean:
2490	$(MAKE) -r -C "lib/motifHack" clean
2491
2492	# --------------------------------------------------------------------------------
2493	# special targets for SOURCE_TOOLS/remake_after_change.pl
2494
2495	rac_arb_dist: di
2496	rac_arb_edit4: e4
2497	rac_arb_ntree: nt
2498	rac_arb_pars: pa
2499	rac_arb_phylo: ph
2500	rac_arb_wetc: wetc
2501	rac_arb_naligner: nal
2502	rac_arb_pt_server: pt
2503	rac_arb_db_server: ds
2504	rac_arb_name_server: na
2505	rac_arb_convert_aln: convert
2506	rac_arb_treegen: tg
2507	rac_arb_rnacma: cma
2508	rac_arb_help2xml: help
2509
2510	rac_arb_a2ps: tools
2511	rac_arb_consensus_tree: tools
2512	rac_arb_dnarates: tools
2513	rac_arb_export_rates: tools
2514	rac_arb_export_tree: tools
2515	rac_arb_gene_probe: tools
2516	rac_arb_message: tools
2517	rac_arb_primer: tools
2518	rac_arb_probe: tools
2519	rac_arb_read_tree: tools
2520
2521	# --------------------------------------------------------------------------------
2522	# unit testing
2523	# @@@ work in progress
2524	#
2525	# goal is to automatically test all libraries/executables using TESTED_UNITS_AUTO
2526	# currently not all test executables link w/o error.
2527	# therefor units are organized in three sets:
2528	#
2529	# TESTED_UNITS = testable and contain tests
2530	# UNTESTED_UNITS = testable, but no tests written yet
2531	# UNTESTABLE_UNITS = not testable
2532
2533	# always define OPENGL units manually:
2534	OPENGL_TESTS :=
2535	ifeq ($(OPENGL),1)
2536	OPENGL_TESTS += \
2537	$(subst .a,.test,$(RNA3D_LIB)) \
2538	GL/glAW/libglAW.test \
2539	GL/glpng/libglpng_arb.test \
2540
2541	endif
2542
2543	UNITS_NOT_AUTODETECTED = \
2544	HELP_SOURCE/HELP_SOURCE.tooltests
2545
2546	TESTED_UNITS_AUTO = \
2547	$(OPENGL_TESTS) \
2548	$(TL_ARCHIVES:.a=.test) \
2549	$(TL_SHARED_ARCHIVES:.so=.test) \
2550	$(CL_ARCHIVES:.a=.test) \
2551	$(TL_TOOLS_COLLECTIONS:.toolColl=.tooltests) \
2552	$(UNITS_NOT_AUTODETECTED) \
2553
2554	UNTESTED_UNITS = \
2555	$(OPENGL_TESTS) \
2556	EISPACK/EISPACK.test \
2557	GENOM/GENOM.test \
2558	ISLAND_HOPPING/ISLAND_HOPPING.test \
2559	NALIGNER/NALIGNER.test \
2560	NAMES/NAMES.test \
2561	PHYLO/PHYLO.test \
2562	PRIMER_DESIGN/PRIMER_DESIGN.test \
2563	PROBE_DESIGN/PROBE_DESIGN.test \
2564	READSEQ/READSEQ.tooltests \
2565	SECEDIT/SECEDIT.test \
2566	SEQ_QUALITY/SEQ_QUALITY.test \
2567	SERVERCNTRL/SERVERCNTRL.test \
2568	SL/ALIVIEW/ALIVIEW.test \
2569	SL/AP_TREE/AP_TREE.test \
2570	SL/ARB_TREE/ARB_TREE.test \
2571	SL/AW_HELIX/AW_HELIX.test \
2572	SL/AW_NAME/AW_NAME.test \
2573	SL/DB_SCANNER/DB_SCANNER.test \
2574	SL/DB_UI/DB_UI.test \
2575	SL/GUI_ALIVIEW/GUI_ALIVIEW.test \
2576	SL/HELIX/HELIX.test \
2577	SL/QUERY/QUERY.test \
2578	SL/REFENTRIES/REFENTRIES.test \
2579	SL/SEQUENCE/SEQUENCE.test \
2580	SL/TREE_ADMIN/TREE_ADMIN.test \
2581	SL/TREE_WRITE/TREE_WRITE.test \
2582	SL/XFERGUI/XFERGUI.test \
2583	STAT/STAT.test \
2584	TREEGEN/TREEGEN.test \
2585	WETC/WETC.test \
2586	XML/XML.test \
2587
2588	# untestable units
2589
2590	UNTESTABLE_UNITS = \
2591	AISC/AISC.test \
2592	NAMES_COM/server.test \
2593	PROBE_COM/server.test \
2594
2595	# --------------------
2596	# put all units containing tests into the following 4 sections (see also TESTED_UNITS below)
2597
2598	# recent development
2599	UNITS_TESTED_FIRST = \
2600	SL/MATRIX/MATRIX.test \
2601	AWTI/AWTI.test \
2602	SL/FILTSEQEXP/FILTSEQEXP.test \
2603	SL/GROUP_SEARCH/GROUP_SEARCH.test \
2604	SL/PVP/PVP.test \
2605	SL/SAICALC/SAICALC.test \
2606	SL/TRANSLATE/TRANSLATE.test \
2607	SL/XFERSET/XFERSET.test \
2608
2609	# start units with long duration early
2610	UNITS_RUNNING_LONG = \
2611	ARBDB/libARBDB.test \
2612	AWTC/AWTC.test \
2613	TOOLS/TOOLS.tooltests \
2614
2615	# plain test-libaries that are not linked anywhere
2616	TEST_SANDBOXES = \
2617	SL/CB/CB.test \
2618
2619	UNITS_TESTED = \
2620	AISC_MKPTPS/AISC_MKPTPS.tooltests \
2621	ARB_GDE/ARB_GDE.test \
2622	AWT/libAWT.test \
2623	CONSENSUS_TREE/CONSENSUS_TREE.test \
2624	CONVERTALN/CONVERTALN.test \
2625	CORE/libCORE.test \
2626	DBSERVER/DBSERVER.test \
2627	DIST/DIST.test \
2628	EDIT4/EDIT4.test \
2629	GENOM_IMPORT/GENOM_IMPORT.test \
2630	HELP_SOURCE/HELP_SOURCE.tooltests \
2631	MERGE/MERGE.test \
2632	MULTI_PROBE/MULTI_PROBE.test \
2633	NTREE/NTREE.test \
2634	PARSIMONY/PARSIMONY.test \
2635	PERLTOOLS/PERLTOOLS.tooltests \
2636	PROBE/PROBE.test \
2637	PROBE_SET/PROBE_SET.tooltests \
2638	RNACMA/RNACMA.test \
2639	SL/ALILINK/ALILINK.test \
2640	SL/CONSENSUS/CONSENSUS.test \
2641	SL/DB_QUERY/DB_QUERY.test \
2642	SL/FAST_ALIGNER/FAST_ALIGNER.test \
2643	SL/FILTER/FILTER.test \
2644	SL/INSDEL/INSDEL.test \
2645	SL/ITEM_SHADER/ITEM_SHADER.test \
2646	SL/ITEMS/ITEMS.test \
2647	SL/LOCATION/LOCATION.test \
2648	SL/MACROS/MACROS.test \
2649	SL/NDS/NDS.test \
2650	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.test \
2651	SL/PRONUC/PRONUC.test \
2652	SL/PTCLEAN/PTCLEAN.test \
2653	SL/REGEXPR/REGEXPR.test \
2654	SL/SEQIO/SEQIO.test \
2655	SL/TREE_READ/TREE_READ.test \
2656	SL/TREEDISP/TREEDISP.test \
2657	WINDOW/libWINDOW.test \
2658
2659	TESTED_UNITS = \
2660	$(UNITS_TESTED_FIRST) \
2661	$(UNITS_RUNNING_LONG) \
2662	$(TEST_SANDBOXES) \
2663	$(UNITS_TESTED) \
2664
2665	# ----------------------------------------
2666
2667	ifeq ($(DEVELOPER),RALF)
2668
2669	DEFINED_TEST_UNITS = \
2670	$(TESTED_UNITS) \
2671	$(UNTESTED_UNITS) \
2672	$(UNTESTABLE_UNITS) \
2673
2674	list_undefined_units:
2675	@UNIT_TESTER/list_undefined_units.pl $(DEFINED_TEST_UNITS) -- $(TESTED_UNITS_AUTO)
2676
2677	else
2678
2679	list_undefined_units:
2680
2681	endif
2682
2683	# ----------------------------------------
2684
2685	TEST_LOG_DIR = UNIT_TESTER/logs
2686	TEST_RUN_SUITE=$(MAKE) $(NODIR) -C UNIT_TESTER -f Makefile.suite -r
2687	# -> UNIT_TESTER/Makefile.suite
2688	TEST_MAKE_FLAGS=
2689	TEST_POST_CLEAN=
2690	ifeq ($(COVERAGE),1)
2691	TEST_POST_CLEAN=$(MAKE) clean_cov
2692	TEST_MAKE_FLAGS+=-j1
2693	endif
2694
2695
2696	%.test:
2697	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
2698	( \
2699	echo "take[1]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
2700	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
2701	"UNITDIR=$(@D)" \
2702	"UNITLIBNAME=$(@F:.test=)" \
2703	"COVERAGE=$(COVERAGE)" \
2704	"ARB_PID=$(ARB_PID)_$(@F)" \
2705	runtest; \
2706	echo "take[1]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"; \
2707	$(TEST_POST_CLEAN) \
2708	) >$(TEST_LOG_DIR)/$(@F).log 2>&1; \
2709	UNIT_TESTER/log_result.pl $(TEST_LOG_DIR)/$(@F).log )
2710
2711	%.notest:
2712	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
2713	( \
2714	echo "take[4]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
2715	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
2716	"UNITDIR=$(@D)" \
2717	"UNITLIBNAME=$(@F:.notest=)" \
2718	"COVERAGE=0" \
2719	"ARB_PID=$(ARB_PID)_$(@F)" \
2720	check_no_test; \
2721	echo "take[4]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'" \
2722	) >$(TEST_LOG_DIR)/$(@F).log 2>&1 )
2723
2724
2725	# tool test aliases (used to test one or multiple executable(s) in a single subdir):
2726	%.tooltests:
2727	$(error please define an explicit tooltest alias for $@)
2728
2729	AISC_MKPTPS/AISC_MKPTPS.tooltests : AISC_MKPTPS/mkptypes.test
2730	@echo "aliasing $@ -> $^"
2731	PERLTOOLS/PERLTOOLS.tooltests : PERLTOOLS/arb_proto_2_xsub.test
2732	@echo "aliasing $@ -> $^"
2733	PROBE_SET/PROBE_SET.tooltests : PROBE_SET/fb_test.test
2734	@echo "aliasing $@ -> $^"
2735	HELP_SOURCE/HELP_SOURCE.tooltests : HELP_SOURCE/arb_help2xml.test
2736	@echo "aliasing $@ -> $^"
2737	TOOLS/TOOLS.tooltests : TOOLS/arb_consensus_tree.test TOOLS/arb_probe.test TOOLS/arb_test.test
2738	@echo "aliasing $@ -> $^"
2739
2740	# aliases for tools w/o tests:
2741	READSEQ/READSEQ.tooltests:
2742	@echo "Note: no tests for $@"
2743
2744
2745	test_base: $(UNIT_TESTER_LIB:.a=.dummy) $(subst .test,.dummy,$(TEST_SANDBOXES))
2746
2747	clean_cov:
2748	find . $ -name ".gcda" -o -name ".gcov" -o -name "*.cov" $ -exec rm {} \;
2749
2750	clean_cov_all: clean_cov
2751	find . $ -name "*.gcno" $ -exec rm {} \;
2752
2753	cleanup_faked_arbpids:
2754	@rm ~/.arb_tmp/tmp/arb_pids_${USER}_${ARB_PID}_* \|\| true
2755
2756	cleanup_faked_arbpids_and_fail: cleanup_faked_arbpids
2757	@false
2758
2759	NOTESTS_IN_UNTESTED = $(subst .test,.notest,$(UNTESTED_UNITS))
2760
2761	run_tests_faked_arbpid:
2762	+@$(TEST_RUN_SUITE) init
2763	@echo "take[2]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2764	@$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(TESTED_UNITS) $(NOTESTS_IN_UNTESTED) \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2765	@echo "take[2]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2766	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2767	@$(MAKE) clean_cov >/dev/null
2768	@$(MAKE) cleanup_faked_arbpids
2769
2770	# @@@ instead of only running UNIT, this should as well run all tests this unit depends on? according to 'needs_libs'
2771	# @@@ '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
2772
2773	run_onetest_faked_arbpid:
2774	+@$(TEST_RUN_SUITE) init
2775	@echo "take[3]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2776	test -n "$(UNIT)" \|\| (echo "Error: UNIT has to be defined for target 'run_onetest_faked_arbpid'!"; false)
2777	$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(UNIT).test \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2778	@echo "take[3]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2779	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2780	@$(MAKE) clean_cov >/dev/null
2781	@$(MAKE) cleanup_faked_arbpids
2782
2783	run_tests: test_base clean_cov
2784	$(MAKE) "ARB_PID=UT_$$$$" run_tests_faked_arbpid list_undefined_units
2785
2786	run_oneunitstests: test_base
2787	$(MAKE) "ARB_PID=UT_$$$$" run_onetest_faked_arbpid
2788
2789
2790	ut:
2791	ifeq ($(UNIT_TESTS),1)
2792	@echo $(MAKE) run_tests
2793	@$(MAKE) run_tests
2794	else
2795	@echo "Not compiled with unit tests"
2796	endif
2797
2798
2799	aut:
2800	+@$(TEST_RUN_SUITE) unskip
2801	$(MAKE) ut
2802
2803	# --------------------------------------------------------------------------------
2804
2805	TIMELOG=$(ARBHOME)/arb_time.log
2806	TIMEARGS=--append --output=$(TIMELOG) --format=" * %E(%S+%U) %P [%C]"
2807	TIMECMD=$(TIME) $(TIMEARGS)
2808
2809	time_one:
2810	ifeq ($(ONE_TIMED_TARGET),)
2811	@echo "Error: You have to pass ONE_TIMED_TARGET to $@"
2812	false
2813	else
2814	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET)"
2815	@$(TIMECMD) $(MAKE) $(ONE_TIMED_TARGET)
2816	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET) [done]"
2817	endif
2818
2819	timed_target:
2820	ifeq ($(TIMED_TARGET),)
2821	@echo "Error: You have to pass TIMED_TARGET to $@"
2822	false
2823	else
2824	@echo "Build time:" > $(TIMELOG)
2825	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2826	@cat $(TIMELOG)
2827	@rm $(TIMELOG)
2828	endif
2829
2830	timed_target_tested:
2831	ifeq ($(TIMED_TARGET),)
2832	@echo "Error: You have to pass TIMED_TARGET to $@"
2833	false
2834	else
2835	@echo "Build time:" > $(TIMELOG)
2836	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2837	$(MAKE) "ONE_TIMED_TARGET=ut" time_one
2838	@cat $(TIMELOG)
2839	@rm $(TIMELOG)
2840	endif
2841
2842	clean_timed_target:
2843	ifeq ($(TIMED_TARGET),)
2844	@echo "Error: You have to pass TIMED_TARGET to $@"
2845	false
2846	else
2847	@echo "Build time:" > $(TIMELOG)
2848	$(MAKE) "ONE_TIMED_TARGET=clean" time_one
2849	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2850	@cat $(TIMELOG)
2851	@rm $(TIMELOG)
2852	endif
2853
2854	# --------------------------------------------------------------------------------
2855
2856	CHECKOUT_MODIFIED=0# set to 1 to temporarily skip test for modifications (do not check in if set to 1)
2857
2858	check_svn_does_not_contain_generated:
2859	ifeq ($(CHECKOUT_MODIFIED),0)
2860	@echo "Testing that build does not modify files in SVN"
2861	@test 0 = `svn status \| wc -l` \|\| ( \
2862	echo "The checkout is not/no longer clean:"; \
2863	svn status; \
2864	echo "- if this fails instantly, your checkout is not clean"; \
2865	echo "- if this fails after other targets, these targets modify checked in data"; \
2866	echo " (a common cause may be that depends are not up to date)"; \
2867	false)
2868	else
2869	grep -Hn 'CHECKOUT_MODIFIED' Makefile
2870	endif
2871
2872	check_svn_ignores_generated:
2873	@test 0 = `svn status \| grep '^\?' \| wc -l` \|\| ( \
2874	echo "There are svn-unignored files:"; \
2875	svn status \| grep '^\?'; \
2876	echo "(all generated files should be svn-ignored)"; \
2877	false)
2878
2879	check_svn_state: check_svn_does_not_contain_generated
2880	$(MAKE) check_svn_ignores_generated
2881	$(MAKE) savetest
2882
2883	things_that_always_should_work: depends proto
2884
2885	post_commit_check:
2886	@echo "---------------------------------------- [Initial]"
2887	$(MAKE) check_svn_state
2888
2889	$(MAKE) clean
2890	@echo "---------------------------------------- [After 'make clean']"
2891	$(MAKE) check_svn_state
2892
2893	$(MAKE) things_that_always_should_work
2894	@echo "---------------------------------------- [After 'make things_that_always_should_work']"
2895	$(MAKE) check_svn_state
2896
2897	$(MAKE) all
2898	@echo "---------------------------------------- [After 'make all']"
2899	$(MAKE) check_svn_state
2900
2901	$(MAKE) things_that_always_should_work
2902	@echo "---------------------------------------- [Final]"
2903	$(MAKE) check_svn_state
2904
2905	# --------------------------------------------------------------------------------
2906	# sanitize arb_ntree; also works for clients (arb_edit4, ...) started from there.
2907
2908	sanitize: all
2909	( \
2910	export "LSAN_OPTIONS=max_leaks=30:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp"; \
2911	echo "sake[1]: Entering directory \`$(ARBHOME)'"; \
2912	$(ARBHOME)/bin/arb_ntree --execute _logged ~/data/test.arb 2>&1 ; \
2913	echo "sake[1]: Leaving directory \`$(ARBHOME)'" \
2914	) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
2915
2916	# --------------------------------------------------------------------------------
2917	# build and test one unit:
2918
2919	build_oneunit:
2920	$(MAKE) "WITHPERL=1" $(UNIT).dummy
2921
2922	oneunit:
2923	ifndef UNIT
2924	@echo "Please define UNIT, e.g. using"
2925	@echo " make \"UNIT=ARBDB/libARBDB\" oneunit"
2926	@echo " make \"UNIT=SL/TREEDISP/TREEDISP\" oneunit"
2927	@echo "(Note: 1st is a shared library, 2nd isn't)"
2928	false
2929	else
2930	@echo "Build time" > $(TIMELOG)
2931	@echo "$(SEP) $(MAKE) build_oneunit"
2932	@$(TIMECMD) $(MAKE) build_oneunit
2933	ifeq ($(UNIT_TESTS),1)
2934	@echo "$(SEP) $(MAKE) run_oneunitstests"
2935	@$(TIMECMD) $(MAKE) run_oneunitstests
2936	endif
2937	@cat $(TIMELOG)
2938	@rm $(TIMELOG)
2939	endif
2940
2941	# --------------------------------------------------------------------------------
2942
2943	build: arb
2944	$(MAKE) check_bin_dep preplib compile_compatibility fig_cure
2945
2946	all:
2947	@echo "Build time" > $(TIMELOG)
2948	# $(MAKE) clean_checked_vect # uncomment to rebuild sources where expected vectorization gets tested
2949	@echo "$(SEP) $(MAKE) all"
2950	@$(TIMECMD) $(MAKE) build
2951	@echo $(SEP)
2952	@echo "made 'all' with success."
2953	@echo "to start arb enter 'arb'"
2954	ifeq ($(UNIT_TESTS),1)
2955	@echo "$(SEP) $(MAKE) run_tests"
2956	@$(TIMECMD) $(MAKE) run_tests
2957	endif
2958	@echo "$(SEP) $(MAKE) all [done]"
2959	ifeq ($(DEBUG),1)
2960	@$(MAKE) save_test_no_error >/dev/null # just show hints
2961	endif
2962	@cat $(TIMELOG)
2963	@rm $(TIMELOG)
2964

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