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source: trunk/Makefile

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Last change on this file was 19446, checked in by westram, 16 months ago
introduce `onlyC_flags` flags used for C compilation only. similar to `cxxflags` (references added). pass down onlyC_flags into AxML, CLUSTAL, CLUSTALW, FASTDNAML, FASTTREE, GL, MrBAYES, PHYLIP, PHYML*, RAxML, SINA(unused), SOURCE_TOOLS, SUPPORT, TOOLS, TREEGEN + TREEPUZZLE. set flags to `-Werror-implicit-function-declaration` error is only effective in a small part of these modules. TODO need to activate warnings → will activate the error as well.
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 87.6 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
65	ifndef ARB_ORG_MAKEFLAGS
66	ARB_ORG_MAKEFLAGS=$(MAKEFLAGS)
67	else
68	ifeq ($(ARB_ORG_MAKEFLAGS),)
69	ARB_ORG_MAKEFLAGS=$(MAKEFLAGS)
70	endif
71	endif
72
73	# Read configuration
74	include config.makefile
75	CONFIG_MAKEFILE_FOUND=$(strip $(wildcard config.makefile))
76
77	# strip spaces from values defined in config.makefile
78	# (otherwise they easily have spaces appended)
79	ifdef DEVELOPER
80	DEVELOPER := $(strip $(DEVELOPER))
81	endif
82	ifdef OPENGL
83	OPENGL := $(strip $(OPENGL))
84	endif
85	ifdef ISINA
86	ISINA := $(strip $(ISINA))
87	endif
88	ifdef DEBUG
89	DEBUG := $(strip $(DEBUG))
90	endif
91	ifdef UNIT_TESTS
92	UNIT_TESTS := $(strip $(UNIT_TESTS))
93	endif
94	ifdef COVERAGE
95	COVERAGE := $(strip $(COVERAGE))
96	endif
97	ifdef SHOWTODO
98	SHOWTODO := $(strip $(SHOWTODO))
99	endif
100	ifdef STABS
101	STABS := $(strip $(STABS))
102	endif
103	ifdef TRACESYM
104	TRACESYM := $(strip $(TRACESYM))
105	endif
106	ifdef DEBUG_GRAPHICS
107	DEBUG_GRAPHICS := $(strip $(DEBUG_GRAPHICS))
108	endif
109
110	# set defaults for (or strip) variables commented out in config.makefile:
111	ifdef SANITIZE
112	SANITIZE := $(strip $(SANITIZE))
113	else
114	SANITIZE:=0
115	endif
116	ifdef IGNORE_LEAKS
117	IGNORE_LEAKS := $(strip $(IGNORE_LEAKS))
118	else
119	IGNORE_LEAKS:=0
120	endif
121	ifndef DARWIN
122	DARWIN:=0
123	else
124	DARWIN := $(strip $(DARWIN))
125	endif
126	ifndef LINUX
127	LINUX:=0
128	else
129	LINUX := $(strip $(LINUX))
130	endif
131	ifndef DEBIAN
132	DEBIAN:=0
133	else
134	DEBIAN := $(strip $(DEBIAN))
135	endif
136	ifndef ARB_64
137	ARB_64=1#default to 64bit
138	else
139	ARB_64 := $(strip $(ARB_64))
140	endif
141
142	# Variables allowed for injection [InjectedEnvironment]
143	# (alternatively initialize them with '?=', e.g. done for XLIBS and XINCLUDES)
144	# In both cases add them to SOURCE_TOOLS/export2sub
145	ifndef XML_INCLUDES
146	XML_INCLUDES=
147	endif
148	ifndef XAW_LIBS
149	XAW_LIBS=
150	endif
151
152
153	ifneq ($(CONFIG_MAKEFILE_FOUND),)
154	ifneq ($(DARWIN)$(LINUX),10)
155	ifneq ($(DARWIN)$(LINUX),01)
156	$(error exactly one of DARWIN=1 or LINUX=1 has to be defined (got:$(DARWIN)$(LINUX)))
157	endif
158	endif
159	endif
160
161	# compiler settings:
162	ifneq ($(CC),use__A_CC__instead_of__CC)
163	A_CC:=$(CC)# compile C
164	A_CXX:=$(CXX)# compile C++
165
166	# uncomment to ensure no submakefile uses CC and CXX directly
167	override CC:=use__A_CC__instead_of__CC
168	override CXX:=use__A_CXX__instead_of__CXX
169	endif
170
171	export CC CXX A_CC A_CXX
172
173	# unconditionally prepend $(ARBHOME)/lib to LD_LIBRARY_PATH if not found
174	ifeq ($(findstring $(ARBHOME)/lib,$(LD_LIBRARY_PATH)),)
175	LD_LIBRARY_PATH:=${ARBHOME}/lib:$(LD_LIBRARY_PATH)
176	endif
177
178	# store LD_LIBRARY_PATH to circumvent SIP restrictions:
179	ARBBUILD_LIBRARY_PATH:=$(LD_LIBRARY_PATH)
180
181	FORCEMASK = umask 002
182	NODIR=--no-print-directory
183
184	SED:=$(ARBHOME)/SH/arb_sed
185	READLINK:=$(ARBHOME)/SH/arb_readlink
186
187	# ---------------------- compiler version detection
188
189	# supported gcc versions:
190	ALLOWED_gcc_VERSIONS=\
191	4.4.3 4.4.5 4.4.6 4.4.7 \
192	4.5.2 \
193	4.6.1 4.6.2 4.6.3 4.6.4 \
194	4.7.1 4.7.2 4.7.3 4.7.4 \
195	4.8.0 4.8.1 4.8.2 4.8.3 4.8.4 4.8.5 \
196	4.9.0 4.9.1 4.9.2 4.9.3 4.9.4 \
197	5.1.0 5.2.0 5.3.0 5.4.0 5.5.0 \
198	6.1.0 6.2.0 6.3.0 6.4.0 6.5.0 \
199	7.1.0 7.2.0 7.3.0 7.4.0 7.5.0 \
200	8.1.0 8.2.0 8.3.0 8.4.0 8.5.0 \
201	9.1.0 9.2.0 9.3.0 9.4.0 9.5.0 \
202	10.1.0 10.2.0 10.3.0 10.4.0 10.5.0 \
203
204	# Note: starting with version 5, arb silently accepts any subversion number
205	# above zero. See SOURCE_TOOLS/arb_compiler_version.pl@acceptSubVersions
206	#
207	# This may cause problems when manually checking for compiler versions in code
208	# (GCC_VERSION_CODE is not affected, GCC_PATCHLEVEL_CODE may cause problems!)
209	# ----------------------
210
211	COMPILER_INFO:=$(shell SOURCE_TOOLS/arb_compiler_version.pl $(A_CXX))
212	COMPILER_NAME:=$(word 1,$(COMPILER_INFO))
213	COMPILER_VERSION:=$(word 2,$(COMPILER_INFO))
214
215	USE_CLANG:=0
216	ifneq ($(COMPILER_NAME),gcc)
217	ifeq ($(COMPILER_NAME),clang)
218	USE_CLANG:=1
219	else
220	ifeq ($(COMPILER_VERSION),4.6.4)
221	# gcc version 4.6.4 segfaults when dumping symbols for detection (silently accept as gcc)
222	COMPILER_NAME:=gcc
223	else
224	$(error failed to detect COMPILER_NAME (got '$(COMPILER_NAME)', expected 'clang' or 'gcc'))
225	endif
226	endif
227	endif
228
229	ifeq ($(USE_CLANG),1)
230	# accept all clang versions:
231	ALLOWED_COMPILER_VERSIONS=$(COMPILER_VERSION)
232	else
233	ALLOWED_COMPILER_VERSIONS=$(ALLOWED_gcc_VERSIONS)
234	endif
235
236	COMPILER_VERSION_ALLOWED=$(strip $(subst ___,,$(foreach version,$(ALLOWED_COMPILER_VERSIONS),$(findstring ___$(version)___,___$(COMPILER_VERSION)___))))
237
238	#---------------------- split gcc version
239
240	SPLITTED_VERSION:=$(subst ., ,$(COMPILER_VERSION))
241
242	USE_GCC_MAJOR:=$(word 1,$(SPLITTED_VERSION))
243	USE_GCC_MINOR:=$(word 2,$(SPLITTED_VERSION))
244	USE_GCC_PATCHLEVEL:=$(word 3,$(SPLITTED_VERSION))
245
246	USE_GCC_452_OR_HIGHER:=
247	USE_GCC_46_OR_HIGHER:=
248	USE_GCC_47_OR_HIGHER:=
249	USE_GCC_48_OR_HIGHER:=
250	USE_GCC_49_OR_HIGHER:=
251	USE_GCC_50_OR_HIGHER:=
252	USE_GCC_60_OR_HIGHER:=
253	USE_GCC_70_OR_HIGHER:=
254	USE_GCC_80_OR_HIGHER:=
255	USE_GCC_90_OR_HIGHER:=
256
257	ifeq ($(USE_CLANG),0)
258	ifeq ($(USE_GCC_MAJOR),4)
259	ifeq ($(USE_GCC_MINOR),5)
260	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),23456789)','')
261	USE_GCC_452_OR_HIGHER:=yes
262	endif
263	else
264	ifneq ('$(findstring $(USE_GCC_MINOR),6789)','')
265	USE_GCC_452_OR_HIGHER:=yes
266	USE_GCC_46_OR_HIGHER:=yes
267	ifneq ($(USE_GCC_MINOR),6)
268	USE_GCC_47_OR_HIGHER:=yes
269	ifneq ($(USE_GCC_MINOR),7)
270	USE_GCC_48_OR_HIGHER:=yes
271	ifneq ($(USE_GCC_MINOR),8)
272	USE_GCC_49_OR_HIGHER:=yes
273	endif
274	endif
275	endif
276	endif
277	endif
278	else
279	# gcc 5.x or higher
280	USE_GCC_452_OR_HIGHER:=yes
281	USE_GCC_46_OR_HIGHER:=yes
282	USE_GCC_47_OR_HIGHER:=yes
283	USE_GCC_48_OR_HIGHER:=yes
284	USE_GCC_49_OR_HIGHER:=yes
285	USE_GCC_50_OR_HIGHER:=yes
286	ifneq ($(USE_GCC_MAJOR),5)
287	# gcc 6.x or higher
288	USE_GCC_60_OR_HIGHER:=yes
289	ifneq ($(USE_GCC_MAJOR),6)
290	# gcc 7.x or higher
291	USE_GCC_70_OR_HIGHER:=yes
292	ifneq ($(USE_GCC_MAJOR),7)
293	# gcc 8.x or higher
294	USE_GCC_80_OR_HIGHER:=yes
295	ifneq ($(USE_GCC_MAJOR),8)
296	# gcc 9.x or higher
297	USE_GCC_90_OR_HIGHER:=yes
298	endif
299	endif
300	endif
301	endif
302	endif
303	endif
304
305	#---------------------- define special directories for non standard builds
306
307	ifeq ($(DARWIN),1)
308	OSX_FW:=/System/Library/Frameworks
309	OSX_FW_OPENGL:=$(OSX_FW)/OpenGL.framework/Versions/A/Libraries
310	OSX_FW_GLUT:=$(OSX_FW)/GLUT.framework/Versions/A/Libraries
311	OSX_FW_IMAGEIO:=$(OSX_FW)/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources
312	endif
313
314	#---------------------- SSE vectorization
315	# for details about vectorization checks see SOURCE_TOOLS/vectorize.README
316
317	DISABLE_VECTORIZE_CHECK:=0# set to 1 to completely disable vectorization checks
318	TRACE_MISSED_VECTORIZATIONS:=0# set to 1 to activate detailed output about failed vectorizations
319	# (does also show details about successful vectorized loops, which are not optimal)
320	VECTORIZATION_CHECK_CANDIDATES:=0# set to 1 to show vectorizations that may be checked
321	# (for yet unchecked files)
322	# Note: TRACE_MISSED_VECTORIZATIONS and VECTORIZATION_CHECK_CANDIDATES cannot be used together!
323
324	#---------------------- Support for OPENMP
325
326	USE_OPENMP:=1
327	ifeq ($(DARWIN),1)
328	USE_OPENMP:=0
329	endif
330
331	#----------------------
332
333	ifeq ($(DARWIN),1)
334	LINK_STATIC=1# link static
335	else
336	LINK_STATIC=0# link dynamically
337	# LINK_STATIC=1# link static (testing only)
338	endif
339
340	shared_cflags :=# flags for shared lib compilation
341	onlyC_flags :=# flags only suitable for C (not C++; see cxxflags).
342	clflags :=# linker flags (when passed through gcc)
343	extended_warnings :=# warning flags for C and C++-compiler
344	extended_cpp_warnings :=# warning flags for C++-compiler only
345
346	ifeq ($(DEBUG),0)
347	dflags := -DNDEBUG# defines
348	ifeq ($(USE_CLANG),1)
349	cflags := -O3# compiler flags (C and C++)
350	else
351	clflags += -Wl,-O2# passthrough linker flags
352	# ------- standard optimization:
353	cflags := -O3# compiler flags (C and C++)
354	# ------- test changed optimization (DISABLE_VECTORIZE_CHECK for -O2 or lower):
355	# cflags := -O2# do not commit uncommented!
356	# DISABLE_VECTORIZE_CHECK:=1
357	endif
358	endif
359
360	ifeq ($(DEBIAN),1)
361	clflags += -Wl,-rpath=/usr/lib/arb/lib -Wl,-z,relro
362	endif
363
364	ifeq ($(DEBUG),1)
365	dflags := -DDEBUG
366
367	gdb_common := -g -g3 -ggdb -ggdb3
368
369	DBGOPTI:=-O0
370	ifneq ('$(SANITIZE)','0')
371	# sanitizer report several bogus buffer-overflows when arb is build with -O0 (e.g. with gcc 7.5.0)
372	DBGOPTI:=-O1
373	endif
374
375	ifeq ($(STABS),1)
376	$(error STABS no longer supported)
377	endif
378
379	cflags := $(DBGOPTI) $(gdb_common)
380	# cflags := -O2 $(gdb_common) # use this for callgrind (force inlining)
381
382	ifeq ($(DARWIN),0)
383	clflags += -Wl,-g
384	# Note:
385	# Previously '-Wl,-noinhibit-exec' was added to 'clflags' here,
386	# to fix some issues with launchpad binutils (see [12972]).
387	# But that change also caused 'undefined symbols' NOT to be reported as errors
388	# at link time, producing executables that fail at runtime :/
389	endif
390
391	ifeq ($(DEBUG_GRAPHICS),1)
392	dflags += -DDEBUG_GRAPHICS
393	endif
394
395	endif # DEBUG only
396
397	# ------------------------------ POST_COMPILE - control how much you get spammed
398	# (please do not change default in SVN)
399	POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl
400
401	# POST_COMPILE += --original # dont modify compiler output
402	# POST_COMPILE += --hide-Noncopyable-advices
403	# POST_COMPILE += --show-useless-Weff++
404	# POST_COMPILE += --no-warnings
405	# POST_COMPILE += --only-first-error
406	# POST_COMPILE += --no-warnings --only-first-error
407
408	# always pass used compiler version to postcompile:
409	POST_COMPILE += --compiler=$(COMPILER_VERSION)
410
411	# ------------------------------
412
413	# Enable extra warnings
414	extended_warnings :=
415	extended_cpp_warnings :=
416
417	# C and C++
418	extended_warnings += -Wwrite-strings -Wunused -Wno-aggregate-return
419
420	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
421	# disable shadow warnings for gcc 4.8 (and lower)
422	# (does e.g. warn if a method-name is used as parameter in another method - even for derived classes. unusable!)
423	extended_warnings += -Wshadow
424	endif
425
426	# C++ only
427	extended_cpp_warnings += -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute
428	extended_cpp_warnings += -Wctor-dtor-privacy
429	# extended_cpp_warnings += -Wfloat-equal
430
431	extended_cpp_warnings += -Wmissing-noreturn
432	# extended_cpp_warnings += -Wold-style-cast# (warns about 28405 old-style casts)
433	extended_cpp_warnings += -Winit-self
434	extended_cpp_warnings += -Wstrict-aliasing
435	extended_cpp_warnings += -Wextra
436
437	# ------- above only warning-options already available in gcc 4.4.3
438
439	# -Weffc++ broken in 4.7.x series
440	# gcc 4.7.3 crashes on GenomeImport.cxx when -Weffc++ is active
441	# (bug reported https://gcc.gnu.org/bugzilla/show_bug.cgi?id=56923; apparently wont be fixed for 4.7-series)
442	# gcc 4.7.4 crashes on DBwriter.cxx when -Weffc++ is active
443	WEFFC_BROKEN:=0
444	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
445	ifneq ('$(USE_GCC_48_OR_HIGHER)','yes')
446	WEFFC_BROKEN:=1
447	endif
448	endif
449	ifeq ('$(WEFFC_BROKEN)','0')
450	extended_cpp_warnings += -Weffc++
451	endif
452
453	# turn off -Wmaybe-uninitialized in debug mode (gets activated with -Wextra). too many bogus warnings
454	ifeq ($(DEBUG),1)
455	ifeq ($(USE_CLANG),0)
456	extended_cpp_warnings += -Wno-maybe-uninitialized
457	endif
458	endif
459
460	SUGGEST_FINAL:=
461
462	ifeq ('$(USE_GCC_452_OR_HIGHER)','yes')
463	extended_cpp_warnings += -Wlogical-op# gcc 4.5.2
464	endif
465	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
466	extended_cpp_warnings += -Wzero-as-null-pointer-constant# gcc 4.7
467	endif
468	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
469	extended_cpp_warnings += -Wunused-local-typedefs# available since gcc 4.7 (but fails for each STATIC_ASSERT, so enable only for Cxx11)
470	endif
471	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
472	extended_cpp_warnings += -Wswitch-bool
473	extended_cpp_warnings += -Wlogical-not-parentheses
474	extended_cpp_warnings += -Wsizeof-array-argument
475	extended_cpp_warnings += -Wbool-compare
476
477	SUGGEST_FINAL:=yes
478	endif
479	ifeq ('$(USE_GCC_60_OR_HIGHER)','yes')
480	extended_cpp_warnings += -Wduplicated-cond
481	endif
482	ifeq ('$(USE_GCC_80_OR_HIGHER)','yes')
483	extended_cpp_warnings += -Wmultistatement-macros
484	endif
485
486	# switch off final suggestions for 8.3.0 and 8.4.0:
487	ifeq ('$(COMPILER_VERSION)','8.3.0')
488	SUGGEST_FINAL:=no
489	endif
490	ifeq ('$(COMPILER_VERSION)','8.4.0')
491	SUGGEST_FINAL:=no
492	endif
493
494	ifeq ($(DEVELOPER),RELEASE)
495	# switch off final suggestions in RELEASE:
496	SUGGEST_FINAL:=no
497	endif
498	# suggest final:
499	ifeq ('$(SUGGEST_FINAL)','yes')
500	extended_cpp_warnings += -Wsuggest-final-types
501	extended_cpp_warnings += -Wsuggest-final-methods
502	dflags += -DSUGGESTS_FINAL
503	endif
504
505	#---------------------- turn off clang bogus warnings
506
507	ifeq ($(USE_CLANG),1)
508	# -Wmismatched-tags warns about struct/class mismatch in forward declarations (which is explicitely allowed)
509	# -Wchar-subscripts reports too many bogus warnings for "array['x']" (when 'x' is known to be in range [0..128])
510	# -Wunused-private-field report too many false positives (currently ~ 2 of 3)
511	# -Wstring-plus-int warns about common ARB coding practice
512	# -Wgnu-static-float-init warns about accepted GNU extension
513	extended_cpp_warnings += -Wno-mismatched-tags -Wno-char-subscripts -Wno-unused-private-field -Wno-string-plus-int
514	ifeq ('$(COMPILER_VERSION)','4.2.1')
515	# jenkins build (doesn't know switch -Wno-gnu-static-float-init)
516	extended_cpp_warnings += -Wno-gnu
517	else
518	extended_cpp_warnings += -Wno-gnu-static-float-init
519	endif
520	endif
521
522	#---------------------- developer
523
524	ifneq ($(DEVELOPER),ANY) # ANY=default setting (skip all developer specific code)
525	dflags += -DDEVEL_$(DEVELOPER)# activate developer/release specific code
526	endif
527
528	#---------------------- activate TODO warnings?
529
530	ifndef SHOWTODO
531	ifeq ($(DEVELOPER),RALF)
532	SHOWTODO:=1
533	else
534	SHOWTODO:=0
535	endif
536	endif
537	ifeq ($(SHOWTODO),1)
538	dflags += -DWARN_TODO# activate "TODO" warnings
539	endif
540
541	#---------------------- activate threads?
542	# only useful if compiler is able to compile Cxx11 or better
543
544	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
545	# see also ./TEMPLATES/cxxforward.h@USE_Cxx11
546	cflags += -pthread
547	clflags += -pthread
548	endif
549
550	#---------------------- activate Sanitizers?
551
552	ASAN_OPTIONS:=handle_segv=0:color=0
553	ifeq ($(IGNORE_LEAKS),1)
554	ASAN_OPTIONS+=:detect_leaks=0 # disable leak-detection
555	else
556	ASAN_OPTIONS+=:detect_leaks=1 # detect leaks (normal setting)
557	endif
558	ASAN_OPTIONS+=:check_initialization_order=1
559	# ASAN_OPTIONS+=:abort_on_error=1
560
561	# suppressions: SOURCE_TOOLS/arb.leaksan.supp
562	LSAN_OPTIONS:=max_leaks=3:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp
563
564	UBSAN_OPTIONS:=print_stacktrace=1
565
566	SANITIZE_ADDRESS:=0
567	SANITIZE_UNDEFINED:=0
568
569	ifneq ($(SANITIZE),0)
570	ifeq ($(SANITIZE),all)
571	SANITIZE:=3
572	endif
573
574	ifeq ($(SANITIZE),1)
575	SANITIZE_ADDRESS:=1
576	else
577	ifeq ($(SANITIZE),2)
578	SANITIZE_UNDEFINED:=1
579	else
580	ifeq ($(SANITIZE),3)
581	SANITIZE_ADDRESS:=1
582	SANITIZE_UNDEFINED:=1
583	else
584	$(error Unknown value '$(SANITIZE)' specified for SANITIZE in config.makefile)
585	endif
586	endif
587	endif
588	endif
589
590	ifeq ($(SANITIZE_ADDRESS),1)
591	ifneq ('$(USE_GCC_48_OR_HIGHER)','yes')
592	$(info AddressSanitizer not usable with gcc $(COMPILER_VERSION) - disabled)
593	SANITIZE_ADDRESS:=0
594	else
595	ifneq ('$(USE_GCC_49_OR_HIGHER)','yes')
596	$(info LeakSanitizer does not work with gcc $(COMPILER_VERSION) - disabled)
597	# need to disable AddressSanitizer (otherwise build fails; only affects gcc 4.8.x series)
598	SANITIZE_ADDRESS:=0
599	endif
600	endif
601	endif
602
603	ifeq ($(SANITIZE_UNDEFINED),1)
604	ifneq ('$(USE_GCC_49_OR_HIGHER)','yes')
605	$(info UndefinedBehaviorSanitizer not usable with gcc $(COMPILER_VERSION) - disabled)
606	SANITIZE_UNDEFINED:=0
607	endif
608	endif
609
610	SANITIZE_ANY:=0
611	ifeq ($(SANITIZE_ADDRESS),1)
612	SANITIZE_ANY:=1
613	endif
614	ifeq ($(SANITIZE_UNDEFINED),1)
615	SANITIZE_ANY:=1
616	endif
617
618	# vectorization fails if sanitizer active where it normally succeeds -> disable check
619	ifeq ($(SANITIZE_ANY),1)
620	$(info disabling vectorize checks. would fail with sanitized code)
621	DISABLE_VECTORIZE_CHECK:=1
622	else
623	$(info no sanitizer enabled. reset: SANITIZE=0)
624	SANITIZE:=0
625	endif
626
627	# deactivate some bogus warnings occurring when sanitizing NDEBUG version
628	# (do not disable for future gcc-version >= 8.x -> test again when available)
629	ifeq ($(SANITIZE_ANY),1)
630	ifeq ($(DEBUG),0)
631	ifneq ('$(USE_GCC_80_OR_HIGHER)','yes')
632	extended_cpp_warnings += -Wno-format-overflow
633	extended_cpp_warnings += -Wno-maybe-uninitialized
634	endif
635	endif
636	endif
637
638	#---------------------- 32 or 64 bit
639
640	cross_cflags:=
641	cross_lflags:=
642	cross_clflags:=
643
644	ifeq ($(ARB_64),1)
645	dflags += -DARB_64
646	shared_cflags += -fPIC
647	CROSS_LIB:=# empty => autodetect below
648	ifeq ($(DARWIN),1)
649	cross_cflags += -arch x86_64
650	cross_lflags += -arch x86_64
651	cross_clflags += -arch x86_64
652	endif
653	else
654	CROSS_LIB:=/lib
655	endif
656
657	cflags += $(cross_cflags)
658	clflags += $(cross_clflags)
659
660	ifeq ('$(CROSS_LIB)','')
661	# autodetect libdir
662	ifeq ($(ARB_64),1)
663	CROSS_LIB:=$(shell (test -d /lib64 && echo lib64) \|\| echo lib)
664	else
665	CROSS_LIB:=$(shell (test -d /lib32 && echo lib32) \|\| echo lib)
666	endif
667	endif
668
669	#---------------------- unit tests
670
671	ifndef UNIT_TESTS
672	UNIT_TESTS=0#default is "no tests"
673	endif
674	ifeq ($(UNIT_TESTS),1)
675	dflags += -DUNIT_TESTS
676	UNIT_TESTER_LIB=UNIT_TESTER/UNIT_TESTER.a
677	else
678	UNIT_TESTER_LIB=
679	endif
680
681	#---------------------- use gcov
682
683	ifndef COVERAGE
684	COVERAGE=0#default is "no"
685	endif
686	ifneq ($(COVERAGE),0)
687	GCOV_FLAGS=--coverage
688	$(info disabling vectorize checks. would fail with COVERAGE on)
689	DISABLE_VECTORIZE_CHECK:=1
690	else
691	GCOV_FLAGS=
692	endif
693
694	cflags += $(GCOV_FLAGS)
695	clflags += $(GCOV_FLAGS)
696	cross_lflags += $(GCOV_FLAGS)
697
698	#---------------------- other flags
699
700	dflags += -D$(MACH) # define machine
701
702	ifeq ($(DARWIN),1)
703	shared_cflags += -fno-common
704	else
705	dflags += $(shell getconf LFS_CFLAGS)
706	endif
707
708	cflags += -pipe
709	cflags += -fmessage-length=0# dont wrap compiler output
710	cflags += -fshow-column# show columns
711	cflags += -funit-at-a-time
712	cflags += -fPIC
713	cflags += -fno-common# link all global data into one namespace
714	cflags += -fstrict-aliasing# gcc 3.4
715
716	onlyC_flags += -Werror-implicit-function-declaration
717
718	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
719	cflags += -fno-diagnostics-show-caret#gcc 4.8 (4.7.?)
720	endif
721	#cflags += -save-temps# uncomment to see preprocessor output
722
723	#---------------------- various sanitizers
724	# There are some disabled tests in CORE/arb_misc.cxx@sanitizers
725	# which trigger sanitizer reports.
726
727	ifeq ($(SANITIZE_ANY),1)
728	cflags += -ggdb3 -fno-omit-frame-pointer
729	endif
730
731	SANI_CFLAGS:=
732	SANI_CLFLAGS:=
733
734	# activate AddressSanitizer+LeakSanitizer?
735	ifeq ($(SANITIZE_ADDRESS),1)
736	SANI_CFLAGS += -fsanitize=address
737	SANI_CLFLAGS += -fsanitize=address
738	dflags += -DLEAKS_SANITIZED
739	endif
740
741	# activate UndefinedBehaviorSanitizer?
742	ifeq ($(SANITIZE_UNDEFINED),1)
743	SANI_CFLAGS += -fsanitize=undefined
744	SANI_CLFLAGS += -fsanitize=undefined
745	dflags += -DUNDEF_SANITIZED
746	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
747	# abort on runtime errors
748	SANI_CFLAGS += -fno-sanitize-recover=all
749	endif
750
751	cflags += $(SANI_CFLAGS)
752	clflags += $(SANI_CLFLAGS)
753
754	#
755	# Note: alignment-sanitizer is deactivated for ARBDB and PROBE!
756	ifeq ('$(DEBUG)','1')
757	ifeq ($(USE_GCC_MAJOR),4)
758	ifeq ($(USE_GCC_MINOR),9)
759	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),01)','')
760	# workaround https://gcc.gnu.org/bugzilla/show_bug.cgi?id=63531 for 4.9.0 + 4.9.1
761	# (problem is fixed in 4.9.2 release)
762	extended_cpp_warnings:=$(subst -Weffc++,,$(extended_cpp_warnings))
763	endif
764	endif
765	endif
766	endif
767	endif
768
769	#---------------------- X11 location
770
771	ifeq ($(DARWIN),1)
772	XHOME:=$(PREFIX)
773	else
774	ifeq ($(DEBIAN),1)
775	XHOME:=$(PREFIX)
776	else
777	XHOME:=/usr/X11R6
778	endif
779	endif
780
781	XINCLUDES ?= -I$(XHOME)/include
782	XLIBS ?= -L$(XHOME)/$(CROSS_LIB)
783	ifeq ($(DARWIN),1)
784	XINCLUDES += -I$(OSX_FW)/GLUT.framework/Headers -I$(OSX_FW)/OpenGL.framework/Headers -I$(OSX_SDK)/usr/include/krb5
785
786	XLIBS += -lXm -lpng -lz -lXt -lX11 -lXext -lXp -lXmu -lXi
787	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGL.dylib:$(OSX_FW_OPENGL)/libGL.dylib
788	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGLU.dylib:$(OSX_FW_OPENGL)/libGLU.dylib
789	else
790	XLIBS += -lXm -lXpm -lXt -lXext -lX11
791	endif
792
793	#---------------------- open GL
794
795	ifeq ($(OPENGL),1)
796	cflags += -DARB_OPENGL # activate OPENGL code
797	GL := gl # this is the name of the OPENGL base target
798	GL_LIB_SYS := -lGL -lGLU
799	GL_LIB_ARB := -L$(ARBHOME)/GL/glAW -lglAW
800
801	ifeq ($(DARWIN),1)
802	GL_LIB_SYS += -lpthread
803	endif
804
805	GL_PNGLIBS_ARB := -L$(ARBHOME)/GL/glpng -lglpng_arb
806	GL_PNGLIBS_SYS := -lpng
807
808	GLEWLIB := -lGLEW -lGLw
809	GLUTLIB := -lglut
810
811	GL_LIBS_SYS := $(GL_LIB_SYS) $(GL_PNGLIBS_SYS) $(GLEWLIB) $(GLUTLIB)
812	GL_LIBS_ARB := $(GL_LIB_ARB) $(GL_PNGLIBS_ARB)
813
814	RNA3D_LIB := RNA3D/RNA3D.a
815	else
816	GL_LIBS_SYS:=# no opengl -> no libs
817	GL_LIBS_ARB:=# no opengl -> no libs
818	GL:=# dont build ARB openGL libs
819
820	RNA3D_LIB :=
821	endif
822
823	RNA3D_LIB_4_DEPENDS := RNA3D/RNA3D.a
824
825	GL_LIBS:=$(GL_LIBS_ARB) $(GL_LIBS_SYS)
826
827	#---------------------- sina:
828
829	ifndef ISINA
830	# build sina delivered with arb?
831	ifeq ($(LINUX),1)
832	ifeq ('$(USE_GCC_70_OR_HIGHER)','yes')
833	ISINA := 1# default to 'yes' for linux with gcc>=7
834	endif
835	endif
836	ifndef ISINA
837	ISINA := 0# 'no' otherwise
838	endif
839	endif
840
841	#---------------------- tiff lib:
842
843	TIFFLIBS := -ltiff
844
845	#---------------------- XML lib:
846
847	XMLLIBS := -lxerces-c
848
849	#---------------------- glib:
850
851	ARB_NEEDED_GLIB=glib-2.0
852
853	ARB_GLIB_INCLUDE:=$(strip $(shell pkg-config --cflags $(ARB_NEEDED_GLIB)))
854	ARB_GLIB_LIBS:=$(strip $(shell pkg-config --libs $(ARB_NEEDED_GLIB)))
855
856	#---------------------- sunrpc lib:
857	# Note: sunrpc has been removed from glibc
858	# (e.g. in SuSE Leap 15.3 and Fedora 28)
859	# see https://fedoraproject.org/wiki/Changes/SunRPCRemoval
860	#
861	HAVE_LIBTIRPC=$(strip $(shell pkg-config --exists libtirpc && echo libtirpc))
862	ifeq ($(HAVE_LIBTIRPC),)
863	ARB_RPC_INCLUDE:=
864	ARB_RPC_LIBS:=
865	else
866	ARB_RPC_INCLUDE:=$(strip $(shell pkg-config --cflags $(HAVE_LIBTIRPC)))
867	ARB_RPC_LIBS:=$(strip $(shell pkg-config --libs $(HAVE_LIBTIRPC)))
868	endif
869
870	#---------------------- basic libs:
871
872	ARB_CORE_LIBS:=$(ARB_GLIB_LIBS) $(ARB_RPC_LIBS)
873
874	SYSLIBS:=
875	ifeq ($(DARWIN),1)
876	SYSLIBS += -lstdc++
877	else
878	SYSLIBS += -lm $(ARB_CORE_LIBS)
879	endif
880
881	#---------------------- system dependent commands
882
883	ifeq ($(DARWIN),1)
884	TIME:=gtime
885	else
886	TIME:=/usr/bin/time
887	endif
888
889	#---------------------- SSE vectorizer
890	# for details see SOURCE_TOOLS/vectorize.README
891
892	ifeq ($(DEBUG),0)
893	ifeq ($(USE_GCC_49_OR_HIGHER),yes)
894	ifeq ($(DISABLE_VECTORIZE_CHECK),0)
895	cflags += -fopt-info-vec
896	cflags += -fopt-info-vec-missed
897	ifeq ($(TRACE_MISSED_VECTORIZATIONS),1)
898	# Shows reasons for unsuccessful vectorization:
899	cflags += -ftree-vectorizer-verbose=10
900	POST_COMPILE += --dump-loop-optimization
901	ifeq ($(VECTORIZATION_CHECK_CANDIDATES),1)
902	$(error TRACE_MISSED_VECTORIZATIONS and VECTORIZATION_CHECK_CANDIDATES may not be used together!)
903	endif
904	endif
905	ifeq ($(VECTORIZATION_CHECK_CANDIDATES),1)
906	POST_COMPILE += --loop-optimization-candi
907	endif
908	POST_COMPILE += --check-loop-optimization
909	endif
910	else
911	ifeq ($(USE_GCC_48_OR_HIGHER),yes)
912	# no automatic vectorization-check for gcc<4.9.0
913	# -> uncomment the next 2 lines and grep the spam it will produce for 'vectorized.*loops'
914	# cflags += -fopt-info -fopt-info-vec-missed
915	# POST_COMPILE += --original
916	endif
917	endif
918	endif
919
920	#---------------------- stop early on broken flags/compiler combination
921
922	ifeq ($(DEBUG),0)
923	ifeq ($(SANITIZE_ANY),1)
924	ifeq ('$(COMPILER_VERSION)','4.9.1')
925	$(error compiling DEBUG=0 + SANITIZE!=0 crashes with gcc $(COMPILER_VERSION) (gcc 4.9.2 works))
926	endif
927	endif
928	endif
929
930	#---------------------- include symbols?
931
932	ifeq ($(TRACESYM),1)
933	ifeq ($(USE_CLANG),0)
934	cflags += -rdynamic
935	clflags += -rdynamic -Wl,--export-dynamic
936	endif
937	endif
938
939	#---------------------- warn about duplicate variable definitions
940
941	ifeq ($(DARWIN),1)
942	clflags += -Wl,-warn_commons
943	else
944	clflags += -Wl,--warn-common
945	endif
946
947	#---------------------- differences between linking executables and shared libs:
948
949	# executables:
950	ifeq ($(DARWIN),1)
951	blflags:=$(clflags)
952	else
953	blflags:=$(clflags) -Wl,--no-undefined
954	endif
955
956	# shared libraries
957	llflags:=$(clflags)
958
959	# dont use clflags below
960	clflags:=
961
962	# -------------------------------------------------------------------------
963	# Don't put any machine/version/etc conditionals below!
964	# (instead define variables above)
965	# -------------------------------------------------------------------------
966
967	cflags += -W -Wall $(dflags) $(extended_warnings)
968	cxxflags := $(extended_cpp_warnings)# flags only suitable for C++ (not C; see onlyC_flags).
969
970	# add CFLAGS + CPPFLAGS from environment for DEBIAN build
971	ifeq ($(DEBIAN),1)
972	cflags := $(CFLAGS) $(cflags)
973	cxxflags += $(CPPFLAGS)
974	endif
975
976	ifeq ('$(USE_CLANG)','1')
977	# none of the following standards works with clang3.3 (under linux) => dont use standard (as done before r15516)
978	# cxxflags += -std=gnu++11
979	# cxxflags += -std=gnu++0x
980	else
981	ifeq ('$(USE_GCC_60_OR_HIGHER)','yes')
982	cxxflags += -std=gnu++14# see also TEMPLATES/cxxforward.h@USE_Cxx14
983	else
984	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
985	cxxflags += -std=gnu++11# see also TEMPLATES/cxxforward.h@USE_Cxx11
986	else
987	# gcc versions between 4.3 (lowest supported) and <4.7
988	cxxflags += -std=gnu++0x
989	endif
990	endif
991	endif
992
993	LINK_STATIC_LIB := $(AR) -csq# link static lib
994	LINK_EXECUTABLE := $(A_CXX) $(blflags) -o# link executable (c++)
995
996	ifeq ($(LINK_STATIC),1)
997	SHARED_LIB_SUFFIX = a# static lib suffix
998	LINK_SHARED_LIB := $(LINK_STATIC_LIB)
999	else
1000	SHARED_LIB_SUFFIX = so# shared lib suffix
1001	LINK_SHARED_LIB := $(A_CXX) $(llflags) -shared -o# link shared lib
1002	endif
1003
1004	ifeq ($(DARWIN),1)
1005	lflags4perl:=
1006	else
1007	lflags4perl:=$(cross_lflags) -shared
1008	endif
1009
1010	# delete variables unused below
1011	blflags:=
1012	llflags:=
1013
1014	# other used tools
1015	MAKEDEPEND_PLAIN = makedepend
1016	MAKEDEPEND = $(FORCEMASK);$(MAKEDEPEND_PLAIN)
1017
1018	SEPNODATE:=--------------------------------------------------------------------------------
1019	SEP=[`date +%M:%S.%N`] ------------------------------------------------
1020	# to analyse timings run
1021	# make -j9 clean; make -j9 all \| grep '^\[' \| sort
1022	# make -j9 "TIMED_TARGET=perl" clean_timed_target \| grep '^\[' \| sort
1023
1024	# ------------------------------------------------------------ DYNLIBDEFS
1025	# various dynamic library definitions for linking executables:
1026	#
1027	# SYSLIBS: system libraries needed by database lib
1028	# ARBDB_LIB: database lib
1029	# DBSYS_LIBS: executable using database (but no GUI)
1030	# GUI_LIBS: executable using database and GUI (arb gui uses database)
1031	#
1032	# Note: definitions exported to sub-makefiles are described in SOURCE_TOOLS/parent_make.txt
1033
1034	CORE_LIB=-lCORE
1035	ARBDB_LIB=-lARBDB $(CORE_LIB)
1036	DBSYS_LIBS = $(ARBDB_LIB) $(SYSLIBS)
1037
1038	GUI_LIBS_PREFIX:=
1039	ifeq ($(DARWIN),1)
1040	# this seem to be added at wrong place, since opengl is only needed to link EDIT4
1041	GUI_LIBS_PREFIX:=-framework GLUT -framework OpenGL
1042	endif
1043
1044	GUI_LIBS=$(GUI_LIBS_PREFIX) $(DBSYS_LIBS) -lAWT -lWINDOW $(XLIBS)
1045
1046	LIBPATH = -L$(ARBHOME)/lib
1047
1048	DEST_LIB = lib
1049	DEST_BIN = bin
1050
1051	CC_INCLUDES := -I. -I$(ARBHOME)/INCLUDE $(XINCLUDES) $(ARB_GLIB_INCLUDE) $(ARB_RPC_INCLUDE)
1052	CXX_INCLUDES := $(CC_INCLUDES)
1053	MAKEDEPENDFLAGS := -- -DARB_OPENGL -DUNIT_TESTS -D__cplusplus -I. -Y$(ARBHOME)/INCLUDE
1054
1055	# ---------------------------------------
1056	# wrap main()
1057
1058	use_ARB_main=$(ARBHOME)/SOURCE_TOOLS/arb_main_cpp.o
1059	use_ARB_main_C=$(ARBHOME)/SOURCE_TOOLS/arb_main_c.o
1060
1061	# -----------------------------------------
1062	# unique build-id
1063	# - different for different calls of make
1064	# - constant in recursive calls
1065
1066	ifndef ARBBID
1067	ARBBID:=$(shell SOURCE_TOOLS/uniqueID.sh)
1068	endif
1069
1070	# -----------------------------------------
1071	# export variables to submakefiles
1072
1073	include SOURCE_TOOLS/export2sub
1074
1075	# do not define (exported) variables below this point
1076
1077	# -------------------------
1078	# Main arb targets:
1079	# -------------------------
1080
1081	first_target:
1082	$(MAKE) checks
1083	@echo $(SEPNODATE)
1084	@echo 'Main targets:'
1085	@echo ''
1086	@echo ' all - Compile ARB + TOOLs + and copy shared libs + link foreign software'
1087	@echo ' (That is most likely the target you want)'
1088	@echo ''
1089	@echo ' clean - remove generated files ("SUBDIR/SUBDIR.clean" to clean only SUBDIR)'
1090	@echo ' rebuild - clean + all'
1091	@echo ' cleanlinked - remove all binaries'
1092	@echo ' relink - cleanlinked + all (=relink all from objects)'
1093	@echo ''
1094	@echo 'Targets for automated builds:'
1095	@echo ''
1096	@echo ' ALL, REBUILD, TARFILE + TARFILE_QUICK '
1097	@echo ' - same as all, rebuild, tarfile + tarfile_quick'
1098	@echo ' - if errors occur, they are extracted and listed at tail of output'
1099	@echo ''
1100	@echo $(SEPNODATE)
1101	@echo ''
1102	@echo 'Development targets:'
1103	@echo ''
1104	@echo ' depends - create or update dependencies ("SUBDIR/SUBDIR.depends" to update only SUBDIR)'
1105	@echo ' proto - create or update prototypes ("SUBDIR/SUBDIR.proto" to update only SUBDIR)'
1106	@echo ' tags - create tags for xemacs'
1107	@echo ' show - show available shortcuts (AKA subtargets)'
1108	@echo ' up - shortcut for depends+proto+tags'
1109	ifeq ($(UNIT_TESTS),1)
1110	@echo ' ut - only run tests'
1111	@echo ' "UNIT=..." oneunit - build one unit and run tests (see also UNIT_TESTER/Makefile.setup.local)'
1112	endif
1113	ifneq ($(SANITIZE),0)
1114	@echo ' sanitize - all + run arb_ntree with sanitizer (test.arb + execute _logged)'
1115	endif
1116	@echo ' modified - rebuild files modified in svn checkout (does touch)'
1117	@echo ' touch - touch files modified in svn checkout'
1118	@echo ''
1119	@echo 'Some often used sub targets:'
1120	@echo ''
1121	@echo ' arb - Just compile ARB (but none of the integrated tools)'
1122	@echo ' menus - create lib/gde/arb.menu from GDEHELP/ARB_GDEmenus.source'
1123	@echo ' perl - Compile the PERL XSUBS into lib/ARB.so and create links in lib to perl'
1124	@echo ' binlink - Create all links in the bin directory'
1125	@echo ''
1126	@echo 'Internal maintenance:'
1127	@echo ''
1128	@echo ' relinfo - show help on release targets'
1129	@echo ' tarfile - make rebuild and create arb version tarfile ("tarfile_quick" to skip rebuild)'
1130	@echo ' save - save all basic ARB sources into arbsrc_DATE ("savetest" to check filelist)'
1131	@echo ' patch - save svn diff to patchfile'
1132	@echo ' source_doc - create doxygen documentation'
1133	@echo ' relocated - rebuild partly (use when you have relocated ARBHOME)'
1134	@echo ' check_res - check resource usage'
1135	@echo ' dep_graph - Build dependency graphs'
1136	@echo ' clean_cov - Clean coverage results'
1137	@echo ''
1138	@echo ' clean_opengl_changed - clean after changing OPENGL setting in config.Makefile'
1139	@echo ' clean_checked_vect - clean units containing vectorization checks'
1140	@echo ' cleanRelinkable - similar to cleanlinked (but skips raxml8 to avoid rebuild)'
1141	@echo ''
1142	@echo ' post_commit_check - Checks whether'
1143	@echo ' * main make targets work,'
1144	@echo ' * dependencies and prototypes are up to date,'
1145	@echo ' * SVN-controlled files remain unaffected by called targets and'
1146	@echo ' * all generated files are ignored.'
1147	@echo ' (has to be called in a clean SVN checkout)'
1148	@echo $(SEPNODATE)
1149	@echo ''
1150
1151	relinfo:
1152	@echo ''
1153	@echo $(SEPNODATE)
1154	@echo 'Release targets:'
1155	@echo ''
1156	@echo ' inc_candi - increase RC candidate-number (only possible in "rc" branch, not needed for RC1)'
1157	@echo ' inc_patch - increase release patchlevel (only possible in "stable" branch)'
1158	@echo ' inc_minor - increase minor version number (only possible in "trunk")'
1159	@echo ' inc_major - increase MAJOR version number (only possible in "trunk")'
1160	@echo ''
1161	@echo ' show_version - show version tag'
1162	@echo ''
1163	@echo $(SEPNODATE)
1164	@echo ''
1165
1166	# auto-generate config.makefile:
1167
1168	config.makefile : config.makefile.template
1169	@echo --------------------------------------------------------------------------------
1170	ifeq ($(CONFIG_MAKEFILE_FOUND),)
1171	@cp $< $@
1172	@echo '$(ARBHOME)/$@:1: has been generated.'
1173	@echo 'Please edit $@ to configure your system!'
1174	@echo --------------------------------------------------------------------------------
1175	@false
1176	else
1177	@echo '$(ARBHOME)/$<:1: is more recent than'
1178	@echo '$(ARBHOME)/$@:1:'
1179	@ls -al config.makefile*
1180	@echo --------------------------------------------------------------------------------
1181	@echo "Updating $@ (if this fails, check manually)"
1182	SOURCE_TOOLS/update_config_makefile.pl
1183	@echo "Sucessfully updated $@"
1184	@echo --------------------------------------------------------------------------------
1185	@ls -al config.makefile*
1186	@echo --------------------------------------------------------------------------------
1187	@echo "Diff to your old config.makefile:"
1188	@echo --------------------------------------------------------------------------------
1189	-diff $@.bak $@
1190	@echo --------------------------------------------------------------------------------
1191	endif
1192
1193	# check if everything is configured correctly
1194
1195	check_DEVELOPER:
1196	ifndef DEVELOPER
1197	@echo 'config.makefile:1: DEVELOPER not defined'
1198	@false
1199	endif
1200
1201	check_DEBUG:
1202	ifndef dflags
1203	@echo 'config.makefile:1: DEBUG has to be defined. Valid values are 0 and 1'
1204	@false
1205	endif
1206
1207	check_ARB_64:
1208	ifndef ARB_64
1209	@echo 'config.makefile:1: ARB_64 has to be defined. Valid values are 0 and 1'
1210	@false
1211	endif
1212
1213	# ---------------------------------------- check gcc version
1214
1215	COMPILER_BROKEN:=0
1216
1217	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.6.4')
1218	COMPILER_BROKEN:=1
1219	endif
1220	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.8.0')
1221	COMPILER_BROKEN:=1
1222	endif
1223
1224	check_same_GCC_VERSION:
1225	$(ARBHOME)/SOURCE_TOOLS/check_same_compiler_version.pl $(COMPILER_NAME) $(COMPILER_VERSION_ALLOWED)
1226
1227	check_GCC_VERSION:
1228	@echo 'Compiler version check:'
1229	# see .@ALLOWED_gcc_VERSIONS
1230	ifeq ('$(COMPILER_VERSION_ALLOWED)', '')
1231	@echo " - Your compiler is '$(COMPILER_NAME)' version '$(COMPILER_VERSION)'"
1232	@echo ' This version is not in the list of supported $(COMPILER_NAME)-versions:'
1233	@$(foreach version,$(ALLOWED_COMPILER_VERSIONS),echo ' * $(version)';)
1234	@echo ' - You may either ..'
1235	@echo ' - add your version to ALLOWED_$(COMPILER_NAME)_VERSIONS in the Makefile and try it out or'
1236	@echo ' - switch to one of the allowed versions (see arb_README_gcc.txt for installing'
1237	@echo ' a different version of gcc)'
1238	$(error Unsupported compiler '$(COMPILER_NAME)' version '$(COMPILER_VERSION)')
1239	else
1240	ifeq ($(COMPILER_BROKEN),1)
1241	$(error compilation refused for $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)'. Refer to http://bugs.arb-home.de/wiki/GccVersionInfo for details.)
1242	else
1243	@echo " - Supported $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)' detected - fine!"
1244	@echo ''
1245	ifeq ($(USE_CLANG),1)
1246	@echo "Dump clang version:"
1247	$(A_CXX) -v
1248	endif
1249	$(MAKE) check_same_GCC_VERSION
1250	endif
1251	endif
1252
1253	#---------------------- check ARBHOME
1254
1255	# use arb_INSTALL.txt to determine whether ARBHOME points to correct directory
1256	ARB_INSTALL_FOUND=$(wildcard $(ARBHOME)/arb_INSTALL.txt)
1257
1258	check_ARBHOME:
1259	ifeq ($(strip $(ARB_INSTALL_FOUND)),)
1260	@echo ------------------------------------------------------------
1261	@echo "ARBHOME is set to '$(ARBHOME)'"
1262	@echo "The environment variable ARBHOME has to point to the top arb source directory."
1263	@echo "If you use bash enter:"
1264	@echo " export ARBHOME='`pwd`'"
1265	@echo ------------------------------------------------------------
1266	@false
1267	endif
1268
1269	ARB_PATH_SET=$(findstring $(ARBHOME)/bin,$(PATH))
1270
1271	check_PATH: check_ARBHOME
1272	ifeq ($(strip $(ARB_PATH_SET)),)
1273	@echo ------------------------------------------------------------
1274	@echo "The environment variable PATH has to contain $(ARBHOME)/bin"
1275	@echo "If you use bash enter:"
1276	@echo ' export PATH=$$ARBHOME/bin:$$PATH'
1277	@echo ------------------------------------------------------------
1278	@false
1279	endif
1280
1281	check_TOOLS:
1282	@util/arb_check_build_env.pl \
1283	"$(A_CC)" \
1284	"$(A_CXX)" \
1285	"$(LINK_SHARED_LIB)" \
1286
1287	have_makedepend:
1288	@util/arb_check_build_env.pl --check-only "$(MAKEDEPEND_PLAIN)"
1289
1290	check_ENVIRONMENT : check_PATH check_TOOLS
1291	@echo "-------------------- Environment [start]"
1292	@echo "ARBHOME='$(ARBHOME)'"
1293	@echo "PATH='$(PATH)'"
1294	@echo "LD_LIBRARY_PATH='$(LD_LIBRARY_PATH)'"
1295	@echo "-------------------- Environment [end]"
1296
1297	check_tabs: check_setup
1298	ifeq ($(DEBUG),1)
1299	@SOURCE_TOOLS/tabBrake.pl
1300	endif
1301
1302	force_tab_check:
1303	@touch -t 198001010000 SOURCE_TOOLS/stamp.tabBrake
1304	@$(MAKE) check_tabs
1305
1306
1307	# ---------------------
1308
1309	check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION
1310	@echo Your setup seems to be ok.
1311
1312	checks: check_setup check_tabs
1313	@rm -f SOURCE_TOOLS/postcompile.sav
1314
1315
1316	# end test section ------------------------------
1317
1318	# ---------------------------------------
1319	# List of standard top level directories
1320	#
1321	# sub-makefiles have to define the targets
1322	# - 'depends' and
1323	# - 'clean'
1324	#
1325	# when adding new libraries/subdirs here, also add a dependency vs 'links' or 'links_non_perl' in .@DD_links_non_perl
1326
1327	TL_ARCHIVES = \
1328	AISC/AISC.a \
1329	ARB_GDE/ARB_GDE.a \
1330	AWTC/AWTC.a \
1331	AWTI/AWTI.a \
1332	CONSENSUS_TREE/CONSENSUS_TREE.a \
1333	CONVERTALN/CONVERTALN.a \
1334	DBSERVER/DBSERVER.a \
1335	DIST/DIST.a \
1336	EDIT4/EDIT4.a \
1337	EISPACK/EISPACK.a \
1338	GENOM/GENOM.a \
1339	GENOM_IMPORT/GENOM_IMPORT.a \
1340	ISLAND_HOPPING/ISLAND_HOPPING.a \
1341	MERGE/MERGE.a \
1342	MULTI_PROBE/MULTI_PROBE.a \
1343	NALIGNER/NALIGNER.a \
1344	NAMES/NAMES.a \
1345	NAMES_COM/server.a \
1346	NTREE/NTREE.a \
1347	PARSIMONY/PARSIMONY.a \
1348	PHYLO/PHYLO.a \
1349	PRIMER_DESIGN/PRIMER_DESIGN.a \
1350	PROBE/PROBE.a \
1351	PROBE_COM/server.a \
1352	PROBE_DESIGN/PROBE_DESIGN.a \
1353	$(RNA3D_LIB) \
1354	RNACMA/RNACMA.a \
1355	SECEDIT/SECEDIT.a \
1356	SEQ_QUALITY/SEQ_QUALITY.a \
1357	SERVERCNTRL/SERVERCNTRL.a \
1358	STAT/STAT.a \
1359	TREEGEN/TREEGEN.a \
1360	WETC/WETC.a \
1361	XML/XML.a \
1362
1363	TL_SHARED_ARCHIVES = \
1364	ARBDB/libARBDB.so \
1365	CORE/libCORE.so \
1366	AWT/libAWT.so \
1367	WINDOW/libWINDOW.so \
1368
1369	TL_ARCHIV_COLLECTIONS = \
1370	SL/SL.archColl \
1371
1372	TL_TOOLS_COLLECTIONS = \
1373	AISC_MKPTPS/AISC_MKPTPS.toolColl \
1374	TOOLS/TOOLS.toolColl \
1375	PERLTOOLS/PERLTOOLS.toolColl \
1376	PROBE_SET/PROBE_SET.toolColl \
1377	READSEQ/READSEQ.toolColl \
1378
1379	RECURSIVE_SUBS = \
1380	GDE/GDE.sub \
1381	UNIT_TESTER/UNIT_TESTER.sub \
1382
1383	SUBDIRS = \
1384	$(RECURSIVE_SUBS) \
1385	$(TL_ARCHIVES:.a=.sub) \
1386	$(TL_SHARED_ARCHIVES:.so=.sub) \
1387	$(TL_ARCHIV_COLLECTIONS:.archColl=.sub) \
1388	$(TL_TOOLS_COLLECTIONS:.toolColl=.sub) \
1389
1390	# sub directories inside TL_ARCHIV_COLLECTIONS
1391	CL_ARCH_DIRS = $(foreach coll,$(TL_ARCHIV_COLLECTIONS),$(shell find $(dir $(coll)) -maxdepth 1 -mindepth 1 -type d))
1392
1393	# archives inside CL_ARCH_DIRS:
1394	CL_ARCHIVES = $(foreach adir,$(CL_ARCH_DIRS),$(dir $(adir))$(notdir $(adir))/$(notdir $(adir)).a)
1395
1396	# -----------------------
1397	# library packets
1398
1399	ARCHS_CLIENT_PROBE = PROBE_COM/client.a
1400	ARCHS_CLIENT_NAMES = NAMES_COM/client.a
1401
1402	ARCHS_MAKEBIN = AISC_MKPTPS/AISC_MKPTPS.a AISC/AISC.a
1403
1404	# communication libs need aisc and aisc_mkpts:
1405
1406	AISC/AISC.dummy: proto_tools
1407
1408	comtools: AISC/AISC.dummy
1409
1410	ARCHS_SEQUENCE = \
1411	SL/SEQUENCE/SEQUENCE.a \
1412	SL/ALIVIEW/ALIVIEW.a \
1413	SL/PRONUC/PRONUC.a \
1414
1415	ARCHS_TREE = \
1416	SL/ARB_TREE/ARB_TREE.a \
1417	SL/FILTER/FILTER.a \
1418	$(ARCHS_SEQUENCE) \
1419
1420	# parsimony tree (used by NTREE, PARSIMONY, STAT(->EDIT4), DIST(obsolete!))
1421	ARCHS_AP_TREE = \
1422	SL/AP_TREE/AP_TREE.a \
1423	$(ARCHS_TREE) \
1424
1425	# --------------------------------------------------------------------------------
1426	# dependencies for linking shared libs
1427
1428	link_core: core
1429	link_db: db link_core
1430	link_aw: aw link_db
1431	link_awt: awt link_aw
1432
1433	#***************************************************************************************
1434	# Individual_Programs_Section
1435	#***************************************************************************************
1436
1437	arbmainwrapper:
1438	$(MAKE) -C SOURCE_TOOLS -r mainwrapper
1439
1440
1441	#********************************* arb_ntree ************************************
1442	NTREE = bin/arb_ntree
1443	ARCHS_NTREE = \
1444	NTREE/NTREE.a \
1445	ARB_GDE/ARB_GDE.a \
1446	SL/GROUP_SEARCH/GROUP_SEARCH.a \
1447	SL/SAICALC/SAICALC.a \
1448	SL/DB_UI/DB_UI.a \
1449	AWTC/AWTC.a \
1450	AWTI/AWTI.a \
1451	CONSENSUS_TREE/CONSENSUS_TREE.a \
1452	GENOM_IMPORT/GENOM_IMPORT.a \
1453	GENOM/GENOM.a \
1454	MERGE/MERGE.a \
1455	MULTI_PROBE/MULTI_PROBE.a \
1456	PRIMER_DESIGN/PRIMER_DESIGN.a \
1457	PROBE_DESIGN/PROBE_DESIGN.a \
1458	SEQ_QUALITY/SEQ_QUALITY.a \
1459	SERVERCNTRL/SERVERCNTRL.a \
1460	SL/ALILINK/ALILINK.a \
1461	SL/AW_NAME/AW_NAME.a \
1462	SL/CONSENSUS/CONSENSUS.a \
1463	SL/DB_SCANNER/DB_SCANNER.a \
1464	SL/DB_QUERY/DB_QUERY.a \
1465	SL/QUERY/QUERY.a \
1466	SL/SEQIO/SEQIO.a \
1467	STAT/STAT.a \
1468	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1469	SL/HELIX/HELIX.a \
1470	SL/REGEXPR/REGEXPR.a \
1471	SL/REFENTRIES/REFENTRIES.a \
1472	SL/NDS/NDS.a \
1473	SL/ITEM_SHADER/ITEM_SHADER.a \
1474	SL/ITEMS/ITEMS.a \
1475	SL/INSDEL/INSDEL.a \
1476	SL/LOCATION/LOCATION.a \
1477	SL/MACROS/MACROS.a \
1478	SL/PVP/PVP.a \
1479	SL/TRANSLATE/TRANSLATE.a \
1480	SL/TREEDISP/TREEDISP.a \
1481	SL/TREE_ADMIN/TREE_ADMIN.a \
1482	SL/TREE_READ/TREE_READ.a \
1483	SL/TREE_WRITE/TREE_WRITE.a \
1484	SL/XFERGUI/XFERGUI.a \
1485	SL/XFERSET/XFERSET.a \
1486	XML/XML.a \
1487	$(ARCHS_AP_TREE) \
1488
1489	ARCHS_NTREE_ALL = $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(XMLLIBS)
1490
1491	$(NTREE): $(ARCHS_NTREE:.a=.dummy) link_awt
1492	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NTREE_ALL) \|\| ( \
1493	echo "$(SEP) Link $@"; \
1494	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE_ALL)" ; \
1495	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE_ALL) && \
1496	echo "$(SEP) Link $@ [done]"; \
1497	)
1498
1499	#********************************* arb_edit4 ************************************
1500	EDIT4 = bin/arb_edit4
1501
1502	ARCHS_EDIT4 := \
1503	EDIT4/EDIT4.a \
1504	ARB_GDE/ARB_GDE.a \
1505	SL/FAST_ALIGNER/FAST_ALIGNER.a \
1506	AWTC/AWTC.a \
1507	ISLAND_HOPPING/ISLAND_HOPPING.a \
1508	SECEDIT/SECEDIT.a \
1509	SERVERCNTRL/SERVERCNTRL.a \
1510	SL/AW_HELIX/AW_HELIX.a \
1511	SL/AW_NAME/AW_NAME.a \
1512	SL/CONSENSUS/CONSENSUS.a \
1513	SL/ITEMS/ITEMS.a \
1514	STAT/STAT.a \
1515	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1516	SL/HELIX/HELIX.a \
1517	SL/TRANSLATE/TRANSLATE.a \
1518	SL/MACROS/MACROS.a \
1519	SL/NDS/NDS.a \
1520	$(ARCHS_AP_TREE) \
1521	XML/XML.a \
1522
1523	ifeq ($(OPENGL),1)
1524	ARCHS_EDIT4 += RNA3D/RNA3D.a
1525	endif
1526
1527	ARCHS_EDIT4_ALL = $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4)
1528
1529	LIBS_EDIT4 := $(GL_LIBS)
1530
1531	$(EDIT4): $(ARCHS_EDIT4:.a=.dummy) link_awt
1532	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_EDIT4_ALL) \|\| ( \
1533	echo "$(SEP) Link $@"; \
1534	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4_ALL)" ; \
1535	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4_ALL) && \
1536	echo "$(SEP) Link $@ [done]"; \
1537	)
1538
1539	#********************************* arb_rnacma ************************************
1540	RNACMA = bin/arb_rnacma
1541	ARCHS_RNACMA = \
1542	RNACMA/RNACMA.a \
1543
1544	ARCHS_RNACMA_ALL = $(ARCHS_RNACMA) $(DBSYS_LIBS)
1545
1546	$(RNACMA) : $(ARCHS_RNACMA:.a=.dummy) link_db
1547	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_RNACMA_ALL) \|\| ( \
1548	echo "$(SEP) Link $@"; \
1549	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_RNACMA_ALL)"; \
1550	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_RNACMA_ALL) && \
1551	echo "$(SEP) Link $@ [done]"; \
1552	)
1553
1554	#********************************* arb_wetc ************************************
1555	WETC = bin/arb_wetc
1556	ARCHS_WETC = \
1557	WETC/WETC.a \
1558	SL/HELIX/HELIX.a \
1559	SL/FILTER/FILTER.a \
1560	XML/XML.a \
1561
1562	ARCHS_WETC_ALL = $(ARCHS_WETC) $(GUI_LIBS)
1563
1564	$(WETC): $(ARCHS_WETC:.a=.dummy) link_awt
1565	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_WETC_ALL) \|\| ( \
1566	echo "$(SEP) Link $@"; \
1567	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC_ALL)" ; \
1568	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC_ALL) && \
1569	echo "$(SEP) Link $@ [done]"; \
1570	)
1571
1572	#********************************* arb_dist ************************************
1573	DIST = bin/arb_dist
1574	ARCHS_DIST = \
1575	DIST/DIST.a \
1576	CONSENSUS_TREE/CONSENSUS_TREE.a \
1577	EISPACK/EISPACK.a \
1578	SERVERCNTRL/SERVERCNTRL.a \
1579	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1580	SL/HELIX/HELIX.a \
1581	SL/MATRIX/MATRIX.a \
1582	SL/MACROS/MACROS.a \
1583	SL/NDS/NDS.a \
1584	SL/ITEMS/ITEMS.a \
1585	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.a \
1586	XML/XML.a \
1587	$(ARCHS_AP_TREE) \
1588
1589	ARCHS_DIST_ALL = $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS)
1590
1591	$(DIST): $(ARCHS_DIST:.a=.dummy) link_awt
1592	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_DIST_ALL) \|\| ( \
1593	echo "$(SEP) Link $@"; \
1594	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST_ALL)" ; \
1595	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST_ALL) && \
1596	echo "$(SEP) Link $@ [done]"; \
1597	)
1598
1599	#********************************* arb_pars ************************************
1600	PARSIMONY = bin/arb_pars
1601	ARCHS_PARSIMONY = \
1602	PARSIMONY/PARSIMONY.a \
1603	SERVERCNTRL/SERVERCNTRL.a \
1604	SL/AW_NAME/AW_NAME.a \
1605	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1606	SL/HELIX/HELIX.a \
1607	SL/MACROS/MACROS.a \
1608	SL/NDS/NDS.a \
1609	SL/ITEMS/ITEMS.a \
1610	SL/TRANSLATE/TRANSLATE.a \
1611	SL/TREEDISP/TREEDISP.a \
1612	XML/XML.a \
1613	$(ARCHS_AP_TREE) \
1614
1615	ARCHS_PARSIMONY_ALL = $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS)
1616
1617	$(PARSIMONY): $(ARCHS_PARSIMONY:.a=.dummy) link_awt
1618	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_PARSIMONY_ALL) \|\| ( \
1619	echo "$(SEP) Link $@"; \
1620	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY_ALL)" ; \
1621	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY_ALL) && \
1622	echo "$(SEP) Link $@ [done]"; \
1623	)
1624
1625	#********************************* arb_convert_aln ************************************
1626	CONVERT_ALN = bin/arb_convert_aln
1627	ARCHS_CONVERT_ALN = \
1628	CONVERTALN/CONVERTALN.a \
1629
1630	ARCHS_CONVERT_ALN_ALL = $(ARCHS_CONVERT_ALN) $(DBSYS_LIBS)
1631
1632	$(CONVERT_ALN) : $(ARCHS_CONVERT_ALN:.a=.dummy) link_db
1633	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_CONVERT_ALN_ALL) \|\| ( \
1634	echo "$(SEP) Link $@"; \
1635	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN_ALL)"; \
1636	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN_ALL) && \
1637	echo "$(SEP) Link $@ [done]"; \
1638	)
1639
1640	#********************************* arb_treegen ************************************
1641
1642	TREEGEN = bin/arb_treegen
1643	ARCHS_TREEGEN = \
1644	TREEGEN/TREEGEN.a \
1645
1646	ARCHS_TREEGEN_ALL = $(ARCHS_TREEGEN)
1647
1648	$(TREEGEN) : $(ARCHS_TREEGEN:.a=.dummy)
1649	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main_C) $(ARCHS_TREEGEN_ALL) \|\| ( \
1650	echo "$(SEP) Link $@"; \
1651	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN_ALL)" ; \
1652	$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN_ALL) && \
1653	echo "$(SEP) Link $@ [done]"; \
1654	)
1655
1656	#********************************* arb_naligner ************************************
1657	NALIGNER = bin/arb_naligner
1658	ARCHS_NALIGNER = \
1659	NALIGNER/NALIGNER.a \
1660	SERVERCNTRL/SERVERCNTRL.a \
1661	SL/HELIX/HELIX.a \
1662
1663	ARCHS_NALIGNER_ALL = $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(DBSYS_LIBS)
1664
1665	$(NALIGNER): $(ARCHS_NALIGNER:.a=.dummy) link_db
1666	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NALIGNER_ALL) \|\| ( \
1667	echo "$(SEP) Link $@"; \
1668	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER_ALL)" ; \
1669	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER_ALL) && \
1670	echo "$(SEP) Link $@ [done]"; \
1671	)
1672
1673	#********************************* arb_phylo ************************************
1674	PHYLO = bin/arb_phylo
1675	ARCHS_PHYLO = \
1676	PHYLO/PHYLO.a \
1677	SL/HELIX/HELIX.a \
1678	SL/FILTER/FILTER.a \
1679	SL/MACROS/MACROS.a \
1680	XML/XML.a \
1681
1682	ARCHS_PHYLO_ALL = $(ARCHS_PHYLO) $(GUI_LIBS)
1683
1684	$(PHYLO): $(ARCHS_PHYLO:.a=.dummy) link_awt
1685	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_PHYLO_ALL) \|\| ( \
1686	echo "$(SEP) Link $@"; \
1687	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO_ALL)" ; \
1688	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO_ALL) && \
1689	echo "$(SEP) Link $@ [done]"; \
1690	)
1691
1692	#***************************************************************************************
1693	# SERVER SECTION
1694	#***************************************************************************************
1695
1696	#********************************* arb_db_server ************************************
1697	DBSERVER = bin/arb_db_server
1698	ARCHS_DBSERVER = \
1699	DBSERVER/DBSERVER.a \
1700	SERVERCNTRL/SERVERCNTRL.a \
1701
1702	ARCHS_DBSERVER_ALL = $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS)
1703
1704	$(DBSERVER): $(ARCHS_DBSERVER:.a=.dummy) link_db
1705	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_DBSERVER_ALL) \|\| ( \
1706	echo "$(SEP) Link $@"; \
1707	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER_ALL)" ; \
1708	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER_ALL) && \
1709	echo "$(SEP) Link $@ [done]"; \
1710	)
1711
1712	#********************************* arb_pt_server ************************************
1713	PROBE = bin/arb_pt_server
1714
1715	ARCHS_PROBE_DEPEND = \
1716	PROBE/PROBE.a \
1717	SL/PTCLEAN/PTCLEAN.a \
1718	SERVERCNTRL/SERVERCNTRL.a \
1719	SL/HELIX/HELIX.a \
1720
1721	ARCHS_PROBE_ALL = $(ARCHS_PROBE_DEPEND) $(ARCHS_CLIENT_PROBE) $(ARBDB_LIB) $(SYSLIBS)
1722
1723	$(PROBE): $(ARCHS_PROBE_DEPEND:.a=.dummy) link_db
1724	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) config.makefile $(ARCHS_PROBE_ALL) \|\| ( \
1725	echo "$(SEP) Link $@"; \
1726	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_ALL)" ; \
1727	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_ALL) && \
1728	echo "$(SEP) Link $@ [done]"; \
1729	)
1730
1731	#********************************* arb_name_server ************************************
1732	NAMES = bin/arb_name_server
1733	ARCHS_NAMES = \
1734	NAMES/NAMES.a \
1735	SERVERCNTRL/SERVERCNTRL.a \
1736
1737	ARCHS_NAMES_ALL = $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS)
1738
1739	$(NAMES): $(ARCHS_NAMES:.a=.dummy) link_db
1740	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NAMES_ALL) \|\| ( \
1741	echo "$(SEP) Link $@"; \
1742	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES_ALL)" ; \
1743	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES_ALL) && \
1744	echo "$(SEP) Link $@ [done]"; \
1745	)
1746
1747	#********************************* SHARED LIBRARIES SECTION ************************************
1748
1749	prepare_libdir: addlibs
1750
1751	addlibs:
1752	(perl $(ARBHOME)/SOURCE_TOOLS/provide_libs.pl \
1753	"arbhome=$(ARBHOME)" \
1754	"opengl=$(OPENGL)" \
1755	"link_static=$(LINK_STATIC)" \
1756	)
1757
1758	#***************************************************************************************
1759	# Recursive calls to sub-makefiles
1760	#***************************************************************************************
1761
1762	%.depends: have_makedepend
1763	@cp -p $(@D)/Makefile $(@D)/Makefile.old # save old Makefile
1764	@$(MAKE) -C $(@D) -r \
1765	"AUTODEPENDS=1" \
1766	"MAIN=nothing" \
1767	"cflags=noCflagsHere_use_MAKEDEPENDFLAGS" \
1768	"cxxflags=noCxxflagsHere_use_MAKEDEPENDFLAGS" \
1769	depends
1770	@grep "^# DO NOT DELETE" $(@D)/Makefile >/dev/null
1771	@cat $(@D)/Makefile \
1772	\| SOURCE_TOOLS/fix_depends.pl "(from main)" \
1773	>$(@D)/Makefile.2
1774	@mv $(@D)/Makefile.old $(@D)/Makefile # restore old Makefile
1775	@$(ARBHOME)/SOURCE_TOOLS/mv_if_diff $(@D)/Makefile.2 $(@D)/Makefile # update Makefile if changed
1776
1777	%.proto:
1778	@($(MAKE) -C $(@D) \
1779	"AUTODEPENDS=0" \
1780	"MAIN=nothing" \
1781	"cflags=noCflags" \
1782	"cxxflags=noCxxflags" \
1783	proto 2>&1 ) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
1784
1785	%.clean:
1786	@$(MAKE) -C $(@D) \
1787	"AUTODEPENDS=0" \
1788	"MAIN=nothing" \
1789	"cflags=noCflags" \
1790	"cxxflags=noCxxflags" \
1791	clean
1792
1793
1794	# stop wrong targets:
1795	target_is_missing_lib_prefix:
1796	@echo "Error: Denied to build shared library target with missing 'lib'-prefix"
1797	false
1798
1799	ARBDB/ARBDB.dummy: target_is_missing_lib_prefix
1800	CORE/CORE.dummy: target_is_missing_lib_prefix
1801	AWT/AWT.dummy: target_is_missing_lib_prefix
1802	WINDOW/WINDOW.dummy: target_is_missing_lib_prefix
1803
1804	# rule to generate main target (normally a library):
1805	# @@@ check effect of setting LANG=C below
1806	%.dummy:
1807	@( export ID=$$$$; LANG=C; \
1808	(( \
1809	echo "$(SEP) Make $(@D)"; \
1810	$(MAKE) -C $(@D) -r \
1811	"AUTODEPENDS=1" \
1812	"MAIN=$(@F:.dummy=.a)" \
1813	"cflags=$(cflags) -DIN_ARB_$(subst /,_,$(@D))" \
1814	&& \
1815	echo "$(SEP) Make $(@D) [done]"; \
1816	) >$(@D).$$ID.log 2>&1 && (cat $(@D).$$ID.log;rm $(@D).$$ID.log)) \|\| (cat $(@D).$$ID.log;rm $(@D).$$ID.log;false))
1817
1818	# Additional dependencies for subtargets:
1819
1820	PROBE_COM/PROBE_COM.dummy : comtools
1821	NAMES_COM/NAMES_COM.dummy : comtools
1822
1823	com: PROBE_COM/PROBE_COM.dummy NAMES_COM/NAMES_COM.dummy
1824
1825	# stop wrong more targets:
1826	PROBE_COM/server.dummy:
1827	@echo Unwanted request to make target $<
1828	false
1829
1830	PROBE_COM/client.dummy:
1831	@echo Unwanted request to make target $<
1832	false
1833
1834	NAMES_COM/server.dummy:
1835	@echo Unwanted request to make target $<
1836	false
1837
1838	NAMES_COM/client.dummy:
1839	@echo Unwanted request to make target $<
1840	false
1841
1842
1843	ARBDB/libARBDB.dummy: links
1844	CORE/libCORE.dummy: links
1845
1846	PERLTOOLS/PERLTOOLS.dummy: core db
1847
1848	# all subdirs perl not depends on go here (ADD_links_non_perl)
1849	AWT/libAWT.dummy: links_non_perl
1850	AWTI/AWTI.dummy: links_non_perl
1851	CONSENSUS_TREE/CONSENSUS_TREE.dummy: links_non_perl
1852	CONVERTALN/CONVERTALN.dummy: links_non_perl
1853	DBSERVER/DBSERVER.dummy: links_non_perl
1854	DIST/DIST.dummy: links_non_perl
1855	EDIT4/EDIT4.dummy: links_non_perl com
1856	EISPACK/EISPACK.dummy: links_non_perl
1857	GDE/GDE.dummy: links_non_perl
1858	GENOM/GENOM.dummy: links_non_perl
1859	GENOM_IMPORT/GENOM_IMPORT.dummy: links_non_perl
1860	ISLAND_HOPPING/ISLAND_HOPPING.dummy: links_non_perl
1861	MERGE/MERGE.dummy: links_non_perl
1862	NTREE/NTREE.dummy: links_non_perl
1863	PARSIMONY/PARSIMONY.dummy: links_non_perl
1864	PHYLO/PHYLO.dummy: links_non_perl
1865	PRIMER_DESIGN/PRIMER_DESIGN.dummy: links_non_perl
1866	PROBE_SET/PROBE_SET.dummy: links_non_perl link_db
1867	READSEQ/READSEQ.dummy: links_non_perl
1868	RNACMA/RNACMA.dummy: links_non_perl header_libs
1869	SECEDIT/SECEDIT.dummy: links_non_perl
1870	SEQ_QUALITY/SEQ_QUALITY.dummy: links_non_perl
1871	SERVERCNTRL/SERVERCNTRL.dummy: links_non_perl com
1872	SL/ALILINK/ALILINK.dummy: links_non_perl
1873	SL/ALIVIEW/ALIVIEW.dummy: links_non_perl
1874	SL/AP_TREE/AP_TREE.dummy: links_non_perl
1875	SL/ARB_TREE/ARB_TREE.dummy: links_non_perl
1876	SL/AW_HELIX/AW_HELIX.dummy: links_non_perl
1877	SL/CONSENSUS/CONSENSUS.dummy: links_non_perl
1878	SL/DB_QUERY/DB_QUERY.dummy: links_non_perl
1879	SL/DB_SCANNER/DB_SCANNER.dummy: links_non_perl
1880	SL/DB_UI/DB_UI.dummy: links_non_perl
1881	SL/FAST_ALIGNER/FAST_ALIGNER.dummy: links_non_perl
1882	SL/FILTER/FILTER.dummy: links_non_perl
1883	SL/FILTSEQEXP/FILTSEQEXP.dummy: links_non_perl
1884	SL/GROUP_SEARCH/GROUP_SEARCH.dummy: links_non_perl
1885	SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy: links_non_perl
1886	SL/HEADERTESTS/HEADERTESTS.dummy: links_non_perl
1887	SL/HELIX/HELIX.dummy: links_non_perl
1888	SL/INSDEL/INSDEL.dummy: links_non_perl
1889	SL/ITEM_SHADER/ITEM_SHADER.dummy: links_non_perl
1890	SL/ITEMS/ITEMS.dummy: links_non_perl
1891	SL/LOCATION/LOCATION.dummy: links_non_perl
1892	SL/MACROS/MACROS.dummy: links_non_perl
1893	SL/MATRIX/MATRIX.dummy: links_non_perl
1894	SL/NDS/NDS.dummy: links_non_perl
1895	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.dummy: links_non_perl
1896	SL/PRONUC/PRONUC.dummy: links_non_perl
1897	SL/PTCLEAN/PTCLEAN.dummy: links_non_perl link_db
1898	SL/PVP/PVP.dummy: links_non_perl
1899	SL/QUERY/QUERY.dummy: links_non_perl link_db
1900	SL/REFENTRIES/REFENTRIES.dummy: links_non_perl
1901	SL/REGEXPR/REGEXPR.dummy: links_non_perl
1902	SL/SAICALC/SAICALC.dummy: links_non_perl
1903	SL/SEQIO/SEQIO.dummy: links_non_perl
1904	SL/SEQUENCE/SEQUENCE.dummy: links_non_perl
1905	SL/TRANSLATE/TRANSLATE.dummy: links_non_perl
1906	SL/TREE_ADMIN/TREE_ADMIN.dummy: links_non_perl
1907	SL/TREE_READ/TREE_READ.dummy: links_non_perl
1908	SL/TREE_WRITE/TREE_WRITE.dummy: links_non_perl
1909	SL/TREEDISP/TREEDISP.dummy: links_non_perl
1910	SL/XFERGUI/XFERGUI.dummy: links_non_perl
1911	SL/XFERSET/XFERSET.dummy: links_non_perl
1912	STAT/STAT.dummy: links_non_perl
1913	TREEGEN/TREEGEN.dummy: links_non_perl
1914	WETC/WETC.dummy: links_non_perl
1915	WINDOW/libWINDOW.dummy: links_non_perl
1916	XML/XML.dummy: links_non_perl
1917
1918	ifeq ($(OPENGL),1)
1919	GL/glAW/glAW.dummy: links_non_perl
1920	GL/glpng/glpng.dummy: links_non_perl
1921	GL/GL.dummy: GL/glAW/glAW.dummy GL/glpng/glpng.dummy
1922	RNA3D/RNA3D.dummy: links_non_perl gl
1923	endif
1924
1925	UNIT_TESTER/UNIT_TESTER.dummy: link_db \
1926	SERVERCNTRL/SERVERCNTRL.dummy \
1927
1928	# see also TOOLS/Makefile@TOOLSLIBDEPENDS
1929	TOOLS/TOOLS.dummy : links_non_perl link_db \
1930	CONSENSUS_TREE/CONSENSUS_TREE.dummy \
1931	SERVERCNTRL/SERVERCNTRL.dummy \
1932	SL/FILTER/FILTER.dummy \
1933	SL/FILTSEQEXP/FILTSEQEXP.dummy \
1934	SL/INSDEL/INSDEL.dummy \
1935	SL/REGEXPR/REGEXPR.dummy \
1936	SL/SEQIO/SEQIO.dummy \
1937	SL/TREE_READ/TREE_READ.dummy \
1938	SL/TREE_WRITE/TREE_WRITE.dummy \
1939	XML/XML.dummy \
1940
1941	AWTC/AWTC.dummy : com
1942
1943	NAMES/NAMES.dummy : com
1944	SL/AW_NAME/AW_NAME.dummy : com
1945
1946	PROBE/PROBE.dummy : com
1947	MULTI_PROBE/MULTI_PROBE.dummy : com
1948	PROBE_DESIGN/PROBE_DESIGN.dummy : com
1949	NALIGNER/NALIGNER.dummy : com
1950
1951	ARB_GDE/ARB_GDE.dummy : proto_tools menus
1952
1953	compile_compatibility: SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.dummy
1954
1955	#***************************************************************************************
1956	# Short aliases to make targets
1957	#***************************************************************************************
1958
1959	show:
1960	@echo $(SEP)
1961	@echo 'Aliases for often needed targets:'
1962	@echo ''
1963	@echo ' executables:'
1964	@echo ''
1965	@echo ' nt arb_ntree'
1966	@echo ' e4 arb_edit4 (includes secedit)'
1967	@echo ' di arb_dist'
1968	@echo ' ph arb_phylo'
1969	@echo ' pa arb_parsimony'
1970	@echo ' tg arb_treegen'
1971	@echo ' ds arb_dbserver'
1972	@echo ' pt arb_pt_server'
1973	@echo ' na arb_name_server'
1974	@echo ''
1975	@echo ' libraries:'
1976	@echo ''
1977	@echo ' com communication libraries'
1978	@echo ' db ARB database'
1979	@echo ' aw GUI lib'
1980	@echo ' awt GUI toolkit'
1981	@echo ' awtc general purpose library'
1982	@echo ' awti import/export library'
1983	@echo ' mp multi probe library'
1984	@echo ' ge genome library'
1985	@echo ' pd probe design lib'
1986	@echo ' prd primer design lib'
1987	@echo ''
1988	@echo ' other targets:'
1989	@echo ''
1990	@echo ' help recompile help files'
1991	@echo ' tools make small tools used by arb'
1992	@echo ''
1993	@echo ' foreign targets:'
1994	@echo ''
1995	@echo ' gde GDE'
1996	@echo ' agde ARB_GDE'
1997	@echo ''
1998	@echo 'for other targets inspect $(ARBHOME)/Makefile'
1999	@echo ''
2000	@echo $(SEP)
2001
2002	source_doc:
2003	@echo "Remove some links (doxygen crashes otherwise):"
2004	find . $ -name "AISC" -o -name "C" -o -name "GDEHELP" $ -type l -exec rm {} \;
2005	doxygen 2>&1 1>/dev/null
2006	$(MAKE) forcelinks
2007
2008	dep_graph:
2009	@echo "Building some dependency graphs"
2010	SOURCE_TOOLS/dependency_graphs.pl
2011
2012	help: HELP_SOURCE/HELP_SOURCE.dummy
2013
2014	HELP_SOURCE/HELP_SOURCE.dummy: link_core xml menus
2015
2016	db: ARBDB/libARBDB.dummy
2017	core: CORE/libCORE.dummy
2018	aw: WINDOW/libWINDOW.dummy
2019	awt: AWT/libAWT.dummy
2020	awtc: AWTC/AWTC.dummy
2021	awti: AWTI/AWTI.dummy
2022
2023	mp: MULTI_PROBE/MULTI_PROBE.dummy
2024	mg: MERGE/MERGE.dummy
2025	ge: GENOM/GENOM.dummy
2026	prd: PRIMER_DESIGN/PRIMER_DESIGN.dummy
2027
2028	nt: menus $(NTREE)
2029
2030	nal: $(NALIGNER)
2031
2032	di: $(DIST)
2033	ph: $(PHYLO)
2034	pa: $(PARSIMONY)
2035	tg: $(TREEGEN)
2036
2037	ifeq ($(OPENGL),1)
2038	3d: RNA3D/RNA3D.dummy
2039	gl: GL/GL.dummy
2040	else
2041	noopengl:
2042	@echo "invalid target for OPENGL=0"
2043	3d: noopengl
2044	gl: noopengl
2045	endif
2046
2047	SL/SL.dummy: com
2048
2049	ds: $(DBSERVER)
2050	pt: $(PROBE)
2051	pst: PROBE_SET/PROBE_SET.dummy
2052	pd: PROBE_DESIGN/PROBE_DESIGN.dummy
2053	na: $(NAMES)
2054	sq: SEQ_QUALITY/SEQ_QUALITY.dummy
2055	cma: $(RNACMA)
2056
2057	sec: SECEDIT/SECEDIT.dummy
2058
2059	e4: $(EDIT4) readseq menus
2060
2061	gi: GENOM_IMPORT/GENOM_IMPORT.dummy
2062	wetc: $(WETC)
2063
2064	xml: XML/XML.dummy
2065	stat: STAT/STAT.dummy $(NTREE) $(EDIT4)
2066	fa: SL/FAST_ALIGNER/FAST_ALIGNER.dummy
2067
2068	#********************************************************************************
2069
2070	up_by_remake: depends proto vectorize_checks
2071
2072	up: up_by_remake tags valgrind_update
2073
2074	#********************************************************************************
2075
2076	touch:
2077	SOURCE_TOOLS/touch_modified.pl
2078
2079	modified: touch
2080	$(MAKE) all
2081
2082	#********************************************************************************
2083
2084	libdepends:
2085	$(MAKE) -C "SOURCE_TOOLS" \
2086	"RNA3D_LIB=$(RNA3D_LIB_4_DEPENDS)" \
2087	libdepends
2088
2089	#********************************************************************************
2090
2091	# create generated headers:
2092	genheaders: TEMPLATES/TEMPLATES.dummy
2093
2094	clrdotdepends:
2095	rm PROBE_COM/.depends \|\| true
2096	rm NAMES_COM/.depends \|\| true
2097	rm PERL2ARB/.depends \|\| true
2098
2099	comdepends: comtools clrdotdepends have_makedepend
2100	@echo "$(SEP) Partially build com interface"
2101	$(MAKE) PROBE_COM/PROBE_COM.depends NAMES_COM/NAMES_COM.depends
2102	$(MAKE) PROBE_COM/server.depends NAMES_COM/server.depends
2103
2104	depends: genheaders comdepends vectorize_checks have_makedepend
2105	@echo "$(SEP) Updating other dependencies"
2106	$(MAKE) $(subst NAMES_COM/server.depends,,$(subst PROBE_COM/server.depends,,$(SUBDIRS:.sub=.depends))) \
2107	HELP_SOURCE/HELP_SOURCE.depends \
2108	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.depends \
2109
2110	$(MAKE) libdepends
2111
2112	depend: depends
2113
2114	# ------------------------------------------------------------
2115	# dependency generation tests for AISC code
2116	#(all should work w/o creating wrong dependencies;
2117	# neither in XXX_COM/Makefile nor in code using AISC interface)
2118	dependstest1: silent_clean
2119	$(MAKE) depends
2120	dependstest2: silent_clean
2121	$(MAKE) com
2122	dependstest3: silent_clean
2123	$(MAKE) aw
2124	dependstest4: silent_clean
2125	$(MAKE) pt
2126	dependstest5: silent_clean
2127	$(MAKE) na
2128	dependstest6: silent_clean
2129	$(MAKE) nt
2130	dependstest7: silent_clean
2131	$(MAKE) all
2132	# ------------------------------------------------------------
2133
2134	vectorize_checks:
2135	$(MAKE) -C SOURCE_TOOLS -r vectorize_checks
2136
2137	clean_checked_vect: lib/lib.clean
2138	SOURCE_TOOLS/clean_checked_vectorizations.sh
2139
2140	# ------------------------------------------------------------
2141
2142	AISC_MKPTPS/AISC_MKPTPS.dummy: links
2143
2144	proto_tools: AISC_MKPTPS/AISC_MKPTPS.dummy
2145
2146	proto: proto_tools
2147	@echo $(SEP) Updating prototypes
2148	$(MAKE) \
2149	ARBDB/ARBDB.proto \
2150	AISC_COM/AISC_COM.proto \
2151	ARB_GDE/ARB_GDE.proto \
2152	CORE/CORE.proto \
2153	CONVERTALN/CONVERTALN.proto \
2154	NTREE/NTREE.proto \
2155	MERGE/MERGE.proto \
2156	PROBE/PROBE.proto \
2157	SERVERCNTRL/SERVERCNTRL.proto \
2158	SL/SL.proto \
2159
2160	#********************************************************************************
2161
2162	valgrind_update: links
2163	@echo $(SEP) Updating for valgrind
2164	$(MAKE) -C SOURCE_TOOLS valgrind_update
2165
2166	#********************************************************************************
2167
2168	TAGFILE=TAGS
2169	UTAGS=TAGS.$(ARBBID)
2170	TAGFILE_TMP=$(UTAGS).tmp
2171
2172	TAG_SOURCE_HEADERS=$(UTAGS).headers.tmp
2173	TAG_SOURCE_CODE=$(UTAGS).codefiles.tmp
2174	TAG_SOURCE_LISTS=$(TAG_SOURCE_HEADERS) $(TAG_SOURCE_CODE)
2175
2176	ETAGS_IGNORE_LIST=SOURCE_TOOLS/etags_ignore.lst
2177
2178	ETAGS=ctags -e -I @$(ETAGS_IGNORE_LIST) --sort=no --if0=no --extra=q
2179	ETAGS_TYPES=--C-kinds=cgnsut --C++-kinds=cgnsut
2180	ETAGS_FUN =--C-kinds=fm --C++-kinds=fm
2181	ETAGS_REST =--C-kinds=dev --C++-kinds=dev
2182
2183	FILTER_TAGS_SOURCES= \
2184	$(SED) -e 's/^.\///g' \| \
2185	grep -vi '^HEADERLIBS\\|^GDE/\\|/GEN[CH]/'
2186
2187	$(TAG_SOURCE_HEADERS): links
2188	@find . $ -name '.hxx' -o -name ".h" $ -type f \| $(FILTER_TAGS_SOURCES) > $@
2189
2190	$(TAG_SOURCE_CODE): links
2191	@find . $ -name '.cxx' -o -name ".c" $ -type f \| $(FILTER_TAGS_SOURCES) > $@
2192
2193	$(UTAGS).1.tmp: $(TAG_SOURCE_HEADERS)
2194	@$(ETAGS) -f $@ $(ETAGS_TYPES) -L $<
2195	$(UTAGS).2.tmp: $(TAG_SOURCE_HEADERS)
2196	@$(ETAGS) -f $@ $(ETAGS_FUN) -L $<
2197	$(UTAGS).3.tmp: $(TAG_SOURCE_HEADERS)
2198	@$(ETAGS) -f $@ $(ETAGS_REST) -L $<
2199	$(UTAGS).4.tmp: $(TAG_SOURCE_CODE)
2200	@$(ETAGS) -f $@ $(ETAGS_TYPES) -L $<
2201	$(UTAGS).5.tmp: $(TAG_SOURCE_CODE)
2202	@$(ETAGS) -f $@ $(ETAGS_FUN) -L $<
2203	$(UTAGS).6.tmp: $(TAG_SOURCE_CODE)
2204	@$(ETAGS) -f $@ $(ETAGS_REST) -L $<
2205
2206	TAGS_ALL_PARTS=$(UTAGS).1.tmp $(UTAGS).2.tmp $(UTAGS).3.tmp $(UTAGS).4.tmp $(UTAGS).5.tmp $(UTAGS).6.tmp
2207
2208	$(TAGFILE_TMP) : $(TAGS_ALL_PARTS)
2209	@cat $(TAGS_ALL_PARTS) > $@
2210	@rm $(TAGS_ALL_PARTS) $(TAG_SOURCE_LISTS)
2211
2212	cleanOldTags:
2213	@find $(ARBHOME) -name 'TAGS.*.tmp' -ctime +2 -exec rm {} \;
2214
2215	tags: $(TAGFILE_TMP) cleanOldTags
2216	@mv_if_diff $(TAGFILE_TMP) $(TAGFILE)
2217
2218	#********************************************************************************
2219
2220	LINKSTAMP=SOURCE_TOOLS/stamp.generate_all_links
2221
2222	links: checks $(LINKSTAMP) arbmainwrapper
2223	links_no_checks: $(LINKSTAMP) arbmainwrapper
2224
2225	forcelinks:
2226	-rm $(LINKSTAMP)
2227	$(MAKE) links
2228
2229	$(LINKSTAMP): SOURCE_TOOLS/generate_all_links.sh genheaders
2230	+SOURCE_TOOLS/generate_all_links.sh
2231	touch $(LINKSTAMP)
2232
2233	clean_links:
2234	# avoid to delete linked pts, nas or arb_tcp.dat:
2235	find . -path './lib' -prune -o -type l -exec rm {} \;
2236	# removed obsolete file - refuses to disappear due to 'prune' above
2237	@rm -f lib/help/GDEHELP
2238	@rm -f $(LINKSTAMP) lib/inputMasks/format.readme
2239
2240	redo_links: clean_links
2241	$(MAKE) links_no_checks
2242
2243	#********************************************************************************
2244
2245	header_libs:
2246	@(( \
2247	echo "$(SEP) Make HEADERLIBS"; \
2248	$(MAKE) -C HEADERLIBS all && \
2249	echo "$(SEP) Make HEADERLIBS [done]"; \
2250	) > HEADERLIBS.log 2>&1 && (cat HEADERLIBS.log;rm HEADERLIBS.log)) \|\| (cat HEADERLIBS.log;rm HEADERLIBS.log;false)
2251
2252	#********************************************************************************
2253
2254	gde: GDE/GDE.dummy
2255	GDE: gde
2256	agde: ARB_GDE/ARB_GDE.dummy
2257	tools: TOOLS/TOOLS.dummy
2258	convert: $(CONVERT_ALN)
2259	readseq: READSEQ/READSEQ.dummy
2260
2261	#***************************************************************************************
2262	# Some user commands
2263	#***************************************************************************************
2264
2265	menus: binlink links
2266	@(( \
2267	echo "$(SEP) Make GDEHELP"; \
2268	$(MAKE) -C GDEHELP -r all && \
2269	echo "$(SEP) Make GDEHELP [done]"; \
2270	) > GDEHELP.log 2>&1 && (cat GDEHELP.log;rm GDEHELP.log)) \|\| (cat GDEHELP.log;rm GDEHELP.log;false)
2271
2272	ifeq ($(DEBUG),1)
2273	BIN_TARGET=develall
2274	else
2275	BIN_TARGET=all
2276	endif
2277
2278
2279	binlink:
2280	$(MAKE) -C bin $(BIN_TARGET)
2281
2282	check_bin_dep: binlink
2283	SOURCE_TOOLS/check_bin_dependencies.pl
2284
2285	fig_cure:
2286	SOURCE_TOOLS/sortfig.pl doit
2287
2288	preplib:
2289	(cd lib;$(MAKE) all)
2290
2291	# --------------------------------------------------------------------------------
2292	# This section is quite tricky:
2293	#
2294	# make 'perl' is a BIG target, so when it has to be made, it has to be started
2295	# as early as possible to reduce overall compile time. Since 'make' does not
2296	# provide any priorities, i force it to build all 'perl'-prerequisites early, by
2297	# adding artificial dependencies to these prerequisites
2298	#
2299	# That behavior is likely to be system-dependent.
2300	# My goal was only to make it work on my current development system,
2301	# where this saves about 20% of overall build time.
2302
2303	ifeq ($(WITHPERL),1)
2304	links_non_perl: PERLTOOLS/PERLTOOLS.dummy
2305	perltools: links_non_perl
2306	perl: realperl
2307	else
2308	links_non_perl: links
2309	perl: links
2310	$(MAKE) "WITHPERL=1" perl
2311	endif
2312
2313	# ---------------------------------------- perl
2314
2315	realperl: perltools
2316	(( \
2317	echo "$(SEP) Make PERL2ARB" ; \
2318	$(TIME) $(MAKE) -C PERL2ARB -r -f Makefile.main \
2319	"AUTODEPENDS=1" \
2320	"dflags=$(dflags)" \
2321	"cflags4perl=$(cflags) $(cxxflags) $(dflags)" \
2322	"lflags4perl=$(lflags4perl)" \
2323	"COMPILER_VERSION=$(COMPILER_VERSION)" \
2324	all && \
2325	$(MAKE) -C PERL_SCRIPTS/test test && \
2326	echo "$(SEP) Make PERL2ARB [done]" ; \
2327	) > PERL2ARB.log 2>&1 && (cat PERL2ARB.log;rm PERL2ARB.log)) \|\| (cat PERL2ARB.log;rm PERL2ARB.log;false)
2328
2329	perl_clean:
2330	@$(MAKE) -C PERL2ARB -r -f Makefile.main \
2331	"AUTODEPENDS=0" \
2332	clean
2333
2334	PERL2ARB/PERL2ARB.clean:
2335	$(MAKE) perl_clean
2336	$(MAKE) -C PERL_SCRIPTS/test clean
2337
2338	# ---------------------------------------- bindings to script languages
2339
2340	bindings: lib/libCORE.so lib/libARBDB.so
2341	$(MAKE) -C BINDINGS all ARBDEPENDS="$(^:%=../%)" DFLAGS="$(dflags)"
2342
2343	bindings_clean:
2344	$(MAKE) -C BINDINGS clean
2345
2346	# ---------------------------------------- check resources
2347
2348	check_res:
2349	$(ARBHOME)/SOURCE_TOOLS/check_resources.pl
2350
2351	# ---------------------------------------- cleaning
2352
2353	rmbak:
2354	@echo "[cleanup backup/core files]"
2355	@find . \( -name '*%' \
2356	-o -name '*.bak' \
2357	-o -name '*~' \) \
2358	-o $ -name 'core' -a \! -type d $ \
2359	-exec rm -v {} \; \|\| \
2360	echo "Warning: target 'rmbak' reported problems when removing misc. backup files (ignored)"
2361	@echo "[cleanup done]"
2362
2363	bin_reinit:
2364	$(MAKE) bin/bin.clean
2365	$(MAKE) -C "bin" all
2366
2367	clean_directories:
2368	-rm -rf \
2369	$(ARBHOME)/PROBE_SET/bin \
2370	$(ARBHOME)/INCLUDE \
2371
2372	libclean:
2373	-find $(ARBHOME) -type f $ -name '*.a' ! -type l $ -exec rm -f {} \;
2374	-find $(ARBHOME) -type f $ -name 'lib*.so' ! -type l $ -exec rm -f {} \;
2375
2376	objclean:
2377	-find $(ARBHOME) -type f $ -name '*.o' ! -type l $ -exec rm -f {} \;
2378
2379	# bin.clean and HELP_SOURCE.clean interfere
2380	clean3:
2381	$(MAKE) bin/bin.clean
2382	$(MAKE) HELP_SOURCE/HELP_SOURCE.clean
2383
2384
2385	# delete all binaries (similar to 'cleanlinked')
2386	cleanRelinkable: libclean UNIT_TESTER/UNIT_TESTER.clean
2387	$(MAKE) -C bin cleanbinariesRelinkable
2388	$(MAKE) -C PROBE_SET cleanLinked
2389
2390
2391	clean2: $(SUBDIRS:.sub=.clean) \
2392	clean3 \
2393	rmbak \
2394	libclean \
2395	objclean \
2396	lib/lib.clean \
2397	GDEHELP/GDEHELP.clean \
2398	HEADERLIBS/HEADERLIBS.clean \
2399	SOURCE_TOOLS/SOURCE_TOOLS.clean \
2400	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.clean \
2401	UNIT_TESTER/UNIT_TESTER.clean \
2402	TEMPLATES/TEMPLATES.clean \
2403	perl_clean \
2404	clean_directories \
2405
2406	rm -f .last_gcc .last_compiler config.makefile.bak
2407
2408	# links are needed for cleanup
2409	clean: redo_links motif_xpm_hack_clean
2410	$(MAKE) clean2
2411	$(MAKE) clean_cov_all clean_links
2412
2413	silent_clean:
2414	$(MAKE) clean >/dev/null
2415
2416	# 'relocated' is about 50% faster than 'rebuild'
2417	reloc_clean: links
2418	@echo "---------------------------------------- Relocation cleanup"
2419	$(MAKE) \
2420	perl_clean \
2421	GDEHELP/GDEHELP.clean \
2422	HELP_SOURCE/genhelp/genhelp.clean \
2423	bin/bin.clean \
2424	libclean \
2425	objclean
2426
2427	relocated: links
2428	$(MAKE) reloc_clean
2429	@echo "---------------------------------------- and remake"
2430	$(MAKE) build
2431
2432	# -----------------------------------
2433	# some stress tests
2434	# (helpful to reveal race conditions with -j)
2435
2436	rebuild4ever: rebuild
2437	$(MAKE) rebuild4ever
2438
2439	build4ever: build
2440	$(MAKE) build4ever
2441
2442	clean4ever: clean
2443	$(MAKE) clean4ever
2444
2445	test4ever: ut
2446	$(MAKE) test4ever
2447
2448	perl4ever: clean
2449	$(MAKE) links
2450	$(MAKE) perl
2451	$(MAKE) perl4ever
2452
2453	help4ever: clean
2454	$(MAKE) help
2455	$(MAKE) help4ever
2456
2457	# -----------------------------------
2458
2459	cleanlinked: bin/bin.clean libclean
2460
2461	relink: cleanlinked
2462	$(MAKE) all
2463
2464	# --------------------------------------------------------------------------------
2465	# source related targets
2466
2467	CLOC=cloc
2468	CLOCFLAGS=--no3 --quiet --progress-rate=0
2469	CLOCARB=--exclude-dir=GDE .
2470	CLOCEXT=GDE
2471	CLOCCODE=--force-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.code.def
2472	CLOCREST=--force-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.rest.def
2473	CLOCFILT=tail --lines=+4
2474
2475	cloc:
2476	@echo 'Arb code:'
2477	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCARB) \| $(CLOCFILT)
2478	@echo 'Arb rest:'
2479	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCARB) \| $(CLOCFILT)
2480	@echo 'External code:'
2481	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCEXT) \| $(CLOCFILT)
2482	@echo 'External rest:'
2483	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCEXT) \| $(CLOCFILT)
2484
2485
2486	# patch generation
2487	patch:
2488	SOURCE_TOOLS/arb_create_patch.sh arbPatch --svn
2489
2490	# source tarball generation
2491	save: sourcetarfile
2492
2493	sourcetarfile: rmbak
2494	util/arb_save
2495
2496	# test early whether save will work
2497	savetest:
2498	@util/arb_srclst.pl >/dev/null
2499
2500	testsave: savetest
2501
2502	save2: rmbak
2503	util/arb_save ignore
2504
2505	save_test: rmbak
2506	@echo "Testing source list.."
2507	@util/arb_srclst.pl > /dev/null
2508
2509	save_test_no_error:
2510	@-$(MAKE) save_test
2511
2512	# --------------------------------------------------------------------------------
2513	# version management
2514
2515	inc_candi:
2516	touch SOURCE_TOOLS/inc_candi.stamp
2517	$(MAKE) do_version_update
2518
2519	inc_patch:
2520	touch SOURCE_TOOLS/inc_patch.stamp
2521	$(MAKE) do_version_update
2522
2523	inc_minor:
2524	touch SOURCE_TOOLS/inc_minor.stamp
2525	$(MAKE) do_version_update
2526
2527	inc_major:
2528	touch SOURCE_TOOLS/inc_major.stamp
2529	$(MAKE) do_version_update
2530
2531	do_version_update:
2532	@echo Incrementing version information
2533	$(MAKE) savetest
2534	$(MAKE) genheaders # auto upgrades version early
2535
2536	show_version:
2537	$(MAKE) genheaders # updates version info
2538	@echo "$(SEP) ARB version info"
2539	@grep ARB_VERSION TEMPLATES/arb_build.h
2540	@echo "$(SEP)"
2541
2542	# --------------------------------------------------------------------------------
2543	# special cleanups
2544
2545	clean_opengl_changed: RNA3D/RNA3D.clean EDIT4/EDIT4.clean WINDOW/WINDOW.clean GL/GL.clean
2546
2547	# --------------------------------------------------------------------------------
2548
2549	arbapplications: nt pa e4 wetc pt na nal di ph ds wetc cma
2550
2551	arb_external: convert tools gde readseq tg pst
2552
2553	arb_no_perl: arbapplications help arb_external
2554
2555	arb: motif_xpm_hack
2556	$(MAKE) "WITHPERL=1" perl arb_no_perl
2557
2558	motif_xpm_hack:
2559	$(MAKE) -r -C "lib/motifHack" all
2560
2561	motif_xpm_hack_clean:
2562	$(MAKE) -r -C "lib/motifHack" clean
2563
2564	# --------------------------------------------------------------------------------
2565	# special targets for SOURCE_TOOLS/remake_after_change.pl
2566
2567	rac_arb_dist: di
2568	rac_arb_edit4: e4
2569	rac_arb_ntree: nt
2570	rac_arb_pars: pa
2571	rac_arb_phylo: ph
2572	rac_arb_wetc: wetc
2573	rac_arb_naligner: nal
2574	rac_arb_pt_server: pt
2575	rac_arb_db_server: ds
2576	rac_arb_name_server: na
2577	rac_arb_convert_aln: convert
2578	rac_arb_treegen: tg
2579	rac_arb_rnacma: cma
2580	rac_arb_help2xml: help
2581
2582	rac_arb_a2ps: tools
2583	rac_arb_consensus_tree: tools
2584	rac_arb_dnarates: tools
2585	rac_arb_export_rates: tools
2586	rac_arb_export_tree: tools
2587	rac_arb_gene_probe: tools
2588	rac_arb_message: tools
2589	rac_arb_primer: tools
2590	rac_arb_probe: tools
2591	rac_arb_read_tree: tools
2592
2593	# --------------------------------------------------------------------------------
2594	# unit testing
2595	# @@@ work in progress
2596	#
2597	# goal is to automatically test all libraries/executables using TESTED_UNITS_AUTO
2598	# currently not all test executables link w/o error.
2599	# therefor units are organized in three sets:
2600	#
2601	# TESTED_UNITS = testable and contain tests
2602	# UNTESTED_UNITS = testable, but no tests written yet
2603	# UNTESTABLE_UNITS = not testable
2604
2605	# always define OPENGL units manually:
2606	OPENGL_TESTS :=
2607	ifeq ($(OPENGL),1)
2608	OPENGL_TESTS += \
2609	$(subst .a,.test,$(RNA3D_LIB)) \
2610	GL/glAW/libglAW.test \
2611	GL/glpng/libglpng_arb.test \
2612
2613	endif
2614
2615	UNITS_NOT_AUTODETECTED = \
2616	HELP_SOURCE/HELP_SOURCE.tooltests
2617
2618	TESTED_UNITS_AUTO = \
2619	$(OPENGL_TESTS) \
2620	$(TL_ARCHIVES:.a=.test) \
2621	$(TL_SHARED_ARCHIVES:.so=.test) \
2622	$(CL_ARCHIVES:.a=.test) \
2623	$(TL_TOOLS_COLLECTIONS:.toolColl=.tooltests) \
2624	$(UNITS_NOT_AUTODETECTED) \
2625
2626	UNTESTED_UNITS = \
2627	$(OPENGL_TESTS) \
2628	EISPACK/EISPACK.test \
2629	GENOM/GENOM.test \
2630	ISLAND_HOPPING/ISLAND_HOPPING.test \
2631	NALIGNER/NALIGNER.test \
2632	NAMES/NAMES.test \
2633	PHYLO/PHYLO.test \
2634	PRIMER_DESIGN/PRIMER_DESIGN.test \
2635	READSEQ/READSEQ.tooltests \
2636	SECEDIT/SECEDIT.test \
2637	SEQ_QUALITY/SEQ_QUALITY.test \
2638	SERVERCNTRL/SERVERCNTRL.test \
2639	SL/ALIVIEW/ALIVIEW.test \
2640	SL/AP_TREE/AP_TREE.test \
2641	SL/ARB_TREE/ARB_TREE.test \
2642	SL/AW_HELIX/AW_HELIX.test \
2643	SL/AW_NAME/AW_NAME.test \
2644	SL/DB_SCANNER/DB_SCANNER.test \
2645	SL/DB_UI/DB_UI.test \
2646	SL/GUI_ALIVIEW/GUI_ALIVIEW.test \
2647	SL/HELIX/HELIX.test \
2648	SL/QUERY/QUERY.test \
2649	SL/REFENTRIES/REFENTRIES.test \
2650	SL/SEQUENCE/SEQUENCE.test \
2651	SL/TREE_ADMIN/TREE_ADMIN.test \
2652	SL/TREE_WRITE/TREE_WRITE.test \
2653	SL/XFERGUI/XFERGUI.test \
2654	STAT/STAT.test \
2655	TREEGEN/TREEGEN.test \
2656	WETC/WETC.test \
2657	XML/XML.test \
2658
2659	# untestable units
2660
2661	UNTESTABLE_UNITS = \
2662	AISC/AISC.test \
2663	NAMES_COM/server.test \
2664	PROBE_COM/server.test \
2665
2666	# --------------------
2667	# put all units containing tests into the following 4 sections (see also TESTED_UNITS below)
2668
2669	# recent development
2670	UNITS_TESTED_FIRST = \
2671	SL/MATRIX/MATRIX.test \
2672	AWTI/AWTI.test \
2673	SL/FILTSEQEXP/FILTSEQEXP.test \
2674	SL/GROUP_SEARCH/GROUP_SEARCH.test \
2675	SL/PVP/PVP.test \
2676	SL/SAICALC/SAICALC.test \
2677	SL/TRANSLATE/TRANSLATE.test \
2678	SL/XFERSET/XFERSET.test \
2679
2680	# start units with long duration early
2681	UNITS_RUNNING_LONG = \
2682	ARBDB/libARBDB.test \
2683	AWTC/AWTC.test \
2684	TOOLS/TOOLS.tooltests \
2685
2686	# plain test-libaries that are not linked anywhere
2687	TEST_SANDBOXES = \
2688	SL/CB/CB.test \
2689	SL/HEADERTESTS/HEADERTESTS.test \
2690
2691	UNITS_TESTED = \
2692	AISC_MKPTPS/AISC_MKPTPS.tooltests \
2693	ARB_GDE/ARB_GDE.test \
2694	AWT/libAWT.test \
2695	CONSENSUS_TREE/CONSENSUS_TREE.test \
2696	CONVERTALN/CONVERTALN.test \
2697	CORE/libCORE.test \
2698	DBSERVER/DBSERVER.test \
2699	DIST/DIST.test \
2700	EDIT4/EDIT4.test \
2701	GENOM_IMPORT/GENOM_IMPORT.test \
2702	HELP_SOURCE/HELP_SOURCE.tooltests \
2703	MERGE/MERGE.test \
2704	MULTI_PROBE/MULTI_PROBE.test \
2705	NTREE/NTREE.test \
2706	PARSIMONY/PARSIMONY.test \
2707	PERLTOOLS/PERLTOOLS.tooltests \
2708	PROBE/PROBE.test \
2709	PROBE_DESIGN/PROBE_DESIGN.test \
2710	PROBE_SET/PROBE_SET.tooltests \
2711	RNACMA/RNACMA.test \
2712	SL/ALILINK/ALILINK.test \
2713	SL/CONSENSUS/CONSENSUS.test \
2714	SL/DB_QUERY/DB_QUERY.test \
2715	SL/FAST_ALIGNER/FAST_ALIGNER.test \
2716	SL/FILTER/FILTER.test \
2717	SL/INSDEL/INSDEL.test \
2718	SL/ITEM_SHADER/ITEM_SHADER.test \
2719	SL/ITEMS/ITEMS.test \
2720	SL/LOCATION/LOCATION.test \
2721	SL/MACROS/MACROS.test \
2722	SL/NDS/NDS.test \
2723	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.test \
2724	SL/PRONUC/PRONUC.test \
2725	SL/PTCLEAN/PTCLEAN.test \
2726	SL/REGEXPR/REGEXPR.test \
2727	SL/SEQIO/SEQIO.test \
2728	SL/TREE_READ/TREE_READ.test \
2729	SL/TREEDISP/TREEDISP.test \
2730	WINDOW/libWINDOW.test \
2731
2732	TESTED_UNITS = \
2733	$(UNITS_TESTED_FIRST) \
2734	$(UNITS_RUNNING_LONG) \
2735	$(TEST_SANDBOXES) \
2736	$(UNITS_TESTED) \
2737
2738	# ----------------------------------------
2739
2740	ifeq ($(DEVELOPER),RALF)
2741
2742	DEFINED_TEST_UNITS = \
2743	$(TESTED_UNITS) \
2744	$(UNTESTED_UNITS) \
2745	$(UNTESTABLE_UNITS) \
2746
2747	list_undefined_units:
2748	@UNIT_TESTER/list_undefined_units.pl $(DEFINED_TEST_UNITS) -- $(TESTED_UNITS_AUTO)
2749
2750	else
2751
2752	list_undefined_units:
2753
2754	endif
2755
2756	# ----------------------------------------
2757
2758	TEST_LOG_DIR = UNIT_TESTER/logs
2759	TEST_RUN_SUITE=$(MAKE) $(NODIR) -C UNIT_TESTER -f Makefile.suite -r
2760	# -> UNIT_TESTER/Makefile.suite
2761	TEST_MAKE_FLAGS=
2762	TEST_POST_CLEAN=
2763	ifeq ($(COVERAGE),1)
2764	TEST_POST_CLEAN=$(MAKE) clean_cov
2765	TEST_MAKE_FLAGS+=-j1
2766	endif
2767
2768
2769	%.test:
2770	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
2771	( \
2772	echo "take[1]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
2773	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
2774	"UNITDIR=$(@D)" \
2775	"UNITLIBNAME=$(@F:.test=)" \
2776	"COVERAGE=$(COVERAGE)" \
2777	"ARB_PID=$(ARB_PID)_$(@F)" \
2778	runtest; \
2779	echo "take[1]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"; \
2780	$(TEST_POST_CLEAN) \
2781	) >$(TEST_LOG_DIR)/$(@F).log 2>&1; \
2782	UNIT_TESTER/log_result.pl $(TEST_LOG_DIR)/$(@F).log )
2783
2784	%.notest:
2785	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
2786	( \
2787	echo "take[4]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
2788	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
2789	"UNITDIR=$(@D)" \
2790	"UNITLIBNAME=$(@F:.notest=)" \
2791	"COVERAGE=0" \
2792	"ARB_PID=$(ARB_PID)_$(@F)" \
2793	check_no_test; \
2794	echo "take[4]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'" \
2795	) >$(TEST_LOG_DIR)/$(@F).log 2>&1 )
2796
2797
2798	# tool test aliases (used to test one or multiple executable(s) in a single subdir):
2799	%.tooltests:
2800	$(error please define an explicit tooltest alias for $@)
2801
2802	AISC_MKPTPS/AISC_MKPTPS.tooltests : AISC_MKPTPS/mkptypes.test
2803	@echo "aliasing $@ -> $^"
2804	PERLTOOLS/PERLTOOLS.tooltests : PERLTOOLS/arb_proto_2_xsub.test
2805	@echo "aliasing $@ -> $^"
2806	PROBE_SET/PROBE_SET.tooltests : PROBE_SET/fb_test.test
2807	@echo "aliasing $@ -> $^"
2808	HELP_SOURCE/HELP_SOURCE.tooltests : HELP_SOURCE/arb_help2xml.test
2809	@echo "aliasing $@ -> $^"
2810	TOOLS/TOOLS.tooltests : TOOLS/arb_consensus_tree.test TOOLS/arb_probe.test TOOLS/arb_test.test
2811	@echo "aliasing $@ -> $^"
2812
2813	# aliases for tools w/o tests:
2814	READSEQ/READSEQ.tooltests:
2815	@echo "Note: no tests for $@"
2816
2817
2818	test_base: $(UNIT_TESTER_LIB:.a=.dummy) $(subst .test,.dummy,$(TEST_SANDBOXES))
2819
2820	clean_cov:
2821	find . $ -name ".gcda" -o -name ".gcov" -o -name "*.cov" $ -exec rm {} \;
2822
2823	clean_cov_all: clean_cov
2824	find . $ -name "*.gcno" $ -exec rm {} \;
2825
2826	cleanup_faked_arbpids:
2827	@rm ~/.arb_tmp/tmp/arb_pids_${USER}_${ARB_PID}_* \|\| true
2828
2829	cleanup_faked_arbpids_and_fail: cleanup_faked_arbpids
2830	@false
2831
2832	NOTESTS_IN_UNTESTED = $(subst .test,.notest,$(UNTESTED_UNITS))
2833
2834	run_tests_faked_arbpid:
2835	+@$(TEST_RUN_SUITE) init
2836	@echo "take[2]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2837	@$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(TESTED_UNITS) $(NOTESTS_IN_UNTESTED) \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2838	@echo "take[2]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2839	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2840	@$(MAKE) clean_cov >/dev/null
2841	@$(MAKE) cleanup_faked_arbpids
2842
2843	# @@@ instead of only running UNIT, this should as well run all tests this unit depends on? according to 'needs_libs'
2844	# @@@ '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
2845
2846	run_onetest_faked_arbpid:
2847	+@$(TEST_RUN_SUITE) init
2848	@echo "take[3]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2849	test -n "$(UNIT)" \|\| (echo "Error: UNIT has to be defined for target 'run_onetest_faked_arbpid'!"; false)
2850	$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(UNIT).test \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2851	@echo "take[3]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2852	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2853	@$(MAKE) clean_cov >/dev/null
2854	@$(MAKE) cleanup_faked_arbpids
2855
2856	run_tests: test_base clean_cov
2857	$(MAKE) "ARB_PID=UT_$$$$" run_tests_faked_arbpid list_undefined_units
2858
2859	run_oneunitstests: test_base
2860	$(MAKE) "ARB_PID=UT_$$$$" run_onetest_faked_arbpid
2861
2862
2863	ut:
2864	ifeq ($(UNIT_TESTS),1)
2865	@echo $(MAKE) run_tests
2866	@$(MAKE) run_tests
2867	else
2868	@echo "Not compiled with unit tests"
2869	endif
2870
2871
2872	aut:
2873	+@$(TEST_RUN_SUITE) unskip
2874	$(MAKE) ut
2875
2876	# --------------------------------------------------------------------------------
2877
2878	TIMELOG=$(ARBHOME)/arb_time.log
2879	TIMEARGS=--append --output=$(TIMELOG) --format=" * %E(%S+%U) %P [%C]"
2880	TIMECMD=$(TIME) $(TIMEARGS)
2881
2882	time_one:
2883	ifeq ($(ONE_TIMED_TARGET),)
2884	@echo "Error: You have to pass ONE_TIMED_TARGET to $@"
2885	false
2886	else
2887	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET)"
2888	@$(TIMECMD) $(MAKE) $(ONE_TIMED_TARGET)
2889	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET) [done]"
2890	endif
2891
2892	timed_target:
2893	ifeq ($(TIMED_TARGET),)
2894	@echo "Error: You have to pass TIMED_TARGET to $@"
2895	false
2896	else
2897	@echo "Build time:" > $(TIMELOG)
2898	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2899	@cat $(TIMELOG)
2900	@rm $(TIMELOG)
2901	endif
2902
2903	timed_target_tested:
2904	ifeq ($(TIMED_TARGET),)
2905	@echo "Error: You have to pass TIMED_TARGET to $@"
2906	false
2907	else
2908	@echo "Build time:" > $(TIMELOG)
2909	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2910	$(MAKE) "ONE_TIMED_TARGET=ut" time_one
2911	@cat $(TIMELOG)
2912	@rm $(TIMELOG)
2913	endif
2914
2915	clean_timed_target:
2916	ifeq ($(TIMED_TARGET),)
2917	@echo "Error: You have to pass TIMED_TARGET to $@"
2918	false
2919	else
2920	@echo "Build time:" > $(TIMELOG)
2921	$(MAKE) "ONE_TIMED_TARGET=clean" time_one
2922	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2923	@cat $(TIMELOG)
2924	@rm $(TIMELOG)
2925	endif
2926
2927	# --------------------------------------------------------------------------------
2928
2929	CHECKOUT_MODIFIED=0# set to 1 to temporarily skip test for modifications (do not check in if set to 1)
2930
2931	check_svn_does_not_contain_generated:
2932	ifeq ($(CHECKOUT_MODIFIED),0)
2933	@echo "Testing that build does not modify files in SVN"
2934	@test 0 = `svn status \| wc -l` \|\| ( \
2935	echo "The checkout is not/no longer clean:"; \
2936	svn status; \
2937	echo "- if this fails instantly, your checkout is not clean"; \
2938	echo "- if this fails after other targets, these targets modify checked in data"; \
2939	echo " (a common cause may be that depends are not up to date)"; \
2940	false)
2941	else
2942	grep -Hn 'CHECKOUT_MODIFIED' Makefile
2943	endif
2944
2945	check_svn_ignores_generated:
2946	@test 0 = `svn status \| grep '^\?' \| wc -l` \|\| ( \
2947	echo "There are svn-unignored files:"; \
2948	svn status \| grep '^\?'; \
2949	echo "(all generated files should be svn-ignored)"; \
2950	false)
2951
2952	check_svn_state: check_svn_does_not_contain_generated
2953	$(MAKE) check_svn_ignores_generated
2954	$(MAKE) savetest
2955
2956	things_that_always_should_work: depends proto
2957
2958	post_commit_check:
2959	@echo "---------------------------------------- [Initial]"
2960	$(MAKE) check_svn_state
2961
2962	$(MAKE) clean
2963	@echo "---------------------------------------- [After 'make clean']"
2964	$(MAKE) check_svn_state
2965
2966	$(MAKE) things_that_always_should_work
2967	@echo "---------------------------------------- [After 'make things_that_always_should_work']"
2968	$(MAKE) check_svn_state
2969
2970	$(MAKE) all
2971	@echo "---------------------------------------- [After 'make all']"
2972	$(MAKE) check_svn_state
2973
2974	$(MAKE) things_that_always_should_work
2975	@echo "---------------------------------------- [Final]"
2976	$(MAKE) check_svn_state
2977
2978	# --------------------------------------------------------------------------------
2979	# sanitize arb_ntree; also works for clients (arb_edit4, ...) started from there.
2980
2981	sanitize: all
2982	( \
2983	export "LSAN_OPTIONS=max_leaks=30:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp"; \
2984	echo "sake[1]: Entering directory \`$(ARBHOME)'"; \
2985	$(ARBHOME)/bin/arb_ntree --execute _logged ~/data/test.arb 2>&1 ; \
2986	echo "sake[1]: Leaving directory \`$(ARBHOME)'" \
2987	) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
2988
2989	# --------------------------------------------------------------------------------
2990	# build and test one unit:
2991
2992	build_oneunit:
2993	$(MAKE) "WITHPERL=1" $(UNIT).dummy
2994
2995	oneunit:
2996	ifndef UNIT
2997	@echo "Please define UNIT, e.g. using"
2998	@echo " make \"UNIT=ARBDB/libARBDB\" oneunit"
2999	@echo " make \"UNIT=SL/TREEDISP/TREEDISP\" oneunit"
3000	@echo "(Note: 1st is a shared library, 2nd isn't)"
3001	false
3002	else
3003	@echo "Build time" > $(TIMELOG)
3004	@echo "$(SEP) $(MAKE) build_oneunit"
3005	@$(TIMECMD) $(MAKE) build_oneunit
3006	ifeq ($(UNIT_TESTS),1)
3007	@echo "$(SEP) $(MAKE) run_oneunitstests"
3008	@$(TIMECMD) $(MAKE) run_oneunitstests
3009	endif
3010	@cat $(TIMELOG)
3011	@rm $(TIMELOG)
3012	endif
3013
3014	# --------------------------------------------------------------------------------
3015	# Main targets:
3016
3017	tarfile: rebuild
3018	$(MAKE) prepare_libdir
3019	util/arb_compress
3020
3021	tarfile_quick: all
3022	$(MAKE) prepare_libdir
3023	util/arb_compress
3024
3025	# -----------------------------------
3026
3027	build: arb
3028	$(MAKE) check_bin_dep preplib compile_compatibility fig_cure
3029
3030	all:
3031	@echo "Build time" > $(TIMELOG)
3032	# $(MAKE) clean_checked_vect # uncomment to rebuild sources where expected vectorization gets tested
3033	@echo "$(SEP) $(MAKE) all"
3034	@$(TIMECMD) $(MAKE) build
3035	@echo $(SEP)
3036	@echo "made 'all' with success."
3037	@echo "to start arb enter 'arb'"
3038	ifeq ($(UNIT_TESTS),1)
3039	@echo "$(SEP) $(MAKE) run_tests"
3040	@$(TIMECMD) $(MAKE) run_tests
3041	endif
3042	@echo "$(SEP) $(MAKE) all [done]"
3043	ifeq ($(DEBUG),1)
3044	@$(MAKE) save_test_no_error >/dev/null # just show hints
3045	endif
3046	@cat $(TIMELOG)
3047	@rm $(TIMELOG)
3048
3049	rebuild: clean
3050	$(MAKE) all
3051
3052	# --------------------------------------------------------------------------------
3053	# special targets showing obvious error at bottom
3054	# (intended to be used from automated builds)
3055
3056	BUILD_LOG=build.log
3057	SHELL=bash
3058	REDIRECT_KEEP_EXITCODE = tee $(BUILD_LOG) ; exit "$${PIPESTATUS[0]}"
3059	EXTRACT_ERROR_SUMMARY = (./SOURCE_TOOLS/short_error_summary.pl $(BUILD_LOG); false)
3060
3061	ALL:
3062	@(($(MAKE) all 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
3063
3064	REBUILD:
3065	@(($(MAKE) rebuild 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
3066
3067	TARFILE:
3068	@(($(MAKE) tarfile 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
3069
3070	TARFILE_QUICK:
3071	@(($(MAKE) tarfile_quick 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
3072

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