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Last change on this file was 19518, checked in by westram, 4 days ago
full update from 'trunk' into 'help' adds: log:branches/ali@19183:19205,19357:19424 log:branches/gde@19228:19233,19460:19479 log:branches/macros@19482:19488 log:branches/nds@18843:18882 log:branches/progress@18885:18958 log:branches/refactor@19286:19345 log:branches/sina@18984:19244 log:branches/split@19077:19099,19102:19166,19169:19221 log:branches/stable@18903:18906,18908 log:trunk@18813:19517
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 87.9 KB

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1	# =============================================================== #
2	# #
3	# File : Makefile #
4	# #
5	# Institute of Microbiology (Technical University Munich) #
6	# http://www.arb-home.de/ #
7	# #
8	# =============================================================== #
9
10	# -----------------------------------------------------
11	# The ARB Makefile is aware of the following defines:
12	#
13	# CC C compiler (should be defined by OS)
14	# CXX C++ compiler (should be defined by OS)
15	#
16	# DEVELOPER=name special compilation (values: ANY,RELEASE,your name)
17	# OPENGL=0/1 whether OPENGL is available
18	#
19	# -----------------------------------------------------
20	# Paths for several libraries may be set from config.makefile by using:
21	#
22	# export XLIBS=$(shell pkg-config --libs xpm xerces-c)
23	# export XINCLUDES=$(shell pkg-config --cflags x11)
24	# export XAW_LIBS=$(shell pkg-config --libs xaw7)
25	# export XML_INCLUDES=$(shell pkg-config --cflags xerces-c)
26	#
27	# You make have to explicitely point pkg-config to the *.pc files needed.
28	# For example, Xquartz X11 libraries on macOS can be located by adding
29	# the following line before those given above:
30	#
31	# export PKG_CONFIG_PATH=/usr/X11/lib/pkgconfig
32	#
33	# If you introduce a new variable that is handled as described above,
34	# please add to section .@InjectedEnvironment
35	#
36	# -----------------------------------------------------
37	# ARB Makefile and ARB source code are aware of the following defines:
38	#
39	# $(MACH) name of the machine (LINUX or DARWIN; see config.makefile)
40	# DEBUG compiles the DEBUG sections
41	# DEBUG_GRAPHICS all X-graphics are flushed immediately (for debugging)
42	# ARB_64=0/1 1=>compile 64 bit version
43	# UNIT_TESTS=0/1 1=>compile in unit tests and call them after build
44	# COVERAGE=0/1/2 compile in gcov support (useful together with UNIT_TESTS=1)
45	# 0=no, 1+2=compile in, 1=show
46	# STABS=0/1 force stabs format? (0 = "use default format")
47	# SANITIZE=0/#/all use Sanitizer? (defaults to 0,
48	# 1=AddressSanitizer+LeakSanitizer,
49	# 2=UndefinedBehaviorSanitizer,
50	# combine bit-values to activate multiple Sanitizers,
51	# specify 'all' to activate all)
52	# IGNORE_LEAKS=1 does not abort when leaks are detected (while using SANITIZE=1/all)
53	# SHOWTODO=0/1 activate TODO-warnings? (defaults to 0, except for ralf)
54	#
55	# -----------------------------------------------------
56	# The ARB source code is aware of the following defines:
57	#
58	# NDEBUG doesn't compile the DEBUG sections
59	# DEVEL_$(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	#---------------------- force no root
239
240	YOU_ARE_ROOT := $(strip $(shell bash -c 'echo $$((EUID == 0))'))
241	ifeq ($(YOU_ARE_ROOT),1)
242	$(error Building arb as root user is not recommended)
243	# To install a custom-compiled arb system-wide, build target 'tarfile' as "normal" user.
244	# Afterwards, use arb_install.sh as root.
245	endif
246
247	#---------------------- split gcc version
248
249	SPLITTED_VERSION:=$(subst ., ,$(COMPILER_VERSION))
250
251	USE_GCC_MAJOR:=$(word 1,$(SPLITTED_VERSION))
252	USE_GCC_MINOR:=$(word 2,$(SPLITTED_VERSION))
253	USE_GCC_PATCHLEVEL:=$(word 3,$(SPLITTED_VERSION))
254
255	USE_GCC_452_OR_HIGHER:=
256	USE_GCC_46_OR_HIGHER:=
257	USE_GCC_47_OR_HIGHER:=
258	USE_GCC_48_OR_HIGHER:=
259	USE_GCC_49_OR_HIGHER:=
260	USE_GCC_50_OR_HIGHER:=
261	USE_GCC_60_OR_HIGHER:=
262	USE_GCC_70_OR_HIGHER:=
263	USE_GCC_80_OR_HIGHER:=
264	USE_GCC_90_OR_HIGHER:=
265
266	ifeq ($(USE_CLANG),0)
267	ifeq ($(USE_GCC_MAJOR),4)
268	ifeq ($(USE_GCC_MINOR),5)
269	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),23456789)','')
270	USE_GCC_452_OR_HIGHER:=yes
271	endif
272	else
273	ifneq ('$(findstring $(USE_GCC_MINOR),6789)','')
274	USE_GCC_452_OR_HIGHER:=yes
275	USE_GCC_46_OR_HIGHER:=yes
276	ifneq ($(USE_GCC_MINOR),6)
277	USE_GCC_47_OR_HIGHER:=yes
278	ifneq ($(USE_GCC_MINOR),7)
279	USE_GCC_48_OR_HIGHER:=yes
280	ifneq ($(USE_GCC_MINOR),8)
281	USE_GCC_49_OR_HIGHER:=yes
282	endif
283	endif
284	endif
285	endif
286	endif
287	else
288	# gcc 5.x or higher
289	USE_GCC_452_OR_HIGHER:=yes
290	USE_GCC_46_OR_HIGHER:=yes
291	USE_GCC_47_OR_HIGHER:=yes
292	USE_GCC_48_OR_HIGHER:=yes
293	USE_GCC_49_OR_HIGHER:=yes
294	USE_GCC_50_OR_HIGHER:=yes
295	ifneq ($(USE_GCC_MAJOR),5)
296	# gcc 6.x or higher
297	USE_GCC_60_OR_HIGHER:=yes
298	ifneq ($(USE_GCC_MAJOR),6)
299	# gcc 7.x or higher
300	USE_GCC_70_OR_HIGHER:=yes
301	ifneq ($(USE_GCC_MAJOR),7)
302	# gcc 8.x or higher
303	USE_GCC_80_OR_HIGHER:=yes
304	ifneq ($(USE_GCC_MAJOR),8)
305	# gcc 9.x or higher
306	USE_GCC_90_OR_HIGHER:=yes
307	endif
308	endif
309	endif
310	endif
311	endif
312	endif
313
314	#---------------------- define special directories for non standard builds
315
316	ifeq ($(DARWIN),1)
317	OSX_FW:=/System/Library/Frameworks
318	OSX_FW_OPENGL:=$(OSX_FW)/OpenGL.framework/Versions/A/Libraries
319	OSX_FW_GLUT:=$(OSX_FW)/GLUT.framework/Versions/A/Libraries
320	OSX_FW_IMAGEIO:=$(OSX_FW)/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources
321	endif
322
323	#---------------------- SSE vectorization
324	# for details about vectorization checks see SOURCE_TOOLS/vectorize.README
325
326	DISABLE_VECTORIZE_CHECK:=0# set to 1 to completely disable vectorization checks
327	TRACE_MISSED_VECTORIZATIONS:=0# set to 1 to activate detailed output about failed vectorizations
328	# (does also show details about successful vectorized loops, which are not optimal)
329	VECTORIZATION_CHECK_CANDIDATES:=0# set to 1 to show vectorizations that may be checked
330	# (for yet unchecked files)
331	# Note: TRACE_MISSED_VECTORIZATIONS and VECTORIZATION_CHECK_CANDIDATES cannot be used together!
332
333	#---------------------- Support for OPENMP
334
335	USE_OPENMP:=1
336	ifeq ($(DARWIN),1)
337	USE_OPENMP:=0
338	endif
339
340	#----------------------
341
342	ifeq ($(DARWIN),1)
343	LINK_STATIC=1# link static
344	else
345	LINK_STATIC=0# link dynamically
346	# LINK_STATIC=1# link static (testing only)
347	endif
348
349	shared_cflags :=# flags for shared lib compilation
350	onlyC_flags :=# flags only suitable for C (not C++; see cxxflags).
351	clflags :=# linker flags (when passed through gcc)
352	extended_warnings :=# warning flags for C and C++-compiler
353	extended_cpp_warnings :=# warning flags for C++-compiler only
354
355	ifeq ($(DEBUG),0)
356	dflags := -DNDEBUG# defines
357	ifeq ($(USE_CLANG),1)
358	cflags := -O3# compiler flags (C and C++)
359	else
360	clflags += -Wl,-O2# passthrough linker flags
361	# ------- standard optimization:
362	cflags := -O3# compiler flags (C and C++)
363	# ------- test changed optimization (DISABLE_VECTORIZE_CHECK for -O2 or lower):
364	# cflags := -O2# do not commit uncommented!
365	# DISABLE_VECTORIZE_CHECK:=1
366	endif
367	endif
368
369	ifeq ($(DEBIAN),1)
370	clflags += -Wl,-rpath=/usr/lib/arb/lib -Wl,-z,relro
371	endif
372
373	ifeq ($(DEBUG),1)
374	dflags := -DDEBUG
375
376	gdb_common := -g -g3 -ggdb -ggdb3
377
378	DBGOPTI:=-O0
379	ifneq ('$(SANITIZE)','0')
380	# sanitizer report several bogus buffer-overflows when arb is build with -O0 (e.g. with gcc 7.5.0)
381	DBGOPTI:=-O1
382	endif
383
384	ifeq ($(STABS),1)
385	$(error STABS no longer supported)
386	endif
387
388	cflags := $(DBGOPTI) $(gdb_common)
389	# cflags := -O2 $(gdb_common) # use this for callgrind (force inlining)
390
391	ifeq ($(DARWIN),0)
392	clflags += -Wl,-g
393	# Note:
394	# Previously '-Wl,-noinhibit-exec' was added to 'clflags' here,
395	# to fix some issues with launchpad binutils (see [12972]).
396	# But that change also caused 'undefined symbols' NOT to be reported as errors
397	# at link time, producing executables that fail at runtime :/
398	endif
399
400	ifeq ($(DEBUG_GRAPHICS),1)
401	dflags += -DDEBUG_GRAPHICS
402	endif
403
404	endif # DEBUG only
405
406	# ------------------------------ POST_COMPILE - control how much you get spammed
407	# (please do not change default in SVN)
408	POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl
409
410	# POST_COMPILE += --original # dont modify compiler output
411	# POST_COMPILE += --hide-Noncopyable-advices
412	# POST_COMPILE += --show-useless-Weff++
413	# POST_COMPILE += --no-warnings
414	# POST_COMPILE += --only-first-error
415	# POST_COMPILE += --no-warnings --only-first-error
416
417	# always pass used compiler version to postcompile:
418	POST_COMPILE += --compiler=$(COMPILER_VERSION)
419
420	# ------------------------------
421
422	# Enable extra warnings
423	extended_warnings :=
424	extended_cpp_warnings :=
425
426	# C and C++
427	extended_warnings += -Wwrite-strings -Wunused -Wno-aggregate-return
428
429	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
430	# disable shadow warnings for gcc 4.8 (and lower)
431	# (does e.g. warn if a method-name is used as parameter in another method - even for derived classes. unusable!)
432	extended_warnings += -Wshadow
433	endif
434
435	# C++ only
436	extended_cpp_warnings += -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute
437	extended_cpp_warnings += -Wctor-dtor-privacy
438	# extended_cpp_warnings += -Wfloat-equal
439
440	extended_cpp_warnings += -Wmissing-noreturn
441	# extended_cpp_warnings += -Wold-style-cast# (warns about 28405 old-style casts)
442	extended_cpp_warnings += -Winit-self
443	extended_cpp_warnings += -Wstrict-aliasing
444	extended_cpp_warnings += -Wextra
445
446	# ------- above only warning-options already available in gcc 4.4.3
447
448	# -Weffc++ broken in 4.7.x series
449	# gcc 4.7.3 crashes on GenomeImport.cxx when -Weffc++ is active
450	# (bug reported https://gcc.gnu.org/bugzilla/show_bug.cgi?id=56923; apparently wont be fixed for 4.7-series)
451	# gcc 4.7.4 crashes on DBwriter.cxx when -Weffc++ is active
452	WEFFC_BROKEN:=0
453	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
454	ifneq ('$(USE_GCC_48_OR_HIGHER)','yes')
455	WEFFC_BROKEN:=1
456	endif
457	endif
458	ifeq ('$(WEFFC_BROKEN)','0')
459	extended_cpp_warnings += -Weffc++
460	endif
461
462	# turn off -Wmaybe-uninitialized in debug mode (gets activated with -Wextra). too many bogus warnings
463	ifeq ($(DEBUG),1)
464	ifeq ($(USE_CLANG),0)
465	extended_cpp_warnings += -Wno-maybe-uninitialized
466	endif
467	endif
468
469	SUGGEST_FINAL:=
470
471	ifeq ('$(USE_GCC_452_OR_HIGHER)','yes')
472	extended_cpp_warnings += -Wlogical-op# gcc 4.5.2
473	endif
474	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
475	extended_cpp_warnings += -Wzero-as-null-pointer-constant# gcc 4.7
476	endif
477	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
478	extended_cpp_warnings += -Wunused-local-typedefs# available since gcc 4.7 (but fails for each STATIC_ASSERT, so enable only for Cxx11)
479	endif
480	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
481	extended_cpp_warnings += -Wswitch-bool
482	extended_cpp_warnings += -Wlogical-not-parentheses
483	extended_cpp_warnings += -Wsizeof-array-argument
484	extended_cpp_warnings += -Wbool-compare
485
486	SUGGEST_FINAL:=yes
487	endif
488	ifeq ('$(USE_GCC_60_OR_HIGHER)','yes')
489	extended_cpp_warnings += -Wduplicated-cond
490	endif
491	ifeq ('$(USE_GCC_80_OR_HIGHER)','yes')
492	extended_cpp_warnings += -Wmultistatement-macros
493	endif
494
495	# switch off final suggestions for 8.3.0 and 8.4.0:
496	ifeq ('$(COMPILER_VERSION)','8.3.0')
497	SUGGEST_FINAL:=no
498	endif
499	ifeq ('$(COMPILER_VERSION)','8.4.0')
500	SUGGEST_FINAL:=no
501	endif
502
503	ifeq ($(DEVELOPER),RELEASE)
504	# switch off final suggestions in RELEASE:
505	SUGGEST_FINAL:=no
506	endif
507	# suggest final:
508	ifeq ('$(SUGGEST_FINAL)','yes')
509	extended_cpp_warnings += -Wsuggest-final-types
510	extended_cpp_warnings += -Wsuggest-final-methods
511	dflags += -DSUGGESTS_FINAL
512	endif
513
514	#---------------------- turn off clang bogus warnings
515
516	ifeq ($(USE_CLANG),1)
517	# -Wmismatched-tags warns about struct/class mismatch in forward declarations (which is explicitely allowed)
518	# -Wchar-subscripts reports too many bogus warnings for "array['x']" (when 'x' is known to be in range [0..128])
519	# -Wunused-private-field report too many false positives (currently ~ 2 of 3)
520	# -Wstring-plus-int warns about common ARB coding practice
521	# -Wgnu-static-float-init warns about accepted GNU extension
522	extended_cpp_warnings += -Wno-mismatched-tags -Wno-char-subscripts -Wno-unused-private-field -Wno-string-plus-int
523	ifeq ('$(COMPILER_VERSION)','4.2.1')
524	# jenkins build (doesn't know switch -Wno-gnu-static-float-init)
525	extended_cpp_warnings += -Wno-gnu
526	else
527	extended_cpp_warnings += -Wno-gnu-static-float-init
528	endif
529	endif
530
531	#---------------------- developer
532
533	ifneq ($(DEVELOPER),ANY) # ANY=default setting (skip all developer specific code)
534	dflags += -DDEVEL_$(DEVELOPER)# activate developer/release specific code
535	endif
536
537	#---------------------- activate TODO warnings?
538
539	ifndef SHOWTODO
540	ifeq ($(DEVELOPER),RALF)
541	SHOWTODO:=1
542	else
543	SHOWTODO:=0
544	endif
545	endif
546	ifeq ($(SHOWTODO),1)
547	dflags += -DWARN_TODO# activate "TODO" warnings
548	endif
549
550	#---------------------- activate threads?
551	# only useful if compiler is able to compile Cxx11 or better
552
553	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
554	# see also ./TEMPLATES/cxxforward.h@USE_Cxx11
555	cflags += -pthread
556	clflags += -pthread
557	endif
558
559	#---------------------- activate Sanitizers?
560
561	ASAN_OPTIONS:=handle_segv=0:color=0
562	ifeq ($(IGNORE_LEAKS),1)
563	ASAN_OPTIONS+=:detect_leaks=0 # disable leak-detection
564	else
565	ASAN_OPTIONS+=:detect_leaks=1 # detect leaks (normal setting)
566	endif
567	ASAN_OPTIONS+=:check_initialization_order=1
568	# ASAN_OPTIONS+=:abort_on_error=1
569
570	# suppressions: SOURCE_TOOLS/arb.leaksan.supp
571	LSAN_OPTIONS:=max_leaks=3:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp
572
573	UBSAN_OPTIONS:=print_stacktrace=1
574
575	SANITIZE_ADDRESS:=0
576	SANITIZE_UNDEFINED:=0
577
578	ifneq ($(SANITIZE),0)
579	ifeq ($(SANITIZE),all)
580	SANITIZE:=3
581	endif
582
583	ifeq ($(SANITIZE),1)
584	SANITIZE_ADDRESS:=1
585	else
586	ifeq ($(SANITIZE),2)
587	SANITIZE_UNDEFINED:=1
588	else
589	ifeq ($(SANITIZE),3)
590	SANITIZE_ADDRESS:=1
591	SANITIZE_UNDEFINED:=1
592	else
593	$(error Unknown value '$(SANITIZE)' specified for SANITIZE in config.makefile)
594	endif
595	endif
596	endif
597	endif
598
599	ifeq ($(SANITIZE_ADDRESS),1)
600	ifneq ('$(USE_GCC_48_OR_HIGHER)','yes')
601	$(info AddressSanitizer not usable with gcc $(COMPILER_VERSION) - disabled)
602	SANITIZE_ADDRESS:=0
603	else
604	ifneq ('$(USE_GCC_49_OR_HIGHER)','yes')
605	$(info LeakSanitizer does not work with gcc $(COMPILER_VERSION) - disabled)
606	# need to disable AddressSanitizer (otherwise build fails; only affects gcc 4.8.x series)
607	SANITIZE_ADDRESS:=0
608	endif
609	endif
610	endif
611
612	ifeq ($(SANITIZE_UNDEFINED),1)
613	ifneq ('$(USE_GCC_49_OR_HIGHER)','yes')
614	$(info UndefinedBehaviorSanitizer not usable with gcc $(COMPILER_VERSION) - disabled)
615	SANITIZE_UNDEFINED:=0
616	endif
617	endif
618
619	SANITIZE_ANY:=0
620	ifeq ($(SANITIZE_ADDRESS),1)
621	SANITIZE_ANY:=1
622	endif
623	ifeq ($(SANITIZE_UNDEFINED),1)
624	SANITIZE_ANY:=1
625	endif
626
627	# vectorization fails if sanitizer active where it normally succeeds -> disable check
628	ifeq ($(SANITIZE_ANY),1)
629	$(info disabling vectorize checks. would fail with sanitized code)
630	DISABLE_VECTORIZE_CHECK:=1
631	else
632	$(info no sanitizer enabled. reset: SANITIZE=0)
633	SANITIZE:=0
634	endif
635
636	# deactivate some bogus warnings occurring when sanitizing NDEBUG version
637	# (do not disable for future gcc-version >= 8.x -> test again when available)
638	ifeq ($(SANITIZE_ANY),1)
639	ifeq ($(DEBUG),0)
640	ifneq ('$(USE_GCC_80_OR_HIGHER)','yes')
641	extended_cpp_warnings += -Wno-format-overflow
642	extended_cpp_warnings += -Wno-maybe-uninitialized
643	endif
644	endif
645	endif
646
647	#---------------------- 32 or 64 bit
648
649	cross_cflags:=
650	cross_lflags:=
651	cross_clflags:=
652
653	ifeq ($(ARB_64),1)
654	dflags += -DARB_64
655	shared_cflags += -fPIC
656	CROSS_LIB:=# empty => autodetect below
657	ifeq ($(DARWIN),1)
658	cross_cflags += -arch x86_64
659	cross_lflags += -arch x86_64
660	cross_clflags += -arch x86_64
661	endif
662	else
663	CROSS_LIB:=/lib
664	endif
665
666	cflags += $(cross_cflags)
667	clflags += $(cross_clflags)
668
669	ifeq ('$(CROSS_LIB)','')
670	# autodetect libdir
671	ifeq ($(ARB_64),1)
672	CROSS_LIB:=$(shell (test -d /lib64 && echo lib64) \|\| echo lib)
673	else
674	CROSS_LIB:=$(shell (test -d /lib32 && echo lib32) \|\| echo lib)
675	endif
676	endif
677
678	#---------------------- unit tests
679
680	ifndef UNIT_TESTS
681	UNIT_TESTS=0#default is "no tests"
682	endif
683	ifeq ($(UNIT_TESTS),1)
684	dflags += -DUNIT_TESTS
685	UNIT_TESTER_LIB=UNIT_TESTER/UNIT_TESTER.a
686	else
687	UNIT_TESTER_LIB=
688	endif
689
690	#---------------------- use gcov
691
692	ifndef COVERAGE
693	COVERAGE=0#default is "no"
694	endif
695	ifneq ($(COVERAGE),0)
696	GCOV_FLAGS=--coverage
697	$(info disabling vectorize checks. would fail with COVERAGE on)
698	DISABLE_VECTORIZE_CHECK:=1
699	else
700	GCOV_FLAGS=
701	endif
702
703	cflags += $(GCOV_FLAGS)
704	clflags += $(GCOV_FLAGS)
705	cross_lflags += $(GCOV_FLAGS)
706
707	#---------------------- other flags
708
709	dflags += -D$(MACH) # define machine
710
711	ifeq ($(DARWIN),1)
712	shared_cflags += -fno-common
713	else
714	dflags += $(shell getconf LFS_CFLAGS)
715	endif
716
717	cflags += -pipe
718	cflags += -fmessage-length=0# dont wrap compiler output
719	cflags += -fshow-column# show columns
720	cflags += -funit-at-a-time
721	cflags += -fPIC
722	cflags += -fno-common# link all global data into one namespace
723	cflags += -fstrict-aliasing# gcc 3.4
724
725	onlyC_flags += -Werror-implicit-function-declaration
726
727	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
728	cflags += -fno-diagnostics-show-caret#gcc 4.8 (4.7.?)
729	endif
730	#cflags += -save-temps# uncomment to see preprocessor output
731
732	#---------------------- various sanitizers
733	# There are some disabled tests in CORE/arb_misc.cxx@sanitizers
734	# which trigger sanitizer reports.
735
736	ifeq ($(SANITIZE_ANY),1)
737	cflags += -ggdb3 -fno-omit-frame-pointer
738	endif
739
740	SANI_CFLAGS:=
741	SANI_CLFLAGS:=
742
743	# activate AddressSanitizer+LeakSanitizer?
744	ifeq ($(SANITIZE_ADDRESS),1)
745	SANI_CFLAGS += -fsanitize=address
746	SANI_CLFLAGS += -fsanitize=address
747	dflags += -DLEAKS_SANITIZED
748	endif
749
750	# activate UndefinedBehaviorSanitizer?
751	ifeq ($(SANITIZE_UNDEFINED),1)
752	SANI_CFLAGS += -fsanitize=undefined
753	SANI_CLFLAGS += -fsanitize=undefined
754	dflags += -DUNDEF_SANITIZED
755	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
756	# abort on runtime errors
757	SANI_CFLAGS += -fno-sanitize-recover=all
758	endif
759
760	cflags += $(SANI_CFLAGS)
761	clflags += $(SANI_CLFLAGS)
762
763	#
764	# Note: alignment-sanitizer is deactivated for ARBDB and PROBE!
765	ifeq ('$(DEBUG)','1')
766	ifeq ($(USE_GCC_MAJOR),4)
767	ifeq ($(USE_GCC_MINOR),9)
768	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),01)','')
769	# workaround https://gcc.gnu.org/bugzilla/show_bug.cgi?id=63531 for 4.9.0 + 4.9.1
770	# (problem is fixed in 4.9.2 release)
771	extended_cpp_warnings:=$(subst -Weffc++,,$(extended_cpp_warnings))
772	endif
773	endif
774	endif
775	endif
776	endif
777
778	#---------------------- X11 location
779
780	ifeq ($(DARWIN),1)
781	XHOME:=$(PREFIX)
782	else
783	ifeq ($(DEBIAN),1)
784	XHOME:=$(PREFIX)
785	else
786	XHOME:=/usr/X11R6
787	endif
788	endif
789
790	XINCLUDES ?= -I$(XHOME)/include
791	XLIBS ?= -L$(XHOME)/$(CROSS_LIB)
792	ifeq ($(DARWIN),1)
793	XINCLUDES += -I$(OSX_FW)/GLUT.framework/Headers -I$(OSX_FW)/OpenGL.framework/Headers -I$(OSX_SDK)/usr/include/krb5
794
795	XLIBS += -lXm -lpng -lz -lXt -lX11 -lXext -lXp -lXmu -lXi
796	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGL.dylib:$(OSX_FW_OPENGL)/libGL.dylib
797	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGLU.dylib:$(OSX_FW_OPENGL)/libGLU.dylib
798	else
799	XLIBS += -lXm -lXpm -lXt -lXext -lX11
800	endif
801
802	#---------------------- open GL
803
804	ifeq ($(OPENGL),1)
805	cflags += -DARB_OPENGL # activate OPENGL code
806	GL := gl # this is the name of the OPENGL base target
807	GL_LIB_SYS := -lGL -lGLU
808	GL_LIB_ARB := -L$(ARBHOME)/GL/glAW -lglAW
809
810	ifeq ($(DARWIN),1)
811	GL_LIB_SYS += -lpthread
812	endif
813
814	GL_PNGLIBS_ARB := -L$(ARBHOME)/GL/glpng -lglpng_arb
815	GL_PNGLIBS_SYS := -lpng
816
817	GLEWLIB := -lGLEW -lGLw
818	GLUTLIB := -lglut
819
820	GL_LIBS_SYS := $(GL_LIB_SYS) $(GL_PNGLIBS_SYS) $(GLEWLIB) $(GLUTLIB)
821	GL_LIBS_ARB := $(GL_LIB_ARB) $(GL_PNGLIBS_ARB)
822
823	RNA3D_LIB := RNA3D/RNA3D.a
824	else
825	GL_LIBS_SYS:=# no opengl -> no libs
826	GL_LIBS_ARB:=# no opengl -> no libs
827	GL:=# dont build ARB openGL libs
828
829	RNA3D_LIB :=
830	endif
831
832	RNA3D_LIB_4_DEPENDS := RNA3D/RNA3D.a
833
834	GL_LIBS:=$(GL_LIBS_ARB) $(GL_LIBS_SYS)
835
836	#---------------------- sina:
837
838	ifndef ISINA
839	# build sina delivered with arb?
840	ifeq ($(LINUX),1)
841	ifeq ('$(USE_GCC_70_OR_HIGHER)','yes')
842	ISINA := 1# default to 'yes' for linux with gcc>=7
843	endif
844	endif
845	ifndef ISINA
846	ISINA := 0# 'no' otherwise
847	endif
848	endif
849
850	#---------------------- tiff lib:
851
852	TIFFLIBS := -ltiff
853
854	#---------------------- XML lib:
855
856	XMLLIBS := -lxerces-c
857
858	#---------------------- glib:
859
860	ARB_NEEDED_GLIB=glib-2.0
861
862	ARB_GLIB_INCLUDE:=$(strip $(shell pkg-config --cflags $(ARB_NEEDED_GLIB)))
863	ARB_GLIB_LIBS:=$(strip $(shell pkg-config --libs $(ARB_NEEDED_GLIB)))
864
865	#---------------------- sunrpc lib:
866	# Note: sunrpc has been removed from glibc
867	# (e.g. in SuSE Leap 15.3 and Fedora 28)
868	# see https://fedoraproject.org/wiki/Changes/SunRPCRemoval
869	#
870	HAVE_LIBTIRPC=$(strip $(shell pkg-config --exists libtirpc && echo libtirpc))
871	ifeq ($(HAVE_LIBTIRPC),)
872	ARB_RPC_INCLUDE:=
873	ARB_RPC_LIBS:=
874	else
875	ARB_RPC_INCLUDE:=$(strip $(shell pkg-config --cflags $(HAVE_LIBTIRPC)))
876	ARB_RPC_LIBS:=$(strip $(shell pkg-config --libs $(HAVE_LIBTIRPC)))
877	endif
878
879	#---------------------- basic libs:
880
881	ARB_CORE_LIBS:=$(ARB_GLIB_LIBS) $(ARB_RPC_LIBS)
882
883	SYSLIBS:=
884	ifeq ($(DARWIN),1)
885	SYSLIBS += -lstdc++
886	else
887	SYSLIBS += -lm $(ARB_CORE_LIBS)
888	endif
889
890	#---------------------- system dependent commands
891
892	ifeq ($(DARWIN),1)
893	TIME:=gtime
894	else
895	TIME:=/usr/bin/time
896	endif
897
898	#---------------------- SSE vectorizer
899	# for details see SOURCE_TOOLS/vectorize.README
900
901	ifeq ($(DEBUG),0)
902	ifeq ($(USE_GCC_49_OR_HIGHER),yes)
903	ifeq ($(DISABLE_VECTORIZE_CHECK),0)
904	cflags += -fopt-info-vec
905	cflags += -fopt-info-vec-missed
906	ifeq ($(TRACE_MISSED_VECTORIZATIONS),1)
907	# Shows reasons for unsuccessful vectorization:
908	cflags += -ftree-vectorizer-verbose=10
909	POST_COMPILE += --dump-loop-optimization
910	ifeq ($(VECTORIZATION_CHECK_CANDIDATES),1)
911	$(error TRACE_MISSED_VECTORIZATIONS and VECTORIZATION_CHECK_CANDIDATES may not be used together!)
912	endif
913	endif
914	ifeq ($(VECTORIZATION_CHECK_CANDIDATES),1)
915	POST_COMPILE += --loop-optimization-candi
916	endif
917	POST_COMPILE += --check-loop-optimization
918	endif
919	else
920	ifeq ($(USE_GCC_48_OR_HIGHER),yes)
921	# no automatic vectorization-check for gcc<4.9.0
922	# -> uncomment the next 2 lines and grep the spam it will produce for 'vectorized.*loops'
923	# cflags += -fopt-info -fopt-info-vec-missed
924	# POST_COMPILE += --original
925	endif
926	endif
927	endif
928
929	#---------------------- stop early on broken flags/compiler combination
930
931	ifeq ($(DEBUG),0)
932	ifeq ($(SANITIZE_ANY),1)
933	ifeq ('$(COMPILER_VERSION)','4.9.1')
934	$(error compiling DEBUG=0 + SANITIZE!=0 crashes with gcc $(COMPILER_VERSION) (gcc 4.9.2 works))
935	endif
936	endif
937	endif
938
939	#---------------------- include symbols?
940
941	ifeq ($(TRACESYM),1)
942	ifeq ($(USE_CLANG),0)
943	cflags += -rdynamic
944	clflags += -rdynamic -Wl,--export-dynamic
945	endif
946	endif
947
948	#---------------------- warn about duplicate variable definitions
949
950	ifeq ($(DARWIN),1)
951	clflags += -Wl,-warn_commons
952	else
953	clflags += -Wl,--warn-common
954	endif
955
956	#---------------------- differences between linking executables and shared libs:
957
958	# executables:
959	ifeq ($(DARWIN),1)
960	blflags:=$(clflags)
961	else
962	blflags:=$(clflags) -Wl,--no-undefined
963	endif
964
965	# shared libraries
966	llflags:=$(clflags)
967
968	# dont use clflags below
969	clflags:=
970
971	# -------------------------------------------------------------------------
972	# Don't put any machine/version/etc conditionals below!
973	# (instead define variables above)
974	# -------------------------------------------------------------------------
975
976	cflags += -W -Wall $(dflags) $(extended_warnings)
977	cxxflags := $(extended_cpp_warnings)# flags only suitable for C++ (not C; see onlyC_flags).
978
979	# add CFLAGS + CPPFLAGS from environment for DEBIAN build
980	ifeq ($(DEBIAN),1)
981	cflags := $(CFLAGS) $(cflags)
982	cxxflags += $(CPPFLAGS)
983	endif
984
985	ifeq ('$(USE_CLANG)','1')
986	# none of the following standards works with clang3.3 (under linux) => dont use standard (as done before r15516)
987	# cxxflags += -std=gnu++11
988	# cxxflags += -std=gnu++0x
989	else
990	ifeq ('$(USE_GCC_60_OR_HIGHER)','yes')
991	cxxflags += -std=gnu++14# see also TEMPLATES/cxxforward.h@USE_Cxx14
992	else
993	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
994	cxxflags += -std=gnu++11# see also TEMPLATES/cxxforward.h@USE_Cxx11
995	else
996	# gcc versions between 4.3 (lowest supported) and <4.7
997	cxxflags += -std=gnu++0x
998	endif
999	endif
1000	endif
1001
1002	LINK_STATIC_LIB := $(AR) -csq# link static lib
1003	LINK_EXECUTABLE := $(A_CXX) $(blflags) -o# link executable (c++)
1004
1005	ifeq ($(LINK_STATIC),1)
1006	SHARED_LIB_SUFFIX = a# static lib suffix
1007	LINK_SHARED_LIB := $(LINK_STATIC_LIB)
1008	else
1009	SHARED_LIB_SUFFIX = so# shared lib suffix
1010	LINK_SHARED_LIB := $(A_CXX) $(llflags) -shared -o# link shared lib
1011	endif
1012
1013	ifeq ($(DARWIN),1)
1014	lflags4perl:=
1015	else
1016	lflags4perl:=$(cross_lflags) -shared
1017	endif
1018
1019	# delete variables unused below
1020	blflags:=
1021	llflags:=
1022
1023	# other used tools
1024	MAKEDEPEND_PLAIN = makedepend
1025	MAKEDEPEND = $(FORCEMASK);$(MAKEDEPEND_PLAIN)
1026
1027	SEPNODATE:=--------------------------------------------------------------------------------
1028	SEP=[`date +%M:%S.%N`] ------------------------------------------------
1029	# to analyse timings run
1030	# make -j9 clean; make -j9 all \| grep '^\[' \| sort
1031	# make -j9 "TIMED_TARGET=perl" clean_timed_target \| grep '^\[' \| sort
1032
1033	# ------------------------------------------------------------ DYNLIBDEFS
1034	# various dynamic library definitions for linking executables:
1035	#
1036	# SYSLIBS: system libraries needed by database lib
1037	# ARBDB_LIB: database lib
1038	# DBSYS_LIBS: executable using database (but no GUI)
1039	# GUI_LIBS: executable using database and GUI (arb gui uses database)
1040	#
1041	# Note: definitions exported to sub-makefiles are described in SOURCE_TOOLS/parent_make.txt
1042
1043	CORE_LIB=-lCORE
1044	ARBDB_LIB=-lARBDB $(CORE_LIB)
1045	DBSYS_LIBS = $(ARBDB_LIB) $(SYSLIBS)
1046
1047	GUI_LIBS_PREFIX:=
1048	ifeq ($(DARWIN),1)
1049	# this seem to be added at wrong place, since opengl is only needed to link EDIT4
1050	GUI_LIBS_PREFIX:=-framework GLUT -framework OpenGL
1051	endif
1052
1053	GUI_LIBS=$(GUI_LIBS_PREFIX) $(DBSYS_LIBS) -lAWT -lWINDOW $(XLIBS)
1054
1055	LIBPATH = -L$(ARBHOME)/lib
1056
1057	DEST_LIB = lib
1058	DEST_BIN = bin
1059
1060	CC_INCLUDES := -I. -I$(ARBHOME)/INCLUDE $(XINCLUDES) $(ARB_GLIB_INCLUDE) $(ARB_RPC_INCLUDE)
1061	CXX_INCLUDES := $(CC_INCLUDES)
1062	MAKEDEPENDFLAGS := -- -DARB_OPENGL -DUNIT_TESTS -D__cplusplus -I. -Y$(ARBHOME)/INCLUDE
1063
1064	# ---------------------------------------
1065	# wrap main()
1066
1067	use_ARB_main=$(ARBHOME)/SOURCE_TOOLS/arb_main_cpp.o
1068	use_ARB_main_C=$(ARBHOME)/SOURCE_TOOLS/arb_main_c.o
1069
1070	# -----------------------------------------
1071	# unique build-id
1072	# - different for different calls of make
1073	# - constant in recursive calls
1074
1075	ifndef ARBBID
1076	ARBBID:=$(shell SOURCE_TOOLS/uniqueID.sh)
1077	endif
1078
1079	# -----------------------------------------
1080	# export variables to submakefiles
1081
1082	include SOURCE_TOOLS/export2sub
1083
1084	# do not define (exported) variables below this point
1085
1086	# -------------------------
1087	# Main arb targets:
1088	# -------------------------
1089
1090	first_target:
1091	$(MAKE) checks
1092	@echo $(SEPNODATE)
1093	@echo 'Main targets:'
1094	@echo ''
1095	@echo ' all - Compile ARB + TOOLs + and copy shared libs + link foreign software'
1096	@echo ' (That is most likely the target you want)'
1097	@echo ''
1098	@echo ' clean - remove generated files ("SUBDIR/SUBDIR.clean" to clean only SUBDIR)'
1099	@echo ' rebuild - clean + all'
1100	@echo ' cleanlinked - remove all binaries'
1101	@echo ' relink - cleanlinked + all (=relink all from objects)'
1102	@echo ''
1103	@echo 'Targets for automated builds:'
1104	@echo ''
1105	@echo ' ALL, REBUILD, TARFILE + TARFILE_QUICK '
1106	@echo ' - same as all, rebuild, tarfile + tarfile_quick'
1107	@echo ' - if errors occur, they are extracted and listed at tail of output'
1108	@echo ''
1109	@echo $(SEPNODATE)
1110	@echo ''
1111	@echo 'Development targets:'
1112	@echo ''
1113	@echo ' depends - create or update dependencies ("SUBDIR/SUBDIR.depends" to update only SUBDIR)'
1114	@echo ' proto - create or update prototypes ("SUBDIR/SUBDIR.proto" to update only SUBDIR)'
1115	@echo ' tags - create tags for xemacs'
1116	@echo ' show - show available shortcuts (AKA subtargets)'
1117	@echo ' up - shortcut for depends+proto+tags'
1118	ifeq ($(UNIT_TESTS),1)
1119	@echo ' ut - only run tests'
1120	@echo ' "UNIT=..." oneunit - build one unit and run tests (see also UNIT_TESTER/Makefile.setup.local)'
1121	endif
1122	ifneq ($(SANITIZE),0)
1123	@echo ' sanitize - all + run arb_ntree with sanitizer (test.arb + execute _logged)'
1124	endif
1125	@echo ' modified - rebuild files modified in svn checkout (does touch)'
1126	@echo ' touch - touch files modified in svn checkout'
1127	@echo ''
1128	@echo 'Some often used sub targets:'
1129	@echo ''
1130	@echo ' arb - Just compile ARB (but none of the integrated tools)'
1131	@echo ' menus - create lib/gde/arb.menu from GDEHELP/ARB_GDEmenus.source'
1132	@echo ' perl - Compile the PERL XSUBS into lib/ARB.so and create links in lib to perl'
1133	@echo ' binlink - Create all links in the bin directory'
1134	@echo ''
1135	@echo 'Internal maintenance:'
1136	@echo ''
1137	@echo ' relinfo - show help on release targets'
1138	@echo ' tarfile - make rebuild and create arb version tarfile ("tarfile_quick" to skip rebuild)'
1139	@echo ' save - save all basic ARB sources into arbsrc_DATE ("savetest" to check filelist)'
1140	@echo ' patch - save svn diff to patchfile'
1141	@echo ' source_doc - create doxygen documentation'
1142	@echo ' relocated - rebuild partly (use when you have relocated ARBHOME)'
1143	@echo ' check_res - check resource usage'
1144	@echo ' dep_graph - Build dependency graphs'
1145	@echo ' clean_cov - Clean coverage results'
1146	@echo ''
1147	@echo ' clean_opengl_changed - clean after changing OPENGL setting in config.Makefile'
1148	@echo ' clean_checked_vect - clean units containing vectorization checks'
1149	@echo ' cleanRelinkable - similar to cleanlinked (but skips raxml8 to avoid rebuild)'
1150	@echo ''
1151	@echo ' post_commit_check - Checks whether'
1152	@echo ' * main make targets work,'
1153	@echo ' * dependencies and prototypes are up to date,'
1154	@echo ' * SVN-controlled files remain unaffected by called targets and'
1155	@echo ' * all generated files are ignored.'
1156	@echo ' (has to be called in a clean SVN checkout)'
1157	@echo $(SEPNODATE)
1158	@echo ''
1159
1160	relinfo:
1161	@echo ''
1162	@echo $(SEPNODATE)
1163	@echo 'Release targets:'
1164	@echo ''
1165	@echo ' inc_candi - increase RC candidate-number (only possible in "rc" branch, not needed for RC1)'
1166	@echo ' inc_patch - increase release patchlevel (only possible in "stable" branch)'
1167	@echo ' inc_minor - increase minor version number (only possible in "trunk")'
1168	@echo ' inc_major - increase MAJOR version number (only possible in "trunk")'
1169	@echo ''
1170	@echo ' show_version - show version tag'
1171	@echo ''
1172	@echo $(SEPNODATE)
1173	@echo ''
1174
1175	# auto-generate config.makefile:
1176
1177	config.makefile : config.makefile.template
1178	@echo --------------------------------------------------------------------------------
1179	ifeq ($(CONFIG_MAKEFILE_FOUND),)
1180	@cp $< $@
1181	@echo '$(ARBHOME)/$@:1: has been generated.'
1182	@echo 'Please edit $@ to configure your system!'
1183	@echo --------------------------------------------------------------------------------
1184	@false
1185	else
1186	@echo '$(ARBHOME)/$<:1: is more recent than'
1187	@echo '$(ARBHOME)/$@:1:'
1188	@ls -al config.makefile*
1189	@echo --------------------------------------------------------------------------------
1190	@echo "Updating $@ (if this fails, check manually)"
1191	SOURCE_TOOLS/update_config_makefile.pl
1192	@echo "Sucessfully updated $@"
1193	@echo --------------------------------------------------------------------------------
1194	@ls -al config.makefile*
1195	@echo --------------------------------------------------------------------------------
1196	@echo "Diff to your old config.makefile:"
1197	@echo --------------------------------------------------------------------------------
1198	-diff $@.bak $@
1199	@echo --------------------------------------------------------------------------------
1200	endif
1201
1202	# check if everything is configured correctly
1203
1204	check_DEVELOPER:
1205	ifndef DEVELOPER
1206	@echo 'config.makefile:1: DEVELOPER not defined'
1207	@false
1208	endif
1209
1210	check_DEBUG:
1211	ifndef dflags
1212	@echo 'config.makefile:1: DEBUG has to be defined. Valid values are 0 and 1'
1213	@false
1214	endif
1215
1216	check_ARB_64:
1217	ifndef ARB_64
1218	@echo 'config.makefile:1: ARB_64 has to be defined. Valid values are 0 and 1'
1219	@false
1220	endif
1221
1222	# ---------------------------------------- check gcc version
1223
1224	COMPILER_BROKEN:=0
1225
1226	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.6.4')
1227	COMPILER_BROKEN:=1
1228	endif
1229	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.8.0')
1230	COMPILER_BROKEN:=1
1231	endif
1232
1233	check_same_GCC_VERSION:
1234	$(ARBHOME)/SOURCE_TOOLS/check_same_compiler_version.pl $(COMPILER_NAME) $(COMPILER_VERSION_ALLOWED)
1235
1236	check_GCC_VERSION:
1237	@echo 'Compiler version check:'
1238	# see .@ALLOWED_gcc_VERSIONS
1239	ifeq ('$(COMPILER_VERSION_ALLOWED)', '')
1240	@echo " - Your compiler is '$(COMPILER_NAME)' version '$(COMPILER_VERSION)'"
1241	@echo ' This version is not in the list of supported $(COMPILER_NAME)-versions:'
1242	@$(foreach version,$(ALLOWED_COMPILER_VERSIONS),echo ' * $(version)';)
1243	@echo ' - You may either ..'
1244	@echo ' - add your version to ALLOWED_$(COMPILER_NAME)_VERSIONS in the Makefile and try it out or'
1245	@echo ' - switch to one of the allowed versions (see arb_README_gcc.txt for installing'
1246	@echo ' a different version of gcc)'
1247	$(error Unsupported compiler '$(COMPILER_NAME)' version '$(COMPILER_VERSION)')
1248	else
1249	ifeq ($(COMPILER_BROKEN),1)
1250	$(error compilation refused for $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)'. Refer to http://bugs.arb-home.de/wiki/GccVersionInfo for details.)
1251	else
1252	@echo " - Supported $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)' detected - fine!"
1253	@echo ''
1254	ifeq ($(USE_CLANG),1)
1255	@echo "Dump clang version:"
1256	$(A_CXX) -v
1257	endif
1258	$(MAKE) check_same_GCC_VERSION
1259	endif
1260	endif
1261
1262	#---------------------- check ARBHOME
1263
1264	# use arb_INSTALL.txt to determine whether ARBHOME points to correct directory
1265	ARB_INSTALL_FOUND=$(wildcard $(ARBHOME)/arb_INSTALL.txt)
1266
1267	check_ARBHOME:
1268	ifeq ($(strip $(ARB_INSTALL_FOUND)),)
1269	@echo ------------------------------------------------------------
1270	@echo "ARBHOME is set to '$(ARBHOME)'"
1271	@echo "The environment variable ARBHOME has to point to the top arb source directory."
1272	@echo "If you use bash enter:"
1273	@echo " export ARBHOME='`pwd`'"
1274	@echo ------------------------------------------------------------
1275	@false
1276	endif
1277
1278	ARB_PATH_SET=$(findstring $(ARBHOME)/bin,$(PATH))
1279
1280	check_PATH: check_ARBHOME
1281	ifeq ($(strip $(ARB_PATH_SET)),)
1282	@echo ------------------------------------------------------------
1283	@echo "The environment variable PATH has to contain $(ARBHOME)/bin"
1284	@echo "If you use bash enter:"
1285	@echo ' export PATH=$$ARBHOME/bin:$$PATH'
1286	@echo ------------------------------------------------------------
1287	@false
1288	endif
1289
1290	check_TOOLS:
1291	@util/arb_check_build_env.pl \
1292	"$(A_CC)" \
1293	"$(A_CXX)" \
1294	"$(LINK_SHARED_LIB)" \
1295
1296	have_makedepend:
1297	@util/arb_check_build_env.pl --check-only "$(MAKEDEPEND_PLAIN)"
1298
1299	check_ENVIRONMENT : check_PATH check_TOOLS
1300	@echo "-------------------- Environment [start]"
1301	@echo "ARBHOME='$(ARBHOME)'"
1302	@echo "PATH='$(PATH)'"
1303	@echo "LD_LIBRARY_PATH='$(LD_LIBRARY_PATH)'"
1304	@echo "-------------------- Environment [end]"
1305
1306	check_tabs: check_setup
1307	ifeq ($(DEBUG),1)
1308	@SOURCE_TOOLS/tabBrake.pl
1309	endif
1310
1311	force_tab_check:
1312	@touch -t 198001010000 SOURCE_TOOLS/stamp.tabBrake
1313	@$(MAKE) check_tabs
1314
1315
1316	# ---------------------
1317
1318	check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION
1319	@echo Your setup seems to be ok.
1320
1321	checks: check_setup check_tabs
1322	@rm -f SOURCE_TOOLS/postcompile.sav
1323
1324
1325	# end test section ------------------------------
1326
1327	# ---------------------------------------
1328	# List of standard top level directories
1329	#
1330	# sub-makefiles have to define the targets
1331	# - 'depends' and
1332	# - 'clean'
1333	#
1334	# when adding new libraries/subdirs here, also add a dependency vs 'links' or 'links_non_perl' in .@DD_links_non_perl
1335
1336	TL_ARCHIVES = \
1337	AISC/AISC.a \
1338	ARB_GDE/ARB_GDE.a \
1339	AWTC/AWTC.a \
1340	AWTI/AWTI.a \
1341	CONSENSUS_TREE/CONSENSUS_TREE.a \
1342	CONVERTALN/CONVERTALN.a \
1343	DBSERVER/DBSERVER.a \
1344	DIST/DIST.a \
1345	EDIT4/EDIT4.a \
1346	EISPACK/EISPACK.a \
1347	GENOM/GENOM.a \
1348	GENOM_IMPORT/GENOM_IMPORT.a \
1349	ISLAND_HOPPING/ISLAND_HOPPING.a \
1350	MERGE/MERGE.a \
1351	MULTI_PROBE/MULTI_PROBE.a \
1352	NALIGNER/NALIGNER.a \
1353	NAMES/NAMES.a \
1354	NAMES_COM/server.a \
1355	NTREE/NTREE.a \
1356	PARSIMONY/PARSIMONY.a \
1357	PHYLO/PHYLO.a \
1358	PRIMER_DESIGN/PRIMER_DESIGN.a \
1359	PROBE/PROBE.a \
1360	PROBE_COM/server.a \
1361	PROBE_DESIGN/PROBE_DESIGN.a \
1362	$(RNA3D_LIB) \
1363	RNACMA/RNACMA.a \
1364	SECEDIT/SECEDIT.a \
1365	SEQ_QUALITY/SEQ_QUALITY.a \
1366	SERVERCNTRL/SERVERCNTRL.a \
1367	STAT/STAT.a \
1368	TREEGEN/TREEGEN.a \
1369	WETC/WETC.a \
1370	XML/XML.a \
1371
1372	TL_SHARED_ARCHIVES = \
1373	ARBDB/libARBDB.so \
1374	CORE/libCORE.so \
1375	AWT/libAWT.so \
1376	WINDOW/libWINDOW.so \
1377
1378	TL_ARCHIV_COLLECTIONS = \
1379	SL/SL.archColl \
1380
1381	TL_TOOLS_COLLECTIONS = \
1382	AISC_MKPTPS/AISC_MKPTPS.toolColl \
1383	TOOLS/TOOLS.toolColl \
1384	PERLTOOLS/PERLTOOLS.toolColl \
1385	PROBE_SET/PROBE_SET.toolColl \
1386	READSEQ/READSEQ.toolColl \
1387
1388	RECURSIVE_SUBS = \
1389	GDE/GDE.sub \
1390	UNIT_TESTER/UNIT_TESTER.sub \
1391
1392	SUBDIRS = \
1393	$(RECURSIVE_SUBS) \
1394	$(TL_ARCHIVES:.a=.sub) \
1395	$(TL_SHARED_ARCHIVES:.so=.sub) \
1396	$(TL_ARCHIV_COLLECTIONS:.archColl=.sub) \
1397	$(TL_TOOLS_COLLECTIONS:.toolColl=.sub) \
1398
1399	# sub directories inside TL_ARCHIV_COLLECTIONS
1400	CL_ARCH_DIRS = $(foreach coll,$(TL_ARCHIV_COLLECTIONS),$(shell find $(dir $(coll)) -maxdepth 1 -mindepth 1 -type d))
1401
1402	# archives inside CL_ARCH_DIRS:
1403	CL_ARCHIVES = $(foreach adir,$(CL_ARCH_DIRS),$(dir $(adir))$(notdir $(adir))/$(notdir $(adir)).a)
1404
1405	# -----------------------
1406	# library packets
1407
1408	ARCHS_CLIENT_PROBE = PROBE_COM/client.a
1409	ARCHS_CLIENT_NAMES = NAMES_COM/client.a
1410
1411	ARCHS_MAKEBIN = AISC_MKPTPS/AISC_MKPTPS.a AISC/AISC.a
1412
1413	# communication libs need aisc and aisc_mkpts:
1414
1415	AISC/AISC.dummy: proto_tools
1416
1417	comtools: AISC/AISC.dummy
1418
1419	ARCHS_SEQUENCE = \
1420	SL/SEQUENCE/SEQUENCE.a \
1421	SL/ALIVIEW/ALIVIEW.a \
1422	SL/PRONUC/PRONUC.a \
1423
1424	ARCHS_TREE = \
1425	SL/ARB_TREE/ARB_TREE.a \
1426	SL/FILTER/FILTER.a \
1427	$(ARCHS_SEQUENCE) \
1428
1429	# parsimony tree (used by NTREE, PARSIMONY, STAT(->EDIT4), DIST(obsolete!))
1430	ARCHS_AP_TREE = \
1431	SL/AP_TREE/AP_TREE.a \
1432	$(ARCHS_TREE) \
1433
1434	# --------------------------------------------------------------------------------
1435	# dependencies for linking shared libs
1436
1437	link_core: core
1438	link_db: db link_core
1439	link_aw: aw link_db
1440	link_awt: awt link_aw
1441
1442	#***************************************************************************************
1443	# Individual_Programs_Section
1444	#***************************************************************************************
1445
1446	arbmainwrapper:
1447	$(MAKE) -C SOURCE_TOOLS -r mainwrapper
1448
1449
1450	#********************************* arb_ntree ************************************
1451	NTREE = bin/arb_ntree
1452	ARCHS_NTREE = \
1453	NTREE/NTREE.a \
1454	ARB_GDE/ARB_GDE.a \
1455	SL/GROUP_SEARCH/GROUP_SEARCH.a \
1456	SL/SAICALC/SAICALC.a \
1457	SL/DB_UI/DB_UI.a \
1458	AWTC/AWTC.a \
1459	AWTI/AWTI.a \
1460	CONSENSUS_TREE/CONSENSUS_TREE.a \
1461	GENOM_IMPORT/GENOM_IMPORT.a \
1462	GENOM/GENOM.a \
1463	MERGE/MERGE.a \
1464	MULTI_PROBE/MULTI_PROBE.a \
1465	PRIMER_DESIGN/PRIMER_DESIGN.a \
1466	PROBE_DESIGN/PROBE_DESIGN.a \
1467	SEQ_QUALITY/SEQ_QUALITY.a \
1468	SERVERCNTRL/SERVERCNTRL.a \
1469	SL/ALILINK/ALILINK.a \
1470	SL/AW_NAME/AW_NAME.a \
1471	SL/CONSENSUS/CONSENSUS.a \
1472	SL/DB_SCANNER/DB_SCANNER.a \
1473	SL/DB_QUERY/DB_QUERY.a \
1474	SL/QUERY/QUERY.a \
1475	SL/SEQIO/SEQIO.a \
1476	STAT/STAT.a \
1477	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1478	SL/HELIX/HELIX.a \
1479	SL/REGEXPR/REGEXPR.a \
1480	SL/REFENTRIES/REFENTRIES.a \
1481	SL/NDS/NDS.a \
1482	SL/ITEM_SHADER/ITEM_SHADER.a \
1483	SL/ITEMS/ITEMS.a \
1484	SL/INSDEL/INSDEL.a \
1485	SL/LOCATION/LOCATION.a \
1486	SL/MACROS/MACROS.a \
1487	SL/PVP/PVP.a \
1488	SL/TRANSLATE/TRANSLATE.a \
1489	SL/TREEDISP/TREEDISP.a \
1490	SL/TREE_ADMIN/TREE_ADMIN.a \
1491	SL/TREE_READ/TREE_READ.a \
1492	SL/TREE_WRITE/TREE_WRITE.a \
1493	SL/XFERGUI/XFERGUI.a \
1494	SL/XFERSET/XFERSET.a \
1495	XML/XML.a \
1496	$(ARCHS_AP_TREE) \
1497
1498	ARCHS_NTREE_ALL = $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(XMLLIBS)
1499
1500	$(NTREE): $(ARCHS_NTREE:.a=.dummy) link_awt
1501	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NTREE_ALL) \|\| ( \
1502	echo "$(SEP) Link $@"; \
1503	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE_ALL)" ; \
1504	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE_ALL) && \
1505	echo "$(SEP) Link $@ [done]"; \
1506	)
1507
1508	#********************************* arb_edit4 ************************************
1509	EDIT4 = bin/arb_edit4
1510
1511	ARCHS_EDIT4 := \
1512	EDIT4/EDIT4.a \
1513	ARB_GDE/ARB_GDE.a \
1514	SL/FAST_ALIGNER/FAST_ALIGNER.a \
1515	AWTC/AWTC.a \
1516	ISLAND_HOPPING/ISLAND_HOPPING.a \
1517	SECEDIT/SECEDIT.a \
1518	SERVERCNTRL/SERVERCNTRL.a \
1519	SL/AW_HELIX/AW_HELIX.a \
1520	SL/AW_NAME/AW_NAME.a \
1521	SL/CONSENSUS/CONSENSUS.a \
1522	SL/ITEMS/ITEMS.a \
1523	STAT/STAT.a \
1524	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1525	SL/HELIX/HELIX.a \
1526	SL/TRANSLATE/TRANSLATE.a \
1527	SL/MACROS/MACROS.a \
1528	SL/NDS/NDS.a \
1529	$(ARCHS_AP_TREE) \
1530	XML/XML.a \
1531
1532	ifeq ($(OPENGL),1)
1533	ARCHS_EDIT4 += RNA3D/RNA3D.a
1534	endif
1535
1536	ARCHS_EDIT4_ALL = $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4)
1537
1538	LIBS_EDIT4 := $(GL_LIBS)
1539
1540	$(EDIT4): $(ARCHS_EDIT4:.a=.dummy) link_awt
1541	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_EDIT4_ALL) \|\| ( \
1542	echo "$(SEP) Link $@"; \
1543	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4_ALL)" ; \
1544	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4_ALL) && \
1545	echo "$(SEP) Link $@ [done]"; \
1546	)
1547
1548	#********************************* arb_rnacma ************************************
1549	RNACMA = bin/arb_rnacma
1550	ARCHS_RNACMA = \
1551	RNACMA/RNACMA.a \
1552
1553	ARCHS_RNACMA_ALL = $(ARCHS_RNACMA) $(DBSYS_LIBS)
1554
1555	$(RNACMA) : $(ARCHS_RNACMA:.a=.dummy) link_db
1556	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_RNACMA_ALL) \|\| ( \
1557	echo "$(SEP) Link $@"; \
1558	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_RNACMA_ALL)"; \
1559	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_RNACMA_ALL) && \
1560	echo "$(SEP) Link $@ [done]"; \
1561	)
1562
1563	#********************************* arb_wetc ************************************
1564	WETC = bin/arb_wetc
1565	ARCHS_WETC = \
1566	WETC/WETC.a \
1567	SL/HELIX/HELIX.a \
1568	SL/FILTER/FILTER.a \
1569	XML/XML.a \
1570
1571	ARCHS_WETC_ALL = $(ARCHS_WETC) $(GUI_LIBS)
1572
1573	$(WETC): $(ARCHS_WETC:.a=.dummy) link_awt
1574	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_WETC_ALL) \|\| ( \
1575	echo "$(SEP) Link $@"; \
1576	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC_ALL)" ; \
1577	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC_ALL) && \
1578	echo "$(SEP) Link $@ [done]"; \
1579	)
1580
1581	#********************************* arb_dist ************************************
1582	DIST = bin/arb_dist
1583	ARCHS_DIST = \
1584	DIST/DIST.a \
1585	CONSENSUS_TREE/CONSENSUS_TREE.a \
1586	EISPACK/EISPACK.a \
1587	SERVERCNTRL/SERVERCNTRL.a \
1588	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1589	SL/HELIX/HELIX.a \
1590	SL/MATRIX/MATRIX.a \
1591	SL/MACROS/MACROS.a \
1592	SL/NDS/NDS.a \
1593	SL/ITEMS/ITEMS.a \
1594	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.a \
1595	XML/XML.a \
1596	$(ARCHS_AP_TREE) \
1597
1598	ARCHS_DIST_ALL = $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS)
1599
1600	$(DIST): $(ARCHS_DIST:.a=.dummy) link_awt
1601	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_DIST_ALL) \|\| ( \
1602	echo "$(SEP) Link $@"; \
1603	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST_ALL)" ; \
1604	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST_ALL) && \
1605	echo "$(SEP) Link $@ [done]"; \
1606	)
1607
1608	#********************************* arb_pars ************************************
1609	PARSIMONY = bin/arb_pars
1610	ARCHS_PARSIMONY = \
1611	PARSIMONY/PARSIMONY.a \
1612	SERVERCNTRL/SERVERCNTRL.a \
1613	SL/AW_NAME/AW_NAME.a \
1614	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1615	SL/HELIX/HELIX.a \
1616	SL/MACROS/MACROS.a \
1617	SL/NDS/NDS.a \
1618	SL/ITEMS/ITEMS.a \
1619	SL/TRANSLATE/TRANSLATE.a \
1620	SL/TREEDISP/TREEDISP.a \
1621	XML/XML.a \
1622	$(ARCHS_AP_TREE) \
1623
1624	ARCHS_PARSIMONY_ALL = $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS)
1625
1626	$(PARSIMONY): $(ARCHS_PARSIMONY:.a=.dummy) link_awt
1627	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_PARSIMONY_ALL) \|\| ( \
1628	echo "$(SEP) Link $@"; \
1629	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY_ALL)" ; \
1630	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY_ALL) && \
1631	echo "$(SEP) Link $@ [done]"; \
1632	)
1633
1634	#********************************* arb_convert_aln ************************************
1635	CONVERT_ALN = bin/arb_convert_aln
1636	ARCHS_CONVERT_ALN = \
1637	CONVERTALN/CONVERTALN.a \
1638
1639	ARCHS_CONVERT_ALN_ALL = $(ARCHS_CONVERT_ALN) $(DBSYS_LIBS)
1640
1641	$(CONVERT_ALN) : $(ARCHS_CONVERT_ALN:.a=.dummy) link_db
1642	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_CONVERT_ALN_ALL) \|\| ( \
1643	echo "$(SEP) Link $@"; \
1644	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN_ALL)"; \
1645	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN_ALL) && \
1646	echo "$(SEP) Link $@ [done]"; \
1647	)
1648
1649	#********************************* arb_treegen ************************************
1650
1651	TREEGEN = bin/arb_treegen
1652	ARCHS_TREEGEN = \
1653	TREEGEN/TREEGEN.a \
1654
1655	ARCHS_TREEGEN_ALL = $(ARCHS_TREEGEN)
1656
1657	$(TREEGEN) : $(ARCHS_TREEGEN:.a=.dummy)
1658	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main_C) $(ARCHS_TREEGEN_ALL) \|\| ( \
1659	echo "$(SEP) Link $@"; \
1660	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN_ALL)" ; \
1661	$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN_ALL) && \
1662	echo "$(SEP) Link $@ [done]"; \
1663	)
1664
1665	#********************************* arb_naligner ************************************
1666	NALIGNER = bin/arb_naligner
1667	ARCHS_NALIGNER = \
1668	NALIGNER/NALIGNER.a \
1669	SERVERCNTRL/SERVERCNTRL.a \
1670	SL/HELIX/HELIX.a \
1671
1672	ARCHS_NALIGNER_ALL = $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(DBSYS_LIBS)
1673
1674	$(NALIGNER): $(ARCHS_NALIGNER:.a=.dummy) link_db
1675	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NALIGNER_ALL) \|\| ( \
1676	echo "$(SEP) Link $@"; \
1677	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER_ALL)" ; \
1678	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER_ALL) && \
1679	echo "$(SEP) Link $@ [done]"; \
1680	)
1681
1682	#********************************* arb_phylo ************************************
1683	PHYLO = bin/arb_phylo
1684	ARCHS_PHYLO = \
1685	PHYLO/PHYLO.a \
1686	SL/HELIX/HELIX.a \
1687	SL/FILTER/FILTER.a \
1688	SL/MACROS/MACROS.a \
1689	XML/XML.a \
1690
1691	ARCHS_PHYLO_ALL = $(ARCHS_PHYLO) $(GUI_LIBS)
1692
1693	$(PHYLO): $(ARCHS_PHYLO:.a=.dummy) link_awt
1694	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_PHYLO_ALL) \|\| ( \
1695	echo "$(SEP) Link $@"; \
1696	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO_ALL)" ; \
1697	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO_ALL) && \
1698	echo "$(SEP) Link $@ [done]"; \
1699	)
1700
1701	#***************************************************************************************
1702	# SERVER SECTION
1703	#***************************************************************************************
1704
1705	#********************************* arb_db_server ************************************
1706	DBSERVER = bin/arb_db_server
1707	ARCHS_DBSERVER = \
1708	DBSERVER/DBSERVER.a \
1709	SERVERCNTRL/SERVERCNTRL.a \
1710
1711	ARCHS_DBSERVER_ALL = $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS)
1712
1713	$(DBSERVER): $(ARCHS_DBSERVER:.a=.dummy) link_db
1714	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_DBSERVER_ALL) \|\| ( \
1715	echo "$(SEP) Link $@"; \
1716	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER_ALL)" ; \
1717	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER_ALL) && \
1718	echo "$(SEP) Link $@ [done]"; \
1719	)
1720
1721	#********************************* arb_pt_server ************************************
1722	PROBE = bin/arb_pt_server
1723
1724	ARCHS_PROBE_DEPEND = \
1725	PROBE/PROBE.a \
1726	SL/PTCLEAN/PTCLEAN.a \
1727	SERVERCNTRL/SERVERCNTRL.a \
1728	SL/HELIX/HELIX.a \
1729
1730	ARCHS_PROBE_ALL = $(ARCHS_PROBE_DEPEND) $(ARCHS_CLIENT_PROBE) $(ARBDB_LIB) $(SYSLIBS)
1731
1732	$(PROBE): $(ARCHS_PROBE_DEPEND:.a=.dummy) link_db
1733	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) config.makefile $(ARCHS_PROBE_ALL) \|\| ( \
1734	echo "$(SEP) Link $@"; \
1735	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_ALL)" ; \
1736	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_ALL) && \
1737	echo "$(SEP) Link $@ [done]"; \
1738	)
1739
1740	#********************************* arb_name_server ************************************
1741	NAMES = bin/arb_name_server
1742	ARCHS_NAMES = \
1743	NAMES/NAMES.a \
1744	SERVERCNTRL/SERVERCNTRL.a \
1745
1746	ARCHS_NAMES_ALL = $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS)
1747
1748	$(NAMES): $(ARCHS_NAMES:.a=.dummy) link_db
1749	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NAMES_ALL) \|\| ( \
1750	echo "$(SEP) Link $@"; \
1751	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES_ALL)" ; \
1752	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES_ALL) && \
1753	echo "$(SEP) Link $@ [done]"; \
1754	)
1755
1756	#********************************* SHARED LIBRARIES SECTION ************************************
1757
1758	prepare_libdir: addlibs
1759
1760	addlibs:
1761	(perl $(ARBHOME)/SOURCE_TOOLS/provide_libs.pl \
1762	"arbhome=$(ARBHOME)" \
1763	"opengl=$(OPENGL)" \
1764	"link_static=$(LINK_STATIC)" \
1765	)
1766
1767	#***************************************************************************************
1768	# Recursive calls to sub-makefiles
1769	#***************************************************************************************
1770
1771	%.depends: have_makedepend
1772	@cp -p $(@D)/Makefile $(@D)/Makefile.old # save old Makefile
1773	@$(MAKE) -C $(@D) -r \
1774	"AUTODEPENDS=1" \
1775	"MAIN=nothing" \
1776	"cflags=noCflagsHere_use_MAKEDEPENDFLAGS" \
1777	"cxxflags=noCxxflagsHere_use_MAKEDEPENDFLAGS" \
1778	depends
1779	@grep "^# DO NOT DELETE" $(@D)/Makefile >/dev/null
1780	@cat $(@D)/Makefile \
1781	\| SOURCE_TOOLS/fix_depends.pl "(from main)" \
1782	>$(@D)/Makefile.2
1783	@mv $(@D)/Makefile.old $(@D)/Makefile # restore old Makefile
1784	@$(ARBHOME)/SOURCE_TOOLS/mv_if_diff $(@D)/Makefile.2 $(@D)/Makefile # update Makefile if changed
1785
1786	%.proto:
1787	@($(MAKE) -C $(@D) \
1788	"AUTODEPENDS=0" \
1789	"MAIN=nothing" \
1790	"cflags=noCflags" \
1791	"cxxflags=noCxxflags" \
1792	proto 2>&1 ) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
1793
1794	%.clean:
1795	@$(MAKE) -C $(@D) \
1796	"AUTODEPENDS=0" \
1797	"MAIN=nothing" \
1798	"cflags=noCflags" \
1799	"cxxflags=noCxxflags" \
1800	clean
1801
1802
1803	# stop wrong targets:
1804	target_is_missing_lib_prefix:
1805	@echo "Error: Denied to build shared library target with missing 'lib'-prefix"
1806	false
1807
1808	ARBDB/ARBDB.dummy: target_is_missing_lib_prefix
1809	CORE/CORE.dummy: target_is_missing_lib_prefix
1810	AWT/AWT.dummy: target_is_missing_lib_prefix
1811	WINDOW/WINDOW.dummy: target_is_missing_lib_prefix
1812
1813	# rule to generate main target (normally a library):
1814	# @@@ check effect of setting LANG=C below
1815	%.dummy:
1816	@( export ID=$$$$; LANG=C; \
1817	(( \
1818	echo "$(SEP) Make $(@D)"; \
1819	$(MAKE) -C $(@D) -r \
1820	"AUTODEPENDS=1" \
1821	"MAIN=$(@F:.dummy=.a)" \
1822	"cflags=$(cflags) -DIN_ARB_$(subst /,_,$(@D))" \
1823	&& \
1824	echo "$(SEP) Make $(@D) [done]"; \
1825	) >$(@D).$$ID.log 2>&1 && (cat $(@D).$$ID.log;rm $(@D).$$ID.log)) \|\| (cat $(@D).$$ID.log;rm $(@D).$$ID.log;false))
1826
1827	# Additional dependencies for subtargets:
1828
1829	PROBE_COM/PROBE_COM.dummy : comtools
1830	NAMES_COM/NAMES_COM.dummy : comtools
1831
1832	com: PROBE_COM/PROBE_COM.dummy NAMES_COM/NAMES_COM.dummy
1833
1834	# stop wrong more targets:
1835	PROBE_COM/server.dummy:
1836	@echo Unwanted request to make target $<
1837	false
1838
1839	PROBE_COM/client.dummy:
1840	@echo Unwanted request to make target $<
1841	false
1842
1843	NAMES_COM/server.dummy:
1844	@echo Unwanted request to make target $<
1845	false
1846
1847	NAMES_COM/client.dummy:
1848	@echo Unwanted request to make target $<
1849	false
1850
1851
1852	ARBDB/libARBDB.dummy: links
1853	CORE/libCORE.dummy: links
1854
1855	PERLTOOLS/PERLTOOLS.dummy: core db
1856
1857	# all subdirs perl not depends on go here (ADD_links_non_perl)
1858	AWT/libAWT.dummy: links_non_perl
1859	AWTI/AWTI.dummy: links_non_perl
1860	CONSENSUS_TREE/CONSENSUS_TREE.dummy: links_non_perl
1861	CONVERTALN/CONVERTALN.dummy: links_non_perl
1862	DBSERVER/DBSERVER.dummy: links_non_perl
1863	DIST/DIST.dummy: links_non_perl
1864	EDIT4/EDIT4.dummy: links_non_perl com
1865	EISPACK/EISPACK.dummy: links_non_perl
1866	GDE/GDE.dummy: links_non_perl
1867	GENOM/GENOM.dummy: links_non_perl
1868	GENOM_IMPORT/GENOM_IMPORT.dummy: links_non_perl
1869	ISLAND_HOPPING/ISLAND_HOPPING.dummy: links_non_perl
1870	MERGE/MERGE.dummy: links_non_perl
1871	NTREE/NTREE.dummy: links_non_perl
1872	PARSIMONY/PARSIMONY.dummy: links_non_perl
1873	PHYLO/PHYLO.dummy: links_non_perl
1874	PRIMER_DESIGN/PRIMER_DESIGN.dummy: links_non_perl
1875	PROBE_SET/PROBE_SET.dummy: links_non_perl link_db
1876	READSEQ/READSEQ.dummy: links_non_perl
1877	RNACMA/RNACMA.dummy: links_non_perl header_libs
1878	SECEDIT/SECEDIT.dummy: links_non_perl
1879	SEQ_QUALITY/SEQ_QUALITY.dummy: links_non_perl
1880	SERVERCNTRL/SERVERCNTRL.dummy: links_non_perl com
1881	SL/ALILINK/ALILINK.dummy: links_non_perl
1882	SL/ALIVIEW/ALIVIEW.dummy: links_non_perl
1883	SL/AP_TREE/AP_TREE.dummy: links_non_perl
1884	SL/ARB_TREE/ARB_TREE.dummy: links_non_perl
1885	SL/AW_HELIX/AW_HELIX.dummy: links_non_perl
1886	SL/CONSENSUS/CONSENSUS.dummy: links_non_perl
1887	SL/DB_QUERY/DB_QUERY.dummy: links_non_perl
1888	SL/DB_SCANNER/DB_SCANNER.dummy: links_non_perl
1889	SL/DB_UI/DB_UI.dummy: links_non_perl
1890	SL/FAST_ALIGNER/FAST_ALIGNER.dummy: links_non_perl
1891	SL/FILTER/FILTER.dummy: links_non_perl
1892	SL/FILTSEQEXP/FILTSEQEXP.dummy: links_non_perl
1893	SL/GROUP_SEARCH/GROUP_SEARCH.dummy: links_non_perl
1894	SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy: links_non_perl
1895	SL/HEADERTESTS/HEADERTESTS.dummy: links_non_perl
1896	SL/HELIX/HELIX.dummy: links_non_perl
1897	SL/INSDEL/INSDEL.dummy: links_non_perl
1898	SL/ITEM_SHADER/ITEM_SHADER.dummy: links_non_perl
1899	SL/ITEMS/ITEMS.dummy: links_non_perl
1900	SL/LOCATION/LOCATION.dummy: links_non_perl
1901	SL/MACROS/MACROS.dummy: links_non_perl
1902	SL/MATRIX/MATRIX.dummy: links_non_perl
1903	SL/NDS/NDS.dummy: links_non_perl
1904	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.dummy: links_non_perl
1905	SL/PRONUC/PRONUC.dummy: links_non_perl
1906	SL/PTCLEAN/PTCLEAN.dummy: links_non_perl link_db
1907	SL/PVP/PVP.dummy: links_non_perl
1908	SL/QUERY/QUERY.dummy: links_non_perl link_db
1909	SL/REFENTRIES/REFENTRIES.dummy: links_non_perl
1910	SL/REGEXPR/REGEXPR.dummy: links_non_perl
1911	SL/SAICALC/SAICALC.dummy: links_non_perl
1912	SL/SEQIO/SEQIO.dummy: links_non_perl
1913	SL/SEQUENCE/SEQUENCE.dummy: links_non_perl
1914	SL/TRANSLATE/TRANSLATE.dummy: links_non_perl
1915	SL/TREE_ADMIN/TREE_ADMIN.dummy: links_non_perl
1916	SL/TREE_READ/TREE_READ.dummy: links_non_perl
1917	SL/TREE_WRITE/TREE_WRITE.dummy: links_non_perl
1918	SL/TREEDISP/TREEDISP.dummy: links_non_perl
1919	SL/XFERGUI/XFERGUI.dummy: links_non_perl
1920	SL/XFERSET/XFERSET.dummy: links_non_perl
1921	STAT/STAT.dummy: links_non_perl
1922	TREEGEN/TREEGEN.dummy: links_non_perl
1923	WETC/WETC.dummy: links_non_perl
1924	WINDOW/libWINDOW.dummy: links_non_perl
1925	XML/XML.dummy: links_non_perl
1926
1927	ifeq ($(OPENGL),1)
1928	GL/glAW/glAW.dummy: links_non_perl
1929	GL/glpng/glpng.dummy: links_non_perl
1930	GL/GL.dummy: GL/glAW/glAW.dummy GL/glpng/glpng.dummy
1931	RNA3D/RNA3D.dummy: links_non_perl gl
1932	endif
1933
1934	UNIT_TESTER/UNIT_TESTER.dummy: link_db \
1935	SERVERCNTRL/SERVERCNTRL.dummy \
1936
1937	# see also TOOLS/Makefile@TOOLSLIBDEPENDS
1938	TOOLS/TOOLS.dummy : links_non_perl link_db \
1939	CONSENSUS_TREE/CONSENSUS_TREE.dummy \
1940	SERVERCNTRL/SERVERCNTRL.dummy \
1941	SL/FILTER/FILTER.dummy \
1942	SL/FILTSEQEXP/FILTSEQEXP.dummy \
1943	SL/INSDEL/INSDEL.dummy \
1944	SL/REGEXPR/REGEXPR.dummy \
1945	SL/SEQIO/SEQIO.dummy \
1946	SL/TREE_READ/TREE_READ.dummy \
1947	SL/TREE_WRITE/TREE_WRITE.dummy \
1948	XML/XML.dummy \
1949
1950	AWTC/AWTC.dummy : com
1951
1952	NAMES/NAMES.dummy : com
1953	SL/AW_NAME/AW_NAME.dummy : com
1954
1955	PROBE/PROBE.dummy : com
1956	MULTI_PROBE/MULTI_PROBE.dummy : com
1957	PROBE_DESIGN/PROBE_DESIGN.dummy : com
1958	NALIGNER/NALIGNER.dummy : com
1959
1960	ARB_GDE/ARB_GDE.dummy : proto_tools menus
1961
1962	compile_compatibility: SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.dummy
1963
1964	#***************************************************************************************
1965	# Short aliases to make targets
1966	#***************************************************************************************
1967
1968	show:
1969	@echo $(SEP)
1970	@echo 'Aliases for often needed targets:'
1971	@echo ''
1972	@echo ' executables:'
1973	@echo ''
1974	@echo ' nt arb_ntree'
1975	@echo ' e4 arb_edit4 (includes secedit)'
1976	@echo ' di arb_dist'
1977	@echo ' ph arb_phylo'
1978	@echo ' pa arb_parsimony'
1979	@echo ' tg arb_treegen'
1980	@echo ' ds arb_dbserver'
1981	@echo ' pt arb_pt_server'
1982	@echo ' na arb_name_server'
1983	@echo ''
1984	@echo ' libraries:'
1985	@echo ''
1986	@echo ' com communication libraries'
1987	@echo ' db ARB database'
1988	@echo ' aw GUI lib'
1989	@echo ' awt GUI toolkit'
1990	@echo ' awtc general purpose library'
1991	@echo ' awti import/export library'
1992	@echo ' mp multi probe library'
1993	@echo ' ge genome library'
1994	@echo ' pd probe design lib'
1995	@echo ' prd primer design lib'
1996	@echo ''
1997	@echo ' other targets:'
1998	@echo ''
1999	@echo ' help recompile help files'
2000	@echo ' tools make small tools used by arb'
2001	@echo ''
2002	@echo ' foreign targets:'
2003	@echo ''
2004	@echo ' gde GDE'
2005	@echo ' agde ARB_GDE'
2006	@echo ''
2007	@echo 'for other targets inspect $(ARBHOME)/Makefile'
2008	@echo ''
2009	@echo $(SEP)
2010
2011	source_doc:
2012	@echo "Remove some links (doxygen crashes otherwise):"
2013	find . $ -name "AISC" -o -name "C" -o -name "GDEHELP" $ -type l -exec rm {} \;
2014	doxygen 2>&1 1>/dev/null
2015	$(MAKE) forcelinks
2016
2017	dep_graph:
2018	@echo "Building some dependency graphs"
2019	SOURCE_TOOLS/dependency_graphs.pl
2020
2021	help: HELP_SOURCE/HELP_SOURCE.dummy
2022
2023	HELP_SOURCE/HELP_SOURCE.dummy: link_core xml menus
2024
2025	db: ARBDB/libARBDB.dummy
2026	core: CORE/libCORE.dummy
2027	aw: WINDOW/libWINDOW.dummy
2028	awt: AWT/libAWT.dummy
2029	awtc: AWTC/AWTC.dummy
2030	awti: AWTI/AWTI.dummy
2031
2032	mp: MULTI_PROBE/MULTI_PROBE.dummy
2033	mg: MERGE/MERGE.dummy
2034	ge: GENOM/GENOM.dummy
2035	prd: PRIMER_DESIGN/PRIMER_DESIGN.dummy
2036
2037	nt: menus $(NTREE)
2038
2039	nal: $(NALIGNER)
2040
2041	di: $(DIST)
2042	ph: $(PHYLO)
2043	pa: $(PARSIMONY)
2044	tg: $(TREEGEN)
2045
2046	ifeq ($(OPENGL),1)
2047	3d: RNA3D/RNA3D.dummy
2048	gl: GL/GL.dummy
2049	else
2050	noopengl:
2051	@echo "invalid target for OPENGL=0"
2052	3d: noopengl
2053	gl: noopengl
2054	endif
2055
2056	SL/SL.dummy: com
2057
2058	ds: $(DBSERVER)
2059	pt: $(PROBE)
2060	pst: PROBE_SET/PROBE_SET.dummy
2061	pd: PROBE_DESIGN/PROBE_DESIGN.dummy
2062	na: $(NAMES)
2063	sq: SEQ_QUALITY/SEQ_QUALITY.dummy
2064	cma: $(RNACMA)
2065
2066	sec: SECEDIT/SECEDIT.dummy
2067
2068	e4: $(EDIT4) readseq menus
2069
2070	gi: GENOM_IMPORT/GENOM_IMPORT.dummy
2071	wetc: $(WETC)
2072
2073	xml: XML/XML.dummy
2074	stat: STAT/STAT.dummy $(NTREE) $(EDIT4)
2075	fa: SL/FAST_ALIGNER/FAST_ALIGNER.dummy
2076
2077	#********************************************************************************
2078
2079	up_by_remake: depends proto vectorize_checks
2080
2081	up: up_by_remake tags valgrind_update
2082
2083	#********************************************************************************
2084
2085	touch:
2086	SOURCE_TOOLS/touch_modified.pl
2087
2088	modified: touch
2089	$(MAKE) all
2090
2091	#********************************************************************************
2092
2093	libdepends:
2094	$(MAKE) -C "SOURCE_TOOLS" \
2095	"RNA3D_LIB=$(RNA3D_LIB_4_DEPENDS)" \
2096	libdepends
2097
2098	#********************************************************************************
2099
2100	# create generated headers:
2101	genheaders: TEMPLATES/TEMPLATES.dummy
2102
2103	clrdotdepends:
2104	rm PROBE_COM/.depends \|\| true
2105	rm NAMES_COM/.depends \|\| true
2106	rm PERL2ARB/.depends \|\| true
2107
2108	comdepends: comtools clrdotdepends have_makedepend
2109	@echo "$(SEP) Partially build com interface"
2110	$(MAKE) PROBE_COM/PROBE_COM.depends NAMES_COM/NAMES_COM.depends
2111	$(MAKE) PROBE_COM/server.depends NAMES_COM/server.depends
2112
2113	depends: genheaders comdepends vectorize_checks have_makedepend
2114	@echo "$(SEP) Updating other dependencies"
2115	$(MAKE) $(subst NAMES_COM/server.depends,,$(subst PROBE_COM/server.depends,,$(SUBDIRS:.sub=.depends))) \
2116	HELP_SOURCE/HELP_SOURCE.depends \
2117	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.depends \
2118
2119	$(MAKE) libdepends
2120
2121	depend: depends
2122
2123	# ------------------------------------------------------------
2124	# dependency generation tests for AISC code
2125	#(all should work w/o creating wrong dependencies;
2126	# neither in XXX_COM/Makefile nor in code using AISC interface)
2127	dependstest1: silent_clean
2128	$(MAKE) depends
2129	dependstest2: silent_clean
2130	$(MAKE) com
2131	dependstest3: silent_clean
2132	$(MAKE) aw
2133	dependstest4: silent_clean
2134	$(MAKE) pt
2135	dependstest5: silent_clean
2136	$(MAKE) na
2137	dependstest6: silent_clean
2138	$(MAKE) nt
2139	dependstest7: silent_clean
2140	$(MAKE) all
2141	# ------------------------------------------------------------
2142
2143	vectorize_checks:
2144	$(MAKE) -C SOURCE_TOOLS -r vectorize_checks
2145
2146	clean_checked_vect: lib/lib.clean
2147	SOURCE_TOOLS/clean_checked_vectorizations.sh
2148
2149	# ------------------------------------------------------------
2150
2151	AISC_MKPTPS/AISC_MKPTPS.dummy: links
2152
2153	proto_tools: AISC_MKPTPS/AISC_MKPTPS.dummy
2154
2155	proto: proto_tools
2156	@echo $(SEP) Updating prototypes
2157	$(MAKE) \
2158	ARBDB/ARBDB.proto \
2159	AISC_COM/AISC_COM.proto \
2160	ARB_GDE/ARB_GDE.proto \
2161	CORE/CORE.proto \
2162	CONVERTALN/CONVERTALN.proto \
2163	NTREE/NTREE.proto \
2164	MERGE/MERGE.proto \
2165	PROBE/PROBE.proto \
2166	SERVERCNTRL/SERVERCNTRL.proto \
2167	SL/SL.proto \
2168
2169	#********************************************************************************
2170
2171	valgrind_update: links
2172	@echo $(SEP) Updating for valgrind
2173	$(MAKE) -C SOURCE_TOOLS valgrind_update
2174
2175	#********************************************************************************
2176
2177	TAGFILE=TAGS
2178	UTAGS=TAGS.$(ARBBID)
2179	TAGFILE_TMP=$(UTAGS).tmp
2180
2181	TAG_SOURCE_HEADERS=$(UTAGS).headers.tmp
2182	TAG_SOURCE_CODE=$(UTAGS).codefiles.tmp
2183	TAG_SOURCE_LISTS=$(TAG_SOURCE_HEADERS) $(TAG_SOURCE_CODE)
2184
2185	ETAGS_IGNORE_LIST=SOURCE_TOOLS/etags_ignore.lst
2186
2187	ETAGS=ctags -e -I @$(ETAGS_IGNORE_LIST) --sort=no --if0=no --extra=q
2188	ETAGS_TYPES=--C-kinds=cgnsut --C++-kinds=cgnsut
2189	ETAGS_FUN =--C-kinds=fm --C++-kinds=fm
2190	ETAGS_REST =--C-kinds=dev --C++-kinds=dev
2191
2192	FILTER_TAGS_SOURCES= \
2193	$(SED) -e 's/^.\///g' \| \
2194	grep -vi '^HEADERLIBS\\|^GDE/\\|/GEN[CH]/'
2195
2196	$(TAG_SOURCE_HEADERS): links
2197	@find . $ -name '.hxx' -o -name ".h" $ -type f \| $(FILTER_TAGS_SOURCES) > $@
2198
2199	$(TAG_SOURCE_CODE): links
2200	@find . $ -name '.cxx' -o -name ".c" $ -type f \| $(FILTER_TAGS_SOURCES) > $@
2201
2202	$(UTAGS).1.tmp: $(TAG_SOURCE_HEADERS)
2203	@$(ETAGS) -f $@ $(ETAGS_TYPES) -L $<
2204	$(UTAGS).2.tmp: $(TAG_SOURCE_HEADERS)
2205	@$(ETAGS) -f $@ $(ETAGS_FUN) -L $<
2206	$(UTAGS).3.tmp: $(TAG_SOURCE_HEADERS)
2207	@$(ETAGS) -f $@ $(ETAGS_REST) -L $<
2208	$(UTAGS).4.tmp: $(TAG_SOURCE_CODE)
2209	@$(ETAGS) -f $@ $(ETAGS_TYPES) -L $<
2210	$(UTAGS).5.tmp: $(TAG_SOURCE_CODE)
2211	@$(ETAGS) -f $@ $(ETAGS_FUN) -L $<
2212	$(UTAGS).6.tmp: $(TAG_SOURCE_CODE)
2213	@$(ETAGS) -f $@ $(ETAGS_REST) -L $<
2214
2215	TAGS_ALL_PARTS=$(UTAGS).1.tmp $(UTAGS).2.tmp $(UTAGS).3.tmp $(UTAGS).4.tmp $(UTAGS).5.tmp $(UTAGS).6.tmp
2216
2217	$(TAGFILE_TMP) : $(TAGS_ALL_PARTS)
2218	@cat $(TAGS_ALL_PARTS) > $@
2219	@rm $(TAGS_ALL_PARTS) $(TAG_SOURCE_LISTS)
2220
2221	cleanOldTags:
2222	@find $(ARBHOME) -name 'TAGS.*.tmp' -ctime +2 -exec rm {} \;
2223
2224	tags: $(TAGFILE_TMP) cleanOldTags
2225	@mv_if_diff $(TAGFILE_TMP) $(TAGFILE)
2226
2227	#********************************************************************************
2228
2229	LINKSTAMP=SOURCE_TOOLS/stamp.generate_all_links
2230
2231	links: checks $(LINKSTAMP) arbmainwrapper
2232	links_no_checks: $(LINKSTAMP) arbmainwrapper
2233
2234	forcelinks:
2235	-rm $(LINKSTAMP)
2236	$(MAKE) links
2237
2238	$(LINKSTAMP): SOURCE_TOOLS/generate_all_links.sh genheaders
2239	+SOURCE_TOOLS/generate_all_links.sh
2240	touch $(LINKSTAMP)
2241
2242	clean_links:
2243	# avoid to delete linked pts, nas or arb_tcp.dat:
2244	find . -path './lib' -prune -o -type l -exec rm {} \;
2245	# removed obsolete file - refuses to disappear due to 'prune' above
2246	@rm -f lib/help/GDEHELP
2247	@rm -f $(LINKSTAMP) lib/inputMasks/format.readme
2248
2249	redo_links: clean_links
2250	$(MAKE) links_no_checks
2251
2252	#********************************************************************************
2253
2254	header_libs:
2255	@(( \
2256	echo "$(SEP) Make HEADERLIBS"; \
2257	$(MAKE) -C HEADERLIBS all && \
2258	echo "$(SEP) Make HEADERLIBS [done]"; \
2259	) > HEADERLIBS.log 2>&1 && (cat HEADERLIBS.log;rm HEADERLIBS.log)) \|\| (cat HEADERLIBS.log;rm HEADERLIBS.log;false)
2260
2261	#********************************************************************************
2262
2263	gde: GDE/GDE.dummy
2264	GDE: gde
2265	agde: ARB_GDE/ARB_GDE.dummy
2266	tools: TOOLS/TOOLS.dummy
2267	convert: $(CONVERT_ALN)
2268	readseq: READSEQ/READSEQ.dummy
2269
2270	#***************************************************************************************
2271	# Some user commands
2272	#***************************************************************************************
2273
2274	menus: binlink links
2275	@(( \
2276	echo "$(SEP) Make GDEHELP"; \
2277	$(MAKE) -C GDEHELP -r all && \
2278	echo "$(SEP) Make GDEHELP [done]"; \
2279	) > GDEHELP.log 2>&1 && (cat GDEHELP.log;rm GDEHELP.log)) \|\| (cat GDEHELP.log;rm GDEHELP.log;false)
2280
2281	ifeq ($(DEBUG),1)
2282	BIN_TARGET=develall
2283	else
2284	BIN_TARGET=all
2285	endif
2286
2287
2288	binlink:
2289	$(MAKE) -C bin $(BIN_TARGET)
2290
2291	check_bin_dep: binlink
2292	SOURCE_TOOLS/check_bin_dependencies.pl
2293
2294	fig_cure:
2295	SOURCE_TOOLS/sortfig.pl doit
2296
2297	preplib:
2298	(cd lib;$(MAKE) all)
2299
2300	# --------------------------------------------------------------------------------
2301	# This section is quite tricky:
2302	#
2303	# make 'perl' is a BIG target, so when it has to be made, it has to be started
2304	# as early as possible to reduce overall compile time. Since 'make' does not
2305	# provide any priorities, i force it to build all 'perl'-prerequisites early, by
2306	# adding artificial dependencies to these prerequisites
2307	#
2308	# That behavior is likely to be system-dependent.
2309	# My goal was only to make it work on my current development system,
2310	# where this saves about 20% of overall build time.
2311
2312	ifeq ($(WITHPERL),1)
2313	links_non_perl: PERLTOOLS/PERLTOOLS.dummy
2314	perltools: links_non_perl
2315	perl: realperl
2316	else
2317	links_non_perl: links
2318	perl: links
2319	$(MAKE) "WITHPERL=1" perl
2320	endif
2321
2322	# ---------------------------------------- perl
2323
2324	realperl: perltools
2325	(( \
2326	echo "$(SEP) Make PERL2ARB" ; \
2327	$(TIME) $(MAKE) -C PERL2ARB -r -f Makefile.main \
2328	"AUTODEPENDS=1" \
2329	"dflags=$(dflags)" \
2330	"cflags4perl=$(cflags) $(cxxflags) $(dflags)" \
2331	"lflags4perl=$(lflags4perl)" \
2332	"COMPILER_VERSION=$(COMPILER_VERSION)" \
2333	all && \
2334	$(MAKE) -C PERL_SCRIPTS/test test && \
2335	echo "$(SEP) Make PERL2ARB [done]" ; \
2336	) > PERL2ARB.log 2>&1 && (cat PERL2ARB.log;rm PERL2ARB.log)) \|\| (cat PERL2ARB.log;rm PERL2ARB.log;false)
2337
2338	perl_clean:
2339	@$(MAKE) -C PERL2ARB -r -f Makefile.main \
2340	"AUTODEPENDS=0" \
2341	clean
2342
2343	PERL2ARB/PERL2ARB.clean:
2344	$(MAKE) perl_clean
2345	$(MAKE) -C PERL_SCRIPTS/test clean
2346
2347	# ---------------------------------------- bindings to script languages
2348
2349	bindings: lib/libCORE.so lib/libARBDB.so
2350	$(MAKE) -C BINDINGS all ARBDEPENDS="$(^:%=../%)" DFLAGS="$(dflags)"
2351
2352	bindings_clean:
2353	$(MAKE) -C BINDINGS clean
2354
2355	# ---------------------------------------- check resources
2356
2357	check_res:
2358	$(ARBHOME)/SOURCE_TOOLS/check_resources.pl
2359
2360	# ---------------------------------------- cleaning
2361
2362	rmbak:
2363	@echo "[cleanup backup/core files]"
2364	@find . \( -name '*%' \
2365	-o -name '*.bak' \
2366	-o -name '*~' \) \
2367	-o $ -name 'core' -a \! -type d $ \
2368	-exec rm -v {} \; \|\| \
2369	echo "Warning: target 'rmbak' reported problems when removing misc. backup files (ignored)"
2370	@echo "[cleanup done]"
2371
2372	bin_reinit:
2373	$(MAKE) bin/bin.clean
2374	$(MAKE) -C "bin" all
2375
2376	clean_directories:
2377	-rm -rf \
2378	$(ARBHOME)/PROBE_SET/bin \
2379	$(ARBHOME)/INCLUDE \
2380
2381	libclean:
2382	-find $(ARBHOME) -type f $ -name '*.a' ! -type l $ -exec rm -f {} \;
2383	-find $(ARBHOME) -type f $ -name 'lib*.so' ! -type l $ -exec rm -f {} \;
2384
2385	objclean:
2386	-find $(ARBHOME) -type f $ -name '*.o' ! -type l $ -exec rm -f {} \;
2387
2388	# bin.clean and HELP_SOURCE.clean interfere
2389	clean3:
2390	$(MAKE) bin/bin.clean
2391	$(MAKE) HELP_SOURCE/HELP_SOURCE.clean
2392
2393
2394	# delete all binaries (similar to 'cleanlinked')
2395	cleanRelinkable: libclean UNIT_TESTER/UNIT_TESTER.clean
2396	$(MAKE) -C bin cleanbinariesRelinkable
2397	$(MAKE) -C PROBE_SET cleanLinked
2398
2399
2400	clean2: $(SUBDIRS:.sub=.clean) \
2401	clean3 \
2402	rmbak \
2403	libclean \
2404	objclean \
2405	lib/lib.clean \
2406	GDEHELP/GDEHELP.clean \
2407	HEADERLIBS/HEADERLIBS.clean \
2408	SOURCE_TOOLS/SOURCE_TOOLS.clean \
2409	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.clean \
2410	UNIT_TESTER/UNIT_TESTER.clean \
2411	TEMPLATES/TEMPLATES.clean \
2412	perl_clean \
2413	clean_directories \
2414
2415	rm -f .last_gcc .last_compiler config.makefile.bak
2416
2417	# links are needed for cleanup
2418	clean: redo_links motif_xpm_hack_clean
2419	$(MAKE) clean2
2420	$(MAKE) clean_cov_all clean_links
2421
2422	silent_clean:
2423	$(MAKE) clean >/dev/null
2424
2425	# 'relocated' is about 50% faster than 'rebuild'
2426	reloc_clean: links
2427	@echo "---------------------------------------- Relocation cleanup"
2428	$(MAKE) \
2429	perl_clean \
2430	GDEHELP/GDEHELP.clean \
2431	HELP_SOURCE/genhelp/genhelp.clean \
2432	bin/bin.clean \
2433	libclean \
2434	objclean
2435
2436	relocated: links
2437	$(MAKE) reloc_clean
2438	@echo "---------------------------------------- and remake"
2439	$(MAKE) build
2440
2441	# -----------------------------------
2442	# some stress tests
2443	# (helpful to reveal race conditions with -j)
2444
2445	rebuild4ever: rebuild
2446	$(MAKE) rebuild4ever
2447
2448	build4ever: build
2449	$(MAKE) build4ever
2450
2451	clean4ever: clean
2452	$(MAKE) clean4ever
2453
2454	test4ever: ut
2455	$(MAKE) test4ever
2456
2457	perl4ever: clean
2458	$(MAKE) links
2459	$(MAKE) perl
2460	$(MAKE) perl4ever
2461
2462	help4ever: clean
2463	$(MAKE) help
2464	$(MAKE) help4ever
2465
2466	# -----------------------------------
2467
2468	cleanlinked: bin/bin.clean libclean
2469
2470	relink: cleanlinked
2471	$(MAKE) all
2472
2473	# --------------------------------------------------------------------------------
2474	# source related targets
2475
2476	CLOC=cloc
2477	CLOCFLAGS=--no3 --quiet --progress-rate=0
2478	CLOCARB=--exclude-dir=GDE .
2479	CLOCEXT=GDE
2480	CLOCCODE=--force-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.code.def
2481	CLOCREST=--force-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.rest.def
2482	CLOCFILT=tail --lines=+4
2483
2484	cloc:
2485	@echo 'Arb code:'
2486	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCARB) \| $(CLOCFILT)
2487	@echo 'Arb rest:'
2488	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCARB) \| $(CLOCFILT)
2489	@echo 'External code:'
2490	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCEXT) \| $(CLOCFILT)
2491	@echo 'External rest:'
2492	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCEXT) \| $(CLOCFILT)
2493
2494
2495	# patch generation
2496	patch:
2497	SOURCE_TOOLS/arb_create_patch.sh arbPatch --svn
2498
2499	# source tarball generation
2500	save: sourcetarfile
2501
2502	sourcetarfile: rmbak
2503	util/arb_save
2504
2505	# test early whether save will work
2506	savetest:
2507	@util/arb_srclst.pl >/dev/null
2508
2509	testsave: savetest
2510
2511	save2: rmbak
2512	util/arb_save ignore
2513
2514	save_test: rmbak
2515	@echo "Testing source list.."
2516	@util/arb_srclst.pl > /dev/null
2517
2518	save_test_no_error:
2519	@-$(MAKE) save_test
2520
2521	# --------------------------------------------------------------------------------
2522	# version management
2523
2524	inc_candi:
2525	touch SOURCE_TOOLS/inc_candi.stamp
2526	$(MAKE) do_version_update
2527
2528	inc_patch:
2529	touch SOURCE_TOOLS/inc_patch.stamp
2530	$(MAKE) do_version_update
2531
2532	inc_minor:
2533	touch SOURCE_TOOLS/inc_minor.stamp
2534	$(MAKE) do_version_update
2535
2536	inc_major:
2537	touch SOURCE_TOOLS/inc_major.stamp
2538	$(MAKE) do_version_update
2539
2540	do_version_update:
2541	@echo Incrementing version information
2542	$(MAKE) savetest
2543	$(MAKE) genheaders # auto upgrades version early
2544
2545	show_version:
2546	$(MAKE) genheaders # updates version info
2547	@echo "$(SEP) ARB version info"
2548	@grep ARB_VERSION TEMPLATES/arb_build.h
2549	@echo "$(SEP)"
2550
2551	# --------------------------------------------------------------------------------
2552	# special cleanups
2553
2554	clean_opengl_changed: RNA3D/RNA3D.clean EDIT4/EDIT4.clean WINDOW/WINDOW.clean GL/GL.clean
2555
2556	# --------------------------------------------------------------------------------
2557
2558	arbapplications: nt pa e4 wetc pt na nal di ph ds wetc cma
2559
2560	arb_external: convert tools gde readseq tg pst
2561
2562	arb_no_perl: arbapplications help arb_external
2563
2564	arb: motif_xpm_hack
2565	$(MAKE) "WITHPERL=1" perl arb_no_perl
2566
2567	motif_xpm_hack:
2568	$(MAKE) -r -C "lib/motifHack" all
2569
2570	motif_xpm_hack_clean:
2571	$(MAKE) -r -C "lib/motifHack" clean
2572
2573	# --------------------------------------------------------------------------------
2574	# special targets for SOURCE_TOOLS/remake_after_change.pl
2575
2576	rac_arb_dist: di
2577	rac_arb_edit4: e4
2578	rac_arb_ntree: nt
2579	rac_arb_pars: pa
2580	rac_arb_phylo: ph
2581	rac_arb_wetc: wetc
2582	rac_arb_naligner: nal
2583	rac_arb_pt_server: pt
2584	rac_arb_db_server: ds
2585	rac_arb_name_server: na
2586	rac_arb_convert_aln: convert
2587	rac_arb_treegen: tg
2588	rac_arb_rnacma: cma
2589	rac_arb_help2xml: help
2590
2591	rac_arb_a2ps: tools
2592	rac_arb_consensus_tree: tools
2593	rac_arb_dnarates: tools
2594	rac_arb_export_rates: tools
2595	rac_arb_export_tree: tools
2596	rac_arb_gene_probe: tools
2597	rac_arb_message: tools
2598	rac_arb_primer: tools
2599	rac_arb_probe: tools
2600	rac_arb_read_tree: tools
2601
2602	# --------------------------------------------------------------------------------
2603	# unit testing
2604	# @@@ work in progress
2605	#
2606	# goal is to automatically test all libraries/executables using TESTED_UNITS_AUTO
2607	# currently not all test executables link w/o error.
2608	# therefor units are organized in three sets:
2609	#
2610	# TESTED_UNITS = testable and contain tests
2611	# UNTESTED_UNITS = testable, but no tests written yet
2612	# UNTESTABLE_UNITS = not testable
2613
2614	# always define OPENGL units manually:
2615	OPENGL_TESTS :=
2616	ifeq ($(OPENGL),1)
2617	OPENGL_TESTS += \
2618	$(subst .a,.test,$(RNA3D_LIB)) \
2619	GL/glAW/libglAW.test \
2620	GL/glpng/libglpng_arb.test \
2621
2622	endif
2623
2624	UNITS_NOT_AUTODETECTED = \
2625	HELP_SOURCE/HELP_SOURCE.tooltests
2626
2627	TESTED_UNITS_AUTO = \
2628	$(OPENGL_TESTS) \
2629	$(TL_ARCHIVES:.a=.test) \
2630	$(TL_SHARED_ARCHIVES:.so=.test) \
2631	$(CL_ARCHIVES:.a=.test) \
2632	$(TL_TOOLS_COLLECTIONS:.toolColl=.tooltests) \
2633	$(UNITS_NOT_AUTODETECTED) \
2634
2635	UNTESTED_UNITS = \
2636	$(OPENGL_TESTS) \
2637	EISPACK/EISPACK.test \
2638	GENOM/GENOM.test \
2639	ISLAND_HOPPING/ISLAND_HOPPING.test \
2640	NALIGNER/NALIGNER.test \
2641	NAMES/NAMES.test \
2642	PHYLO/PHYLO.test \
2643	PRIMER_DESIGN/PRIMER_DESIGN.test \
2644	READSEQ/READSEQ.tooltests \
2645	SECEDIT/SECEDIT.test \
2646	SEQ_QUALITY/SEQ_QUALITY.test \
2647	SERVERCNTRL/SERVERCNTRL.test \
2648	SL/ALIVIEW/ALIVIEW.test \
2649	SL/AP_TREE/AP_TREE.test \
2650	SL/ARB_TREE/ARB_TREE.test \
2651	SL/AW_HELIX/AW_HELIX.test \
2652	SL/AW_NAME/AW_NAME.test \
2653	SL/DB_SCANNER/DB_SCANNER.test \
2654	SL/DB_UI/DB_UI.test \
2655	SL/GUI_ALIVIEW/GUI_ALIVIEW.test \
2656	SL/HELIX/HELIX.test \
2657	SL/QUERY/QUERY.test \
2658	SL/REFENTRIES/REFENTRIES.test \
2659	SL/SEQUENCE/SEQUENCE.test \
2660	SL/TREE_ADMIN/TREE_ADMIN.test \
2661	SL/TREE_WRITE/TREE_WRITE.test \
2662	SL/XFERGUI/XFERGUI.test \
2663	STAT/STAT.test \
2664	TREEGEN/TREEGEN.test \
2665	WETC/WETC.test \
2666	XML/XML.test \
2667
2668	# untestable units
2669
2670	UNTESTABLE_UNITS = \
2671	AISC/AISC.test \
2672	NAMES_COM/server.test \
2673	PROBE_COM/server.test \
2674
2675	# --------------------
2676	# put all units containing tests into the following 4 sections (see also TESTED_UNITS below)
2677
2678	# recent development
2679	UNITS_TESTED_FIRST = \
2680	SL/MATRIX/MATRIX.test \
2681	AWTI/AWTI.test \
2682	SL/FILTSEQEXP/FILTSEQEXP.test \
2683	SL/GROUP_SEARCH/GROUP_SEARCH.test \
2684	SL/PVP/PVP.test \
2685	SL/SAICALC/SAICALC.test \
2686	SL/TRANSLATE/TRANSLATE.test \
2687	SL/XFERSET/XFERSET.test \
2688
2689	# start units with long duration early
2690	UNITS_RUNNING_LONG = \
2691	ARBDB/libARBDB.test \
2692	AWTC/AWTC.test \
2693	TOOLS/TOOLS.tooltests \
2694
2695	# plain test-libaries that are not linked anywhere
2696	TEST_SANDBOXES = \
2697	SL/CB/CB.test \
2698	SL/HEADERTESTS/HEADERTESTS.test \
2699
2700	UNITS_TESTED = \
2701	AISC_MKPTPS/AISC_MKPTPS.tooltests \
2702	ARB_GDE/ARB_GDE.test \
2703	AWT/libAWT.test \
2704	CONSENSUS_TREE/CONSENSUS_TREE.test \
2705	CONVERTALN/CONVERTALN.test \
2706	CORE/libCORE.test \
2707	DBSERVER/DBSERVER.test \
2708	DIST/DIST.test \
2709	EDIT4/EDIT4.test \
2710	GENOM_IMPORT/GENOM_IMPORT.test \
2711	HELP_SOURCE/HELP_SOURCE.tooltests \
2712	MERGE/MERGE.test \
2713	MULTI_PROBE/MULTI_PROBE.test \
2714	NTREE/NTREE.test \
2715	PARSIMONY/PARSIMONY.test \
2716	PERLTOOLS/PERLTOOLS.tooltests \
2717	PROBE/PROBE.test \
2718	PROBE_DESIGN/PROBE_DESIGN.test \
2719	PROBE_SET/PROBE_SET.tooltests \
2720	RNACMA/RNACMA.test \
2721	SL/ALILINK/ALILINK.test \
2722	SL/CONSENSUS/CONSENSUS.test \
2723	SL/DB_QUERY/DB_QUERY.test \
2724	SL/FAST_ALIGNER/FAST_ALIGNER.test \
2725	SL/FILTER/FILTER.test \
2726	SL/INSDEL/INSDEL.test \
2727	SL/ITEM_SHADER/ITEM_SHADER.test \
2728	SL/ITEMS/ITEMS.test \
2729	SL/LOCATION/LOCATION.test \
2730	SL/MACROS/MACROS.test \
2731	SL/NDS/NDS.test \
2732	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.test \
2733	SL/PRONUC/PRONUC.test \
2734	SL/PTCLEAN/PTCLEAN.test \
2735	SL/REGEXPR/REGEXPR.test \
2736	SL/SEQIO/SEQIO.test \
2737	SL/TREE_READ/TREE_READ.test \
2738	SL/TREEDISP/TREEDISP.test \
2739	WINDOW/libWINDOW.test \
2740
2741	TESTED_UNITS = \
2742	$(UNITS_TESTED_FIRST) \
2743	$(UNITS_RUNNING_LONG) \
2744	$(TEST_SANDBOXES) \
2745	$(UNITS_TESTED) \
2746
2747	# ----------------------------------------
2748
2749	ifeq ($(DEVELOPER),RALF)
2750
2751	DEFINED_TEST_UNITS = \
2752	$(TESTED_UNITS) \
2753	$(UNTESTED_UNITS) \
2754	$(UNTESTABLE_UNITS) \
2755
2756	list_undefined_units:
2757	@UNIT_TESTER/list_undefined_units.pl $(DEFINED_TEST_UNITS) -- $(TESTED_UNITS_AUTO)
2758
2759	else
2760
2761	list_undefined_units:
2762
2763	endif
2764
2765	# ----------------------------------------
2766
2767	TEST_LOG_DIR = UNIT_TESTER/logs
2768	TEST_RUN_SUITE=$(MAKE) $(NODIR) -C UNIT_TESTER -f Makefile.suite -r
2769	# -> UNIT_TESTER/Makefile.suite
2770	TEST_MAKE_FLAGS=
2771	TEST_POST_CLEAN=
2772	ifeq ($(COVERAGE),1)
2773	TEST_POST_CLEAN=$(MAKE) clean_cov
2774	TEST_MAKE_FLAGS+=-j1
2775	endif
2776
2777
2778	%.test:
2779	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
2780	( \
2781	echo "take[1]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
2782	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
2783	"UNITDIR=$(@D)" \
2784	"UNITLIBNAME=$(@F:.test=)" \
2785	"COVERAGE=$(COVERAGE)" \
2786	"ARB_PID=$(ARB_PID)_$(@F)" \
2787	runtest; \
2788	echo "take[1]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"; \
2789	$(TEST_POST_CLEAN) \
2790	) >$(TEST_LOG_DIR)/$(@F).log 2>&1; \
2791	UNIT_TESTER/log_result.pl $(TEST_LOG_DIR)/$(@F).log )
2792
2793	%.notest:
2794	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
2795	( \
2796	echo "take[4]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
2797	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
2798	"UNITDIR=$(@D)" \
2799	"UNITLIBNAME=$(@F:.notest=)" \
2800	"COVERAGE=0" \
2801	"ARB_PID=$(ARB_PID)_$(@F)" \
2802	check_no_test; \
2803	echo "take[4]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'" \
2804	) >$(TEST_LOG_DIR)/$(@F).log 2>&1 )
2805
2806
2807	# tool test aliases (used to test one or multiple executable(s) in a single subdir):
2808	%.tooltests:
2809	$(error please define an explicit tooltest alias for $@)
2810
2811	AISC_MKPTPS/AISC_MKPTPS.tooltests : AISC_MKPTPS/mkptypes.test
2812	@echo "aliasing $@ -> $^"
2813	PERLTOOLS/PERLTOOLS.tooltests : PERLTOOLS/arb_proto_2_xsub.test
2814	@echo "aliasing $@ -> $^"
2815	PROBE_SET/PROBE_SET.tooltests : PROBE_SET/fb_test.test
2816	@echo "aliasing $@ -> $^"
2817	HELP_SOURCE/HELP_SOURCE.tooltests : HELP_SOURCE/arb_help2xml.test
2818	@echo "aliasing $@ -> $^"
2819	TOOLS/TOOLS.tooltests : TOOLS/arb_consensus_tree.test TOOLS/arb_probe.test TOOLS/arb_test.test
2820	@echo "aliasing $@ -> $^"
2821
2822	# aliases for tools w/o tests:
2823	READSEQ/READSEQ.tooltests:
2824	@echo "Note: no tests for $@"
2825
2826
2827	test_base: $(UNIT_TESTER_LIB:.a=.dummy) $(subst .test,.dummy,$(TEST_SANDBOXES))
2828
2829	clean_cov:
2830	find . $ -name ".gcda" -o -name ".gcov" -o -name "*.cov" $ -exec rm {} \;
2831
2832	clean_cov_all: clean_cov
2833	find . $ -name "*.gcno" $ -exec rm {} \;
2834
2835	cleanup_faked_arbpids:
2836	@rm ~/.arb_tmp/tmp/arb_pids_${USER}_${ARB_PID}_* \|\| true
2837
2838	cleanup_faked_arbpids_and_fail: cleanup_faked_arbpids
2839	@false
2840
2841	NOTESTS_IN_UNTESTED = $(subst .test,.notest,$(UNTESTED_UNITS))
2842
2843	run_tests_faked_arbpid:
2844	+@$(TEST_RUN_SUITE) init
2845	@echo "take[2]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2846	@$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(TESTED_UNITS) $(NOTESTS_IN_UNTESTED) \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2847	@echo "take[2]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2848	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2849	@$(MAKE) clean_cov >/dev/null
2850	@$(MAKE) cleanup_faked_arbpids
2851
2852	# @@@ instead of only running UNIT, this should as well run all tests this unit depends on? according to 'needs_libs'
2853	# @@@ '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
2854
2855	run_onetest_faked_arbpid:
2856	+@$(TEST_RUN_SUITE) init
2857	@echo "take[3]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2858	test -n "$(UNIT)" \|\| (echo "Error: UNIT has to be defined for target 'run_onetest_faked_arbpid'!"; false)
2859	$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(UNIT).test \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2860	@echo "take[3]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2861	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2862	@$(MAKE) clean_cov >/dev/null
2863	@$(MAKE) cleanup_faked_arbpids
2864
2865	run_tests: test_base clean_cov
2866	$(MAKE) "ARB_PID=UT_$$$$" run_tests_faked_arbpid list_undefined_units
2867
2868	run_oneunitstests: test_base
2869	$(MAKE) "ARB_PID=UT_$$$$" run_onetest_faked_arbpid
2870
2871
2872	ut:
2873	ifeq ($(UNIT_TESTS),1)
2874	@echo $(MAKE) run_tests
2875	@$(MAKE) run_tests
2876	else
2877	@echo "Not compiled with unit tests"
2878	endif
2879
2880
2881	aut:
2882	+@$(TEST_RUN_SUITE) unskip
2883	$(MAKE) ut
2884
2885	# --------------------------------------------------------------------------------
2886
2887	TIMELOG=$(ARBHOME)/arb_time.log
2888	TIMEARGS=--append --output=$(TIMELOG) --format=" * %E(%S+%U) %P [%C]"
2889	TIMECMD=$(TIME) $(TIMEARGS)
2890
2891	time_one:
2892	ifeq ($(ONE_TIMED_TARGET),)
2893	@echo "Error: You have to pass ONE_TIMED_TARGET to $@"
2894	false
2895	else
2896	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET)"
2897	@$(TIMECMD) $(MAKE) $(ONE_TIMED_TARGET)
2898	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET) [done]"
2899	endif
2900
2901	timed_target:
2902	ifeq ($(TIMED_TARGET),)
2903	@echo "Error: You have to pass TIMED_TARGET to $@"
2904	false
2905	else
2906	@echo "Build time:" > $(TIMELOG)
2907	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2908	@cat $(TIMELOG)
2909	@rm $(TIMELOG)
2910	endif
2911
2912	timed_target_tested:
2913	ifeq ($(TIMED_TARGET),)
2914	@echo "Error: You have to pass TIMED_TARGET to $@"
2915	false
2916	else
2917	@echo "Build time:" > $(TIMELOG)
2918	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2919	$(MAKE) "ONE_TIMED_TARGET=ut" time_one
2920	@cat $(TIMELOG)
2921	@rm $(TIMELOG)
2922	endif
2923
2924	clean_timed_target:
2925	ifeq ($(TIMED_TARGET),)
2926	@echo "Error: You have to pass TIMED_TARGET to $@"
2927	false
2928	else
2929	@echo "Build time:" > $(TIMELOG)
2930	$(MAKE) "ONE_TIMED_TARGET=clean" time_one
2931	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2932	@cat $(TIMELOG)
2933	@rm $(TIMELOG)
2934	endif
2935
2936	# --------------------------------------------------------------------------------
2937
2938	CHECKOUT_MODIFIED=0# set to 1 to temporarily skip test for modifications (do not check in if set to 1)
2939
2940	check_svn_does_not_contain_generated:
2941	ifeq ($(CHECKOUT_MODIFIED),0)
2942	@echo "Testing that build does not modify files in SVN"
2943	@test 0 = `svn status \| wc -l` \|\| ( \
2944	echo "The checkout is not/no longer clean:"; \
2945	svn status; \
2946	echo "- if this fails instantly, your checkout is not clean"; \
2947	echo "- if this fails after other targets, these targets modify checked in data"; \
2948	echo " (a common cause may be that depends are not up to date)"; \
2949	false)
2950	else
2951	grep -Hn 'CHECKOUT_MODIFIED' Makefile
2952	endif
2953
2954	check_svn_ignores_generated:
2955	@test 0 = `svn status \| grep '^\?' \| wc -l` \|\| ( \
2956	echo "There are svn-unignored files:"; \
2957	svn status \| grep '^\?'; \
2958	echo "(all generated files should be svn-ignored)"; \
2959	false)
2960
2961	check_svn_state: check_svn_does_not_contain_generated
2962	$(MAKE) check_svn_ignores_generated
2963	$(MAKE) savetest
2964
2965	things_that_always_should_work: depends proto
2966
2967	post_commit_check:
2968	@echo "---------------------------------------- [Initial]"
2969	$(MAKE) check_svn_state
2970
2971	$(MAKE) clean
2972	@echo "---------------------------------------- [After 'make clean']"
2973	$(MAKE) check_svn_state
2974
2975	$(MAKE) things_that_always_should_work
2976	@echo "---------------------------------------- [After 'make things_that_always_should_work']"
2977	$(MAKE) check_svn_state
2978
2979	$(MAKE) all
2980	@echo "---------------------------------------- [After 'make all']"
2981	$(MAKE) check_svn_state
2982
2983	$(MAKE) things_that_always_should_work
2984	@echo "---------------------------------------- [Final]"
2985	$(MAKE) check_svn_state
2986
2987	# --------------------------------------------------------------------------------
2988	# sanitize arb_ntree; also works for clients (arb_edit4, ...) started from there.
2989
2990	sanitize: all
2991	( \
2992	export "LSAN_OPTIONS=max_leaks=30:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp"; \
2993	echo "sake[1]: Entering directory \`$(ARBHOME)'"; \
2994	$(ARBHOME)/bin/arb_ntree --execute _logged ~/data/test.arb 2>&1 ; \
2995	echo "sake[1]: Leaving directory \`$(ARBHOME)'" \
2996	) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
2997
2998	# --------------------------------------------------------------------------------
2999	# build and test one unit:
3000
3001	build_oneunit:
3002	$(MAKE) "WITHPERL=1" $(UNIT).dummy
3003
3004	oneunit:
3005	ifndef UNIT
3006	@echo "Please define UNIT, e.g. using"
3007	@echo " make \"UNIT=ARBDB/libARBDB\" oneunit"
3008	@echo " make \"UNIT=SL/TREEDISP/TREEDISP\" oneunit"
3009	@echo "(Note: 1st is a shared library, 2nd isn't)"
3010	false
3011	else
3012	@echo "Build time" > $(TIMELOG)
3013	@echo "$(SEP) $(MAKE) build_oneunit"
3014	@$(TIMECMD) $(MAKE) build_oneunit
3015	ifeq ($(UNIT_TESTS),1)
3016	@echo "$(SEP) $(MAKE) run_oneunitstests"
3017	@$(TIMECMD) $(MAKE) run_oneunitstests
3018	endif
3019	@cat $(TIMELOG)
3020	@rm $(TIMELOG)
3021	endif
3022
3023	# --------------------------------------------------------------------------------
3024	# Main targets:
3025
3026	tarfile: rebuild
3027	$(MAKE) prepare_libdir
3028	util/arb_compress
3029
3030	tarfile_quick: all
3031	$(MAKE) prepare_libdir
3032	util/arb_compress
3033
3034	# -----------------------------------
3035
3036	build: arb
3037	$(MAKE) check_bin_dep preplib compile_compatibility fig_cure
3038
3039	all:
3040	@echo "Build time" > $(TIMELOG)
3041	# $(MAKE) clean_checked_vect # uncomment to rebuild sources where expected vectorization gets tested
3042	@echo "$(SEP) $(MAKE) all"
3043	@$(TIMECMD) $(MAKE) build
3044	@echo $(SEP)
3045	@echo "made 'all' with success."
3046	@echo "to start arb enter 'arb'"
3047	ifeq ($(UNIT_TESTS),1)
3048	@echo "$(SEP) $(MAKE) run_tests"
3049	@$(TIMECMD) $(MAKE) run_tests
3050	endif
3051	@echo "$(SEP) $(MAKE) all [done]"
3052	ifeq ($(DEBUG),1)
3053	@$(MAKE) save_test_no_error >/dev/null # just show hints
3054	endif
3055	@cat $(TIMELOG)
3056	@rm $(TIMELOG)
3057
3058	rebuild: clean
3059	$(MAKE) all
3060
3061	# --------------------------------------------------------------------------------
3062	# special targets showing obvious error at bottom
3063	# (intended to be used from automated builds)
3064
3065	BUILD_LOG=build.log
3066	SHELL=bash
3067	REDIRECT_KEEP_EXITCODE = tee $(BUILD_LOG) ; exit "$${PIPESTATUS[0]}"
3068	EXTRACT_ERROR_SUMMARY = (./SOURCE_TOOLS/short_error_summary.pl $(BUILD_LOG); false)
3069
3070	ALL:
3071	@(($(MAKE) all 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
3072
3073	REBUILD:
3074	@(($(MAKE) rebuild 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
3075
3076	TARFILE:
3077	@(($(MAKE) tarfile 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
3078
3079	TARFILE_QUICK:
3080	@(($(MAKE) tarfile_quick 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
3081

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