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source: trunk/Makefile

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Last change on this file was 19916, checked in by westram, 7 hours ago
fix compile with clang 6 under linux parts of `TEST_naninf` also fails using clang under linux. parse real clang version from detailed version info AFAIK this effectively already happens under OSX (since change r12860). also set USE_OPENMP=0 for clang under linux. fix undefined code: variable length arrays (VLAs) cannot be initialized at declaration. use `-std=gnu++17` for clang. `str_iequal` + `count_spaces` fail to build as `constexpr` under clang.
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 89.3 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 ($(USE_CLANG),1)
337	USE_OPENMP:=0
338	endif
339
340	#----------------------
341
342	ifeq ($(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	#---------------------- be strict while building documentation?
551
552	STRICT_DOC:=0
553	ifeq ($(DEVELOPER),RALF)
554	STRICT_DOC:=1
555	endif
556
557	#---------------------- activate threads?
558	# only useful if compiler is able to compile Cxx11 or better
559
560	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
561	# see also ./TEMPLATES/cxxforward.h@USE_Cxx11
562	cflags += -pthread
563	clflags += -pthread
564	endif
565
566	#---------------------- activate Sanitizers?
567
568	ASAN_OPTIONS:=handle_segv=0:color=0
569	ifeq ($(IGNORE_LEAKS),1)
570	ASAN_OPTIONS+=:detect_leaks=0 # disable leak-detection
571	else
572	ASAN_OPTIONS+=:detect_leaks=1 # detect leaks (normal setting)
573	endif
574	ASAN_OPTIONS+=:check_initialization_order=1
575	# ASAN_OPTIONS+=:abort_on_error=1
576
577	# suppressions: SOURCE_TOOLS/arb.leaksan.supp
578	LSAN_OPTIONS:=max_leaks=3:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp
579
580	UBSAN_OPTIONS:=print_stacktrace=1
581
582	SANITIZE_ADDRESS:=0
583	SANITIZE_UNDEFINED:=0
584
585	ifneq ($(SANITIZE),0)
586	ifeq ($(SANITIZE),all)
587	SANITIZE:=3
588	endif
589
590	ifeq ($(SANITIZE),1)
591	SANITIZE_ADDRESS:=1
592	else
593	ifeq ($(SANITIZE),2)
594	SANITIZE_UNDEFINED:=1
595	else
596	ifeq ($(SANITIZE),3)
597	SANITIZE_ADDRESS:=1
598	SANITIZE_UNDEFINED:=1
599	else
600	$(error Unknown value '$(SANITIZE)' specified for SANITIZE in config.makefile)
601	endif
602	endif
603	endif
604	endif
605
606	ifeq ($(SANITIZE_ADDRESS),1)
607	ifneq ('$(USE_GCC_48_OR_HIGHER)','yes')
608	$(info AddressSanitizer not usable with gcc $(COMPILER_VERSION) - disabled)
609	SANITIZE_ADDRESS:=0
610	else
611	ifneq ('$(USE_GCC_49_OR_HIGHER)','yes')
612	$(info LeakSanitizer does not work with gcc $(COMPILER_VERSION) - disabled)
613	# need to disable AddressSanitizer (otherwise build fails; only affects gcc 4.8.x series)
614	SANITIZE_ADDRESS:=0
615	endif
616	endif
617	endif
618
619	ifeq ($(SANITIZE_UNDEFINED),1)
620	ifneq ('$(USE_GCC_49_OR_HIGHER)','yes')
621	$(info UndefinedBehaviorSanitizer not usable with gcc $(COMPILER_VERSION) - disabled)
622	SANITIZE_UNDEFINED:=0
623	endif
624	endif
625
626	SANITIZE_ANY:=0
627	ifeq ($(SANITIZE_ADDRESS),1)
628	SANITIZE_ANY:=1
629	endif
630	ifeq ($(SANITIZE_UNDEFINED),1)
631	SANITIZE_ANY:=1
632	endif
633
634	# vectorization fails if sanitizer active where it normally succeeds -> disable check
635	ifeq ($(SANITIZE_ANY),1)
636	$(info disabling vectorize checks. would fail with sanitized code)
637	DISABLE_VECTORIZE_CHECK:=1
638	else
639	$(info no sanitizer enabled. reset: SANITIZE=0)
640	SANITIZE:=0
641	endif
642
643	# deactivate some bogus warnings occurring when sanitizing NDEBUG version
644	# (do not disable for future gcc-version >= 8.x -> test again when available)
645	ifeq ($(SANITIZE_ANY),1)
646	ifeq ($(DEBUG),0)
647	ifneq ('$(USE_GCC_80_OR_HIGHER)','yes')
648	extended_cpp_warnings += -Wno-format-overflow
649	extended_cpp_warnings += -Wno-maybe-uninitialized
650	endif
651	endif
652	endif
653
654	#---------------------- 32 or 64 bit
655
656	cross_cflags:=
657	cross_lflags:=
658	cross_clflags:=
659
660	ifeq ($(ARB_64),1)
661	dflags += -DARB_64
662	shared_cflags += -fPIC
663	CROSS_LIB:=# empty => autodetect below
664	ifeq ($(DARWIN),1)
665	cross_cflags += -arch x86_64
666	cross_lflags += -arch x86_64
667	cross_clflags += -arch x86_64
668	endif
669	else
670	CROSS_LIB:=/lib
671	endif
672
673	cflags += $(cross_cflags)
674	clflags += $(cross_clflags)
675
676	ifeq ('$(CROSS_LIB)','')
677	# autodetect libdir
678	ifeq ($(ARB_64),1)
679	CROSS_LIB:=$(shell (test -d /lib64 && echo lib64) \|\| echo lib)
680	else
681	CROSS_LIB:=$(shell (test -d /lib32 && echo lib32) \|\| echo lib)
682	endif
683	endif
684
685	#---------------------- unit tests
686
687	ifndef UNIT_TESTS
688	UNIT_TESTS=0#default is "no tests"
689	endif
690	ifeq ($(UNIT_TESTS),1)
691	dflags += -DUNIT_TESTS
692	UNIT_TESTER_LIB=UNIT_TESTER/UNIT_TESTER.a
693	else
694	UNIT_TESTER_LIB=
695	endif
696
697	#---------------------- use gcov
698
699	ifndef COVERAGE
700	COVERAGE=0#default is "no"
701	endif
702	ifneq ($(COVERAGE),0)
703	GCOV_FLAGS=--coverage
704	$(info disabling vectorize checks. would fail with COVERAGE on)
705	DISABLE_VECTORIZE_CHECK:=1
706	else
707	GCOV_FLAGS=
708	endif
709
710	cflags += $(GCOV_FLAGS)
711	clflags += $(GCOV_FLAGS)
712	cross_lflags += $(GCOV_FLAGS)
713
714	#---------------------- other flags
715
716	dflags += -D$(MACH) # define machine
717
718	ifeq ($(DARWIN),1)
719	shared_cflags += -fno-common
720	else
721	dflags += $(shell getconf LFS_CFLAGS)
722	endif
723
724	cflags += -pipe
725	cflags += -fmessage-length=0# dont wrap compiler output
726	cflags += -fshow-column# show columns
727	cflags += -funit-at-a-time
728	cflags += -fPIC
729	cflags += -fno-common# link all global data into one namespace
730	cflags += -fstrict-aliasing# gcc 3.4
731
732	onlyC_flags += -Werror-implicit-function-declaration
733
734	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
735	cflags += -fno-diagnostics-show-caret#gcc 4.8 (4.7.?)
736	endif
737	#cflags += -save-temps# uncomment to see preprocessor output
738
739	#---------------------- various sanitizers
740	# There are some disabled tests in CORE/arb_misc.cxx@sanitizers
741	# which trigger sanitizer reports.
742
743	ifeq ($(SANITIZE_ANY),1)
744	cflags += -ggdb3 -fno-omit-frame-pointer
745	endif
746
747	SANI_CFLAGS:=
748	SANI_CLFLAGS:=
749
750	# activate AddressSanitizer+LeakSanitizer?
751	ifeq ($(SANITIZE_ADDRESS),1)
752	SANI_CFLAGS += -fsanitize=address
753	SANI_CLFLAGS += -fsanitize=address
754	dflags += -DLEAKS_SANITIZED
755	endif
756
757	# activate UndefinedBehaviorSanitizer?
758	ifeq ($(SANITIZE_UNDEFINED),1)
759	SANI_CFLAGS += -fsanitize=undefined
760	SANI_CLFLAGS += -fsanitize=undefined
761	dflags += -DUNDEF_SANITIZED
762	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
763	# abort on runtime errors
764	SANI_CFLAGS += -fno-sanitize-recover=all
765	endif
766
767	cflags += $(SANI_CFLAGS)
768	clflags += $(SANI_CLFLAGS)
769
770	#
771	# Note: alignment-sanitizer is deactivated for ARBDB and PROBE!
772	ifeq ('$(DEBUG)','1')
773	ifeq ($(USE_GCC_MAJOR),4)
774	ifeq ($(USE_GCC_MINOR),9)
775	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),01)','')
776	# workaround https://gcc.gnu.org/bugzilla/show_bug.cgi?id=63531 for 4.9.0 + 4.9.1
777	# (problem is fixed in 4.9.2 release)
778	extended_cpp_warnings:=$(subst -Weffc++,,$(extended_cpp_warnings))
779	endif
780	endif
781	endif
782	endif
783	endif
784
785	#---------------------- X11 location
786
787	ifeq ($(DARWIN),1)
788	XHOME:=$(PREFIX)
789	else
790	ifeq ($(DEBIAN),1)
791	XHOME:=$(PREFIX)
792	else
793	XHOME:=/usr/X11R6
794	endif
795	endif
796
797	XINCLUDES ?= -I$(XHOME)/include
798	XLIBS ?= -L$(XHOME)/$(CROSS_LIB)
799	ifeq ($(DARWIN),1)
800	XINCLUDES += -I$(OSX_FW)/GLUT.framework/Headers -I$(OSX_FW)/OpenGL.framework/Headers -I$(OSX_SDK)/usr/include/krb5
801
802	XLIBS += -lXm -lpng -lz -lXt -lX11 -lXext -lXp -lXmu -lXi
803	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGL.dylib:$(OSX_FW_OPENGL)/libGL.dylib
804	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGLU.dylib:$(OSX_FW_OPENGL)/libGLU.dylib
805	else
806	XLIBS += -lXm -lXpm -lXt -lXext -lX11
807	endif
808
809	#---------------------- open GL
810
811	ifeq ($(OPENGL),1)
812	cflags += -DARB_OPENGL # activate OPENGL code
813	GL := gl # this is the name of the OPENGL base target
814	GL_LIB_SYS := -lGL -lGLU
815	GL_LIB_ARB := -L$(ARBHOME)/GL/glAW -lglAW
816
817	ifeq ($(DARWIN),1)
818	GL_LIB_SYS += -lpthread
819	endif
820
821	GL_PNGLIBS_ARB := -L$(ARBHOME)/GL/glpng -lglpng_arb
822	GL_PNGLIBS_SYS := -lpng
823
824	GLEWLIB := -lGLEW -lGLw
825	GLUTLIB := -lglut
826
827	GL_LIBS_SYS := $(GL_LIB_SYS) $(GL_PNGLIBS_SYS) $(GLEWLIB) $(GLUTLIB)
828	GL_LIBS_ARB := $(GL_LIB_ARB) $(GL_PNGLIBS_ARB)
829
830	RNA3D_LIB := RNA3D/RNA3D.a
831	else
832	GL_LIBS_SYS:=# no opengl -> no libs
833	GL_LIBS_ARB:=# no opengl -> no libs
834	GL:=# dont build ARB openGL libs
835
836	RNA3D_LIB :=
837	endif
838
839	RNA3D_LIB_4_DEPENDS := RNA3D/RNA3D.a
840
841	GL_LIBS:=$(GL_LIBS_ARB) $(GL_LIBS_SYS)
842
843	#---------------------- sina:
844
845	ifndef ISINA
846	# build sina delivered with arb?
847	ifeq ($(LINUX),1)
848	ifeq ('$(USE_GCC_70_OR_HIGHER)','yes')
849	ISINA := 1# default to 'yes' for linux with gcc>=7
850	endif
851	endif
852	ifndef ISINA
853	ISINA := 0# 'no' otherwise
854	endif
855	endif
856
857	#---------------------- tiff lib:
858
859	TIFFLIBS := -ltiff
860
861	#---------------------- XML lib:
862
863	XMLLIBS := -lxerces-c
864
865	#---------------------- glib:
866
867	ARB_NEEDED_GLIB=glib-2.0
868
869	ARB_GLIB_INCLUDE:=$(strip $(shell pkg-config --cflags $(ARB_NEEDED_GLIB)))
870	ARB_GLIB_LIBS:=$(strip $(shell pkg-config --libs $(ARB_NEEDED_GLIB)))
871
872	#---------------------- sunrpc lib:
873	# Note: sunrpc has been removed from glibc
874	# (e.g. in SuSE Leap 15.3 and Fedora 28)
875	# see https://fedoraproject.org/wiki/Changes/SunRPCRemoval
876	#
877	HAVE_LIBTIRPC=$(strip $(shell pkg-config --exists libtirpc && echo libtirpc))
878	ifeq ($(HAVE_LIBTIRPC),)
879	ARB_RPC_INCLUDE:=
880	ARB_RPC_LIBS:=
881	else
882	ARB_RPC_INCLUDE:=$(strip $(shell pkg-config --cflags $(HAVE_LIBTIRPC)))
883	ARB_RPC_LIBS:=$(strip $(shell pkg-config --libs $(HAVE_LIBTIRPC)))
884	endif
885
886	#---------------------- basic libs:
887
888	ARB_CORE_LIBS:=$(ARB_GLIB_LIBS) $(ARB_RPC_LIBS)
889
890	SYSLIBS:=
891	ifeq ($(DARWIN),1)
892	SYSLIBS += -lstdc++
893	else
894	SYSLIBS += -lm $(ARB_CORE_LIBS)
895	endif
896
897	#---------------------- system dependent commands
898
899	ifeq ($(DARWIN),1)
900	TIME:=gtime
901	else
902	TIME:=/usr/bin/time
903	endif
904
905	#---------------------- SSE vectorizer
906	# for details see SOURCE_TOOLS/vectorize.README
907
908	ifeq ($(DEBUG),0)
909	ifeq ($(USE_GCC_49_OR_HIGHER),yes)
910	ifeq ($(DISABLE_VECTORIZE_CHECK),0)
911	cflags += -fopt-info-vec
912	cflags += -fopt-info-vec-missed
913	ifeq ($(TRACE_MISSED_VECTORIZATIONS),1)
914	# Shows reasons for unsuccessful vectorization:
915	cflags += -ftree-vectorizer-verbose=10
916	POST_COMPILE += --dump-loop-optimization
917	ifeq ($(VECTORIZATION_CHECK_CANDIDATES),1)
918	$(error TRACE_MISSED_VECTORIZATIONS and VECTORIZATION_CHECK_CANDIDATES may not be used together!)
919	endif
920	endif
921	ifeq ($(VECTORIZATION_CHECK_CANDIDATES),1)
922	POST_COMPILE += --loop-optimization-candi
923	endif
924	POST_COMPILE += --check-loop-optimization
925	endif
926	else
927	ifeq ($(USE_GCC_48_OR_HIGHER),yes)
928	# no automatic vectorization-check for gcc<4.9.0
929	# -> uncomment the next 2 lines and grep the spam it will produce for 'vectorized.*loops'
930	# cflags += -fopt-info -fopt-info-vec-missed
931	# POST_COMPILE += --original
932	endif
933	endif
934	endif
935
936	#---------------------- stop early on broken flags/compiler combination
937
938	ifeq ($(DEBUG),0)
939	ifeq ($(SANITIZE_ANY),1)
940	ifeq ('$(COMPILER_VERSION)','4.9.1')
941	$(error compiling DEBUG=0 + SANITIZE!=0 crashes with gcc $(COMPILER_VERSION) (gcc 4.9.2 works))
942	endif
943	endif
944	endif
945
946	#---------------------- include symbols?
947
948	ifeq ($(TRACESYM),1)
949	ifeq ($(USE_CLANG),0)
950	cflags += -rdynamic
951	clflags += -rdynamic -Wl,--export-dynamic
952	endif
953	endif
954
955	#---------------------- warn about duplicate variable definitions
956
957	ifeq ($(DARWIN),1)
958	clflags += -Wl,-warn_commons
959	else
960	clflags += -Wl,--warn-common
961	endif
962
963	#---------------------- differences between linking executables and shared libs:
964
965	# executables:
966	ifeq ($(DARWIN),1)
967	blflags:=$(clflags)
968	else
969	blflags:=$(clflags) -Wl,--no-undefined
970	endif
971
972	# shared libraries
973	llflags:=$(clflags)
974
975	# dont use clflags below
976	clflags:=
977
978	# -------------------------------------------------------------------------
979	# Don't put any machine/version/etc conditionals below!
980	# (instead define variables above)
981	# -------------------------------------------------------------------------
982
983	cflags += -W -Wall $(dflags) $(extended_warnings)
984	cxxflags := $(extended_cpp_warnings)# flags only suitable for C++ (not C; see onlyC_flags).
985
986	# add CFLAGS + CPPFLAGS from environment for DEBIAN build
987	ifeq ($(DEBIAN),1)
988	cflags := $(CFLAGS) $(cflags)
989	cxxflags += $(CPPFLAGS)
990	endif
991
992	ifeq ('$(USE_CLANG)','1')
993	# the following standards also work with clang 6.0.0 (under linux):
994	# -std=gnu++17 -std=gnu++14 -std=gnu++11 -std=gnu++0x
995	cxxflags += -std=gnu++17
996	else
997	# standard mostly supported by gcc version (according to https://gcc.gnu.org/projects/cxx-status.html)
998	# C++20 with gcc>=12
999	# C++23 with gcc>=15 (or 16 for reflection)
1000
1001	ifeq ('$(USE_GCC_80_OR_HIGHER)','yes')
1002	# C++17 mostly supported by gcc>=8
1003	cxxflags += -std=gnu++17 # see also TEMPLATES/cxxforward.h@USE_Cxx17
1004	else
1005	ifeq ('$(USE_GCC_60_OR_HIGHER)','yes')
1006	cxxflags += -std=gnu++14 # see also TEMPLATES/cxxforward.h@USE_Cxx14
1007	else
1008	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
1009	cxxflags += -std=gnu++11 # see also TEMPLATES/cxxforward.h@USE_Cxx11
1010	else
1011	# gcc versions between 4.3 (lowest supported) and <4.7
1012	cxxflags += -std=gnu++0x
1013	endif # 47
1014	endif # 60
1015	endif # 80
1016	endif # USE_CLANG
1017
1018	LINK_STATIC_LIB := $(AR) -csq# link static lib
1019	LINK_EXECUTABLE := $(A_CXX) $(blflags) -o# link executable (c++)
1020
1021	ifeq ($(LINK_STATIC),1)
1022	SHARED_LIB_SUFFIX = a# static lib suffix
1023	LINK_SHARED_LIB := $(LINK_STATIC_LIB)
1024	else
1025	SHARED_LIB_SUFFIX = so# shared lib suffix
1026	LINK_SHARED_LIB := $(A_CXX) $(llflags) -shared -o# link shared lib
1027	endif
1028
1029	ifeq ($(DARWIN),1)
1030	lflags4perl:=
1031	else
1032	lflags4perl:=$(cross_lflags) -shared
1033	endif
1034
1035	# delete variables unused below
1036	blflags:=
1037	llflags:=
1038
1039	# other used tools
1040	MAKEDEPEND_PLAIN = makedepend
1041	MAKEDEPEND = $(FORCEMASK);$(MAKEDEPEND_PLAIN)
1042
1043	SEPNODATE:=--------------------------------------------------------------------------------
1044	SEP=[`date +%M:%S.%N`] ------------------------------------------------
1045	# to analyse timings run
1046	# make -j9 clean; make -j9 all \| grep '^\[' \| sort
1047	# make -j9 "TIMED_TARGET=perl" clean_timed_target \| grep '^\[' \| sort
1048
1049	# ------------------------------------------------------------ DYNLIBDEFS
1050	# various dynamic library definitions for linking executables:
1051	#
1052	# SYSLIBS: system libraries needed by database lib
1053	# ARBDB_LIB: database lib
1054	# DBSYS_LIBS: executable using database (but no GUI)
1055	# GUI_LIBS: executable using database and GUI (arb gui uses database)
1056	#
1057	# Note: definitions exported to sub-makefiles are described in SOURCE_TOOLS/parent_make.txt
1058
1059	CORE_LIB=-lCORE
1060	ARBDB_LIB=-lARBDB $(CORE_LIB)
1061	DBSYS_LIBS = $(ARBDB_LIB) $(SYSLIBS)
1062
1063	GUI_LIBS_PREFIX:=
1064	ifeq ($(DARWIN),1)
1065	# this seem to be added at wrong place, since opengl is only needed to link EDIT4
1066	GUI_LIBS_PREFIX:=-framework GLUT -framework OpenGL
1067	endif
1068
1069	GUI_LIBS=$(GUI_LIBS_PREFIX) $(DBSYS_LIBS) -lWINDOW $(XLIBS)
1070
1071	LIBPATH = -L$(ARBHOME)/lib
1072
1073	DEST_LIB = lib
1074	DEST_BIN = bin
1075
1076	CC_INCLUDES := -I. -I$(ARBHOME)/INCLUDE $(XINCLUDES) $(ARB_GLIB_INCLUDE) $(ARB_RPC_INCLUDE)
1077	CXX_INCLUDES := $(CC_INCLUDES)
1078	MAKEDEPENDFLAGS := -- -DARB_OPENGL -DUNIT_TESTS -D__cplusplus -I. -Y$(ARBHOME)/INCLUDE
1079
1080	# ---------------------------------------
1081	# wrap main()
1082
1083	use_ARB_main=$(ARBHOME)/SOURCE_TOOLS/arb_main_cpp.o
1084	use_ARB_main_C=$(ARBHOME)/SOURCE_TOOLS/arb_main_c.o
1085
1086	# -----------------------------------------
1087	# unique build-id
1088	# - different for different calls of make
1089	# - constant in recursive calls
1090
1091	ifndef ARBBID
1092	ARBBID:=$(shell SOURCE_TOOLS/uniqueID.sh)
1093	endif
1094
1095	# -----------------------------------------
1096	# export variables to submakefiles
1097
1098	include SOURCE_TOOLS/export2sub
1099
1100	# do not define (exported) variables below this point
1101
1102	# -------------------------
1103	# Main arb targets:
1104	# -------------------------
1105
1106	first_target:
1107	$(MAKE) checks
1108	@echo $(SEPNODATE)
1109	@echo 'Main targets:'
1110	@echo ''
1111	@echo ' all - Compile ARB + TOOLs + and copy shared libs + link foreign software'
1112	@echo ' (That is most likely the target you want)'
1113	@echo ''
1114	@echo ' clean - remove generated files ("SUBDIR/SUBDIR.clean" to clean only SUBDIR)'
1115	@echo ' rebuild - clean + all'
1116	@echo ' cleanlinked - remove all binaries'
1117	@echo ' relink - cleanlinked + all (=relink all from objects)'
1118	@echo ''
1119	@echo 'Targets for automated builds:'
1120	@echo ''
1121	@echo ' ALL, REBUILD, TARFILE + TARFILE_QUICK '
1122	@echo ' - same as all, rebuild, tarfile + tarfile_quick'
1123	@echo ' - if errors occur, they are extracted and listed at tail of output'
1124	@echo ''
1125	@echo $(SEPNODATE)
1126	@echo ''
1127	@echo 'Development targets:'
1128	@echo ''
1129	@echo ' depends - create or update dependencies ("SUBDIR/SUBDIR.depends" to update only SUBDIR)'
1130	@echo ' proto - create or update prototypes ("SUBDIR/SUBDIR.proto" to update only SUBDIR)'
1131	@echo ' tags - create tags for xemacs'
1132	@echo ' show - show available shortcuts (AKA subtargets)'
1133	@echo ' up - shortcut for depends+proto+tags'
1134	ifeq ($(UNIT_TESTS),1)
1135	@echo ' ut - only run tests'
1136	@echo ' "UNIT=..." oneunit - build one unit and run tests (see also UNIT_TESTER/Makefile.setup.local)'
1137	endif
1138	ifneq ($(SANITIZE),0)
1139	@echo ' sanitize - all + run arb_ntree with sanitizer (test.arb + execute _logged)'
1140	endif
1141	@echo ' modified - rebuild files modified in svn checkout (does touch)'
1142	@echo ' touch - touch files modified in svn checkout'
1143	@echo ''
1144	@echo 'Some often used sub targets:'
1145	@echo ''
1146	@echo ' arb - Just compile ARB (but none of the integrated tools)'
1147	@echo ' menus - create lib/gde/arb.menu from GDEHELP/ARB_GDEmenus.source'
1148	@echo ' perl - Compile the PERL XSUBS into lib/ARB.so and create links in lib to perl'
1149	@echo ' binlink - Create all links in the bin directory'
1150	@echo ''
1151	@echo 'Internal maintenance:'
1152	@echo ''
1153	@echo ' relinfo - show help on release targets'
1154	@echo ' tarfile - make rebuild and create arb version tarfile ("tarfile_quick" to skip rebuild)'
1155	@echo ' save - save all basic ARB sources into arbsrc_DATE ("savetest" to check filelist)'
1156	@echo ' patch - save svn diff to patchfile'
1157	@echo ' source_doc - create doxygen documentation'
1158	@echo ' relocated - rebuild partly (use when you have relocated ARBHOME)'
1159	@echo ' check_res - check resource usage'
1160	@echo ' dep_graph - Build dependency graphs'
1161	@echo ' clean_cov - Clean coverage results'
1162	@echo ''
1163	@echo ' clean_opengl_changed - clean after changing OPENGL setting in config.Makefile'
1164	@echo ' clean_checked_vect - clean units containing vectorization checks'
1165	@echo ' cleanRelinkable - similar to cleanlinked (but skips raxml8 to avoid rebuild)'
1166	@echo ''
1167	@echo ' post_commit_check - Checks whether'
1168	@echo ' * main make targets work,'
1169	@echo ' * dependencies and prototypes are up to date,'
1170	@echo ' * SVN-controlled files remain unaffected by called targets and'
1171	@echo ' * all generated files are ignored.'
1172	@echo ' (has to be called in a clean SVN checkout)'
1173	@echo $(SEPNODATE)
1174	@echo ''
1175
1176	relinfo:
1177	@echo ''
1178	@echo $(SEPNODATE)
1179	@echo 'Release targets:'
1180	@echo ''
1181	@echo ' inc_candi - increase RC candidate-number (only possible in "rc" branch, not needed for RC1)'
1182	@echo ' inc_patch - increase release patchlevel (only possible in "stable" branch)'
1183	@echo ' inc_minor - increase minor version number (only possible in "trunk")'
1184	@echo ' inc_major - increase MAJOR version number (only possible in "trunk")'
1185	@echo ''
1186	@echo ' show_version - show version tag'
1187	@echo ''
1188	@echo $(SEPNODATE)
1189	@echo ''
1190
1191	# auto-generate config.makefile:
1192
1193	config.makefile : config.makefile.template
1194	@echo --------------------------------------------------------------------------------
1195	ifeq ($(CONFIG_MAKEFILE_FOUND),)
1196	@cp $< $@
1197	@echo '$(ARBHOME)/$@:1: has been generated.'
1198	@echo 'Please edit $@ to configure your system!'
1199	@echo --------------------------------------------------------------------------------
1200	@false
1201	else
1202	@echo '$(ARBHOME)/$<:1: is more recent than'
1203	@echo '$(ARBHOME)/$@:1:'
1204	@ls -al config.makefile*
1205	@echo --------------------------------------------------------------------------------
1206	@echo "Updating $@ (if this fails, check manually)"
1207	SOURCE_TOOLS/update_config_makefile.pl
1208	@echo "Sucessfully updated $@"
1209	@echo --------------------------------------------------------------------------------
1210	@ls -al config.makefile*
1211	@echo --------------------------------------------------------------------------------
1212	@echo "Diff to your old config.makefile:"
1213	@echo --------------------------------------------------------------------------------
1214	-diff $@.bak $@
1215	@echo --------------------------------------------------------------------------------
1216	endif
1217
1218	# check if everything is configured correctly
1219
1220	check_DEVELOPER:
1221	ifndef DEVELOPER
1222	@echo 'config.makefile:1: DEVELOPER not defined'
1223	@false
1224	endif
1225
1226	check_DEBUG:
1227	ifndef dflags
1228	@echo 'config.makefile:1: DEBUG has to be defined. Valid values are 0 and 1'
1229	@false
1230	endif
1231
1232	check_ARB_64:
1233	ifndef ARB_64
1234	@echo 'config.makefile:1: ARB_64 has to be defined. Valid values are 0 and 1'
1235	@false
1236	endif
1237
1238	# ---------------------------------------- check gcc version
1239
1240	COMPILER_BROKEN:=0
1241
1242	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.6.4')
1243	COMPILER_BROKEN:=1
1244	endif
1245	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.8.0')
1246	COMPILER_BROKEN:=1
1247	endif
1248
1249	check_same_GCC_VERSION:
1250	$(ARBHOME)/SOURCE_TOOLS/check_same_compiler_version.pl $(COMPILER_NAME) $(COMPILER_VERSION_ALLOWED)
1251
1252	check_GCC_VERSION:
1253	@echo 'Compiler version check:'
1254	# see .@ALLOWED_gcc_VERSIONS
1255	ifeq ('$(COMPILER_VERSION_ALLOWED)', '')
1256	@echo " - Your compiler is '$(COMPILER_NAME)' version '$(COMPILER_VERSION)'"
1257	@echo ' This version is not in the list of supported $(COMPILER_NAME)-versions:'
1258	@$(foreach version,$(ALLOWED_COMPILER_VERSIONS),echo ' * $(version)';)
1259	@echo ' - You may either ..'
1260	@echo ' - add your version to ALLOWED_$(COMPILER_NAME)_VERSIONS in the Makefile and try it out or'
1261	@echo ' - switch to one of the allowed versions (see arb_README_gcc.txt for installing'
1262	@echo ' a different version of gcc)'
1263	$(error Unsupported compiler '$(COMPILER_NAME)' version '$(COMPILER_VERSION)')
1264	else
1265	ifeq ($(COMPILER_BROKEN),1)
1266	$(error compilation refused for $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)'. Refer to http://bugs.arb-home.de/wiki/GccVersionInfo for details.)
1267	else
1268	@echo " - Supported $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)' detected - fine!"
1269	@echo ''
1270	$(MAKE) check_same_GCC_VERSION
1271	endif
1272	endif
1273
1274	#---------------------- check ARBHOME
1275
1276	# use arb_INSTALL.txt to determine whether ARBHOME points to correct directory
1277	ARB_INSTALL_FOUND=$(wildcard $(ARBHOME)/arb_INSTALL.txt)
1278
1279	check_ARBHOME:
1280	ifeq ($(strip $(ARB_INSTALL_FOUND)),)
1281	@echo ------------------------------------------------------------
1282	@echo "ARBHOME is set to '$(ARBHOME)'"
1283	@echo "The environment variable ARBHOME has to point to the top arb source directory."
1284	@echo "If you use bash enter:"
1285	@echo " export ARBHOME='`pwd`'"
1286	@echo ------------------------------------------------------------
1287	@false
1288	endif
1289
1290	ARB_PATH_SET=$(findstring $(ARBHOME)/bin,$(PATH))
1291
1292	check_PATH: check_ARBHOME
1293	ifeq ($(strip $(ARB_PATH_SET)),)
1294	@echo ------------------------------------------------------------
1295	@echo "The environment variable PATH has to contain $(ARBHOME)/bin"
1296	@echo "If you use bash enter:"
1297	@echo ' export PATH=$$ARBHOME/bin:$$PATH'
1298	@echo ------------------------------------------------------------
1299	@false
1300	endif
1301
1302	check_TOOLS:
1303	@util/arb_check_build_env.pl \
1304	"$(A_CC)" \
1305	"$(A_CXX)" \
1306	"$(LINK_SHARED_LIB)" \
1307
1308	have_makedepend:
1309	@util/arb_check_build_env.pl --check-only "$(MAKEDEPEND_PLAIN)"
1310
1311	check_ENVIRONMENT : check_PATH check_TOOLS
1312	@echo "-------------------- Environment [start]"
1313	@echo "ARBHOME='$(ARBHOME)'"
1314	@echo "PATH='$(PATH)'"
1315	@echo "LD_LIBRARY_PATH='$(LD_LIBRARY_PATH)'"
1316	@echo "-------------------- Environment [end]"
1317
1318	check_tabs: check_setup
1319	ifeq ($(DEBUG),1)
1320	@SOURCE_TOOLS/tabBrake.pl
1321	endif
1322
1323	force_tab_check:
1324	@touch -t 198001010000 SOURCE_TOOLS/stamp.tabBrake
1325	@$(MAKE) check_tabs
1326
1327
1328	# ---------------------
1329
1330	check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION
1331	@echo Your setup seems to be ok.
1332
1333	checks: check_setup check_tabs
1334	@rm -f SOURCE_TOOLS/postcompile.sav
1335
1336
1337	# end test section ------------------------------
1338
1339	# ---------------------------------------
1340	# List of standard top level directories
1341	#
1342	# sub-makefiles have to define the targets
1343	# - 'depends' and
1344	# - 'clean'
1345	#
1346	# when adding new libraries/subdirs here, also add a dependency vs 'links' or 'links_non_perl' in .@DD_links_non_perl
1347
1348	TL_ARCHIVES = \
1349	AISC/AISC.a \
1350	ARB_GDE/ARB_GDE.a \
1351	AWTC/AWTC.a \
1352	AWTI/AWTI.a \
1353	CONSENSUS_TREE/CONSENSUS_TREE.a \
1354	CONVERTALN/CONVERTALN.a \
1355	DBSERVER/DBSERVER.a \
1356	DIST/DIST.a \
1357	EDIT4/EDIT4.a \
1358	EISPACK/EISPACK.a \
1359	GENOM/GENOM.a \
1360	GENOM_IMPORT/GENOM_IMPORT.a \
1361	ISLAND_HOPPING/ISLAND_HOPPING.a \
1362	MERGE/MERGE.a \
1363	MULTI_PROBE/MULTI_PROBE.a \
1364	NALIGNER/NALIGNER.a \
1365	NAMES/NAMES.a \
1366	NAMES_COM/server.a \
1367	NTREE/NTREE.a \
1368	PARSIMONY/PARSIMONY.a \
1369	PHYLO/PHYLO.a \
1370	PRIMER_DESIGN/PRIMER_DESIGN.a \
1371	PROBE/PROBE.a \
1372	PROBE_COM/server.a \
1373	PROBE_DESIGN/PROBE_DESIGN.a \
1374	$(RNA3D_LIB) \
1375	RNACMA/RNACMA.a \
1376	SECEDIT/SECEDIT.a \
1377	SEQ_QUALITY/SEQ_QUALITY.a \
1378	SERVERCNTRL/SERVERCNTRL.a \
1379	STAT/STAT.a \
1380	TREEGEN/TREEGEN.a \
1381	WETC/WETC.a \
1382	XML/XML.a \
1383
1384	TL_SHARED_ARCHIVES = \
1385	ARBDB/libARBDB.so \
1386	CORE/libCORE.so \
1387	WINDOW/libWINDOW.so \
1388
1389	TL_ARCHIV_COLLECTIONS = \
1390	SL/SL.archColl \
1391
1392	TL_TOOLS_COLLECTIONS = \
1393	AISC_MKPTPS/AISC_MKPTPS.toolColl \
1394	TOOLS/TOOLS.toolColl \
1395	PERLTOOLS/PERLTOOLS.toolColl \
1396	PROBE_SET/PROBE_SET.toolColl \
1397	READSEQ/READSEQ.toolColl \
1398
1399	RECURSIVE_SUBS = \
1400	GDE/GDE.sub \
1401	UNIT_TESTER/UNIT_TESTER.sub \
1402
1403	SUBDIRS = \
1404	$(RECURSIVE_SUBS) \
1405	$(TL_ARCHIVES:.a=.sub) \
1406	$(TL_SHARED_ARCHIVES:.so=.sub) \
1407	$(TL_ARCHIV_COLLECTIONS:.archColl=.sub) \
1408	$(TL_TOOLS_COLLECTIONS:.toolColl=.sub) \
1409
1410	# sub directories inside TL_ARCHIV_COLLECTIONS
1411	CL_ARCH_DIRS = $(foreach coll,$(TL_ARCHIV_COLLECTIONS),$(shell find $(dir $(coll)) -maxdepth 1 -mindepth 1 -type d))
1412
1413	# archives inside CL_ARCH_DIRS:
1414	CL_ARCHIVES = $(foreach adir,$(CL_ARCH_DIRS),$(dir $(adir))$(notdir $(adir))/$(notdir $(adir)).a)
1415
1416	# -----------------------
1417	# library packets
1418
1419	ARCHS_CLIENT_PROBE = PROBE_COM/client.a
1420	ARCHS_CLIENT_NAMES = NAMES_COM/client.a
1421
1422	ARCHS_MAKEBIN = AISC_MKPTPS/AISC_MKPTPS.a AISC/AISC.a
1423
1424	# communication libs need aisc and aisc_mkpts:
1425
1426	AISC/AISC.dummy: proto_tools
1427
1428	comtools: AISC/AISC.dummy
1429
1430	ARCHS_SEQUENCE = \
1431	SL/SEQUENCE/SEQUENCE.a \
1432	SL/ALIVIEW/ALIVIEW.a \
1433	SL/PRONUC/PRONUC.a \
1434
1435	ARCHS_TREE = \
1436	SL/ARB_TREE/ARB_TREE.a \
1437	SL/FILTER/FILTER.a \
1438	$(ARCHS_SEQUENCE) \
1439
1440	# parsimony tree (used by NTREE, PARSIMONY, STAT(->EDIT4), DIST(obsolete!))
1441	ARCHS_AP_TREE = \
1442	SL/AP_TREE/AP_TREE.a \
1443	$(ARCHS_TREE) \
1444
1445	# --------------------------------------------------------------------------------
1446	# dependencies for linking shared libs
1447
1448	link_core: core
1449	link_db: db link_core
1450	link_aw: aw link_db
1451
1452	#***************************************************************************************
1453	# Individual_Programs_Section
1454	#***************************************************************************************
1455
1456	arbmainwrapper:
1457	$(MAKE) -C SOURCE_TOOLS -r mainwrapper
1458
1459
1460	#********************************* arb_ntree ************************************
1461	NTREE = bin/arb_ntree
1462	ARCHS_NTREE = \
1463	NTREE/NTREE.a \
1464	ARB_GDE/ARB_GDE.a \
1465	SL/SPECSEL/SPECSEL.a \
1466	SL/GROUP_SEARCH/GROUP_SEARCH.a \
1467	SL/SAICALC/SAICALC.a \
1468	SL/DB_UI/DB_UI.a \
1469	SL/ARB_SPEC/ARB_SPEC.a \
1470	SL/MASKS/MASKS.a \
1471	AWTC/AWTC.a \
1472	AWTI/AWTI.a \
1473	CONSENSUS_TREE/CONSENSUS_TREE.a \
1474	GENOM_IMPORT/GENOM_IMPORT.a \
1475	GENOM/GENOM.a \
1476	MERGE/MERGE.a \
1477	MULTI_PROBE/MULTI_PROBE.a \
1478	PRIMER_DESIGN/PRIMER_DESIGN.a \
1479	PROBE_DESIGN/PROBE_DESIGN.a \
1480	SEQ_QUALITY/SEQ_QUALITY.a \
1481	SERVERCNTRL/SERVERCNTRL.a \
1482	SL/ALILINK/ALILINK.a \
1483	SL/AW_NAME/AW_NAME.a \
1484	SL/APP/APP.a \
1485	SL/CONSENSUS/CONSENSUS.a \
1486	SL/CANVAS/CANVAS.a \
1487	SL/DB_SCANNER/DB_SCANNER.a \
1488	SL/DB_QUERY/DB_QUERY.a \
1489	SL/QUERY/QUERY.a \
1490	SL/SEQIO/SEQIO.a \
1491	STAT/STAT.a \
1492	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1493	SL/GUI_TK/GUI_TK.a \
1494	SL/HELIX/HELIX.a \
1495	SL/REGEXPR/REGEXPR.a \
1496	SL/REFENTRIES/REFENTRIES.a \
1497	SL/NDS/NDS.a \
1498	SL/ITEM_SHADER/ITEM_SHADER.a \
1499	SL/ITEMS/ITEMS.a \
1500	SL/INSDEL/INSDEL.a \
1501	SL/LOCATION/LOCATION.a \
1502	SL/MACROS/MACROS.a \
1503	SL/PVP/PVP.a \
1504	SL/TRANSLATE/TRANSLATE.a \
1505	SL/TREEDISP/TREEDISP.a \
1506	SL/TREE_ADMIN/TREE_ADMIN.a \
1507	SL/TREE_READ/TREE_READ.a \
1508	SL/TREE_WRITE/TREE_WRITE.a \
1509	SL/XFERGUI/XFERGUI.a \
1510	SL/XFERSET/XFERSET.a \
1511	XML/XML.a \
1512	$(ARCHS_AP_TREE) \
1513
1514	ARCHS_NTREE_ALL = $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(XMLLIBS)
1515
1516	$(NTREE): $(ARCHS_NTREE:.a=.dummy) link_aw
1517	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NTREE_ALL) \|\| ( \
1518	echo "$(SEP) Link $@"; \
1519	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE_ALL)" ; \
1520	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE_ALL) && \
1521	echo "$(SEP) Link $@ [done]"; \
1522	)
1523
1524	#********************************* arb_edit4 ************************************
1525	EDIT4 = bin/arb_edit4
1526
1527	ARCHS_EDIT4 := \
1528	EDIT4/EDIT4.a \
1529	ARB_GDE/ARB_GDE.a \
1530	SL/FAST_ALIGNER/FAST_ALIGNER.a \
1531	AWTC/AWTC.a \
1532	ISLAND_HOPPING/ISLAND_HOPPING.a \
1533	SECEDIT/SECEDIT.a \
1534	SERVERCNTRL/SERVERCNTRL.a \
1535	SL/APP/APP.a \
1536	SL/GUI_TK/GUI_TK.a \
1537	SL/ARB_SPEC/ARB_SPEC.a \
1538	SL/AW_HELIX/AW_HELIX.a \
1539	SL/AW_NAME/AW_NAME.a \
1540	SL/CONSENSUS/CONSENSUS.a \
1541	SL/CANVAS/CANVAS.a \
1542	SL/ITEMS/ITEMS.a \
1543	STAT/STAT.a \
1544	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1545	SL/HELIX/HELIX.a \
1546	SL/TRANSLATE/TRANSLATE.a \
1547	SL/MACROS/MACROS.a \
1548	SL/MAPKEY/MAPKEY.a \
1549	SL/NDS/NDS.a \
1550	$(ARCHS_AP_TREE) \
1551	XML/XML.a \
1552
1553	ifeq ($(OPENGL),1)
1554	ARCHS_EDIT4 += RNA3D/RNA3D.a
1555	endif
1556
1557	ARCHS_EDIT4_ALL = $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4)
1558
1559	LIBS_EDIT4 := $(GL_LIBS)
1560
1561	$(EDIT4): $(ARCHS_EDIT4:.a=.dummy) link_aw
1562	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_EDIT4_ALL) \|\| ( \
1563	echo "$(SEP) Link $@"; \
1564	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4_ALL)" ; \
1565	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4_ALL) && \
1566	echo "$(SEP) Link $@ [done]"; \
1567	)
1568
1569	#********************************* arb_rnacma ************************************
1570	RNACMA = bin/arb_rnacma
1571	ARCHS_RNACMA = \
1572	RNACMA/RNACMA.a \
1573
1574	ARCHS_RNACMA_ALL = $(ARCHS_RNACMA) $(DBSYS_LIBS)
1575
1576	$(RNACMA) : $(ARCHS_RNACMA:.a=.dummy) link_db
1577	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_RNACMA_ALL) \|\| ( \
1578	echo "$(SEP) Link $@"; \
1579	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_RNACMA_ALL)"; \
1580	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_RNACMA_ALL) && \
1581	echo "$(SEP) Link $@ [done]"; \
1582	)
1583
1584	#********************************* arb_wetc ************************************
1585	WETC = bin/arb_wetc
1586	ARCHS_WETC = \
1587	WETC/WETC.a \
1588	SL/APP/APP.a \
1589	SL/MACROS/MACROS.a \
1590	SL/GUI_TK/GUI_TK.a \
1591	SL/HELIX/HELIX.a \
1592	SL/FILTER/FILTER.a \
1593	XML/XML.a \
1594
1595	ARCHS_WETC_ALL = $(ARCHS_WETC) $(GUI_LIBS)
1596
1597	$(WETC): $(ARCHS_WETC:.a=.dummy) link_aw
1598	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_WETC_ALL) \|\| ( \
1599	echo "$(SEP) Link $@"; \
1600	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC_ALL)" ; \
1601	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC_ALL) && \
1602	echo "$(SEP) Link $@ [done]"; \
1603	)
1604
1605	#********************************* arb_dist ************************************
1606	DIST = bin/arb_dist
1607	ARCHS_DIST = \
1608	DIST/DIST.a \
1609	CONSENSUS_TREE/CONSENSUS_TREE.a \
1610	EISPACK/EISPACK.a \
1611	SERVERCNTRL/SERVERCNTRL.a \
1612	SL/APP/APP.a \
1613	SL/GUI_TK/GUI_TK.a \
1614	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1615	SL/HELIX/HELIX.a \
1616	SL/MATRIX/MATRIX.a \
1617	SL/MACROS/MACROS.a \
1618	SL/NDS/NDS.a \
1619	SL/ITEMS/ITEMS.a \
1620	SL/ARB_SPEC/ARB_SPEC.a \
1621	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.a \
1622	XML/XML.a \
1623	$(ARCHS_AP_TREE) \
1624
1625	ARCHS_DIST_ALL = $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS)
1626
1627	$(DIST): $(ARCHS_DIST:.a=.dummy) link_aw
1628	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_DIST_ALL) \|\| ( \
1629	echo "$(SEP) Link $@"; \
1630	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST_ALL)" ; \
1631	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST_ALL) && \
1632	echo "$(SEP) Link $@ [done]"; \
1633	)
1634
1635	#********************************* arb_pars ************************************
1636	PARSIMONY = bin/arb_pars
1637	ARCHS_PARSIMONY = \
1638	PARSIMONY/PARSIMONY.a \
1639	SERVERCNTRL/SERVERCNTRL.a \
1640	SL/APP/APP.a \
1641	SL/GUI_TK/GUI_TK.a \
1642	SL/AW_NAME/AW_NAME.a \
1643	SL/CANVAS/CANVAS.a \
1644	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1645	SL/HELIX/HELIX.a \
1646	SL/MACROS/MACROS.a \
1647	SL/NDS/NDS.a \
1648	SL/ITEMS/ITEMS.a \
1649	SL/TRANSLATE/TRANSLATE.a \
1650	SL/TREEDISP/TREEDISP.a \
1651	XML/XML.a \
1652	$(ARCHS_AP_TREE) \
1653
1654	ARCHS_PARSIMONY_ALL = $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS)
1655
1656	$(PARSIMONY): $(ARCHS_PARSIMONY:.a=.dummy) link_aw
1657	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_PARSIMONY_ALL) \|\| ( \
1658	echo "$(SEP) Link $@"; \
1659	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY_ALL)" ; \
1660	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY_ALL) && \
1661	echo "$(SEP) Link $@ [done]"; \
1662	)
1663
1664	#********************************* arb_convert_aln ************************************
1665	CONVERT_ALN = bin/arb_convert_aln
1666	ARCHS_CONVERT_ALN = \
1667	CONVERTALN/CONVERTALN.a \
1668
1669	ARCHS_CONVERT_ALN_ALL = $(ARCHS_CONVERT_ALN) $(DBSYS_LIBS)
1670
1671	$(CONVERT_ALN) : $(ARCHS_CONVERT_ALN:.a=.dummy) link_db
1672	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_CONVERT_ALN_ALL) \|\| ( \
1673	echo "$(SEP) Link $@"; \
1674	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN_ALL)"; \
1675	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN_ALL) && \
1676	echo "$(SEP) Link $@ [done]"; \
1677	)
1678
1679	#********************************* arb_treegen ************************************
1680
1681	TREEGEN = bin/arb_treegen
1682	ARCHS_TREEGEN = \
1683	TREEGEN/TREEGEN.a \
1684
1685	ARCHS_TREEGEN_ALL = $(ARCHS_TREEGEN)
1686
1687	$(TREEGEN) : $(ARCHS_TREEGEN:.a=.dummy)
1688	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main_C) $(ARCHS_TREEGEN_ALL) \|\| ( \
1689	echo "$(SEP) Link $@"; \
1690	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN_ALL)" ; \
1691	$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN_ALL) && \
1692	echo "$(SEP) Link $@ [done]"; \
1693	)
1694
1695	#********************************* arb_naligner ************************************
1696	NALIGNER = bin/arb_naligner
1697	ARCHS_NALIGNER = \
1698	NALIGNER/NALIGNER.a \
1699	SERVERCNTRL/SERVERCNTRL.a \
1700	SL/HELIX/HELIX.a \
1701
1702	ARCHS_NALIGNER_ALL = $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(DBSYS_LIBS)
1703
1704	$(NALIGNER): $(ARCHS_NALIGNER:.a=.dummy) link_db
1705	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NALIGNER_ALL) \|\| ( \
1706	echo "$(SEP) Link $@"; \
1707	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER_ALL)" ; \
1708	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER_ALL) && \
1709	echo "$(SEP) Link $@ [done]"; \
1710	)
1711
1712	#********************************* arb_phylo ************************************
1713	PHYLO = bin/arb_phylo
1714	ARCHS_PHYLO = \
1715	PHYLO/PHYLO.a \
1716	SL/APP/APP.a \
1717	SL/GUI_TK/GUI_TK.a \
1718	SL/HELIX/HELIX.a \
1719	SL/FILTER/FILTER.a \
1720	SL/MACROS/MACROS.a \
1721	XML/XML.a \
1722
1723	ARCHS_PHYLO_ALL = $(ARCHS_PHYLO) $(GUI_LIBS)
1724
1725	$(PHYLO): $(ARCHS_PHYLO:.a=.dummy) link_aw
1726	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_PHYLO_ALL) \|\| ( \
1727	echo "$(SEP) Link $@"; \
1728	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO_ALL)" ; \
1729	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO_ALL) && \
1730	echo "$(SEP) Link $@ [done]"; \
1731	)
1732
1733	#***************************************************************************************
1734	# SERVER SECTION
1735	#***************************************************************************************
1736
1737	#********************************* arb_db_server ************************************
1738	DBSERVER = bin/arb_db_server
1739	ARCHS_DBSERVER = \
1740	DBSERVER/DBSERVER.a \
1741	SERVERCNTRL/SERVERCNTRL.a \
1742
1743	ARCHS_DBSERVER_ALL = $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS)
1744
1745	$(DBSERVER): $(ARCHS_DBSERVER:.a=.dummy) link_db
1746	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_DBSERVER_ALL) \|\| ( \
1747	echo "$(SEP) Link $@"; \
1748	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER_ALL)" ; \
1749	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER_ALL) && \
1750	echo "$(SEP) Link $@ [done]"; \
1751	)
1752
1753	#********************************* arb_pt_server ************************************
1754	PROBE = bin/arb_pt_server
1755
1756	ARCHS_PROBE_DEPEND = \
1757	PROBE/PROBE.a \
1758	SL/PTCLEAN/PTCLEAN.a \
1759	SERVERCNTRL/SERVERCNTRL.a \
1760	SL/HELIX/HELIX.a \
1761
1762	ARCHS_PROBE_ALL = $(ARCHS_PROBE_DEPEND) $(ARCHS_CLIENT_PROBE) $(ARBDB_LIB) $(SYSLIBS)
1763
1764	$(PROBE): $(ARCHS_PROBE_DEPEND:.a=.dummy) link_db
1765	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) config.makefile $(ARCHS_PROBE_ALL) \|\| ( \
1766	echo "$(SEP) Link $@"; \
1767	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_ALL)" ; \
1768	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_ALL) && \
1769	echo "$(SEP) Link $@ [done]"; \
1770	)
1771
1772	#********************************* arb_name_server ************************************
1773	NAMES = bin/arb_name_server
1774	ARCHS_NAMES = \
1775	NAMES/NAMES.a \
1776	SERVERCNTRL/SERVERCNTRL.a \
1777
1778	ARCHS_NAMES_ALL = $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS)
1779
1780	$(NAMES): $(ARCHS_NAMES:.a=.dummy) link_db
1781	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NAMES_ALL) \|\| ( \
1782	echo "$(SEP) Link $@"; \
1783	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES_ALL)" ; \
1784	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES_ALL) && \
1785	echo "$(SEP) Link $@ [done]"; \
1786	)
1787
1788	#********************************* SHARED LIBRARIES SECTION ************************************
1789
1790	prepare_libdir: addlibs
1791
1792	addlibs:
1793	(perl $(ARBHOME)/SOURCE_TOOLS/provide_libs.pl \
1794	"arbhome=$(ARBHOME)" \
1795	"opengl=$(OPENGL)" \
1796	"link_static=$(LINK_STATIC)" \
1797	)
1798
1799	#***************************************************************************************
1800	# Recursive calls to sub-makefiles
1801	#***************************************************************************************
1802
1803	%.depends: have_makedepend
1804	@cp -p $(@D)/Makefile $(@D)/Makefile.old # save old Makefile
1805	@$(MAKE) -C $(@D) -r \
1806	"AUTODEPENDS=1" \
1807	"MAIN=nothing" \
1808	"cflags=noCflagsHere_use_MAKEDEPENDFLAGS" \
1809	"cxxflags=noCxxflagsHere_use_MAKEDEPENDFLAGS" \
1810	depends
1811	@grep "^# DO NOT DELETE" $(@D)/Makefile >/dev/null
1812	@cat $(@D)/Makefile \
1813	\| SOURCE_TOOLS/fix_depends.pl "(from main)" \
1814	>$(@D)/Makefile.2
1815	@mv $(@D)/Makefile.old $(@D)/Makefile # restore old Makefile
1816	@$(ARBHOME)/SOURCE_TOOLS/mv_if_diff $(@D)/Makefile.2 $(@D)/Makefile # update Makefile if changed
1817
1818	%.proto:
1819	@($(MAKE) -C $(@D) \
1820	"AUTODEPENDS=0" \
1821	"MAIN=nothing" \
1822	"cflags=noCflags" \
1823	"cxxflags=noCxxflags" \
1824	proto 2>&1 ) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
1825
1826	%.clean:
1827	@$(MAKE) -C $(@D) \
1828	"AUTODEPENDS=0" \
1829	"MAIN=nothing" \
1830	"cflags=noCflags" \
1831	"cxxflags=noCxxflags" \
1832	clean
1833
1834
1835	# stop wrong targets:
1836	target_is_missing_lib_prefix:
1837	@echo "Error: Denied to build shared library target with missing 'lib'-prefix"
1838	false
1839
1840	ARBDB/ARBDB.dummy: target_is_missing_lib_prefix
1841	CORE/CORE.dummy: target_is_missing_lib_prefix
1842	AWT/AWT.dummy: target_is_missing_lib_prefix
1843	WINDOW/WINDOW.dummy: target_is_missing_lib_prefix
1844
1845	# rule to generate main target (normally a library):
1846	# @@@ check effect of setting LANG=C below
1847	%.dummy:
1848	@( export ID=$$$$; LANG=C; \
1849	(( \
1850	echo "$(SEP) Make $(@D)"; \
1851	$(MAKE) -C $(@D) -r \
1852	"AUTODEPENDS=1" \
1853	"MAIN=$(@F:.dummy=.a)" \
1854	"cflags=$(cflags) -DIN_ARB_$(subst /,_,$(@D))" \
1855	&& \
1856	echo "$(SEP) Make $(@D) [done]"; \
1857	) >$(@D).$$ID.log 2>&1 && (cat $(@D).$$ID.log;rm $(@D).$$ID.log)) \|\| (cat $(@D).$$ID.log;rm $(@D).$$ID.log;false))
1858
1859	# Additional dependencies for subtargets:
1860
1861	PROBE_COM/PROBE_COM.dummy : comtools
1862	NAMES_COM/NAMES_COM.dummy : comtools
1863
1864	com: PROBE_COM/PROBE_COM.dummy NAMES_COM/NAMES_COM.dummy
1865
1866	# stop wrong more targets:
1867	PROBE_COM/server.dummy:
1868	@echo Unwanted request to make target $<
1869	false
1870
1871	PROBE_COM/client.dummy:
1872	@echo Unwanted request to make target $<
1873	false
1874
1875	NAMES_COM/server.dummy:
1876	@echo Unwanted request to make target $<
1877	false
1878
1879	NAMES_COM/client.dummy:
1880	@echo Unwanted request to make target $<
1881	false
1882
1883
1884	ARBDB/libARBDB.dummy: links
1885	CORE/libCORE.dummy: links
1886
1887	PERLTOOLS/PERLTOOLS.dummy: core db
1888
1889	# all subdirs perl not depends on go here (ADD_links_non_perl)
1890	AWTI/AWTI.dummy: links_non_perl
1891	CONSENSUS_TREE/CONSENSUS_TREE.dummy: links_non_perl
1892	CONVERTALN/CONVERTALN.dummy: links_non_perl
1893	DBSERVER/DBSERVER.dummy: links_non_perl
1894	DIST/DIST.dummy: links_non_perl
1895	EDIT4/EDIT4.dummy: links_non_perl com
1896	EISPACK/EISPACK.dummy: links_non_perl
1897	GDE/GDE.dummy: links_non_perl
1898	GENOM/GENOM.dummy: links_non_perl
1899	GENOM_IMPORT/GENOM_IMPORT.dummy: links_non_perl
1900	ISLAND_HOPPING/ISLAND_HOPPING.dummy: links_non_perl
1901	MERGE/MERGE.dummy: links_non_perl
1902	NTREE/NTREE.dummy: links_non_perl
1903	PARSIMONY/PARSIMONY.dummy: links_non_perl
1904	PHYLO/PHYLO.dummy: links_non_perl
1905	PRIMER_DESIGN/PRIMER_DESIGN.dummy: links_non_perl
1906	PROBE_SET/PROBE_SET.dummy: links_non_perl link_db
1907	READSEQ/READSEQ.dummy: links_non_perl
1908	RNACMA/RNACMA.dummy: links_non_perl header_libs
1909	SECEDIT/SECEDIT.dummy: links_non_perl
1910	SEQ_QUALITY/SEQ_QUALITY.dummy: links_non_perl
1911	SERVERCNTRL/SERVERCNTRL.dummy: links_non_perl com
1912	SL/ALILINK/ALILINK.dummy: links_non_perl
1913	SL/ALIVIEW/ALIVIEW.dummy: links_non_perl
1914	SL/AP_TREE/AP_TREE.dummy: links_non_perl
1915	SL/APP/APP.dummy: links_non_perl
1916	SL/ARB_SPEC/ARB_SPEC.dummy: links_non_perl
1917	SL/ARB_TREE/ARB_TREE.dummy: links_non_perl
1918	SL/AW_HELIX/AW_HELIX.dummy: links_non_perl
1919	SL/CONSENSUS/CONSENSUS.dummy: links_non_perl
1920	SL/CANVAS/CANVAS.dummy: links_non_perl
1921	SL/DB_QUERY/DB_QUERY.dummy: links_non_perl
1922	SL/DB_SCANNER/DB_SCANNER.dummy: links_non_perl
1923	SL/DB_UI/DB_UI.dummy: links_non_perl
1924	SL/FAST_ALIGNER/FAST_ALIGNER.dummy: links_non_perl
1925	SL/FILTER/FILTER.dummy: links_non_perl
1926	SL/FILTSEQEXP/FILTSEQEXP.dummy: links_non_perl
1927	SL/GROUP_SEARCH/GROUP_SEARCH.dummy: links_non_perl
1928	SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy: links_non_perl
1929	SL/GUI_TK/GUI_TK.dummy: links_non_perl
1930	SL/HEADERTESTS/HEADERTESTS.dummy: links_non_perl
1931	SL/HELIX/HELIX.dummy: links_non_perl
1932	SL/INSDEL/INSDEL.dummy: links_non_perl
1933	SL/ITEM_SHADER/ITEM_SHADER.dummy: links_non_perl
1934	SL/ITEMS/ITEMS.dummy: links_non_perl
1935	SL/LOCATION/LOCATION.dummy: links_non_perl
1936	SL/MACROS/MACROS.dummy: links_non_perl
1937	SL/MASKS/MASKS.dummy: links_non_perl
1938	SL/MATRIX/MATRIX.dummy: links_non_perl
1939	SL/MAPKEY/MAPKEY.dummy: links_non_perl
1940	SL/NDS/NDS.dummy: links_non_perl
1941	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.dummy: links_non_perl
1942	SL/PRONUC/PRONUC.dummy: links_non_perl
1943	SL/PTCLEAN/PTCLEAN.dummy: links_non_perl link_db
1944	SL/PVP/PVP.dummy: links_non_perl
1945	SL/QUERY/QUERY.dummy: links_non_perl link_db
1946	SL/REFENTRIES/REFENTRIES.dummy: links_non_perl
1947	SL/REGEXPR/REGEXPR.dummy: links_non_perl
1948	SL/SAICALC/SAICALC.dummy: links_non_perl
1949	SL/SPECSEL/SPECSEL.dummy: links_non_perl
1950	SL/SEQIO/SEQIO.dummy: links_non_perl
1951	SL/SEQUENCE/SEQUENCE.dummy: links_non_perl
1952	SL/TRANSLATE/TRANSLATE.dummy: links_non_perl
1953	SL/TREE_ADMIN/TREE_ADMIN.dummy: links_non_perl
1954	SL/TREE_READ/TREE_READ.dummy: links_non_perl
1955	SL/TREE_WRITE/TREE_WRITE.dummy: links_non_perl
1956	SL/TREEDISP/TREEDISP.dummy: links_non_perl
1957	SL/XFERGUI/XFERGUI.dummy: links_non_perl
1958	SL/XFERSET/XFERSET.dummy: links_non_perl
1959	STAT/STAT.dummy: links_non_perl
1960	TREEGEN/TREEGEN.dummy: links_non_perl
1961	WETC/WETC.dummy: links_non_perl
1962	WINDOW/libWINDOW.dummy: links_non_perl
1963	XML/XML.dummy: links_non_perl
1964
1965	ifeq ($(OPENGL),1)
1966	GL/glAW/glAW.dummy: links_non_perl
1967	GL/glpng/glpng.dummy: links_non_perl
1968	GL/GL.dummy: GL/glAW/glAW.dummy GL/glpng/glpng.dummy
1969	RNA3D/RNA3D.dummy: links_non_perl gl
1970	endif
1971
1972	UNIT_TESTER/UNIT_TESTER.dummy: link_db \
1973	SERVERCNTRL/SERVERCNTRL.dummy \
1974
1975	# see also TOOLS/Makefile@TOOLSLIBDEPENDS
1976	TOOLS/TOOLS.dummy : links_non_perl link_db \
1977	CONSENSUS_TREE/CONSENSUS_TREE.dummy \
1978	SERVERCNTRL/SERVERCNTRL.dummy \
1979	SL/FILTER/FILTER.dummy \
1980	SL/FILTSEQEXP/FILTSEQEXP.dummy \
1981	SL/INSDEL/INSDEL.dummy \
1982	SL/REGEXPR/REGEXPR.dummy \
1983	SL/SEQIO/SEQIO.dummy \
1984	SL/TREE_READ/TREE_READ.dummy \
1985	SL/TREE_WRITE/TREE_WRITE.dummy \
1986	XML/XML.dummy \
1987
1988	AWTC/AWTC.dummy : com
1989
1990	NAMES/NAMES.dummy : com
1991	SL/AW_NAME/AW_NAME.dummy : com
1992
1993	PROBE/PROBE.dummy : com
1994	MULTI_PROBE/MULTI_PROBE.dummy : com
1995	PROBE_DESIGN/PROBE_DESIGN.dummy : com
1996	NALIGNER/NALIGNER.dummy : com
1997
1998	ARB_GDE/ARB_GDE.dummy : proto_tools menus
1999
2000	compile_compatibility: SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.dummy
2001
2002	#***************************************************************************************
2003	# Short aliases to make targets
2004	#***************************************************************************************
2005
2006	show:
2007	@echo $(SEP)
2008	@echo 'Aliases for often needed targets:'
2009	@echo ''
2010	@echo ' executables:'
2011	@echo ''
2012	@echo ' nt arb_ntree'
2013	@echo ' e4 arb_edit4 (includes secedit)'
2014	@echo ' di arb_dist'
2015	@echo ' ph arb_phylo'
2016	@echo ' pa arb_parsimony'
2017	@echo ' tg arb_treegen'
2018	@echo ' ds arb_dbserver'
2019	@echo ' pt arb_pt_server'
2020	@echo ' na arb_name_server'
2021	@echo ''
2022	@echo ' libraries:'
2023	@echo ''
2024	@echo ' com communication libraries'
2025	@echo ' db ARB database'
2026	@echo ' aw GUI lib'
2027	@echo ' awt GUI toolkit'
2028	@echo ' awtc general purpose library'
2029	@echo ' awti import/export library'
2030	@echo ' mp multi probe library'
2031	@echo ' ge genome library'
2032	@echo ' pd probe design lib'
2033	@echo ' prd primer design lib'
2034	@echo ''
2035	@echo ' other targets:'
2036	@echo ''
2037	@echo ' help recompile help files'
2038	@echo ' tools make small tools used by arb'
2039	@echo ''
2040	@echo ' foreign targets:'
2041	@echo ''
2042	@echo ' gde GDE'
2043	@echo ' agde ARB_GDE'
2044	@echo ''
2045	@echo 'for other targets inspect $(ARBHOME)/Makefile'
2046	@echo ''
2047	@echo $(SEP)
2048
2049	source_doc:
2050	@echo "Remove some links (doxygen crashes otherwise):"
2051	find . $ -name "AISC" -o -name "C" -o -name "GDEHELP" $ -type l -exec rm {} \;
2052	doxygen 2>&1 1>/dev/null
2053	$(MAKE) forcelinks
2054
2055	dep_graph:
2056	@echo "Building some dependency graphs"
2057	SOURCE_TOOLS/dependency_graphs.pl
2058
2059	help: HELP_SOURCE/HELP_SOURCE.dummy
2060
2061	HELP_SOURCE/HELP_SOURCE.dummy: link_core xml menus
2062
2063	db: ARBDB/libARBDB.dummy
2064	core: CORE/libCORE.dummy
2065	aw: WINDOW/libWINDOW.dummy
2066	awtc: AWTC/AWTC.dummy
2067	awti: AWTI/AWTI.dummy
2068
2069	mp: MULTI_PROBE/MULTI_PROBE.dummy
2070	mg: MERGE/MERGE.dummy
2071	ge: GENOM/GENOM.dummy
2072	prd: PRIMER_DESIGN/PRIMER_DESIGN.dummy
2073
2074	nt: menus $(NTREE)
2075
2076	nal: $(NALIGNER)
2077
2078	di: $(DIST)
2079	ph: $(PHYLO)
2080	pa: $(PARSIMONY)
2081	tg: $(TREEGEN)
2082
2083	ifeq ($(OPENGL),1)
2084	3d: RNA3D/RNA3D.dummy
2085	gl: GL/GL.dummy
2086	else
2087	noopengl:
2088	@echo "invalid target for OPENGL=0"
2089	3d: noopengl
2090	gl: noopengl
2091	endif
2092
2093	SL/SL.dummy: com
2094
2095	ds: $(DBSERVER)
2096	pt: $(PROBE)
2097	pst: PROBE_SET/PROBE_SET.dummy
2098	pd: PROBE_DESIGN/PROBE_DESIGN.dummy
2099	na: $(NAMES)
2100	sq: SEQ_QUALITY/SEQ_QUALITY.dummy
2101	cma: $(RNACMA)
2102
2103	sec: SECEDIT/SECEDIT.dummy
2104
2105	e4: $(EDIT4) readseq menus
2106
2107	gi: GENOM_IMPORT/GENOM_IMPORT.dummy
2108	wetc: $(WETC)
2109
2110	xml: XML/XML.dummy
2111	stat: STAT/STAT.dummy $(NTREE) $(EDIT4)
2112	fa: SL/FAST_ALIGNER/FAST_ALIGNER.dummy
2113
2114	#********************************************************************************
2115
2116	up_by_remake: depends proto vectorize_checks
2117
2118	up: up_by_remake tags valgrind_update
2119
2120	#********************************************************************************
2121
2122	touch:
2123	SOURCE_TOOLS/touch_modified.pl
2124
2125	modified: touch
2126	$(MAKE) all
2127
2128	#********************************************************************************
2129
2130	libdepends:
2131	$(MAKE) -C "SOURCE_TOOLS" \
2132	"RNA3D_LIB=$(RNA3D_LIB_4_DEPENDS)" \
2133	libdepends
2134
2135	#********************************************************************************
2136
2137	# create generated headers:
2138	genheaders: TEMPLATES/TEMPLATES.dummy
2139
2140	clrdotdepends:
2141	rm PROBE_COM/.depends \|\| true
2142	rm NAMES_COM/.depends \|\| true
2143	rm PERL2ARB/.depends \|\| true
2144
2145	comdepends: comtools clrdotdepends have_makedepend
2146	@echo "$(SEP) Partially build com interface"
2147	$(MAKE) PROBE_COM/PROBE_COM.depends NAMES_COM/NAMES_COM.depends
2148	$(MAKE) PROBE_COM/server.depends NAMES_COM/server.depends
2149
2150	depends: genheaders comdepends vectorize_checks have_makedepend
2151	@echo "$(SEP) Updating other dependencies"
2152	$(MAKE) $(subst NAMES_COM/server.depends,,$(subst PROBE_COM/server.depends,,$(SUBDIRS:.sub=.depends))) \
2153	HELP_SOURCE/HELP_SOURCE.depends \
2154	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.depends \
2155
2156	$(MAKE) libdepends
2157
2158	depend: depends
2159
2160	# ------------------------------------------------------------
2161	# dependency generation tests for AISC code
2162	#(all should work w/o creating wrong dependencies;
2163	# neither in XXX_COM/Makefile nor in code using AISC interface)
2164	dependstest1: silent_clean
2165	$(MAKE) depends
2166	dependstest2: silent_clean
2167	$(MAKE) com
2168	dependstest3: silent_clean
2169	$(MAKE) aw
2170	dependstest4: silent_clean
2171	$(MAKE) pt
2172	dependstest5: silent_clean
2173	$(MAKE) na
2174	dependstest6: silent_clean
2175	$(MAKE) nt
2176	dependstest7: silent_clean
2177	$(MAKE) all
2178	# ------------------------------------------------------------
2179
2180	vectorize_checks:
2181	$(MAKE) -C SOURCE_TOOLS -r vectorize_checks
2182
2183	clean_checked_vect: lib/lib.clean
2184	SOURCE_TOOLS/clean_checked_vectorizations.sh
2185
2186	# ------------------------------------------------------------
2187
2188	AISC_MKPTPS/AISC_MKPTPS.dummy: links
2189
2190	proto_tools: AISC_MKPTPS/AISC_MKPTPS.dummy
2191
2192	proto: proto_tools
2193	@echo $(SEP) Updating prototypes
2194	$(MAKE) \
2195	ARBDB/ARBDB.proto \
2196	AISC_COM/AISC_COM.proto \
2197	ARB_GDE/ARB_GDE.proto \
2198	CORE/CORE.proto \
2199	CONVERTALN/CONVERTALN.proto \
2200	NTREE/NTREE.proto \
2201	MERGE/MERGE.proto \
2202	PROBE/PROBE.proto \
2203	SERVERCNTRL/SERVERCNTRL.proto \
2204	SL/SL.proto \
2205
2206	#********************************************************************************
2207
2208	valgrind_update: links
2209	@echo $(SEP) Updating for valgrind
2210	$(MAKE) -C SOURCE_TOOLS valgrind_update
2211
2212	#********************************************************************************
2213
2214	TAGFILE=TAGS
2215	UTAGS=TAGS.$(ARBBID)
2216	TAGFILE_TMP=$(UTAGS).tmp
2217
2218	TAG_SOURCE_HEADERS=$(UTAGS).headers.tmp
2219	TAG_SOURCE_CODE=$(UTAGS).codefiles.tmp
2220	TAG_SOURCE_LISTS=$(TAG_SOURCE_HEADERS) $(TAG_SOURCE_CODE)
2221
2222	ETAGS_IGNORE_LIST=SOURCE_TOOLS/etags_ignore.lst
2223
2224	ETAGS=ctags -e -I @$(ETAGS_IGNORE_LIST) --sort=no --if0=no --extra=q
2225	ETAGS_TYPES=--C-kinds=cgnsut --C++-kinds=cgnsut
2226	ETAGS_FUN =--C-kinds=fm --C++-kinds=fm
2227	ETAGS_REST =--C-kinds=dev --C++-kinds=dev
2228
2229	FILTER_TAGS_SOURCES= \
2230	$(SED) -e 's/^.\///g' \| \
2231	grep -vi '^HEADERLIBS\\|^GDE/\\|/GEN[CH]/'
2232
2233	$(TAG_SOURCE_HEADERS): links
2234	@find . $ -name '.hxx' -o -name ".h" $ -type f \| $(FILTER_TAGS_SOURCES) > $@
2235
2236	$(TAG_SOURCE_CODE): links
2237	@find . $ -name '.cxx' -o -name ".c" $ -type f \| $(FILTER_TAGS_SOURCES) > $@
2238
2239	$(UTAGS).1.tmp: $(TAG_SOURCE_HEADERS)
2240	@$(ETAGS) -f $@ $(ETAGS_TYPES) -L $<
2241	$(UTAGS).2.tmp: $(TAG_SOURCE_HEADERS)
2242	@$(ETAGS) -f $@ $(ETAGS_FUN) -L $<
2243	$(UTAGS).3.tmp: $(TAG_SOURCE_HEADERS)
2244	@$(ETAGS) -f $@ $(ETAGS_REST) -L $<
2245	$(UTAGS).4.tmp: $(TAG_SOURCE_CODE)
2246	@$(ETAGS) -f $@ $(ETAGS_TYPES) -L $<
2247	$(UTAGS).5.tmp: $(TAG_SOURCE_CODE)
2248	@$(ETAGS) -f $@ $(ETAGS_FUN) -L $<
2249	$(UTAGS).6.tmp: $(TAG_SOURCE_CODE)
2250	@$(ETAGS) -f $@ $(ETAGS_REST) -L $<
2251
2252	TAGS_ALL_PARTS=$(UTAGS).1.tmp $(UTAGS).2.tmp $(UTAGS).3.tmp $(UTAGS).4.tmp $(UTAGS).5.tmp $(UTAGS).6.tmp
2253
2254	$(TAGFILE_TMP) : $(TAGS_ALL_PARTS)
2255	@cat $(TAGS_ALL_PARTS) > $@
2256	@rm $(TAGS_ALL_PARTS) $(TAG_SOURCE_LISTS)
2257
2258	cleanOldTags:
2259	@find $(ARBHOME) -name 'TAGS.*.tmp' -ctime +2 -exec rm {} \;
2260
2261	tags: $(TAGFILE_TMP) cleanOldTags
2262	@mv_if_diff $(TAGFILE_TMP) $(TAGFILE)
2263
2264	#********************************************************************************
2265
2266	LINKSTAMP=SOURCE_TOOLS/stamp.generate_all_links
2267
2268	links: checks $(LINKSTAMP) arbmainwrapper
2269	links_no_checks: $(LINKSTAMP) arbmainwrapper
2270
2271	forcelinks:
2272	-rm $(LINKSTAMP)
2273	$(MAKE) links
2274
2275	$(LINKSTAMP): SOURCE_TOOLS/generate_all_links.sh genheaders
2276	+SOURCE_TOOLS/generate_all_links.sh
2277	touch $(LINKSTAMP)
2278
2279	clean_links:
2280	# avoid to delete linked pts, nas or arb_tcp.dat:
2281	find . -path './lib' -prune -o -type l -exec rm {} \;
2282	# removed obsolete file - refuses to disappear due to 'prune' above
2283	@rm -f lib/help/GDEHELP
2284	@rm -f $(LINKSTAMP) lib/inputMasks/format.readme
2285
2286	redo_links: clean_links
2287	$(MAKE) links_no_checks
2288
2289	#********************************************************************************
2290
2291	header_libs:
2292	@(( \
2293	echo "$(SEP) Make HEADERLIBS"; \
2294	$(MAKE) -C HEADERLIBS all && \
2295	echo "$(SEP) Make HEADERLIBS [done]"; \
2296	) > HEADERLIBS.log 2>&1 && (cat HEADERLIBS.log;rm HEADERLIBS.log)) \|\| (cat HEADERLIBS.log;rm HEADERLIBS.log;false)
2297
2298	#********************************************************************************
2299
2300	gde: GDE/GDE.dummy
2301	GDE: gde
2302	agde: ARB_GDE/ARB_GDE.dummy
2303	tools: TOOLS/TOOLS.dummy
2304	convert: $(CONVERT_ALN)
2305	readseq: READSEQ/READSEQ.dummy
2306
2307	#***************************************************************************************
2308	# Some user commands
2309	#***************************************************************************************
2310
2311	menus: binlink links
2312	@(( \
2313	echo "$(SEP) Make GDEHELP"; \
2314	$(MAKE) -C GDEHELP -r all && \
2315	echo "$(SEP) Make GDEHELP [done]"; \
2316	) > GDEHELP.log 2>&1 && (cat GDEHELP.log;rm GDEHELP.log)) \|\| (cat GDEHELP.log;rm GDEHELP.log;false)
2317
2318	ifeq ($(DEBUG),1)
2319	BIN_TARGET=develall
2320	else
2321	BIN_TARGET=all
2322	endif
2323
2324
2325	binlink:
2326	$(MAKE) -C bin $(BIN_TARGET)
2327
2328	check_bin_dep: binlink
2329	SOURCE_TOOLS/check_bin_dependencies.pl
2330
2331	fig_cure:
2332	SOURCE_TOOLS/sortfig.pl doit
2333
2334	preplib:
2335	(cd lib;$(MAKE) all)
2336
2337	# --------------------------------------------------------------------------------
2338	# This section is quite tricky:
2339	#
2340	# make 'perl' is a BIG target, so when it has to be made, it has to be started
2341	# as early as possible to reduce overall compile time. Since 'make' does not
2342	# provide any priorities, i force it to build all 'perl'-prerequisites early, by
2343	# adding artificial dependencies to these prerequisites
2344	#
2345	# That behavior is likely to be system-dependent.
2346	# My goal was only to make it work on my current development system,
2347	# where this saves about 20% of overall build time.
2348
2349	ifeq ($(WITHPERL),1)
2350	links_non_perl: PERLTOOLS/PERLTOOLS.dummy
2351	perltools: links_non_perl
2352	perl: realperl
2353	else
2354	links_non_perl: links
2355	perl: links
2356	$(MAKE) "WITHPERL=1" perl
2357	endif
2358
2359	# ---------------------------------------- perl
2360
2361	realperl: perltools
2362	(( \
2363	echo "$(SEP) Make PERL2ARB" ; \
2364	$(TIME) $(MAKE) -C PERL2ARB -r -f Makefile.main \
2365	"AUTODEPENDS=1" \
2366	"dflags=$(dflags)" \
2367	"cflags4perl=$(cflags) $(cxxflags) $(dflags)" \
2368	"lflags4perl=$(lflags4perl)" \
2369	"COMPILER_VERSION=$(COMPILER_VERSION)" \
2370	all && \
2371	$(MAKE) -C PERL_SCRIPTS/test test && \
2372	echo "$(SEP) Make PERL2ARB [done]" ; \
2373	) > PERL2ARB.log 2>&1 && (cat PERL2ARB.log;rm PERL2ARB.log)) \|\| (cat PERL2ARB.log;rm PERL2ARB.log;false)
2374
2375	perl_clean:
2376	@$(MAKE) -C PERL2ARB -r -f Makefile.main \
2377	"AUTODEPENDS=0" \
2378	clean
2379
2380	PERL2ARB/PERL2ARB.clean:
2381	$(MAKE) perl_clean
2382	$(MAKE) -C PERL_SCRIPTS/test clean
2383
2384	# ---------------------------------------- bindings to script languages
2385
2386	bindings: lib/libCORE.so lib/libARBDB.so
2387	$(MAKE) -C BINDINGS all ARBDEPENDS="$(^:%=../%)" DFLAGS="$(dflags)"
2388
2389	bindings_clean:
2390	$(MAKE) -C BINDINGS clean
2391
2392	# ---------------------------------------- check resources
2393
2394	check_res:
2395	$(ARBHOME)/SOURCE_TOOLS/check_resources.pl
2396
2397	# ---------------------------------------- cleaning
2398
2399	rmbak:
2400	@echo "[cleanup backup/core files]"
2401	@find . \( -name '*%' \
2402	-o -name '*.bak' \
2403	-o -name '*~' \) \
2404	-o $ -name 'core' -a \! -type d $ \
2405	-exec rm -v {} \; \|\| \
2406	echo "Warning: target 'rmbak' reported problems when removing misc. backup files (ignored)"
2407	@echo "[cleanup done]"
2408
2409	bin_reinit:
2410	$(MAKE) bin/bin.clean
2411	$(MAKE) -C "bin" all
2412
2413	clean_directories:
2414	-rm -rf \
2415	$(ARBHOME)/PROBE_SET/bin \
2416	$(ARBHOME)/INCLUDE \
2417
2418	libclean:
2419	-find $(ARBHOME) -type f $ -name '*.a' ! -type l $ -exec rm -f {} \;
2420	-find $(ARBHOME) -type f $ -name 'lib*.so' ! -type l $ -exec rm -f {} \;
2421
2422	objclean:
2423	-find $(ARBHOME) -type f $ -name '*.o' ! -type l $ -exec rm -f {} \;
2424
2425	# bin.clean and HELP_SOURCE.clean interfere
2426	clean3:
2427	$(MAKE) bin/bin.clean
2428	$(MAKE) HELP_SOURCE/HELP_SOURCE.clean
2429
2430
2431	# delete all binaries (similar to 'cleanlinked')
2432	cleanRelinkable: libclean UNIT_TESTER/UNIT_TESTER.clean
2433	$(MAKE) -C bin cleanbinariesRelinkable
2434	$(MAKE) -C PROBE_SET cleanLinked
2435
2436
2437	clean2: $(SUBDIRS:.sub=.clean) \
2438	clean3 \
2439	rmbak \
2440	libclean \
2441	objclean \
2442	lib/lib.clean \
2443	GDEHELP/GDEHELP.clean \
2444	HEADERLIBS/HEADERLIBS.clean \
2445	SOURCE_TOOLS/SOURCE_TOOLS.clean \
2446	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.clean \
2447	UNIT_TESTER/UNIT_TESTER.clean \
2448	TEMPLATES/TEMPLATES.clean \
2449	perl_clean \
2450
2451	rm -f .last_gcc .last_compiler config.makefile.bak
2452	$(MAKE) clean_directories
2453
2454	# links are needed for cleanup
2455	clean: redo_links motif_xpm_hack_clean
2456	$(MAKE) clean2
2457	$(MAKE) clean_cov_all clean_links
2458
2459	silent_clean:
2460	$(MAKE) clean >/dev/null
2461
2462	# 'relocated' is about 50% faster than 'rebuild'
2463	reloc_clean: links
2464	@echo "---------------------------------------- Relocation cleanup"
2465	$(MAKE) \
2466	perl_clean \
2467	GDEHELP/GDEHELP.clean \
2468	HELP_SOURCE/genhelp/genhelp.clean \
2469	bin/bin.clean \
2470	libclean \
2471	objclean
2472
2473	relocated: links
2474	$(MAKE) reloc_clean
2475	@echo "---------------------------------------- and remake"
2476	$(MAKE) build
2477
2478	# -----------------------------------
2479	# some stress tests
2480	# (helpful to reveal race conditions with -j)
2481
2482	rebuild4ever: rebuild
2483	$(MAKE) rebuild4ever
2484
2485	build4ever: build
2486	$(MAKE) build4ever
2487
2488	clean4ever: clean
2489	$(MAKE) clean4ever
2490
2491	test4ever: ut
2492	$(MAKE) test4ever
2493
2494	perl4ever: clean
2495	$(MAKE) links
2496	$(MAKE) perl
2497	$(MAKE) perl4ever
2498
2499	help4ever: clean
2500	$(MAKE) help
2501	$(MAKE) help4ever
2502
2503	# -----------------------------------
2504
2505	cleanlinked: bin/bin.clean libclean
2506
2507	relink: cleanlinked
2508	$(MAKE) all
2509
2510	# --------------------------------------------------------------------------------
2511	# source related targets
2512
2513	CLOC=cloc
2514	CLOCFLAGS=--no3 --quiet --progress-rate=0
2515	CLOCARB=--exclude-dir=GDE .
2516	CLOCEXT=GDE
2517	CLOCCODE=--force-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.code.def
2518	CLOCREST=--force-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.rest.def
2519	CLOCFILT=tail --lines=+4
2520
2521	cloc:
2522	@echo 'Arb code:'
2523	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCARB) \| $(CLOCFILT)
2524	@echo 'Arb rest:'
2525	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCARB) \| $(CLOCFILT)
2526	@echo 'External code:'
2527	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCEXT) \| $(CLOCFILT)
2528	@echo 'External rest:'
2529	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCEXT) \| $(CLOCFILT)
2530
2531
2532	# patch generation
2533	patch:
2534	SOURCE_TOOLS/arb_create_patch.sh arbPatch --svn
2535
2536	# source tarball generation
2537	save: sourcetarfile
2538
2539	sourcetarfile: rmbak
2540	util/arb_save
2541
2542	# test early whether save will work
2543	savetest:
2544	@util/arb_srclst.pl >/dev/null
2545
2546	testsave: savetest
2547
2548	save2: rmbak
2549	util/arb_save ignore
2550
2551	save_test: rmbak
2552	@echo "Testing source list.."
2553	@util/arb_srclst.pl > /dev/null
2554
2555	save_test_no_error:
2556	@-$(MAKE) save_test
2557
2558	# --------------------------------------------------------------------------------
2559	# version management
2560
2561	inc_candi:
2562	touch SOURCE_TOOLS/inc_candi.stamp
2563	$(MAKE) do_version_update
2564
2565	inc_patch:
2566	touch SOURCE_TOOLS/inc_patch.stamp
2567	$(MAKE) do_version_update
2568
2569	inc_minor:
2570	touch SOURCE_TOOLS/inc_minor.stamp
2571	$(MAKE) do_version_update
2572
2573	inc_major:
2574	touch SOURCE_TOOLS/inc_major.stamp
2575	$(MAKE) do_version_update
2576
2577	do_version_update:
2578	@echo Incrementing version information
2579	$(MAKE) savetest
2580	$(MAKE) genheaders # auto upgrades version early
2581
2582	show_version:
2583	$(MAKE) genheaders # updates version info
2584	@echo "$(SEP) ARB version info"
2585	@grep ARB_VERSION TEMPLATES/arb_build.h
2586	@echo "$(SEP)"
2587
2588	# --------------------------------------------------------------------------------
2589	# special cleanups
2590
2591	clean_opengl_changed: RNA3D/RNA3D.clean EDIT4/EDIT4.clean WINDOW/WINDOW.clean GL/GL.clean
2592
2593	# --------------------------------------------------------------------------------
2594
2595	arbapplications: nt pa e4 wetc pt na nal di ph ds wetc cma
2596
2597	arb_external: convert tools gde readseq tg pst
2598
2599	arb_no_perl: arbapplications help arb_external
2600
2601	arb: motif_xpm_hack
2602	$(MAKE) "WITHPERL=1" perl arb_no_perl
2603
2604	motif_xpm_hack:
2605	$(MAKE) -r -C "lib/motifHack" all
2606
2607	motif_xpm_hack_clean:
2608	$(MAKE) -r -C "lib/motifHack" clean
2609
2610	# --------------------------------------------------------------------------------
2611	# special targets for SOURCE_TOOLS/remake_after_change.pl
2612
2613	rac_arb_dist: di
2614	rac_arb_edit4: e4
2615	rac_arb_ntree: nt
2616	rac_arb_pars: pa
2617	rac_arb_phylo: ph
2618	rac_arb_wetc: wetc
2619	rac_arb_naligner: nal
2620	rac_arb_pt_server: pt
2621	rac_arb_db_server: ds
2622	rac_arb_name_server: na
2623	rac_arb_convert_aln: convert
2624	rac_arb_treegen: tg
2625	rac_arb_rnacma: cma
2626	rac_arb_help2xml: help
2627
2628	rac_arb_a2ps: tools
2629	rac_arb_consensus_tree: tools
2630	rac_arb_dnarates: tools
2631	rac_arb_export_rates: tools
2632	rac_arb_export_tree: tools
2633	rac_arb_gene_probe: tools
2634	rac_arb_message: tools
2635	rac_arb_primer: tools
2636	rac_arb_probe: tools
2637	rac_arb_read_tree: tools
2638
2639	# --------------------------------------------------------------------------------
2640	# unit testing
2641	# @@@ work in progress
2642	#
2643	# goal is to automatically test all libraries/executables using TESTED_UNITS_AUTO
2644	# currently not all test executables link w/o error.
2645	# therefor units are organized in three sets:
2646	#
2647	# TESTED_UNITS = testable and contain tests
2648	# UNTESTED_UNITS = testable, but no tests written yet
2649	# UNTESTABLE_UNITS = not testable
2650
2651	# always define OPENGL units manually:
2652	OPENGL_TESTS :=
2653	ifeq ($(OPENGL),1)
2654	# this section defines RNA3D.test
2655	OPENGL_TESTS += \
2656	$(subst .a,.test,$(RNA3D_LIB)) \
2657	GL/glAW/libglAW.test \
2658	GL/glpng/libglpng_arb.test \
2659
2660	endif
2661
2662	UNITS_NOT_AUTODETECTED = \
2663	HELP_SOURCE/HELP_SOURCE.tooltests
2664
2665	TESTED_UNITS_AUTO = \
2666	$(OPENGL_TESTS) \
2667	$(TL_ARCHIVES:.a=.test) \
2668	$(TL_SHARED_ARCHIVES:.so=.test) \
2669	$(CL_ARCHIVES:.a=.test) \
2670	$(TL_TOOLS_COLLECTIONS:.toolColl=.tooltests) \
2671	$(UNITS_NOT_AUTODETECTED) \
2672
2673	UNTESTED_UNITS = \
2674	$(OPENGL_TESTS) \
2675	EISPACK/EISPACK.test \
2676	GENOM/GENOM.test \
2677	ISLAND_HOPPING/ISLAND_HOPPING.test \
2678	NALIGNER/NALIGNER.test \
2679	NAMES/NAMES.test \
2680	PHYLO/PHYLO.test \
2681	PRIMER_DESIGN/PRIMER_DESIGN.test \
2682	READSEQ/READSEQ.tooltests \
2683	SECEDIT/SECEDIT.test \
2684	SEQ_QUALITY/SEQ_QUALITY.test \
2685	SERVERCNTRL/SERVERCNTRL.test \
2686	SL/ALIVIEW/ALIVIEW.test \
2687	SL/AP_TREE/AP_TREE.test \
2688	SL/ARB_SPEC/ARB_SPEC.test \
2689	SL/ARB_TREE/ARB_TREE.test \
2690	SL/AW_HELIX/AW_HELIX.test \
2691	SL/AW_NAME/AW_NAME.test \
2692	SL/CANVAS/CANVAS.test \
2693	SL/DB_SCANNER/DB_SCANNER.test \
2694	SL/DB_UI/DB_UI.test \
2695	SL/GUI_ALIVIEW/GUI_ALIVIEW.test \
2696	SL/GUI_TK/GUI_TK.test \
2697	SL/HELIX/HELIX.test \
2698	SL/MASKS/MASKS.test \
2699	SL/MAPKEY/MAPKEY.test \
2700	SL/QUERY/QUERY.test \
2701	SL/REFENTRIES/REFENTRIES.test \
2702	SL/SEQUENCE/SEQUENCE.test \
2703	SL/TREE_ADMIN/TREE_ADMIN.test \
2704	SL/TREE_WRITE/TREE_WRITE.test \
2705	SL/XFERGUI/XFERGUI.test \
2706	STAT/STAT.test \
2707	TREEGEN/TREEGEN.test \
2708	WETC/WETC.test \
2709	XML/XML.test \
2710
2711	# untestable units
2712
2713	UNTESTABLE_UNITS = \
2714	AISC/AISC.test \
2715	NAMES_COM/server.test \
2716	PROBE_COM/server.test \
2717
2718	# --------------------
2719	# put all units containing tests into the following 4 sections (see also TESTED_UNITS below)
2720
2721	# recent development
2722	UNITS_TESTED_FIRST = \
2723	SL/SPECSEL/SPECSEL.test \
2724	SL/MATRIX/MATRIX.test \
2725	AWTI/AWTI.test \
2726	SL/FILTSEQEXP/FILTSEQEXP.test \
2727	SL/GROUP_SEARCH/GROUP_SEARCH.test \
2728	SL/PVP/PVP.test \
2729	SL/SAICALC/SAICALC.test \
2730	SL/TRANSLATE/TRANSLATE.test \
2731	SL/XFERSET/XFERSET.test \
2732
2733	# start units with long duration early
2734	UNITS_RUNNING_LONG = \
2735	ARBDB/libARBDB.test \
2736	AWTC/AWTC.test \
2737	TOOLS/TOOLS.tooltests \
2738
2739	# plain test-libaries that are not linked anywhere
2740	TEST_SANDBOXES = \
2741	SL/CB/CB.test \
2742	SL/HEADERTESTS/HEADERTESTS.test \
2743
2744	UNITS_TESTED = \
2745	AISC_MKPTPS/AISC_MKPTPS.tooltests \
2746	ARB_GDE/ARB_GDE.test \
2747	CONSENSUS_TREE/CONSENSUS_TREE.test \
2748	CONVERTALN/CONVERTALN.test \
2749	CORE/libCORE.test \
2750	DBSERVER/DBSERVER.test \
2751	DIST/DIST.test \
2752	EDIT4/EDIT4.test \
2753	GENOM_IMPORT/GENOM_IMPORT.test \
2754	HELP_SOURCE/HELP_SOURCE.tooltests \
2755	MERGE/MERGE.test \
2756	MULTI_PROBE/MULTI_PROBE.test \
2757	NTREE/NTREE.test \
2758	PARSIMONY/PARSIMONY.test \
2759	PERLTOOLS/PERLTOOLS.tooltests \
2760	PROBE/PROBE.test \
2761	PROBE_DESIGN/PROBE_DESIGN.test \
2762	PROBE_SET/PROBE_SET.tooltests \
2763	RNACMA/RNACMA.test \
2764	SL/ALILINK/ALILINK.test \
2765	SL/APP/APP.test \
2766	SL/CONSENSUS/CONSENSUS.test \
2767	SL/DB_QUERY/DB_QUERY.test \
2768	SL/FAST_ALIGNER/FAST_ALIGNER.test \
2769	SL/FILTER/FILTER.test \
2770	SL/INSDEL/INSDEL.test \
2771	SL/ITEM_SHADER/ITEM_SHADER.test \
2772	SL/ITEMS/ITEMS.test \
2773	SL/LOCATION/LOCATION.test \
2774	SL/MACROS/MACROS.test \
2775	SL/NDS/NDS.test \
2776	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.test \
2777	SL/PRONUC/PRONUC.test \
2778	SL/PTCLEAN/PTCLEAN.test \
2779	SL/REGEXPR/REGEXPR.test \
2780	SL/SEQIO/SEQIO.test \
2781	SL/TREE_READ/TREE_READ.test \
2782	SL/TREEDISP/TREEDISP.test \
2783	WINDOW/libWINDOW.test \
2784
2785	TESTED_UNITS = \
2786	$(UNITS_TESTED_FIRST) \
2787	$(UNITS_RUNNING_LONG) \
2788	$(TEST_SANDBOXES) \
2789	$(UNITS_TESTED) \
2790
2791	# ----------------------------------------
2792
2793	ifeq ($(DEVELOPER),RALF)
2794
2795	DEFINED_TEST_UNITS = \
2796	$(TESTED_UNITS) \
2797	$(UNTESTED_UNITS) \
2798	$(UNTESTABLE_UNITS) \
2799
2800	list_undefined_units:
2801	@UNIT_TESTER/list_undefined_units.pl $(DEFINED_TEST_UNITS) -- $(TESTED_UNITS_AUTO)
2802
2803	else
2804
2805	list_undefined_units:
2806
2807	endif
2808
2809	# ----------------------------------------
2810
2811	TEST_LOG_DIR = UNIT_TESTER/logs
2812	TEST_RUN_SUITE=$(MAKE) $(NODIR) -C UNIT_TESTER -f Makefile.suite -r
2813	# -> UNIT_TESTER/Makefile.suite
2814	TEST_MAKE_FLAGS=
2815	TEST_POST_CLEAN=
2816	ifeq ($(COVERAGE),1)
2817	TEST_POST_CLEAN=$(MAKE) clean_cov
2818	TEST_MAKE_FLAGS+=-j1
2819	endif
2820
2821
2822	%.test:
2823	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
2824	( \
2825	echo "take[1]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
2826	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
2827	"UNITDIR=$(@D)" \
2828	"UNITLIBNAME=$(@F:.test=)" \
2829	"COVERAGE=$(COVERAGE)" \
2830	"ARB_PID=$(ARB_PID)_$(@F)" \
2831	"DEVELOPER=$(DEVELOPER)" \
2832	runtest; \
2833	echo "take[1]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"; \
2834	$(TEST_POST_CLEAN) \
2835	) >$(TEST_LOG_DIR)/$(@F).log 2>&1; \
2836	UNIT_TESTER/log_result.pl $(TEST_LOG_DIR)/$(@F).log )
2837
2838	%.notest:
2839	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
2840	( \
2841	echo "take[4]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
2842	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
2843	"UNITDIR=$(@D)" \
2844	"UNITLIBNAME=$(@F:.notest=)" \
2845	"COVERAGE=0" \
2846	"ARB_PID=$(ARB_PID)_$(@F)" \
2847	"DEVELOPER=$(DEVELOPER)" \
2848	check_no_test; \
2849	echo "take[4]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'" \
2850	) >$(TEST_LOG_DIR)/$(@F).log 2>&1 )
2851
2852
2853	# tool test aliases (used to test one or multiple executable(s) in a single subdir):
2854	%.tooltests:
2855	$(error please define an explicit tooltest alias for $@)
2856
2857	AISC_MKPTPS/AISC_MKPTPS.tooltests : AISC_MKPTPS/mkptypes.test
2858	@echo "aliasing $@ -> $^"
2859	PERLTOOLS/PERLTOOLS.tooltests : PERLTOOLS/arb_proto_2_xsub.test
2860	@echo "aliasing $@ -> $^"
2861	PROBE_SET/PROBE_SET.tooltests : PROBE_SET/fb_test.test
2862	@echo "aliasing $@ -> $^"
2863	HELP_SOURCE/HELP_SOURCE.tooltests : HELP_SOURCE/arb_help2xml.test
2864	@echo "aliasing $@ -> $^"
2865	TOOLS/TOOLS.tooltests : TOOLS/arb_consensus_tree.test TOOLS/arb_probe.test TOOLS/arb_test.test
2866	@echo "aliasing $@ -> $^"
2867
2868	# aliases for tools w/o tests:
2869	READSEQ/READSEQ.tooltests:
2870	@echo "Note: no tests for $@"
2871
2872
2873	test_base: $(UNIT_TESTER_LIB:.a=.dummy) $(subst .test,.dummy,$(TEST_SANDBOXES))
2874
2875	clean_cov:
2876	find . $ -name ".gcda" -o -name ".gcov" -o -name "*.cov" $ -exec rm {} \;
2877
2878	clean_cov_all: clean_cov
2879	find . $ -name "*.gcno" $ -exec rm {} \;
2880
2881	cleanup_faked_arbpids:
2882	@rm ~/.arb_tmp/tmp/arb_pids_${USER}_${ARB_PID}_* \|\| true
2883
2884	cleanup_faked_arbpids_and_fail: cleanup_faked_arbpids
2885	@false
2886
2887	NOTESTS_IN_UNTESTED = $(subst .test,.notest,$(UNTESTED_UNITS))
2888
2889	run_tests_faked_arbpid:
2890	+@$(TEST_RUN_SUITE) init
2891	@echo "take[2]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2892	@$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(TESTED_UNITS) $(NOTESTS_IN_UNTESTED) \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2893	@echo "take[2]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2894	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2895	@$(MAKE) clean_cov >/dev/null
2896	@$(MAKE) cleanup_faked_arbpids
2897
2898	# @@@ instead of only running UNIT, this should as well run all tests this unit depends on? according to 'needs_libs'
2899	# @@@ '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
2900
2901	run_onetest_faked_arbpid:
2902	+@$(TEST_RUN_SUITE) init
2903	@echo "take[3]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2904	@test -n "$(UNIT)" \|\| (echo "Error: UNIT has to be defined for target 'run_onetest_faked_arbpid'!"; false)
2905	$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(UNIT).test \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2906	@echo "take[3]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2907	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2908	@$(MAKE) clean_cov >/dev/null
2909	@$(MAKE) cleanup_faked_arbpids
2910
2911	run_tests: test_base clean_cov
2912	$(MAKE) "ARB_PID=UT_$$$$" run_tests_faked_arbpid list_undefined_units
2913
2914	run_oneunitstests: test_base
2915	$(MAKE) "ARB_PID=UT_$$$$" run_onetest_faked_arbpid
2916
2917
2918	ut:
2919	ifeq ($(UNIT_TESTS),1)
2920	@echo $(MAKE) run_tests
2921	@$(MAKE) run_tests
2922	else
2923	@echo "Not compiled with unit tests"
2924	endif
2925
2926
2927	aut:
2928	+@$(TEST_RUN_SUITE) unskip
2929	$(MAKE) ut
2930
2931	# --------------------------------------------------------------------------------
2932
2933	TIMELOG=$(ARBHOME)/arb_time.log
2934	TIMEARGS=--append --output=$(TIMELOG) --format=" * %E(%S+%U) %P [%C]"
2935	TIMECMD=$(TIME) $(TIMEARGS)
2936
2937	time_one:
2938	ifeq ($(ONE_TIMED_TARGET),)
2939	@echo "Error: You have to pass ONE_TIMED_TARGET to $@"
2940	false
2941	else
2942	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET)"
2943	@$(TIMECMD) $(MAKE) $(ONE_TIMED_TARGET)
2944	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET) [done]"
2945	endif
2946
2947	timed_target:
2948	ifeq ($(TIMED_TARGET),)
2949	@echo "Error: You have to pass TIMED_TARGET to $@"
2950	false
2951	else
2952	@echo "Build time:" > $(TIMELOG)
2953	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2954	@cat $(TIMELOG)
2955	@rm $(TIMELOG)
2956	endif
2957
2958	timed_target_tested:
2959	ifeq ($(TIMED_TARGET),)
2960	@echo "Error: You have to pass TIMED_TARGET to $@"
2961	false
2962	else
2963	@echo "Build time:" > $(TIMELOG)
2964	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2965	$(MAKE) "ONE_TIMED_TARGET=ut" time_one
2966	@cat $(TIMELOG)
2967	@rm $(TIMELOG)
2968	endif
2969
2970	clean_timed_target:
2971	ifeq ($(TIMED_TARGET),)
2972	@echo "Error: You have to pass TIMED_TARGET to $@"
2973	false
2974	else
2975	@echo "Build time:" > $(TIMELOG)
2976	$(MAKE) "ONE_TIMED_TARGET=clean" time_one
2977	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2978	@cat $(TIMELOG)
2979	@rm $(TIMELOG)
2980	endif
2981
2982	# --------------------------------------------------------------------------------
2983
2984	CHECKOUT_MODIFIED=0# set to 1 to temporarily skip test for modifications (do not check in if set to 1)
2985
2986	check_svn_does_not_contain_generated:
2987	ifeq ($(CHECKOUT_MODIFIED),0)
2988	@echo "Testing that build does not modify files in SVN"
2989	@test 0 = `svn status \| wc -l` \|\| ( \
2990	echo "The checkout is not/no longer clean:"; \
2991	svn status; \
2992	echo "- if this fails instantly, your checkout is not clean"; \
2993	echo "- if this fails after other targets, these targets modify checked in data"; \
2994	echo " (a common cause may be that depends are not up to date)"; \
2995	false)
2996	else
2997	grep -Hn 'CHECKOUT_MODIFIED' Makefile
2998	endif
2999
3000	check_svn_ignores_generated:
3001	@test 0 = `svn status \| grep '^\?' \| wc -l` \|\| ( \
3002	echo "There are svn-unignored files:"; \
3003	svn status \| grep '^\?'; \
3004	echo "(all generated files should be svn-ignored)"; \
3005	false)
3006
3007	check_svn_state: check_svn_does_not_contain_generated
3008	$(MAKE) check_svn_ignores_generated
3009	$(MAKE) savetest
3010
3011	things_that_always_should_work: depends proto
3012
3013	post_commit_check:
3014	@echo "---------------------------------------- [Initial]"
3015	$(MAKE) check_svn_state
3016
3017	$(MAKE) clean
3018	@echo "---------------------------------------- [After 'make clean']"
3019	$(MAKE) check_svn_state
3020
3021	$(MAKE) things_that_always_should_work
3022	@echo "---------------------------------------- [After 'make things_that_always_should_work']"
3023	$(MAKE) check_svn_state
3024
3025	$(MAKE) all
3026	@echo "---------------------------------------- [After 'make all']"
3027	$(MAKE) check_svn_state
3028
3029	$(MAKE) things_that_always_should_work
3030	@echo "---------------------------------------- [Final]"
3031	$(MAKE) check_svn_state
3032
3033	# --------------------------------------------------------------------------------
3034	# sanitize arb_ntree; also works for clients (arb_edit4, ...) started from there.
3035
3036	sanitize: all
3037	( \
3038	export "LSAN_OPTIONS=max_leaks=30:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp"; \
3039	echo "sake[1]: Entering directory \`$(ARBHOME)'"; \
3040	$(ARBHOME)/bin/arb_ntree --execute _logged ~/data/test.arb 2>&1 ; \
3041	echo "sake[1]: Leaving directory \`$(ARBHOME)'" \
3042	) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
3043
3044	# --------------------------------------------------------------------------------
3045	# build and test one unit:
3046
3047	build_oneunit:
3048	$(MAKE) "WITHPERL=1" $(UNIT).dummy
3049
3050	oneunit:
3051	ifndef UNIT
3052	@echo "Please define UNIT, e.g. using"
3053	@echo " make \"UNIT=ARBDB/libARBDB\" oneunit"
3054	@echo " make \"UNIT=SL/TREEDISP/TREEDISP\" oneunit"
3055	@echo "(Note: 1st is a shared library, 2nd isn't)"
3056	false
3057	else
3058	@echo "Build time" > $(TIMELOG)
3059	@echo "$(SEP) $(MAKE) build_oneunit"
3060	@$(TIMECMD) $(MAKE) build_oneunit
3061	ifeq ($(UNIT_TESTS),1)
3062	@echo "$(SEP) $(MAKE) run_oneunitstests"
3063	@$(TIMECMD) $(MAKE) run_oneunitstests
3064	endif
3065	@cat $(TIMELOG)
3066	@rm $(TIMELOG)
3067	endif
3068
3069	# --------------------------------------------------------------------------------
3070	# Main targets:
3071
3072	tarfile: rebuild
3073	$(MAKE) prepare_libdir
3074	util/arb_compress
3075
3076	tarfile_quick: all
3077	$(MAKE) prepare_libdir
3078	util/arb_compress
3079
3080	# -----------------------------------
3081
3082	build: arb
3083	$(MAKE) check_bin_dep preplib compile_compatibility fig_cure
3084
3085	all:
3086	@echo "Build time" > $(TIMELOG)
3087	# $(MAKE) clean_checked_vect # uncomment to rebuild sources where expected vectorization gets tested
3088	@echo "$(SEP) $(MAKE) all"
3089	@$(TIMECMD) $(MAKE) build
3090	@echo $(SEP)
3091	@echo "made 'all' with success."
3092	@echo "to start arb enter 'arb'"
3093	ifeq ($(UNIT_TESTS),1)
3094	@echo "$(SEP) $(MAKE) run_tests"
3095	@$(TIMECMD) $(MAKE) run_tests
3096	endif
3097	@echo "$(SEP) $(MAKE) all [done]"
3098	ifeq ($(DEBUG),1)
3099	@$(MAKE) save_test_no_error >/dev/null # just show hints
3100	endif
3101	@cat $(TIMELOG)
3102	@rm $(TIMELOG)
3103
3104	rebuild: clean
3105	$(MAKE) all
3106
3107	# --------------------------------------------------------------------------------
3108	# special targets showing obvious error at bottom
3109	# (intended to be used from automated builds)
3110
3111	BUILD_LOG=build.log
3112	SHELL=bash
3113	REDIRECT_KEEP_EXITCODE = tee $(BUILD_LOG) ; exit "$${PIPESTATUS[0]}"
3114	EXTRACT_ERROR_SUMMARY = (./SOURCE_TOOLS/short_error_summary.pl $(BUILD_LOG); false)
3115
3116	REEXTRACT:
3117	@echo "Note: Re-extracting errors from $(BUILD_LOG):"
3118	@$(EXTRACT_ERROR_SUMMARY)
3119
3120	ALL:
3121	@(($(MAKE) all 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
3122
3123	REBUILD:
3124	@(($(MAKE) rebuild 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
3125
3126	TARFILE:
3127	@(($(MAKE) tarfile 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
3128
3129	TARFILE_QUICK:
3130	@(($(MAKE) tarfile_quick 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
3131

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