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Last change on this file was 19695, checked in by westram, 7 days ago
refactored selection list admin uses `SelectionAdmin` to provide global data moved code from `NTREE` to `SPECSEL`
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 88.9 KB

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1	# =============================================================== #
2	# #
3	# File : Makefile #
4	# #
5	# Institute of Microbiology (Technical University Munich) #
6	# http://www.arb-home.de/ #
7	# #
8	# =============================================================== #
9
10	# -----------------------------------------------------
11	# The ARB Makefile is aware of the following defines:
12	#
13	# CC C compiler (should be defined by OS)
14	# CXX C++ compiler (should be defined by OS)
15	#
16	# DEVELOPER=name special compilation (values: ANY,RELEASE,your name)
17	# OPENGL=0/1 whether OPENGL is available
18	#
19	# -----------------------------------------------------
20	# Paths for several libraries may be set from config.makefile by using:
21	#
22	# export XLIBS=$(shell pkg-config --libs xpm xerces-c)
23	# export XINCLUDES=$(shell pkg-config --cflags x11)
24	# export XAW_LIBS=$(shell pkg-config --libs xaw7)
25	# export XML_INCLUDES=$(shell pkg-config --cflags xerces-c)
26	#
27	# You make have to explicitely point pkg-config to the *.pc files needed.
28	# For example, Xquartz X11 libraries on macOS can be located by adding
29	# the following line before those given above:
30	#
31	# export PKG_CONFIG_PATH=/usr/X11/lib/pkgconfig
32	#
33	# If you introduce a new variable that is handled as described above,
34	# please add to section .@InjectedEnvironment
35	#
36	# -----------------------------------------------------
37	# ARB Makefile and ARB source code are aware of the following defines:
38	#
39	# $(MACH) name of the machine (LINUX or DARWIN; see config.makefile)
40	# DEBUG compiles the DEBUG sections
41	# DEBUG_GRAPHICS all X-graphics are flushed immediately (for debugging)
42	# ARB_64=0/1 1=>compile 64 bit version
43	# UNIT_TESTS=0/1 1=>compile in unit tests and call them after build
44	# COVERAGE=0/1/2 compile in gcov support (useful together with UNIT_TESTS=1)
45	# 0=no, 1+2=compile in, 1=show
46	# STABS=0/1 force stabs format? (0 = "use default format")
47	# SANITIZE=0/#/all use Sanitizer? (defaults to 0,
48	# 1=AddressSanitizer+LeakSanitizer,
49	# 2=UndefinedBehaviorSanitizer,
50	# combine bit-values to activate multiple Sanitizers,
51	# specify 'all' to activate all)
52	# IGNORE_LEAKS=1 does not abort when leaks are detected (while using SANITIZE=1/all)
53	# SHOWTODO=0/1 activate TODO-warnings? (defaults to 0, except for ralf)
54	#
55	# -----------------------------------------------------
56	# The ARB source code is aware of the following defines:
57	#
58	# NDEBUG doesn't compile the DEBUG sections
59	# DEVEL_$(DEVELOPER) developer-dependent flag (enables you to have private sections in code)
60	# DEVELOPER='ANY' (default setting) will be ignored
61	# configurable in config.makefile
62	#
63	# -----------------------------------------------------
64
65	ifndef ARB_ORG_MAKEFLAGS
66	ARB_ORG_MAKEFLAGS=$(MAKEFLAGS)
67	else
68	ifeq ($(ARB_ORG_MAKEFLAGS),)
69	ARB_ORG_MAKEFLAGS=$(MAKEFLAGS)
70	endif
71	endif
72
73	# Read configuration
74	include config.makefile
75	CONFIG_MAKEFILE_FOUND=$(strip $(wildcard config.makefile))
76
77	# strip spaces from values defined in config.makefile
78	# (otherwise they easily have spaces appended)
79	ifdef DEVELOPER
80	DEVELOPER := $(strip $(DEVELOPER))
81	endif
82	ifdef OPENGL
83	OPENGL := $(strip $(OPENGL))
84	endif
85	ifdef ISINA
86	ISINA := $(strip $(ISINA))
87	endif
88	ifdef DEBUG
89	DEBUG := $(strip $(DEBUG))
90	endif
91	ifdef UNIT_TESTS
92	UNIT_TESTS := $(strip $(UNIT_TESTS))
93	endif
94	ifdef COVERAGE
95	COVERAGE := $(strip $(COVERAGE))
96	endif
97	ifdef SHOWTODO
98	SHOWTODO := $(strip $(SHOWTODO))
99	endif
100	ifdef STABS
101	STABS := $(strip $(STABS))
102	endif
103	ifdef TRACESYM
104	TRACESYM := $(strip $(TRACESYM))
105	endif
106	ifdef DEBUG_GRAPHICS
107	DEBUG_GRAPHICS := $(strip $(DEBUG_GRAPHICS))
108	endif
109
110	# set defaults for (or strip) variables commented out in config.makefile:
111	ifdef SANITIZE
112	SANITIZE := $(strip $(SANITIZE))
113	else
114	SANITIZE:=0
115	endif
116	ifdef IGNORE_LEAKS
117	IGNORE_LEAKS := $(strip $(IGNORE_LEAKS))
118	else
119	IGNORE_LEAKS:=0
120	endif
121	ifndef DARWIN
122	DARWIN:=0
123	else
124	DARWIN := $(strip $(DARWIN))
125	endif
126	ifndef LINUX
127	LINUX:=0
128	else
129	LINUX := $(strip $(LINUX))
130	endif
131	ifndef DEBIAN
132	DEBIAN:=0
133	else
134	DEBIAN := $(strip $(DEBIAN))
135	endif
136	ifndef ARB_64
137	ARB_64=1#default to 64bit
138	else
139	ARB_64 := $(strip $(ARB_64))
140	endif
141
142	# Variables allowed for injection [InjectedEnvironment]
143	# (alternatively initialize them with '?=', e.g. done for XLIBS and XINCLUDES)
144	# In both cases add them to SOURCE_TOOLS/export2sub
145	ifndef XML_INCLUDES
146	XML_INCLUDES=
147	endif
148	ifndef XAW_LIBS
149	XAW_LIBS=
150	endif
151
152
153	ifneq ($(CONFIG_MAKEFILE_FOUND),)
154	ifneq ($(DARWIN)$(LINUX),10)
155	ifneq ($(DARWIN)$(LINUX),01)
156	$(error exactly one of DARWIN=1 or LINUX=1 has to be defined (got:$(DARWIN)$(LINUX)))
157	endif
158	endif
159	endif
160
161	# compiler settings:
162	ifneq ($(CC),use__A_CC__instead_of__CC)
163	A_CC:=$(CC)# compile C
164	A_CXX:=$(CXX)# compile C++
165
166	# uncomment to ensure no submakefile uses CC and CXX directly
167	override CC:=use__A_CC__instead_of__CC
168	override CXX:=use__A_CXX__instead_of__CXX
169	endif
170
171	export CC CXX A_CC A_CXX
172
173	# unconditionally prepend $(ARBHOME)/lib to LD_LIBRARY_PATH if not found
174	ifeq ($(findstring $(ARBHOME)/lib,$(LD_LIBRARY_PATH)),)
175	LD_LIBRARY_PATH:=${ARBHOME}/lib:$(LD_LIBRARY_PATH)
176	endif
177
178	# store LD_LIBRARY_PATH to circumvent SIP restrictions:
179	ARBBUILD_LIBRARY_PATH:=$(LD_LIBRARY_PATH)
180
181	FORCEMASK = umask 002
182	NODIR=--no-print-directory
183
184	SED:=$(ARBHOME)/SH/arb_sed
185	READLINK:=$(ARBHOME)/SH/arb_readlink
186
187	# ---------------------- compiler version detection
188
189	# supported gcc versions:
190	ALLOWED_gcc_VERSIONS=\
191	4.4.3 4.4.5 4.4.6 4.4.7 \
192	4.5.2 \
193	4.6.1 4.6.2 4.6.3 4.6.4 \
194	4.7.1 4.7.2 4.7.3 4.7.4 \
195	4.8.0 4.8.1 4.8.2 4.8.3 4.8.4 4.8.5 \
196	4.9.0 4.9.1 4.9.2 4.9.3 4.9.4 \
197	5.1.0 5.2.0 5.3.0 5.4.0 5.5.0 \
198	6.1.0 6.2.0 6.3.0 6.4.0 6.5.0 \
199	7.1.0 7.2.0 7.3.0 7.4.0 7.5.0 \
200	8.1.0 8.2.0 8.3.0 8.4.0 8.5.0 \
201	9.1.0 9.2.0 9.3.0 9.4.0 9.5.0 \
202	10.1.0 10.2.0 10.3.0 10.4.0 10.5.0 \
203
204	# Note: starting with version 5, arb silently accepts any subversion number
205	# above zero. See SOURCE_TOOLS/arb_compiler_version.pl@acceptSubVersions
206	#
207	# This may cause problems when manually checking for compiler versions in code
208	# (GCC_VERSION_CODE is not affected, GCC_PATCHLEVEL_CODE may cause problems!)
209	# ----------------------
210
211	COMPILER_INFO:=$(shell SOURCE_TOOLS/arb_compiler_version.pl $(A_CXX))
212	COMPILER_NAME:=$(word 1,$(COMPILER_INFO))
213	COMPILER_VERSION:=$(word 2,$(COMPILER_INFO))
214
215	USE_CLANG:=0
216	ifneq ($(COMPILER_NAME),gcc)
217	ifeq ($(COMPILER_NAME),clang)
218	USE_CLANG:=1
219	else
220	ifeq ($(COMPILER_VERSION),4.6.4)
221	# gcc version 4.6.4 segfaults when dumping symbols for detection (silently accept as gcc)
222	COMPILER_NAME:=gcc
223	else
224	$(error failed to detect COMPILER_NAME (got '$(COMPILER_NAME)', expected 'clang' or 'gcc'))
225	endif
226	endif
227	endif
228
229	ifeq ($(USE_CLANG),1)
230	# accept all clang versions:
231	ALLOWED_COMPILER_VERSIONS=$(COMPILER_VERSION)
232	else
233	ALLOWED_COMPILER_VERSIONS=$(ALLOWED_gcc_VERSIONS)
234	endif
235
236	COMPILER_VERSION_ALLOWED=$(strip $(subst ___,,$(foreach version,$(ALLOWED_COMPILER_VERSIONS),$(findstring ___$(version)___,___$(COMPILER_VERSION)___))))
237
238	#---------------------- force no root
239
240	YOU_ARE_ROOT := $(strip $(shell bash -c 'echo $$((EUID == 0))'))
241	ifeq ($(YOU_ARE_ROOT),1)
242	$(error Building arb as root user is not recommended)
243	# To install a custom-compiled arb system-wide, build target 'tarfile' as "normal" user.
244	# Afterwards, use arb_install.sh as root.
245	endif
246
247	#---------------------- split gcc version
248
249	SPLITTED_VERSION:=$(subst ., ,$(COMPILER_VERSION))
250
251	USE_GCC_MAJOR:=$(word 1,$(SPLITTED_VERSION))
252	USE_GCC_MINOR:=$(word 2,$(SPLITTED_VERSION))
253	USE_GCC_PATCHLEVEL:=$(word 3,$(SPLITTED_VERSION))
254
255	USE_GCC_452_OR_HIGHER:=
256	USE_GCC_46_OR_HIGHER:=
257	USE_GCC_47_OR_HIGHER:=
258	USE_GCC_48_OR_HIGHER:=
259	USE_GCC_49_OR_HIGHER:=
260	USE_GCC_50_OR_HIGHER:=
261	USE_GCC_60_OR_HIGHER:=
262	USE_GCC_70_OR_HIGHER:=
263	USE_GCC_80_OR_HIGHER:=
264	USE_GCC_90_OR_HIGHER:=
265
266	ifeq ($(USE_CLANG),0)
267	ifeq ($(USE_GCC_MAJOR),4)
268	ifeq ($(USE_GCC_MINOR),5)
269	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),23456789)','')
270	USE_GCC_452_OR_HIGHER:=yes
271	endif
272	else
273	ifneq ('$(findstring $(USE_GCC_MINOR),6789)','')
274	USE_GCC_452_OR_HIGHER:=yes
275	USE_GCC_46_OR_HIGHER:=yes
276	ifneq ($(USE_GCC_MINOR),6)
277	USE_GCC_47_OR_HIGHER:=yes
278	ifneq ($(USE_GCC_MINOR),7)
279	USE_GCC_48_OR_HIGHER:=yes
280	ifneq ($(USE_GCC_MINOR),8)
281	USE_GCC_49_OR_HIGHER:=yes
282	endif
283	endif
284	endif
285	endif
286	endif
287	else
288	# gcc 5.x or higher
289	USE_GCC_452_OR_HIGHER:=yes
290	USE_GCC_46_OR_HIGHER:=yes
291	USE_GCC_47_OR_HIGHER:=yes
292	USE_GCC_48_OR_HIGHER:=yes
293	USE_GCC_49_OR_HIGHER:=yes
294	USE_GCC_50_OR_HIGHER:=yes
295	ifneq ($(USE_GCC_MAJOR),5)
296	# gcc 6.x or higher
297	USE_GCC_60_OR_HIGHER:=yes
298	ifneq ($(USE_GCC_MAJOR),6)
299	# gcc 7.x or higher
300	USE_GCC_70_OR_HIGHER:=yes
301	ifneq ($(USE_GCC_MAJOR),7)
302	# gcc 8.x or higher
303	USE_GCC_80_OR_HIGHER:=yes
304	ifneq ($(USE_GCC_MAJOR),8)
305	# gcc 9.x or higher
306	USE_GCC_90_OR_HIGHER:=yes
307	endif
308	endif
309	endif
310	endif
311	endif
312	endif
313
314	#---------------------- define special directories for non standard builds
315
316	ifeq ($(DARWIN),1)
317	OSX_FW:=/System/Library/Frameworks
318	OSX_FW_OPENGL:=$(OSX_FW)/OpenGL.framework/Versions/A/Libraries
319	OSX_FW_GLUT:=$(OSX_FW)/GLUT.framework/Versions/A/Libraries
320	OSX_FW_IMAGEIO:=$(OSX_FW)/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources
321	endif
322
323	#---------------------- SSE vectorization
324	# for details about vectorization checks see SOURCE_TOOLS/vectorize.README
325
326	DISABLE_VECTORIZE_CHECK:=0# set to 1 to completely disable vectorization checks
327	TRACE_MISSED_VECTORIZATIONS:=0# set to 1 to activate detailed output about failed vectorizations
328	# (does also show details about successful vectorized loops, which are not optimal)
329	VECTORIZATION_CHECK_CANDIDATES:=0# set to 1 to show vectorizations that may be checked
330	# (for yet unchecked files)
331	# Note: TRACE_MISSED_VECTORIZATIONS and VECTORIZATION_CHECK_CANDIDATES cannot be used together!
332
333	#---------------------- Support for OPENMP
334
335	USE_OPENMP:=1
336	ifeq ($(DARWIN),1)
337	USE_OPENMP:=0
338	endif
339
340	#----------------------
341
342	ifeq ($(DARWIN),1)
343	LINK_STATIC=1# link static
344	else
345	LINK_STATIC=0# link dynamically
346	# LINK_STATIC=1# link static (testing only)
347	endif
348
349	shared_cflags :=# flags for shared lib compilation
350	onlyC_flags :=# flags only suitable for C (not C++; see cxxflags).
351	clflags :=# linker flags (when passed through gcc)
352	extended_warnings :=# warning flags for C and C++-compiler
353	extended_cpp_warnings :=# warning flags for C++-compiler only
354
355	ifeq ($(DEBUG),0)
356	dflags := -DNDEBUG# defines
357	ifeq ($(USE_CLANG),1)
358	cflags := -O3# compiler flags (C and C++)
359	else
360	clflags += -Wl,-O2# passthrough linker flags
361	# ------- standard optimization:
362	cflags := -O3# compiler flags (C and C++)
363	# ------- test changed optimization (DISABLE_VECTORIZE_CHECK for -O2 or lower):
364	# cflags := -O2# do not commit uncommented!
365	# DISABLE_VECTORIZE_CHECK:=1
366	endif
367	endif
368
369	ifeq ($(DEBIAN),1)
370	clflags += -Wl,-rpath=/usr/lib/arb/lib -Wl,-z,relro
371	endif
372
373	ifeq ($(DEBUG),1)
374	dflags := -DDEBUG
375
376	gdb_common := -g -g3 -ggdb -ggdb3
377
378	DBGOPTI:=-O0
379	ifneq ('$(SANITIZE)','0')
380	# sanitizer report several bogus buffer-overflows when arb is build with -O0 (e.g. with gcc 7.5.0)
381	DBGOPTI:=-O1
382	endif
383
384	ifeq ($(STABS),1)
385	$(error STABS no longer supported)
386	endif
387
388	cflags := $(DBGOPTI) $(gdb_common)
389	# cflags := -O2 $(gdb_common) # use this for callgrind (force inlining)
390
391	ifeq ($(DARWIN),0)
392	clflags += -Wl,-g
393	# Note:
394	# Previously '-Wl,-noinhibit-exec' was added to 'clflags' here,
395	# to fix some issues with launchpad binutils (see [12972]).
396	# But that change also caused 'undefined symbols' NOT to be reported as errors
397	# at link time, producing executables that fail at runtime :/
398	endif
399
400	ifeq ($(DEBUG_GRAPHICS),1)
401	dflags += -DDEBUG_GRAPHICS
402	endif
403
404	endif # DEBUG only
405
406	# ------------------------------ POST_COMPILE - control how much you get spammed
407	# (please do not change default in SVN)
408	POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl
409
410	# POST_COMPILE += --original # dont modify compiler output
411	# POST_COMPILE += --hide-Noncopyable-advices
412	# POST_COMPILE += --show-useless-Weff++
413	# POST_COMPILE += --no-warnings
414	# POST_COMPILE += --only-first-error
415	# POST_COMPILE += --no-warnings --only-first-error
416
417	# always pass used compiler version to postcompile:
418	POST_COMPILE += --compiler=$(COMPILER_VERSION)
419
420	# ------------------------------
421
422	# Enable extra warnings
423	extended_warnings :=
424	extended_cpp_warnings :=
425
426	# C and C++
427	extended_warnings += -Wwrite-strings -Wunused -Wno-aggregate-return
428
429	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
430	# disable shadow warnings for gcc 4.8 (and lower)
431	# (does e.g. warn if a method-name is used as parameter in another method - even for derived classes. unusable!)
432	extended_warnings += -Wshadow
433	endif
434
435	# C++ only
436	extended_cpp_warnings += -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute
437	extended_cpp_warnings += -Wctor-dtor-privacy
438	# extended_cpp_warnings += -Wfloat-equal
439
440	extended_cpp_warnings += -Wmissing-noreturn
441	# extended_cpp_warnings += -Wold-style-cast# (warns about 28405 old-style casts)
442	extended_cpp_warnings += -Winit-self
443	extended_cpp_warnings += -Wstrict-aliasing
444	extended_cpp_warnings += -Wextra
445
446	# ------- above only warning-options already available in gcc 4.4.3
447
448	# -Weffc++ broken in 4.7.x series
449	# gcc 4.7.3 crashes on GenomeImport.cxx when -Weffc++ is active
450	# (bug reported https://gcc.gnu.org/bugzilla/show_bug.cgi?id=56923; apparently wont be fixed for 4.7-series)
451	# gcc 4.7.4 crashes on DBwriter.cxx when -Weffc++ is active
452	WEFFC_BROKEN:=0
453	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
454	ifneq ('$(USE_GCC_48_OR_HIGHER)','yes')
455	WEFFC_BROKEN:=1
456	endif
457	endif
458	ifeq ('$(WEFFC_BROKEN)','0')
459	extended_cpp_warnings += -Weffc++
460	endif
461
462	# turn off -Wmaybe-uninitialized in debug mode (gets activated with -Wextra). too many bogus warnings
463	ifeq ($(DEBUG),1)
464	ifeq ($(USE_CLANG),0)
465	extended_cpp_warnings += -Wno-maybe-uninitialized
466	endif
467	endif
468
469	SUGGEST_FINAL:=
470
471	ifeq ('$(USE_GCC_452_OR_HIGHER)','yes')
472	extended_cpp_warnings += -Wlogical-op# gcc 4.5.2
473	endif
474	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
475	extended_cpp_warnings += -Wzero-as-null-pointer-constant# gcc 4.7
476	endif
477	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
478	extended_cpp_warnings += -Wunused-local-typedefs# available since gcc 4.7 (but fails for each STATIC_ASSERT, so enable only for Cxx11)
479	endif
480	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
481	extended_cpp_warnings += -Wswitch-bool
482	extended_cpp_warnings += -Wlogical-not-parentheses
483	extended_cpp_warnings += -Wsizeof-array-argument
484	extended_cpp_warnings += -Wbool-compare
485
486	SUGGEST_FINAL:=yes
487	endif
488	ifeq ('$(USE_GCC_60_OR_HIGHER)','yes')
489	extended_cpp_warnings += -Wduplicated-cond
490	endif
491	ifeq ('$(USE_GCC_80_OR_HIGHER)','yes')
492	extended_cpp_warnings += -Wmultistatement-macros
493	endif
494
495	# switch off final suggestions for 8.3.0 and 8.4.0:
496	ifeq ('$(COMPILER_VERSION)','8.3.0')
497	SUGGEST_FINAL:=no
498	endif
499	ifeq ('$(COMPILER_VERSION)','8.4.0')
500	SUGGEST_FINAL:=no
501	endif
502
503	ifeq ($(DEVELOPER),RELEASE)
504	# switch off final suggestions in RELEASE:
505	SUGGEST_FINAL:=no
506	endif
507	# suggest final:
508	ifeq ('$(SUGGEST_FINAL)','yes')
509	extended_cpp_warnings += -Wsuggest-final-types
510	extended_cpp_warnings += -Wsuggest-final-methods
511	dflags += -DSUGGESTS_FINAL
512	endif
513
514	#---------------------- turn off clang bogus warnings
515
516	ifeq ($(USE_CLANG),1)
517	# -Wmismatched-tags warns about struct/class mismatch in forward declarations (which is explicitely allowed)
518	# -Wchar-subscripts reports too many bogus warnings for "array['x']" (when 'x' is known to be in range [0..128])
519	# -Wunused-private-field report too many false positives (currently ~ 2 of 3)
520	# -Wstring-plus-int warns about common ARB coding practice
521	# -Wgnu-static-float-init warns about accepted GNU extension
522	extended_cpp_warnings += -Wno-mismatched-tags -Wno-char-subscripts -Wno-unused-private-field -Wno-string-plus-int
523	ifeq ('$(COMPILER_VERSION)','4.2.1')
524	# jenkins build (doesn't know switch -Wno-gnu-static-float-init)
525	extended_cpp_warnings += -Wno-gnu
526	else
527	extended_cpp_warnings += -Wno-gnu-static-float-init
528	endif
529	endif
530
531	#---------------------- developer
532
533	ifneq ($(DEVELOPER),ANY) # ANY=default setting (skip all developer specific code)
534	dflags += -DDEVEL_$(DEVELOPER)# activate developer/release specific code
535	endif
536
537	#---------------------- activate TODO warnings?
538
539	ifndef SHOWTODO
540	ifeq ($(DEVELOPER),RALF)
541	SHOWTODO:=1
542	else
543	SHOWTODO:=0
544	endif
545	endif
546	ifeq ($(SHOWTODO),1)
547	dflags += -DWARN_TODO# activate "TODO" warnings
548	endif
549
550	#---------------------- 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	# none of the following standards works with clang3.3 (under linux) => dont use standard (as done before r15516)
994	# cxxflags += -std=gnu++11
995	# cxxflags += -std=gnu++0x
996	else
997	ifeq ('$(USE_GCC_60_OR_HIGHER)','yes')
998	cxxflags += -std=gnu++14# see also TEMPLATES/cxxforward.h@USE_Cxx14
999	else
1000	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
1001	cxxflags += -std=gnu++11# see also TEMPLATES/cxxforward.h@USE_Cxx11
1002	else
1003	# gcc versions between 4.3 (lowest supported) and <4.7
1004	cxxflags += -std=gnu++0x
1005	endif
1006	endif
1007	endif
1008
1009	LINK_STATIC_LIB := $(AR) -csq# link static lib
1010	LINK_EXECUTABLE := $(A_CXX) $(blflags) -o# link executable (c++)
1011
1012	ifeq ($(LINK_STATIC),1)
1013	SHARED_LIB_SUFFIX = a# static lib suffix
1014	LINK_SHARED_LIB := $(LINK_STATIC_LIB)
1015	else
1016	SHARED_LIB_SUFFIX = so# shared lib suffix
1017	LINK_SHARED_LIB := $(A_CXX) $(llflags) -shared -o# link shared lib
1018	endif
1019
1020	ifeq ($(DARWIN),1)
1021	lflags4perl:=
1022	else
1023	lflags4perl:=$(cross_lflags) -shared
1024	endif
1025
1026	# delete variables unused below
1027	blflags:=
1028	llflags:=
1029
1030	# other used tools
1031	MAKEDEPEND_PLAIN = makedepend
1032	MAKEDEPEND = $(FORCEMASK);$(MAKEDEPEND_PLAIN)
1033
1034	SEPNODATE:=--------------------------------------------------------------------------------
1035	SEP=[`date +%M:%S.%N`] ------------------------------------------------
1036	# to analyse timings run
1037	# make -j9 clean; make -j9 all \| grep '^\[' \| sort
1038	# make -j9 "TIMED_TARGET=perl" clean_timed_target \| grep '^\[' \| sort
1039
1040	# ------------------------------------------------------------ DYNLIBDEFS
1041	# various dynamic library definitions for linking executables:
1042	#
1043	# SYSLIBS: system libraries needed by database lib
1044	# ARBDB_LIB: database lib
1045	# DBSYS_LIBS: executable using database (but no GUI)
1046	# GUI_LIBS: executable using database and GUI (arb gui uses database)
1047	#
1048	# Note: definitions exported to sub-makefiles are described in SOURCE_TOOLS/parent_make.txt
1049
1050	CORE_LIB=-lCORE
1051	ARBDB_LIB=-lARBDB $(CORE_LIB)
1052	DBSYS_LIBS = $(ARBDB_LIB) $(SYSLIBS)
1053
1054	GUI_LIBS_PREFIX:=
1055	ifeq ($(DARWIN),1)
1056	# this seem to be added at wrong place, since opengl is only needed to link EDIT4
1057	GUI_LIBS_PREFIX:=-framework GLUT -framework OpenGL
1058	endif
1059
1060	GUI_LIBS=$(GUI_LIBS_PREFIX) $(DBSYS_LIBS) -lWINDOW $(XLIBS)
1061
1062	LIBPATH = -L$(ARBHOME)/lib
1063
1064	DEST_LIB = lib
1065	DEST_BIN = bin
1066
1067	CC_INCLUDES := -I. -I$(ARBHOME)/INCLUDE $(XINCLUDES) $(ARB_GLIB_INCLUDE) $(ARB_RPC_INCLUDE)
1068	CXX_INCLUDES := $(CC_INCLUDES)
1069	MAKEDEPENDFLAGS := -- -DARB_OPENGL -DUNIT_TESTS -D__cplusplus -I. -Y$(ARBHOME)/INCLUDE
1070
1071	# ---------------------------------------
1072	# wrap main()
1073
1074	use_ARB_main=$(ARBHOME)/SOURCE_TOOLS/arb_main_cpp.o
1075	use_ARB_main_C=$(ARBHOME)/SOURCE_TOOLS/arb_main_c.o
1076
1077	# -----------------------------------------
1078	# unique build-id
1079	# - different for different calls of make
1080	# - constant in recursive calls
1081
1082	ifndef ARBBID
1083	ARBBID:=$(shell SOURCE_TOOLS/uniqueID.sh)
1084	endif
1085
1086	# -----------------------------------------
1087	# export variables to submakefiles
1088
1089	include SOURCE_TOOLS/export2sub
1090
1091	# do not define (exported) variables below this point
1092
1093	# -------------------------
1094	# Main arb targets:
1095	# -------------------------
1096
1097	first_target:
1098	$(MAKE) checks
1099	@echo $(SEPNODATE)
1100	@echo 'Main targets:'
1101	@echo ''
1102	@echo ' all - Compile ARB + TOOLs + and copy shared libs + link foreign software'
1103	@echo ' (That is most likely the target you want)'
1104	@echo ''
1105	@echo ' clean - remove generated files ("SUBDIR/SUBDIR.clean" to clean only SUBDIR)'
1106	@echo ' rebuild - clean + all'
1107	@echo ' cleanlinked - remove all binaries'
1108	@echo ' relink - cleanlinked + all (=relink all from objects)'
1109	@echo ''
1110	@echo 'Targets for automated builds:'
1111	@echo ''
1112	@echo ' ALL, REBUILD, TARFILE + TARFILE_QUICK '
1113	@echo ' - same as all, rebuild, tarfile + tarfile_quick'
1114	@echo ' - if errors occur, they are extracted and listed at tail of output'
1115	@echo ''
1116	@echo $(SEPNODATE)
1117	@echo ''
1118	@echo 'Development targets:'
1119	@echo ''
1120	@echo ' depends - create or update dependencies ("SUBDIR/SUBDIR.depends" to update only SUBDIR)'
1121	@echo ' proto - create or update prototypes ("SUBDIR/SUBDIR.proto" to update only SUBDIR)'
1122	@echo ' tags - create tags for xemacs'
1123	@echo ' show - show available shortcuts (AKA subtargets)'
1124	@echo ' up - shortcut for depends+proto+tags'
1125	ifeq ($(UNIT_TESTS),1)
1126	@echo ' ut - only run tests'
1127	@echo ' "UNIT=..." oneunit - build one unit and run tests (see also UNIT_TESTER/Makefile.setup.local)'
1128	endif
1129	ifneq ($(SANITIZE),0)
1130	@echo ' sanitize - all + run arb_ntree with sanitizer (test.arb + execute _logged)'
1131	endif
1132	@echo ' modified - rebuild files modified in svn checkout (does touch)'
1133	@echo ' touch - touch files modified in svn checkout'
1134	@echo ''
1135	@echo 'Some often used sub targets:'
1136	@echo ''
1137	@echo ' arb - Just compile ARB (but none of the integrated tools)'
1138	@echo ' menus - create lib/gde/arb.menu from GDEHELP/ARB_GDEmenus.source'
1139	@echo ' perl - Compile the PERL XSUBS into lib/ARB.so and create links in lib to perl'
1140	@echo ' binlink - Create all links in the bin directory'
1141	@echo ''
1142	@echo 'Internal maintenance:'
1143	@echo ''
1144	@echo ' relinfo - show help on release targets'
1145	@echo ' tarfile - make rebuild and create arb version tarfile ("tarfile_quick" to skip rebuild)'
1146	@echo ' save - save all basic ARB sources into arbsrc_DATE ("savetest" to check filelist)'
1147	@echo ' patch - save svn diff to patchfile'
1148	@echo ' source_doc - create doxygen documentation'
1149	@echo ' relocated - rebuild partly (use when you have relocated ARBHOME)'
1150	@echo ' check_res - check resource usage'
1151	@echo ' dep_graph - Build dependency graphs'
1152	@echo ' clean_cov - Clean coverage results'
1153	@echo ''
1154	@echo ' clean_opengl_changed - clean after changing OPENGL setting in config.Makefile'
1155	@echo ' clean_checked_vect - clean units containing vectorization checks'
1156	@echo ' cleanRelinkable - similar to cleanlinked (but skips raxml8 to avoid rebuild)'
1157	@echo ''
1158	@echo ' post_commit_check - Checks whether'
1159	@echo ' * main make targets work,'
1160	@echo ' * dependencies and prototypes are up to date,'
1161	@echo ' * SVN-controlled files remain unaffected by called targets and'
1162	@echo ' * all generated files are ignored.'
1163	@echo ' (has to be called in a clean SVN checkout)'
1164	@echo $(SEPNODATE)
1165	@echo ''
1166
1167	relinfo:
1168	@echo ''
1169	@echo $(SEPNODATE)
1170	@echo 'Release targets:'
1171	@echo ''
1172	@echo ' inc_candi - increase RC candidate-number (only possible in "rc" branch, not needed for RC1)'
1173	@echo ' inc_patch - increase release patchlevel (only possible in "stable" branch)'
1174	@echo ' inc_minor - increase minor version number (only possible in "trunk")'
1175	@echo ' inc_major - increase MAJOR version number (only possible in "trunk")'
1176	@echo ''
1177	@echo ' show_version - show version tag'
1178	@echo ''
1179	@echo $(SEPNODATE)
1180	@echo ''
1181
1182	# auto-generate config.makefile:
1183
1184	config.makefile : config.makefile.template
1185	@echo --------------------------------------------------------------------------------
1186	ifeq ($(CONFIG_MAKEFILE_FOUND),)
1187	@cp $< $@
1188	@echo '$(ARBHOME)/$@:1: has been generated.'
1189	@echo 'Please edit $@ to configure your system!'
1190	@echo --------------------------------------------------------------------------------
1191	@false
1192	else
1193	@echo '$(ARBHOME)/$<:1: is more recent than'
1194	@echo '$(ARBHOME)/$@:1:'
1195	@ls -al config.makefile*
1196	@echo --------------------------------------------------------------------------------
1197	@echo "Updating $@ (if this fails, check manually)"
1198	SOURCE_TOOLS/update_config_makefile.pl
1199	@echo "Sucessfully updated $@"
1200	@echo --------------------------------------------------------------------------------
1201	@ls -al config.makefile*
1202	@echo --------------------------------------------------------------------------------
1203	@echo "Diff to your old config.makefile:"
1204	@echo --------------------------------------------------------------------------------
1205	-diff $@.bak $@
1206	@echo --------------------------------------------------------------------------------
1207	endif
1208
1209	# check if everything is configured correctly
1210
1211	check_DEVELOPER:
1212	ifndef DEVELOPER
1213	@echo 'config.makefile:1: DEVELOPER not defined'
1214	@false
1215	endif
1216
1217	check_DEBUG:
1218	ifndef dflags
1219	@echo 'config.makefile:1: DEBUG has to be defined. Valid values are 0 and 1'
1220	@false
1221	endif
1222
1223	check_ARB_64:
1224	ifndef ARB_64
1225	@echo 'config.makefile:1: ARB_64 has to be defined. Valid values are 0 and 1'
1226	@false
1227	endif
1228
1229	# ---------------------------------------- check gcc version
1230
1231	COMPILER_BROKEN:=0
1232
1233	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.6.4')
1234	COMPILER_BROKEN:=1
1235	endif
1236	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.8.0')
1237	COMPILER_BROKEN:=1
1238	endif
1239
1240	check_same_GCC_VERSION:
1241	$(ARBHOME)/SOURCE_TOOLS/check_same_compiler_version.pl $(COMPILER_NAME) $(COMPILER_VERSION_ALLOWED)
1242
1243	check_GCC_VERSION:
1244	@echo 'Compiler version check:'
1245	# see .@ALLOWED_gcc_VERSIONS
1246	ifeq ('$(COMPILER_VERSION_ALLOWED)', '')
1247	@echo " - Your compiler is '$(COMPILER_NAME)' version '$(COMPILER_VERSION)'"
1248	@echo ' This version is not in the list of supported $(COMPILER_NAME)-versions:'
1249	@$(foreach version,$(ALLOWED_COMPILER_VERSIONS),echo ' * $(version)';)
1250	@echo ' - You may either ..'
1251	@echo ' - add your version to ALLOWED_$(COMPILER_NAME)_VERSIONS in the Makefile and try it out or'
1252	@echo ' - switch to one of the allowed versions (see arb_README_gcc.txt for installing'
1253	@echo ' a different version of gcc)'
1254	$(error Unsupported compiler '$(COMPILER_NAME)' version '$(COMPILER_VERSION)')
1255	else
1256	ifeq ($(COMPILER_BROKEN),1)
1257	$(error compilation refused for $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)'. Refer to http://bugs.arb-home.de/wiki/GccVersionInfo for details.)
1258	else
1259	@echo " - Supported $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)' detected - fine!"
1260	@echo ''
1261	ifeq ($(USE_CLANG),1)
1262	@echo "Dump clang version:"
1263	$(A_CXX) -v
1264	endif
1265	$(MAKE) check_same_GCC_VERSION
1266	endif
1267	endif
1268
1269	#---------------------- check ARBHOME
1270
1271	# use arb_INSTALL.txt to determine whether ARBHOME points to correct directory
1272	ARB_INSTALL_FOUND=$(wildcard $(ARBHOME)/arb_INSTALL.txt)
1273
1274	check_ARBHOME:
1275	ifeq ($(strip $(ARB_INSTALL_FOUND)),)
1276	@echo ------------------------------------------------------------
1277	@echo "ARBHOME is set to '$(ARBHOME)'"
1278	@echo "The environment variable ARBHOME has to point to the top arb source directory."
1279	@echo "If you use bash enter:"
1280	@echo " export ARBHOME='`pwd`'"
1281	@echo ------------------------------------------------------------
1282	@false
1283	endif
1284
1285	ARB_PATH_SET=$(findstring $(ARBHOME)/bin,$(PATH))
1286
1287	check_PATH: check_ARBHOME
1288	ifeq ($(strip $(ARB_PATH_SET)),)
1289	@echo ------------------------------------------------------------
1290	@echo "The environment variable PATH has to contain $(ARBHOME)/bin"
1291	@echo "If you use bash enter:"
1292	@echo ' export PATH=$$ARBHOME/bin:$$PATH'
1293	@echo ------------------------------------------------------------
1294	@false
1295	endif
1296
1297	check_TOOLS:
1298	@util/arb_check_build_env.pl \
1299	"$(A_CC)" \
1300	"$(A_CXX)" \
1301	"$(LINK_SHARED_LIB)" \
1302
1303	have_makedepend:
1304	@util/arb_check_build_env.pl --check-only "$(MAKEDEPEND_PLAIN)"
1305
1306	check_ENVIRONMENT : check_PATH check_TOOLS
1307	@echo "-------------------- Environment [start]"
1308	@echo "ARBHOME='$(ARBHOME)'"
1309	@echo "PATH='$(PATH)'"
1310	@echo "LD_LIBRARY_PATH='$(LD_LIBRARY_PATH)'"
1311	@echo "-------------------- Environment [end]"
1312
1313	check_tabs: check_setup
1314	ifeq ($(DEBUG),1)
1315	@SOURCE_TOOLS/tabBrake.pl
1316	endif
1317
1318	force_tab_check:
1319	@touch -t 198001010000 SOURCE_TOOLS/stamp.tabBrake
1320	@$(MAKE) check_tabs
1321
1322
1323	# ---------------------
1324
1325	check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION
1326	@echo Your setup seems to be ok.
1327
1328	checks: check_setup check_tabs
1329	@rm -f SOURCE_TOOLS/postcompile.sav
1330
1331
1332	# end test section ------------------------------
1333
1334	# ---------------------------------------
1335	# List of standard top level directories
1336	#
1337	# sub-makefiles have to define the targets
1338	# - 'depends' and
1339	# - 'clean'
1340	#
1341	# when adding new libraries/subdirs here, also add a dependency vs 'links' or 'links_non_perl' in .@DD_links_non_perl
1342
1343	TL_ARCHIVES = \
1344	AISC/AISC.a \
1345	ARB_GDE/ARB_GDE.a \
1346	AWTC/AWTC.a \
1347	AWTI/AWTI.a \
1348	CONSENSUS_TREE/CONSENSUS_TREE.a \
1349	CONVERTALN/CONVERTALN.a \
1350	DBSERVER/DBSERVER.a \
1351	DIST/DIST.a \
1352	EDIT4/EDIT4.a \
1353	EISPACK/EISPACK.a \
1354	GENOM/GENOM.a \
1355	GENOM_IMPORT/GENOM_IMPORT.a \
1356	ISLAND_HOPPING/ISLAND_HOPPING.a \
1357	MERGE/MERGE.a \
1358	MULTI_PROBE/MULTI_PROBE.a \
1359	NALIGNER/NALIGNER.a \
1360	NAMES/NAMES.a \
1361	NAMES_COM/server.a \
1362	NTREE/NTREE.a \
1363	PARSIMONY/PARSIMONY.a \
1364	PHYLO/PHYLO.a \
1365	PRIMER_DESIGN/PRIMER_DESIGN.a \
1366	PROBE/PROBE.a \
1367	PROBE_COM/server.a \
1368	PROBE_DESIGN/PROBE_DESIGN.a \
1369	$(RNA3D_LIB) \
1370	RNACMA/RNACMA.a \
1371	SECEDIT/SECEDIT.a \
1372	SEQ_QUALITY/SEQ_QUALITY.a \
1373	SERVERCNTRL/SERVERCNTRL.a \
1374	STAT/STAT.a \
1375	TREEGEN/TREEGEN.a \
1376	WETC/WETC.a \
1377	XML/XML.a \
1378
1379	TL_SHARED_ARCHIVES = \
1380	ARBDB/libARBDB.so \
1381	CORE/libCORE.so \
1382	WINDOW/libWINDOW.so \
1383
1384	TL_ARCHIV_COLLECTIONS = \
1385	SL/SL.archColl \
1386
1387	TL_TOOLS_COLLECTIONS = \
1388	AISC_MKPTPS/AISC_MKPTPS.toolColl \
1389	TOOLS/TOOLS.toolColl \
1390	PERLTOOLS/PERLTOOLS.toolColl \
1391	PROBE_SET/PROBE_SET.toolColl \
1392	READSEQ/READSEQ.toolColl \
1393
1394	RECURSIVE_SUBS = \
1395	GDE/GDE.sub \
1396	UNIT_TESTER/UNIT_TESTER.sub \
1397
1398	SUBDIRS = \
1399	$(RECURSIVE_SUBS) \
1400	$(TL_ARCHIVES:.a=.sub) \
1401	$(TL_SHARED_ARCHIVES:.so=.sub) \
1402	$(TL_ARCHIV_COLLECTIONS:.archColl=.sub) \
1403	$(TL_TOOLS_COLLECTIONS:.toolColl=.sub) \
1404
1405	# sub directories inside TL_ARCHIV_COLLECTIONS
1406	CL_ARCH_DIRS = $(foreach coll,$(TL_ARCHIV_COLLECTIONS),$(shell find $(dir $(coll)) -maxdepth 1 -mindepth 1 -type d))
1407
1408	# archives inside CL_ARCH_DIRS:
1409	CL_ARCHIVES = $(foreach adir,$(CL_ARCH_DIRS),$(dir $(adir))$(notdir $(adir))/$(notdir $(adir)).a)
1410
1411	# -----------------------
1412	# library packets
1413
1414	ARCHS_CLIENT_PROBE = PROBE_COM/client.a
1415	ARCHS_CLIENT_NAMES = NAMES_COM/client.a
1416
1417	ARCHS_MAKEBIN = AISC_MKPTPS/AISC_MKPTPS.a AISC/AISC.a
1418
1419	# communication libs need aisc and aisc_mkpts:
1420
1421	AISC/AISC.dummy: proto_tools
1422
1423	comtools: AISC/AISC.dummy
1424
1425	ARCHS_SEQUENCE = \
1426	SL/SEQUENCE/SEQUENCE.a \
1427	SL/ALIVIEW/ALIVIEW.a \
1428	SL/PRONUC/PRONUC.a \
1429
1430	ARCHS_TREE = \
1431	SL/ARB_TREE/ARB_TREE.a \
1432	SL/FILTER/FILTER.a \
1433	$(ARCHS_SEQUENCE) \
1434
1435	# parsimony tree (used by NTREE, PARSIMONY, STAT(->EDIT4), DIST(obsolete!))
1436	ARCHS_AP_TREE = \
1437	SL/AP_TREE/AP_TREE.a \
1438	$(ARCHS_TREE) \
1439
1440	# --------------------------------------------------------------------------------
1441	# dependencies for linking shared libs
1442
1443	link_core: core
1444	link_db: db link_core
1445	link_aw: aw link_db
1446
1447	#***************************************************************************************
1448	# Individual_Programs_Section
1449	#***************************************************************************************
1450
1451	arbmainwrapper:
1452	$(MAKE) -C SOURCE_TOOLS -r mainwrapper
1453
1454
1455	#********************************* arb_ntree ************************************
1456	NTREE = bin/arb_ntree
1457	ARCHS_NTREE = \
1458	NTREE/NTREE.a \
1459	ARB_GDE/ARB_GDE.a \
1460	SL/SPECSEL/SPECSEL.a \
1461	SL/GROUP_SEARCH/GROUP_SEARCH.a \
1462	SL/SAICALC/SAICALC.a \
1463	SL/DB_UI/DB_UI.a \
1464	SL/ARB_SPEC/ARB_SPEC.a \
1465	SL/MASKS/MASKS.a \
1466	AWTC/AWTC.a \
1467	AWTI/AWTI.a \
1468	CONSENSUS_TREE/CONSENSUS_TREE.a \
1469	GENOM_IMPORT/GENOM_IMPORT.a \
1470	GENOM/GENOM.a \
1471	MERGE/MERGE.a \
1472	MULTI_PROBE/MULTI_PROBE.a \
1473	PRIMER_DESIGN/PRIMER_DESIGN.a \
1474	PROBE_DESIGN/PROBE_DESIGN.a \
1475	SEQ_QUALITY/SEQ_QUALITY.a \
1476	SERVERCNTRL/SERVERCNTRL.a \
1477	SL/ALILINK/ALILINK.a \
1478	SL/AW_NAME/AW_NAME.a \
1479	SL/APP/APP.a \
1480	SL/CONSENSUS/CONSENSUS.a \
1481	SL/CANVAS/CANVAS.a \
1482	SL/DB_SCANNER/DB_SCANNER.a \
1483	SL/DB_QUERY/DB_QUERY.a \
1484	SL/QUERY/QUERY.a \
1485	SL/SEQIO/SEQIO.a \
1486	STAT/STAT.a \
1487	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1488	SL/GUI_TK/GUI_TK.a \
1489	SL/HELIX/HELIX.a \
1490	SL/REGEXPR/REGEXPR.a \
1491	SL/REFENTRIES/REFENTRIES.a \
1492	SL/NDS/NDS.a \
1493	SL/ITEM_SHADER/ITEM_SHADER.a \
1494	SL/ITEMS/ITEMS.a \
1495	SL/INSDEL/INSDEL.a \
1496	SL/LOCATION/LOCATION.a \
1497	SL/MACROS/MACROS.a \
1498	SL/PVP/PVP.a \
1499	SL/TRANSLATE/TRANSLATE.a \
1500	SL/TREEDISP/TREEDISP.a \
1501	SL/TREE_ADMIN/TREE_ADMIN.a \
1502	SL/TREE_READ/TREE_READ.a \
1503	SL/TREE_WRITE/TREE_WRITE.a \
1504	SL/XFERGUI/XFERGUI.a \
1505	SL/XFERSET/XFERSET.a \
1506	XML/XML.a \
1507	$(ARCHS_AP_TREE) \
1508
1509	ARCHS_NTREE_ALL = $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(XMLLIBS)
1510
1511	$(NTREE): $(ARCHS_NTREE:.a=.dummy) link_aw
1512	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NTREE_ALL) \|\| ( \
1513	echo "$(SEP) Link $@"; \
1514	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE_ALL)" ; \
1515	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE_ALL) && \
1516	echo "$(SEP) Link $@ [done]"; \
1517	)
1518
1519	#********************************* arb_edit4 ************************************
1520	EDIT4 = bin/arb_edit4
1521
1522	ARCHS_EDIT4 := \
1523	EDIT4/EDIT4.a \
1524	ARB_GDE/ARB_GDE.a \
1525	SL/FAST_ALIGNER/FAST_ALIGNER.a \
1526	AWTC/AWTC.a \
1527	ISLAND_HOPPING/ISLAND_HOPPING.a \
1528	SECEDIT/SECEDIT.a \
1529	SERVERCNTRL/SERVERCNTRL.a \
1530	SL/APP/APP.a \
1531	SL/GUI_TK/GUI_TK.a \
1532	SL/ARB_SPEC/ARB_SPEC.a \
1533	SL/AW_HELIX/AW_HELIX.a \
1534	SL/AW_NAME/AW_NAME.a \
1535	SL/CONSENSUS/CONSENSUS.a \
1536	SL/CANVAS/CANVAS.a \
1537	SL/ITEMS/ITEMS.a \
1538	STAT/STAT.a \
1539	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1540	SL/HELIX/HELIX.a \
1541	SL/TRANSLATE/TRANSLATE.a \
1542	SL/MACROS/MACROS.a \
1543	SL/MAPKEY/MAPKEY.a \
1544	SL/NDS/NDS.a \
1545	$(ARCHS_AP_TREE) \
1546	XML/XML.a \
1547
1548	ifeq ($(OPENGL),1)
1549	ARCHS_EDIT4 += RNA3D/RNA3D.a
1550	endif
1551
1552	ARCHS_EDIT4_ALL = $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4)
1553
1554	LIBS_EDIT4 := $(GL_LIBS)
1555
1556	$(EDIT4): $(ARCHS_EDIT4:.a=.dummy) link_aw
1557	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_EDIT4_ALL) \|\| ( \
1558	echo "$(SEP) Link $@"; \
1559	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4_ALL)" ; \
1560	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4_ALL) && \
1561	echo "$(SEP) Link $@ [done]"; \
1562	)
1563
1564	#********************************* arb_rnacma ************************************
1565	RNACMA = bin/arb_rnacma
1566	ARCHS_RNACMA = \
1567	RNACMA/RNACMA.a \
1568
1569	ARCHS_RNACMA_ALL = $(ARCHS_RNACMA) $(DBSYS_LIBS)
1570
1571	$(RNACMA) : $(ARCHS_RNACMA:.a=.dummy) link_db
1572	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_RNACMA_ALL) \|\| ( \
1573	echo "$(SEP) Link $@"; \
1574	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_RNACMA_ALL)"; \
1575	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_RNACMA_ALL) && \
1576	echo "$(SEP) Link $@ [done]"; \
1577	)
1578
1579	#********************************* arb_wetc ************************************
1580	WETC = bin/arb_wetc
1581	ARCHS_WETC = \
1582	WETC/WETC.a \
1583	SL/APP/APP.a \
1584	SL/MACROS/MACROS.a \
1585	SL/GUI_TK/GUI_TK.a \
1586	SL/HELIX/HELIX.a \
1587	SL/FILTER/FILTER.a \
1588	XML/XML.a \
1589
1590	ARCHS_WETC_ALL = $(ARCHS_WETC) $(GUI_LIBS)
1591
1592	$(WETC): $(ARCHS_WETC:.a=.dummy) link_aw
1593	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_WETC_ALL) \|\| ( \
1594	echo "$(SEP) Link $@"; \
1595	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC_ALL)" ; \
1596	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC_ALL) && \
1597	echo "$(SEP) Link $@ [done]"; \
1598	)
1599
1600	#********************************* arb_dist ************************************
1601	DIST = bin/arb_dist
1602	ARCHS_DIST = \
1603	DIST/DIST.a \
1604	CONSENSUS_TREE/CONSENSUS_TREE.a \
1605	EISPACK/EISPACK.a \
1606	SERVERCNTRL/SERVERCNTRL.a \
1607	SL/APP/APP.a \
1608	SL/GUI_TK/GUI_TK.a \
1609	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1610	SL/HELIX/HELIX.a \
1611	SL/MATRIX/MATRIX.a \
1612	SL/MACROS/MACROS.a \
1613	SL/NDS/NDS.a \
1614	SL/ITEMS/ITEMS.a \
1615	SL/ARB_SPEC/ARB_SPEC.a \
1616	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.a \
1617	XML/XML.a \
1618	$(ARCHS_AP_TREE) \
1619
1620	ARCHS_DIST_ALL = $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS)
1621
1622	$(DIST): $(ARCHS_DIST:.a=.dummy) link_aw
1623	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_DIST_ALL) \|\| ( \
1624	echo "$(SEP) Link $@"; \
1625	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST_ALL)" ; \
1626	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST_ALL) && \
1627	echo "$(SEP) Link $@ [done]"; \
1628	)
1629
1630	#********************************* arb_pars ************************************
1631	PARSIMONY = bin/arb_pars
1632	ARCHS_PARSIMONY = \
1633	PARSIMONY/PARSIMONY.a \
1634	SERVERCNTRL/SERVERCNTRL.a \
1635	SL/APP/APP.a \
1636	SL/GUI_TK/GUI_TK.a \
1637	SL/AW_NAME/AW_NAME.a \
1638	SL/CANVAS/CANVAS.a \
1639	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1640	SL/HELIX/HELIX.a \
1641	SL/MACROS/MACROS.a \
1642	SL/NDS/NDS.a \
1643	SL/ITEMS/ITEMS.a \
1644	SL/TRANSLATE/TRANSLATE.a \
1645	SL/TREEDISP/TREEDISP.a \
1646	XML/XML.a \
1647	$(ARCHS_AP_TREE) \
1648
1649	ARCHS_PARSIMONY_ALL = $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS)
1650
1651	$(PARSIMONY): $(ARCHS_PARSIMONY:.a=.dummy) link_aw
1652	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_PARSIMONY_ALL) \|\| ( \
1653	echo "$(SEP) Link $@"; \
1654	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY_ALL)" ; \
1655	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY_ALL) && \
1656	echo "$(SEP) Link $@ [done]"; \
1657	)
1658
1659	#********************************* arb_convert_aln ************************************
1660	CONVERT_ALN = bin/arb_convert_aln
1661	ARCHS_CONVERT_ALN = \
1662	CONVERTALN/CONVERTALN.a \
1663
1664	ARCHS_CONVERT_ALN_ALL = $(ARCHS_CONVERT_ALN) $(DBSYS_LIBS)
1665
1666	$(CONVERT_ALN) : $(ARCHS_CONVERT_ALN:.a=.dummy) link_db
1667	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_CONVERT_ALN_ALL) \|\| ( \
1668	echo "$(SEP) Link $@"; \
1669	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN_ALL)"; \
1670	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN_ALL) && \
1671	echo "$(SEP) Link $@ [done]"; \
1672	)
1673
1674	#********************************* arb_treegen ************************************
1675
1676	TREEGEN = bin/arb_treegen
1677	ARCHS_TREEGEN = \
1678	TREEGEN/TREEGEN.a \
1679
1680	ARCHS_TREEGEN_ALL = $(ARCHS_TREEGEN)
1681
1682	$(TREEGEN) : $(ARCHS_TREEGEN:.a=.dummy)
1683	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main_C) $(ARCHS_TREEGEN_ALL) \|\| ( \
1684	echo "$(SEP) Link $@"; \
1685	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN_ALL)" ; \
1686	$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN_ALL) && \
1687	echo "$(SEP) Link $@ [done]"; \
1688	)
1689
1690	#********************************* arb_naligner ************************************
1691	NALIGNER = bin/arb_naligner
1692	ARCHS_NALIGNER = \
1693	NALIGNER/NALIGNER.a \
1694	SERVERCNTRL/SERVERCNTRL.a \
1695	SL/HELIX/HELIX.a \
1696
1697	ARCHS_NALIGNER_ALL = $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(DBSYS_LIBS)
1698
1699	$(NALIGNER): $(ARCHS_NALIGNER:.a=.dummy) link_db
1700	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NALIGNER_ALL) \|\| ( \
1701	echo "$(SEP) Link $@"; \
1702	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER_ALL)" ; \
1703	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER_ALL) && \
1704	echo "$(SEP) Link $@ [done]"; \
1705	)
1706
1707	#********************************* arb_phylo ************************************
1708	PHYLO = bin/arb_phylo
1709	ARCHS_PHYLO = \
1710	PHYLO/PHYLO.a \
1711	SL/APP/APP.a \
1712	SL/GUI_TK/GUI_TK.a \
1713	SL/HELIX/HELIX.a \
1714	SL/FILTER/FILTER.a \
1715	SL/MACROS/MACROS.a \
1716	XML/XML.a \
1717
1718	ARCHS_PHYLO_ALL = $(ARCHS_PHYLO) $(GUI_LIBS)
1719
1720	$(PHYLO): $(ARCHS_PHYLO:.a=.dummy) link_aw
1721	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_PHYLO_ALL) \|\| ( \
1722	echo "$(SEP) Link $@"; \
1723	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO_ALL)" ; \
1724	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO_ALL) && \
1725	echo "$(SEP) Link $@ [done]"; \
1726	)
1727
1728	#***************************************************************************************
1729	# SERVER SECTION
1730	#***************************************************************************************
1731
1732	#********************************* arb_db_server ************************************
1733	DBSERVER = bin/arb_db_server
1734	ARCHS_DBSERVER = \
1735	DBSERVER/DBSERVER.a \
1736	SERVERCNTRL/SERVERCNTRL.a \
1737
1738	ARCHS_DBSERVER_ALL = $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS)
1739
1740	$(DBSERVER): $(ARCHS_DBSERVER:.a=.dummy) link_db
1741	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_DBSERVER_ALL) \|\| ( \
1742	echo "$(SEP) Link $@"; \
1743	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER_ALL)" ; \
1744	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER_ALL) && \
1745	echo "$(SEP) Link $@ [done]"; \
1746	)
1747
1748	#********************************* arb_pt_server ************************************
1749	PROBE = bin/arb_pt_server
1750
1751	ARCHS_PROBE_DEPEND = \
1752	PROBE/PROBE.a \
1753	SL/PTCLEAN/PTCLEAN.a \
1754	SERVERCNTRL/SERVERCNTRL.a \
1755	SL/HELIX/HELIX.a \
1756
1757	ARCHS_PROBE_ALL = $(ARCHS_PROBE_DEPEND) $(ARCHS_CLIENT_PROBE) $(ARBDB_LIB) $(SYSLIBS)
1758
1759	$(PROBE): $(ARCHS_PROBE_DEPEND:.a=.dummy) link_db
1760	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) config.makefile $(ARCHS_PROBE_ALL) \|\| ( \
1761	echo "$(SEP) Link $@"; \
1762	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_ALL)" ; \
1763	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_ALL) && \
1764	echo "$(SEP) Link $@ [done]"; \
1765	)
1766
1767	#********************************* arb_name_server ************************************
1768	NAMES = bin/arb_name_server
1769	ARCHS_NAMES = \
1770	NAMES/NAMES.a \
1771	SERVERCNTRL/SERVERCNTRL.a \
1772
1773	ARCHS_NAMES_ALL = $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS)
1774
1775	$(NAMES): $(ARCHS_NAMES:.a=.dummy) link_db
1776	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NAMES_ALL) \|\| ( \
1777	echo "$(SEP) Link $@"; \
1778	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES_ALL)" ; \
1779	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES_ALL) && \
1780	echo "$(SEP) Link $@ [done]"; \
1781	)
1782
1783	#********************************* SHARED LIBRARIES SECTION ************************************
1784
1785	prepare_libdir: addlibs
1786
1787	addlibs:
1788	(perl $(ARBHOME)/SOURCE_TOOLS/provide_libs.pl \
1789	"arbhome=$(ARBHOME)" \
1790	"opengl=$(OPENGL)" \
1791	"link_static=$(LINK_STATIC)" \
1792	)
1793
1794	#***************************************************************************************
1795	# Recursive calls to sub-makefiles
1796	#***************************************************************************************
1797
1798	%.depends: have_makedepend
1799	@cp -p $(@D)/Makefile $(@D)/Makefile.old # save old Makefile
1800	@$(MAKE) -C $(@D) -r \
1801	"AUTODEPENDS=1" \
1802	"MAIN=nothing" \
1803	"cflags=noCflagsHere_use_MAKEDEPENDFLAGS" \
1804	"cxxflags=noCxxflagsHere_use_MAKEDEPENDFLAGS" \
1805	depends
1806	@grep "^# DO NOT DELETE" $(@D)/Makefile >/dev/null
1807	@cat $(@D)/Makefile \
1808	\| SOURCE_TOOLS/fix_depends.pl "(from main)" \
1809	>$(@D)/Makefile.2
1810	@mv $(@D)/Makefile.old $(@D)/Makefile # restore old Makefile
1811	@$(ARBHOME)/SOURCE_TOOLS/mv_if_diff $(@D)/Makefile.2 $(@D)/Makefile # update Makefile if changed
1812
1813	%.proto:
1814	@($(MAKE) -C $(@D) \
1815	"AUTODEPENDS=0" \
1816	"MAIN=nothing" \
1817	"cflags=noCflags" \
1818	"cxxflags=noCxxflags" \
1819	proto 2>&1 ) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
1820
1821	%.clean:
1822	@$(MAKE) -C $(@D) \
1823	"AUTODEPENDS=0" \
1824	"MAIN=nothing" \
1825	"cflags=noCflags" \
1826	"cxxflags=noCxxflags" \
1827	clean
1828
1829
1830	# stop wrong targets:
1831	target_is_missing_lib_prefix:
1832	@echo "Error: Denied to build shared library target with missing 'lib'-prefix"
1833	false
1834
1835	ARBDB/ARBDB.dummy: target_is_missing_lib_prefix
1836	CORE/CORE.dummy: target_is_missing_lib_prefix
1837	AWT/AWT.dummy: target_is_missing_lib_prefix
1838	WINDOW/WINDOW.dummy: target_is_missing_lib_prefix
1839
1840	# rule to generate main target (normally a library):
1841	# @@@ check effect of setting LANG=C below
1842	%.dummy:
1843	@( export ID=$$$$; LANG=C; \
1844	(( \
1845	echo "$(SEP) Make $(@D)"; \
1846	$(MAKE) -C $(@D) -r \
1847	"AUTODEPENDS=1" \
1848	"MAIN=$(@F:.dummy=.a)" \
1849	"cflags=$(cflags) -DIN_ARB_$(subst /,_,$(@D))" \
1850	&& \
1851	echo "$(SEP) Make $(@D) [done]"; \
1852	) >$(@D).$$ID.log 2>&1 && (cat $(@D).$$ID.log;rm $(@D).$$ID.log)) \|\| (cat $(@D).$$ID.log;rm $(@D).$$ID.log;false))
1853
1854	# Additional dependencies for subtargets:
1855
1856	PROBE_COM/PROBE_COM.dummy : comtools
1857	NAMES_COM/NAMES_COM.dummy : comtools
1858
1859	com: PROBE_COM/PROBE_COM.dummy NAMES_COM/NAMES_COM.dummy
1860
1861	# stop wrong more targets:
1862	PROBE_COM/server.dummy:
1863	@echo Unwanted request to make target $<
1864	false
1865
1866	PROBE_COM/client.dummy:
1867	@echo Unwanted request to make target $<
1868	false
1869
1870	NAMES_COM/server.dummy:
1871	@echo Unwanted request to make target $<
1872	false
1873
1874	NAMES_COM/client.dummy:
1875	@echo Unwanted request to make target $<
1876	false
1877
1878
1879	ARBDB/libARBDB.dummy: links
1880	CORE/libCORE.dummy: links
1881
1882	PERLTOOLS/PERLTOOLS.dummy: core db
1883
1884	# all subdirs perl not depends on go here (ADD_links_non_perl)
1885	AWTI/AWTI.dummy: links_non_perl
1886	CONSENSUS_TREE/CONSENSUS_TREE.dummy: links_non_perl
1887	CONVERTALN/CONVERTALN.dummy: links_non_perl
1888	DBSERVER/DBSERVER.dummy: links_non_perl
1889	DIST/DIST.dummy: links_non_perl
1890	EDIT4/EDIT4.dummy: links_non_perl com
1891	EISPACK/EISPACK.dummy: links_non_perl
1892	GDE/GDE.dummy: links_non_perl
1893	GENOM/GENOM.dummy: links_non_perl
1894	GENOM_IMPORT/GENOM_IMPORT.dummy: links_non_perl
1895	ISLAND_HOPPING/ISLAND_HOPPING.dummy: links_non_perl
1896	MERGE/MERGE.dummy: links_non_perl
1897	NTREE/NTREE.dummy: links_non_perl
1898	PARSIMONY/PARSIMONY.dummy: links_non_perl
1899	PHYLO/PHYLO.dummy: links_non_perl
1900	PRIMER_DESIGN/PRIMER_DESIGN.dummy: links_non_perl
1901	PROBE_SET/PROBE_SET.dummy: links_non_perl link_db
1902	READSEQ/READSEQ.dummy: links_non_perl
1903	RNACMA/RNACMA.dummy: links_non_perl header_libs
1904	SECEDIT/SECEDIT.dummy: links_non_perl
1905	SEQ_QUALITY/SEQ_QUALITY.dummy: links_non_perl
1906	SERVERCNTRL/SERVERCNTRL.dummy: links_non_perl com
1907	SL/ALILINK/ALILINK.dummy: links_non_perl
1908	SL/ALIVIEW/ALIVIEW.dummy: links_non_perl
1909	SL/AP_TREE/AP_TREE.dummy: links_non_perl
1910	SL/APP/APP.dummy: links_non_perl
1911	SL/ARB_SPEC/ARB_SPEC.dummy: links_non_perl
1912	SL/ARB_TREE/ARB_TREE.dummy: links_non_perl
1913	SL/AW_HELIX/AW_HELIX.dummy: links_non_perl
1914	SL/CONSENSUS/CONSENSUS.dummy: links_non_perl
1915	SL/CANVAS/CANVAS.dummy: links_non_perl
1916	SL/DB_QUERY/DB_QUERY.dummy: links_non_perl
1917	SL/DB_SCANNER/DB_SCANNER.dummy: links_non_perl
1918	SL/DB_UI/DB_UI.dummy: links_non_perl
1919	SL/FAST_ALIGNER/FAST_ALIGNER.dummy: links_non_perl
1920	SL/FILTER/FILTER.dummy: links_non_perl
1921	SL/FILTSEQEXP/FILTSEQEXP.dummy: links_non_perl
1922	SL/GROUP_SEARCH/GROUP_SEARCH.dummy: links_non_perl
1923	SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy: links_non_perl
1924	SL/GUI_TK/GUI_TK.dummy: links_non_perl
1925	SL/HEADERTESTS/HEADERTESTS.dummy: links_non_perl
1926	SL/HELIX/HELIX.dummy: links_non_perl
1927	SL/INSDEL/INSDEL.dummy: links_non_perl
1928	SL/ITEM_SHADER/ITEM_SHADER.dummy: links_non_perl
1929	SL/ITEMS/ITEMS.dummy: links_non_perl
1930	SL/LOCATION/LOCATION.dummy: links_non_perl
1931	SL/MACROS/MACROS.dummy: links_non_perl
1932	SL/MASKS/MASKS.dummy: links_non_perl
1933	SL/MATRIX/MATRIX.dummy: links_non_perl
1934	SL/MAPKEY/MAPKEY.dummy: links_non_perl
1935	SL/NDS/NDS.dummy: links_non_perl
1936	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.dummy: links_non_perl
1937	SL/PRONUC/PRONUC.dummy: links_non_perl
1938	SL/PTCLEAN/PTCLEAN.dummy: links_non_perl link_db
1939	SL/PVP/PVP.dummy: links_non_perl
1940	SL/QUERY/QUERY.dummy: links_non_perl link_db
1941	SL/REFENTRIES/REFENTRIES.dummy: links_non_perl
1942	SL/REGEXPR/REGEXPR.dummy: links_non_perl
1943	SL/SAICALC/SAICALC.dummy: links_non_perl
1944	SL/SPECSEL/SPECSEL.dummy: links_non_perl
1945	SL/SEQIO/SEQIO.dummy: links_non_perl
1946	SL/SEQUENCE/SEQUENCE.dummy: links_non_perl
1947	SL/TRANSLATE/TRANSLATE.dummy: links_non_perl
1948	SL/TREE_ADMIN/TREE_ADMIN.dummy: links_non_perl
1949	SL/TREE_READ/TREE_READ.dummy: links_non_perl
1950	SL/TREE_WRITE/TREE_WRITE.dummy: links_non_perl
1951	SL/TREEDISP/TREEDISP.dummy: links_non_perl
1952	SL/XFERGUI/XFERGUI.dummy: links_non_perl
1953	SL/XFERSET/XFERSET.dummy: links_non_perl
1954	STAT/STAT.dummy: links_non_perl
1955	TREEGEN/TREEGEN.dummy: links_non_perl
1956	WETC/WETC.dummy: links_non_perl
1957	WINDOW/libWINDOW.dummy: links_non_perl
1958	XML/XML.dummy: links_non_perl
1959
1960	ifeq ($(OPENGL),1)
1961	GL/glAW/glAW.dummy: links_non_perl
1962	GL/glpng/glpng.dummy: links_non_perl
1963	GL/GL.dummy: GL/glAW/glAW.dummy GL/glpng/glpng.dummy
1964	RNA3D/RNA3D.dummy: links_non_perl gl
1965	endif
1966
1967	UNIT_TESTER/UNIT_TESTER.dummy: link_db \
1968	SERVERCNTRL/SERVERCNTRL.dummy \
1969
1970	# see also TOOLS/Makefile@TOOLSLIBDEPENDS
1971	TOOLS/TOOLS.dummy : links_non_perl link_db \
1972	CONSENSUS_TREE/CONSENSUS_TREE.dummy \
1973	SERVERCNTRL/SERVERCNTRL.dummy \
1974	SL/FILTER/FILTER.dummy \
1975	SL/FILTSEQEXP/FILTSEQEXP.dummy \
1976	SL/INSDEL/INSDEL.dummy \
1977	SL/REGEXPR/REGEXPR.dummy \
1978	SL/SEQIO/SEQIO.dummy \
1979	SL/TREE_READ/TREE_READ.dummy \
1980	SL/TREE_WRITE/TREE_WRITE.dummy \
1981	XML/XML.dummy \
1982
1983	AWTC/AWTC.dummy : com
1984
1985	NAMES/NAMES.dummy : com
1986	SL/AW_NAME/AW_NAME.dummy : com
1987
1988	PROBE/PROBE.dummy : com
1989	MULTI_PROBE/MULTI_PROBE.dummy : com
1990	PROBE_DESIGN/PROBE_DESIGN.dummy : com
1991	NALIGNER/NALIGNER.dummy : com
1992
1993	ARB_GDE/ARB_GDE.dummy : proto_tools menus
1994
1995	compile_compatibility: SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.dummy
1996
1997	#***************************************************************************************
1998	# Short aliases to make targets
1999	#***************************************************************************************
2000
2001	show:
2002	@echo $(SEP)
2003	@echo 'Aliases for often needed targets:'
2004	@echo ''
2005	@echo ' executables:'
2006	@echo ''
2007	@echo ' nt arb_ntree'
2008	@echo ' e4 arb_edit4 (includes secedit)'
2009	@echo ' di arb_dist'
2010	@echo ' ph arb_phylo'
2011	@echo ' pa arb_parsimony'
2012	@echo ' tg arb_treegen'
2013	@echo ' ds arb_dbserver'
2014	@echo ' pt arb_pt_server'
2015	@echo ' na arb_name_server'
2016	@echo ''
2017	@echo ' libraries:'
2018	@echo ''
2019	@echo ' com communication libraries'
2020	@echo ' db ARB database'
2021	@echo ' aw GUI lib'
2022	@echo ' awt GUI toolkit'
2023	@echo ' awtc general purpose library'
2024	@echo ' awti import/export library'
2025	@echo ' mp multi probe library'
2026	@echo ' ge genome library'
2027	@echo ' pd probe design lib'
2028	@echo ' prd primer design lib'
2029	@echo ''
2030	@echo ' other targets:'
2031	@echo ''
2032	@echo ' help recompile help files'
2033	@echo ' tools make small tools used by arb'
2034	@echo ''
2035	@echo ' foreign targets:'
2036	@echo ''
2037	@echo ' gde GDE'
2038	@echo ' agde ARB_GDE'
2039	@echo ''
2040	@echo 'for other targets inspect $(ARBHOME)/Makefile'
2041	@echo ''
2042	@echo $(SEP)
2043
2044	source_doc:
2045	@echo "Remove some links (doxygen crashes otherwise):"
2046	find . $ -name "AISC" -o -name "C" -o -name "GDEHELP" $ -type l -exec rm {} \;
2047	doxygen 2>&1 1>/dev/null
2048	$(MAKE) forcelinks
2049
2050	dep_graph:
2051	@echo "Building some dependency graphs"
2052	SOURCE_TOOLS/dependency_graphs.pl
2053
2054	help: HELP_SOURCE/HELP_SOURCE.dummy
2055
2056	HELP_SOURCE/HELP_SOURCE.dummy: link_core xml menus
2057
2058	db: ARBDB/libARBDB.dummy
2059	core: CORE/libCORE.dummy
2060	aw: WINDOW/libWINDOW.dummy
2061	awtc: AWTC/AWTC.dummy
2062	awti: AWTI/AWTI.dummy
2063
2064	mp: MULTI_PROBE/MULTI_PROBE.dummy
2065	mg: MERGE/MERGE.dummy
2066	ge: GENOM/GENOM.dummy
2067	prd: PRIMER_DESIGN/PRIMER_DESIGN.dummy
2068
2069	nt: menus $(NTREE)
2070
2071	nal: $(NALIGNER)
2072
2073	di: $(DIST)
2074	ph: $(PHYLO)
2075	pa: $(PARSIMONY)
2076	tg: $(TREEGEN)
2077
2078	ifeq ($(OPENGL),1)
2079	3d: RNA3D/RNA3D.dummy
2080	gl: GL/GL.dummy
2081	else
2082	noopengl:
2083	@echo "invalid target for OPENGL=0"
2084	3d: noopengl
2085	gl: noopengl
2086	endif
2087
2088	SL/SL.dummy: com
2089
2090	ds: $(DBSERVER)
2091	pt: $(PROBE)
2092	pst: PROBE_SET/PROBE_SET.dummy
2093	pd: PROBE_DESIGN/PROBE_DESIGN.dummy
2094	na: $(NAMES)
2095	sq: SEQ_QUALITY/SEQ_QUALITY.dummy
2096	cma: $(RNACMA)
2097
2098	sec: SECEDIT/SECEDIT.dummy
2099
2100	e4: $(EDIT4) readseq menus
2101
2102	gi: GENOM_IMPORT/GENOM_IMPORT.dummy
2103	wetc: $(WETC)
2104
2105	xml: XML/XML.dummy
2106	stat: STAT/STAT.dummy $(NTREE) $(EDIT4)
2107	fa: SL/FAST_ALIGNER/FAST_ALIGNER.dummy
2108
2109	#********************************************************************************
2110
2111	up_by_remake: depends proto vectorize_checks
2112
2113	up: up_by_remake tags valgrind_update
2114
2115	#********************************************************************************
2116
2117	touch:
2118	SOURCE_TOOLS/touch_modified.pl
2119
2120	modified: touch
2121	$(MAKE) all
2122
2123	#********************************************************************************
2124
2125	libdepends:
2126	$(MAKE) -C "SOURCE_TOOLS" \
2127	"RNA3D_LIB=$(RNA3D_LIB_4_DEPENDS)" \
2128	libdepends
2129
2130	#********************************************************************************
2131
2132	# create generated headers:
2133	genheaders: TEMPLATES/TEMPLATES.dummy
2134
2135	clrdotdepends:
2136	rm PROBE_COM/.depends \|\| true
2137	rm NAMES_COM/.depends \|\| true
2138	rm PERL2ARB/.depends \|\| true
2139
2140	comdepends: comtools clrdotdepends have_makedepend
2141	@echo "$(SEP) Partially build com interface"
2142	$(MAKE) PROBE_COM/PROBE_COM.depends NAMES_COM/NAMES_COM.depends
2143	$(MAKE) PROBE_COM/server.depends NAMES_COM/server.depends
2144
2145	depends: genheaders comdepends vectorize_checks have_makedepend
2146	@echo "$(SEP) Updating other dependencies"
2147	$(MAKE) $(subst NAMES_COM/server.depends,,$(subst PROBE_COM/server.depends,,$(SUBDIRS:.sub=.depends))) \
2148	HELP_SOURCE/HELP_SOURCE.depends \
2149	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.depends \
2150
2151	$(MAKE) libdepends
2152
2153	depend: depends
2154
2155	# ------------------------------------------------------------
2156	# dependency generation tests for AISC code
2157	#(all should work w/o creating wrong dependencies;
2158	# neither in XXX_COM/Makefile nor in code using AISC interface)
2159	dependstest1: silent_clean
2160	$(MAKE) depends
2161	dependstest2: silent_clean
2162	$(MAKE) com
2163	dependstest3: silent_clean
2164	$(MAKE) aw
2165	dependstest4: silent_clean
2166	$(MAKE) pt
2167	dependstest5: silent_clean
2168	$(MAKE) na
2169	dependstest6: silent_clean
2170	$(MAKE) nt
2171	dependstest7: silent_clean
2172	$(MAKE) all
2173	# ------------------------------------------------------------
2174
2175	vectorize_checks:
2176	$(MAKE) -C SOURCE_TOOLS -r vectorize_checks
2177
2178	clean_checked_vect: lib/lib.clean
2179	SOURCE_TOOLS/clean_checked_vectorizations.sh
2180
2181	# ------------------------------------------------------------
2182
2183	AISC_MKPTPS/AISC_MKPTPS.dummy: links
2184
2185	proto_tools: AISC_MKPTPS/AISC_MKPTPS.dummy
2186
2187	proto: proto_tools
2188	@echo $(SEP) Updating prototypes
2189	$(MAKE) \
2190	ARBDB/ARBDB.proto \
2191	AISC_COM/AISC_COM.proto \
2192	ARB_GDE/ARB_GDE.proto \
2193	CORE/CORE.proto \
2194	CONVERTALN/CONVERTALN.proto \
2195	NTREE/NTREE.proto \
2196	MERGE/MERGE.proto \
2197	PROBE/PROBE.proto \
2198	SERVERCNTRL/SERVERCNTRL.proto \
2199	SL/SL.proto \
2200
2201	#********************************************************************************
2202
2203	valgrind_update: links
2204	@echo $(SEP) Updating for valgrind
2205	$(MAKE) -C SOURCE_TOOLS valgrind_update
2206
2207	#********************************************************************************
2208
2209	TAGFILE=TAGS
2210	UTAGS=TAGS.$(ARBBID)
2211	TAGFILE_TMP=$(UTAGS).tmp
2212
2213	TAG_SOURCE_HEADERS=$(UTAGS).headers.tmp
2214	TAG_SOURCE_CODE=$(UTAGS).codefiles.tmp
2215	TAG_SOURCE_LISTS=$(TAG_SOURCE_HEADERS) $(TAG_SOURCE_CODE)
2216
2217	ETAGS_IGNORE_LIST=SOURCE_TOOLS/etags_ignore.lst
2218
2219	ETAGS=ctags -e -I @$(ETAGS_IGNORE_LIST) --sort=no --if0=no --extra=q
2220	ETAGS_TYPES=--C-kinds=cgnsut --C++-kinds=cgnsut
2221	ETAGS_FUN =--C-kinds=fm --C++-kinds=fm
2222	ETAGS_REST =--C-kinds=dev --C++-kinds=dev
2223
2224	FILTER_TAGS_SOURCES= \
2225	$(SED) -e 's/^.\///g' \| \
2226	grep -vi '^HEADERLIBS\\|^GDE/\\|/GEN[CH]/'
2227
2228	$(TAG_SOURCE_HEADERS): links
2229	@find . $ -name '.hxx' -o -name ".h" $ -type f \| $(FILTER_TAGS_SOURCES) > $@
2230
2231	$(TAG_SOURCE_CODE): links
2232	@find . $ -name '.cxx' -o -name ".c" $ -type f \| $(FILTER_TAGS_SOURCES) > $@
2233
2234	$(UTAGS).1.tmp: $(TAG_SOURCE_HEADERS)
2235	@$(ETAGS) -f $@ $(ETAGS_TYPES) -L $<
2236	$(UTAGS).2.tmp: $(TAG_SOURCE_HEADERS)
2237	@$(ETAGS) -f $@ $(ETAGS_FUN) -L $<
2238	$(UTAGS).3.tmp: $(TAG_SOURCE_HEADERS)
2239	@$(ETAGS) -f $@ $(ETAGS_REST) -L $<
2240	$(UTAGS).4.tmp: $(TAG_SOURCE_CODE)
2241	@$(ETAGS) -f $@ $(ETAGS_TYPES) -L $<
2242	$(UTAGS).5.tmp: $(TAG_SOURCE_CODE)
2243	@$(ETAGS) -f $@ $(ETAGS_FUN) -L $<
2244	$(UTAGS).6.tmp: $(TAG_SOURCE_CODE)
2245	@$(ETAGS) -f $@ $(ETAGS_REST) -L $<
2246
2247	TAGS_ALL_PARTS=$(UTAGS).1.tmp $(UTAGS).2.tmp $(UTAGS).3.tmp $(UTAGS).4.tmp $(UTAGS).5.tmp $(UTAGS).6.tmp
2248
2249	$(TAGFILE_TMP) : $(TAGS_ALL_PARTS)
2250	@cat $(TAGS_ALL_PARTS) > $@
2251	@rm $(TAGS_ALL_PARTS) $(TAG_SOURCE_LISTS)
2252
2253	cleanOldTags:
2254	@find $(ARBHOME) -name 'TAGS.*.tmp' -ctime +2 -exec rm {} \;
2255
2256	tags: $(TAGFILE_TMP) cleanOldTags
2257	@mv_if_diff $(TAGFILE_TMP) $(TAGFILE)
2258
2259	#********************************************************************************
2260
2261	LINKSTAMP=SOURCE_TOOLS/stamp.generate_all_links
2262
2263	links: checks $(LINKSTAMP) arbmainwrapper
2264	links_no_checks: $(LINKSTAMP) arbmainwrapper
2265
2266	forcelinks:
2267	-rm $(LINKSTAMP)
2268	$(MAKE) links
2269
2270	$(LINKSTAMP): SOURCE_TOOLS/generate_all_links.sh genheaders
2271	+SOURCE_TOOLS/generate_all_links.sh
2272	touch $(LINKSTAMP)
2273
2274	clean_links:
2275	# avoid to delete linked pts, nas or arb_tcp.dat:
2276	find . -path './lib' -prune -o -type l -exec rm {} \;
2277	# removed obsolete file - refuses to disappear due to 'prune' above
2278	@rm -f lib/help/GDEHELP
2279	@rm -f $(LINKSTAMP) lib/inputMasks/format.readme
2280
2281	redo_links: clean_links
2282	$(MAKE) links_no_checks
2283
2284	#********************************************************************************
2285
2286	header_libs:
2287	@(( \
2288	echo "$(SEP) Make HEADERLIBS"; \
2289	$(MAKE) -C HEADERLIBS all && \
2290	echo "$(SEP) Make HEADERLIBS [done]"; \
2291	) > HEADERLIBS.log 2>&1 && (cat HEADERLIBS.log;rm HEADERLIBS.log)) \|\| (cat HEADERLIBS.log;rm HEADERLIBS.log;false)
2292
2293	#********************************************************************************
2294
2295	gde: GDE/GDE.dummy
2296	GDE: gde
2297	agde: ARB_GDE/ARB_GDE.dummy
2298	tools: TOOLS/TOOLS.dummy
2299	convert: $(CONVERT_ALN)
2300	readseq: READSEQ/READSEQ.dummy
2301
2302	#***************************************************************************************
2303	# Some user commands
2304	#***************************************************************************************
2305
2306	menus: binlink links
2307	@(( \
2308	echo "$(SEP) Make GDEHELP"; \
2309	$(MAKE) -C GDEHELP -r all && \
2310	echo "$(SEP) Make GDEHELP [done]"; \
2311	) > GDEHELP.log 2>&1 && (cat GDEHELP.log;rm GDEHELP.log)) \|\| (cat GDEHELP.log;rm GDEHELP.log;false)
2312
2313	ifeq ($(DEBUG),1)
2314	BIN_TARGET=develall
2315	else
2316	BIN_TARGET=all
2317	endif
2318
2319
2320	binlink:
2321	$(MAKE) -C bin $(BIN_TARGET)
2322
2323	check_bin_dep: binlink
2324	SOURCE_TOOLS/check_bin_dependencies.pl
2325
2326	fig_cure:
2327	SOURCE_TOOLS/sortfig.pl doit
2328
2329	preplib:
2330	(cd lib;$(MAKE) all)
2331
2332	# --------------------------------------------------------------------------------
2333	# This section is quite tricky:
2334	#
2335	# make 'perl' is a BIG target, so when it has to be made, it has to be started
2336	# as early as possible to reduce overall compile time. Since 'make' does not
2337	# provide any priorities, i force it to build all 'perl'-prerequisites early, by
2338	# adding artificial dependencies to these prerequisites
2339	#
2340	# That behavior is likely to be system-dependent.
2341	# My goal was only to make it work on my current development system,
2342	# where this saves about 20% of overall build time.
2343
2344	ifeq ($(WITHPERL),1)
2345	links_non_perl: PERLTOOLS/PERLTOOLS.dummy
2346	perltools: links_non_perl
2347	perl: realperl
2348	else
2349	links_non_perl: links
2350	perl: links
2351	$(MAKE) "WITHPERL=1" perl
2352	endif
2353
2354	# ---------------------------------------- perl
2355
2356	realperl: perltools
2357	(( \
2358	echo "$(SEP) Make PERL2ARB" ; \
2359	$(TIME) $(MAKE) -C PERL2ARB -r -f Makefile.main \
2360	"AUTODEPENDS=1" \
2361	"dflags=$(dflags)" \
2362	"cflags4perl=$(cflags) $(cxxflags) $(dflags)" \
2363	"lflags4perl=$(lflags4perl)" \
2364	"COMPILER_VERSION=$(COMPILER_VERSION)" \
2365	all && \
2366	$(MAKE) -C PERL_SCRIPTS/test test && \
2367	echo "$(SEP) Make PERL2ARB [done]" ; \
2368	) > PERL2ARB.log 2>&1 && (cat PERL2ARB.log;rm PERL2ARB.log)) \|\| (cat PERL2ARB.log;rm PERL2ARB.log;false)
2369
2370	perl_clean:
2371	@$(MAKE) -C PERL2ARB -r -f Makefile.main \
2372	"AUTODEPENDS=0" \
2373	clean
2374
2375	PERL2ARB/PERL2ARB.clean:
2376	$(MAKE) perl_clean
2377	$(MAKE) -C PERL_SCRIPTS/test clean
2378
2379	# ---------------------------------------- bindings to script languages
2380
2381	bindings: lib/libCORE.so lib/libARBDB.so
2382	$(MAKE) -C BINDINGS all ARBDEPENDS="$(^:%=../%)" DFLAGS="$(dflags)"
2383
2384	bindings_clean:
2385	$(MAKE) -C BINDINGS clean
2386
2387	# ---------------------------------------- check resources
2388
2389	check_res:
2390	$(ARBHOME)/SOURCE_TOOLS/check_resources.pl
2391
2392	# ---------------------------------------- cleaning
2393
2394	rmbak:
2395	@echo "[cleanup backup/core files]"
2396	@find . \( -name '*%' \
2397	-o -name '*.bak' \
2398	-o -name '*~' \) \
2399	-o $ -name 'core' -a \! -type d $ \
2400	-exec rm -v {} \; \|\| \
2401	echo "Warning: target 'rmbak' reported problems when removing misc. backup files (ignored)"
2402	@echo "[cleanup done]"
2403
2404	bin_reinit:
2405	$(MAKE) bin/bin.clean
2406	$(MAKE) -C "bin" all
2407
2408	clean_directories:
2409	-rm -rf \
2410	$(ARBHOME)/PROBE_SET/bin \
2411	$(ARBHOME)/INCLUDE \
2412
2413	libclean:
2414	-find $(ARBHOME) -type f $ -name '*.a' ! -type l $ -exec rm -f {} \;
2415	-find $(ARBHOME) -type f $ -name 'lib*.so' ! -type l $ -exec rm -f {} \;
2416
2417	objclean:
2418	-find $(ARBHOME) -type f $ -name '*.o' ! -type l $ -exec rm -f {} \;
2419
2420	# bin.clean and HELP_SOURCE.clean interfere
2421	clean3:
2422	$(MAKE) bin/bin.clean
2423	$(MAKE) HELP_SOURCE/HELP_SOURCE.clean
2424
2425
2426	# delete all binaries (similar to 'cleanlinked')
2427	cleanRelinkable: libclean UNIT_TESTER/UNIT_TESTER.clean
2428	$(MAKE) -C bin cleanbinariesRelinkable
2429	$(MAKE) -C PROBE_SET cleanLinked
2430
2431
2432	clean2: $(SUBDIRS:.sub=.clean) \
2433	clean3 \
2434	rmbak \
2435	libclean \
2436	objclean \
2437	lib/lib.clean \
2438	GDEHELP/GDEHELP.clean \
2439	HEADERLIBS/HEADERLIBS.clean \
2440	SOURCE_TOOLS/SOURCE_TOOLS.clean \
2441	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.clean \
2442	UNIT_TESTER/UNIT_TESTER.clean \
2443	TEMPLATES/TEMPLATES.clean \
2444	perl_clean \
2445
2446	rm -f .last_gcc .last_compiler config.makefile.bak
2447	$(MAKE) clean_directories
2448
2449	# links are needed for cleanup
2450	clean: redo_links motif_xpm_hack_clean
2451	$(MAKE) clean2
2452	$(MAKE) clean_cov_all clean_links
2453
2454	silent_clean:
2455	$(MAKE) clean >/dev/null
2456
2457	# 'relocated' is about 50% faster than 'rebuild'
2458	reloc_clean: links
2459	@echo "---------------------------------------- Relocation cleanup"
2460	$(MAKE) \
2461	perl_clean \
2462	GDEHELP/GDEHELP.clean \
2463	HELP_SOURCE/genhelp/genhelp.clean \
2464	bin/bin.clean \
2465	libclean \
2466	objclean
2467
2468	relocated: links
2469	$(MAKE) reloc_clean
2470	@echo "---------------------------------------- and remake"
2471	$(MAKE) build
2472
2473	# -----------------------------------
2474	# some stress tests
2475	# (helpful to reveal race conditions with -j)
2476
2477	rebuild4ever: rebuild
2478	$(MAKE) rebuild4ever
2479
2480	build4ever: build
2481	$(MAKE) build4ever
2482
2483	clean4ever: clean
2484	$(MAKE) clean4ever
2485
2486	test4ever: ut
2487	$(MAKE) test4ever
2488
2489	perl4ever: clean
2490	$(MAKE) links
2491	$(MAKE) perl
2492	$(MAKE) perl4ever
2493
2494	help4ever: clean
2495	$(MAKE) help
2496	$(MAKE) help4ever
2497
2498	# -----------------------------------
2499
2500	cleanlinked: bin/bin.clean libclean
2501
2502	relink: cleanlinked
2503	$(MAKE) all
2504
2505	# --------------------------------------------------------------------------------
2506	# source related targets
2507
2508	CLOC=cloc
2509	CLOCFLAGS=--no3 --quiet --progress-rate=0
2510	CLOCARB=--exclude-dir=GDE .
2511	CLOCEXT=GDE
2512	CLOCCODE=--force-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.code.def
2513	CLOCREST=--force-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.rest.def
2514	CLOCFILT=tail --lines=+4
2515
2516	cloc:
2517	@echo 'Arb code:'
2518	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCARB) \| $(CLOCFILT)
2519	@echo 'Arb rest:'
2520	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCARB) \| $(CLOCFILT)
2521	@echo 'External code:'
2522	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCEXT) \| $(CLOCFILT)
2523	@echo 'External rest:'
2524	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCEXT) \| $(CLOCFILT)
2525
2526
2527	# patch generation
2528	patch:
2529	SOURCE_TOOLS/arb_create_patch.sh arbPatch --svn
2530
2531	# source tarball generation
2532	save: sourcetarfile
2533
2534	sourcetarfile: rmbak
2535	util/arb_save
2536
2537	# test early whether save will work
2538	savetest:
2539	@util/arb_srclst.pl >/dev/null
2540
2541	testsave: savetest
2542
2543	save2: rmbak
2544	util/arb_save ignore
2545
2546	save_test: rmbak
2547	@echo "Testing source list.."
2548	@util/arb_srclst.pl > /dev/null
2549
2550	save_test_no_error:
2551	@-$(MAKE) save_test
2552
2553	# --------------------------------------------------------------------------------
2554	# version management
2555
2556	inc_candi:
2557	touch SOURCE_TOOLS/inc_candi.stamp
2558	$(MAKE) do_version_update
2559
2560	inc_patch:
2561	touch SOURCE_TOOLS/inc_patch.stamp
2562	$(MAKE) do_version_update
2563
2564	inc_minor:
2565	touch SOURCE_TOOLS/inc_minor.stamp
2566	$(MAKE) do_version_update
2567
2568	inc_major:
2569	touch SOURCE_TOOLS/inc_major.stamp
2570	$(MAKE) do_version_update
2571
2572	do_version_update:
2573	@echo Incrementing version information
2574	$(MAKE) savetest
2575	$(MAKE) genheaders # auto upgrades version early
2576
2577	show_version:
2578	$(MAKE) genheaders # updates version info
2579	@echo "$(SEP) ARB version info"
2580	@grep ARB_VERSION TEMPLATES/arb_build.h
2581	@echo "$(SEP)"
2582
2583	# --------------------------------------------------------------------------------
2584	# special cleanups
2585
2586	clean_opengl_changed: RNA3D/RNA3D.clean EDIT4/EDIT4.clean WINDOW/WINDOW.clean GL/GL.clean
2587
2588	# --------------------------------------------------------------------------------
2589
2590	arbapplications: nt pa e4 wetc pt na nal di ph ds wetc cma
2591
2592	arb_external: convert tools gde readseq tg pst
2593
2594	arb_no_perl: arbapplications help arb_external
2595
2596	arb: motif_xpm_hack
2597	$(MAKE) "WITHPERL=1" perl arb_no_perl
2598
2599	motif_xpm_hack:
2600	$(MAKE) -r -C "lib/motifHack" all
2601
2602	motif_xpm_hack_clean:
2603	$(MAKE) -r -C "lib/motifHack" clean
2604
2605	# --------------------------------------------------------------------------------
2606	# special targets for SOURCE_TOOLS/remake_after_change.pl
2607
2608	rac_arb_dist: di
2609	rac_arb_edit4: e4
2610	rac_arb_ntree: nt
2611	rac_arb_pars: pa
2612	rac_arb_phylo: ph
2613	rac_arb_wetc: wetc
2614	rac_arb_naligner: nal
2615	rac_arb_pt_server: pt
2616	rac_arb_db_server: ds
2617	rac_arb_name_server: na
2618	rac_arb_convert_aln: convert
2619	rac_arb_treegen: tg
2620	rac_arb_rnacma: cma
2621	rac_arb_help2xml: help
2622
2623	rac_arb_a2ps: tools
2624	rac_arb_consensus_tree: tools
2625	rac_arb_dnarates: tools
2626	rac_arb_export_rates: tools
2627	rac_arb_export_tree: tools
2628	rac_arb_gene_probe: tools
2629	rac_arb_message: tools
2630	rac_arb_primer: tools
2631	rac_arb_probe: tools
2632	rac_arb_read_tree: tools
2633
2634	# --------------------------------------------------------------------------------
2635	# unit testing
2636	# @@@ work in progress
2637	#
2638	# goal is to automatically test all libraries/executables using TESTED_UNITS_AUTO
2639	# currently not all test executables link w/o error.
2640	# therefor units are organized in three sets:
2641	#
2642	# TESTED_UNITS = testable and contain tests
2643	# UNTESTED_UNITS = testable, but no tests written yet
2644	# UNTESTABLE_UNITS = not testable
2645
2646	# always define OPENGL units manually:
2647	OPENGL_TESTS :=
2648	ifeq ($(OPENGL),1)
2649	# this section defines RNA3D.test
2650	OPENGL_TESTS += \
2651	$(subst .a,.test,$(RNA3D_LIB)) \
2652	GL/glAW/libglAW.test \
2653	GL/glpng/libglpng_arb.test \
2654
2655	endif
2656
2657	UNITS_NOT_AUTODETECTED = \
2658	HELP_SOURCE/HELP_SOURCE.tooltests
2659
2660	TESTED_UNITS_AUTO = \
2661	$(OPENGL_TESTS) \
2662	$(TL_ARCHIVES:.a=.test) \
2663	$(TL_SHARED_ARCHIVES:.so=.test) \
2664	$(CL_ARCHIVES:.a=.test) \
2665	$(TL_TOOLS_COLLECTIONS:.toolColl=.tooltests) \
2666	$(UNITS_NOT_AUTODETECTED) \
2667
2668	UNTESTED_UNITS = \
2669	$(OPENGL_TESTS) \
2670	EISPACK/EISPACK.test \
2671	GENOM/GENOM.test \
2672	ISLAND_HOPPING/ISLAND_HOPPING.test \
2673	NALIGNER/NALIGNER.test \
2674	NAMES/NAMES.test \
2675	PHYLO/PHYLO.test \
2676	PRIMER_DESIGN/PRIMER_DESIGN.test \
2677	READSEQ/READSEQ.tooltests \
2678	SECEDIT/SECEDIT.test \
2679	SEQ_QUALITY/SEQ_QUALITY.test \
2680	SERVERCNTRL/SERVERCNTRL.test \
2681	SL/ALIVIEW/ALIVIEW.test \
2682	SL/AP_TREE/AP_TREE.test \
2683	SL/ARB_SPEC/ARB_SPEC.test \
2684	SL/ARB_TREE/ARB_TREE.test \
2685	SL/AW_HELIX/AW_HELIX.test \
2686	SL/AW_NAME/AW_NAME.test \
2687	SL/CANVAS/CANVAS.test \
2688	SL/DB_SCANNER/DB_SCANNER.test \
2689	SL/DB_UI/DB_UI.test \
2690	SL/GUI_ALIVIEW/GUI_ALIVIEW.test \
2691	SL/GUI_TK/GUI_TK.test \
2692	SL/HELIX/HELIX.test \
2693	SL/MASKS/MASKS.test \
2694	SL/MAPKEY/MAPKEY.test \
2695	SL/QUERY/QUERY.test \
2696	SL/REFENTRIES/REFENTRIES.test \
2697	SL/SEQUENCE/SEQUENCE.test \
2698	SL/TREE_ADMIN/TREE_ADMIN.test \
2699	SL/TREE_WRITE/TREE_WRITE.test \
2700	SL/XFERGUI/XFERGUI.test \
2701	STAT/STAT.test \
2702	TREEGEN/TREEGEN.test \
2703	WETC/WETC.test \
2704	XML/XML.test \
2705
2706	# untestable units
2707
2708	UNTESTABLE_UNITS = \
2709	AISC/AISC.test \
2710	NAMES_COM/server.test \
2711	PROBE_COM/server.test \
2712
2713	# --------------------
2714	# put all units containing tests into the following 4 sections (see also TESTED_UNITS below)
2715
2716	# recent development
2717	UNITS_TESTED_FIRST = \
2718	SL/SPECSEL/SPECSEL.test \
2719	SL/MATRIX/MATRIX.test \
2720	AWTI/AWTI.test \
2721	SL/FILTSEQEXP/FILTSEQEXP.test \
2722	SL/GROUP_SEARCH/GROUP_SEARCH.test \
2723	SL/PVP/PVP.test \
2724	SL/SAICALC/SAICALC.test \
2725	SL/TRANSLATE/TRANSLATE.test \
2726	SL/XFERSET/XFERSET.test \
2727
2728	# start units with long duration early
2729	UNITS_RUNNING_LONG = \
2730	ARBDB/libARBDB.test \
2731	AWTC/AWTC.test \
2732	TOOLS/TOOLS.tooltests \
2733
2734	# plain test-libaries that are not linked anywhere
2735	TEST_SANDBOXES = \
2736	SL/CB/CB.test \
2737	SL/HEADERTESTS/HEADERTESTS.test \
2738
2739	UNITS_TESTED = \
2740	AISC_MKPTPS/AISC_MKPTPS.tooltests \
2741	ARB_GDE/ARB_GDE.test \
2742	CONSENSUS_TREE/CONSENSUS_TREE.test \
2743	CONVERTALN/CONVERTALN.test \
2744	CORE/libCORE.test \
2745	DBSERVER/DBSERVER.test \
2746	DIST/DIST.test \
2747	EDIT4/EDIT4.test \
2748	GENOM_IMPORT/GENOM_IMPORT.test \
2749	HELP_SOURCE/HELP_SOURCE.tooltests \
2750	MERGE/MERGE.test \
2751	MULTI_PROBE/MULTI_PROBE.test \
2752	NTREE/NTREE.test \
2753	PARSIMONY/PARSIMONY.test \
2754	PERLTOOLS/PERLTOOLS.tooltests \
2755	PROBE/PROBE.test \
2756	PROBE_DESIGN/PROBE_DESIGN.test \
2757	PROBE_SET/PROBE_SET.tooltests \
2758	RNACMA/RNACMA.test \
2759	SL/ALILINK/ALILINK.test \
2760	SL/APP/APP.test \
2761	SL/CONSENSUS/CONSENSUS.test \
2762	SL/DB_QUERY/DB_QUERY.test \
2763	SL/FAST_ALIGNER/FAST_ALIGNER.test \
2764	SL/FILTER/FILTER.test \
2765	SL/INSDEL/INSDEL.test \
2766	SL/ITEM_SHADER/ITEM_SHADER.test \
2767	SL/ITEMS/ITEMS.test \
2768	SL/LOCATION/LOCATION.test \
2769	SL/MACROS/MACROS.test \
2770	SL/NDS/NDS.test \
2771	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.test \
2772	SL/PRONUC/PRONUC.test \
2773	SL/PTCLEAN/PTCLEAN.test \
2774	SL/REGEXPR/REGEXPR.test \
2775	SL/SEQIO/SEQIO.test \
2776	SL/TREE_READ/TREE_READ.test \
2777	SL/TREEDISP/TREEDISP.test \
2778	WINDOW/libWINDOW.test \
2779
2780	TESTED_UNITS = \
2781	$(UNITS_TESTED_FIRST) \
2782	$(UNITS_RUNNING_LONG) \
2783	$(TEST_SANDBOXES) \
2784	$(UNITS_TESTED) \
2785
2786	# ----------------------------------------
2787
2788	ifeq ($(DEVELOPER),RALF)
2789
2790	DEFINED_TEST_UNITS = \
2791	$(TESTED_UNITS) \
2792	$(UNTESTED_UNITS) \
2793	$(UNTESTABLE_UNITS) \
2794
2795	list_undefined_units:
2796	@UNIT_TESTER/list_undefined_units.pl $(DEFINED_TEST_UNITS) -- $(TESTED_UNITS_AUTO)
2797
2798	else
2799
2800	list_undefined_units:
2801
2802	endif
2803
2804	# ----------------------------------------
2805
2806	TEST_LOG_DIR = UNIT_TESTER/logs
2807	TEST_RUN_SUITE=$(MAKE) $(NODIR) -C UNIT_TESTER -f Makefile.suite -r
2808	# -> UNIT_TESTER/Makefile.suite
2809	TEST_MAKE_FLAGS=
2810	TEST_POST_CLEAN=
2811	ifeq ($(COVERAGE),1)
2812	TEST_POST_CLEAN=$(MAKE) clean_cov
2813	TEST_MAKE_FLAGS+=-j1
2814	endif
2815
2816
2817	%.test:
2818	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
2819	( \
2820	echo "take[1]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
2821	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
2822	"UNITDIR=$(@D)" \
2823	"UNITLIBNAME=$(@F:.test=)" \
2824	"COVERAGE=$(COVERAGE)" \
2825	"ARB_PID=$(ARB_PID)_$(@F)" \
2826	"DEVELOPER=$(DEVELOPER)" \
2827	runtest; \
2828	echo "take[1]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"; \
2829	$(TEST_POST_CLEAN) \
2830	) >$(TEST_LOG_DIR)/$(@F).log 2>&1; \
2831	UNIT_TESTER/log_result.pl $(TEST_LOG_DIR)/$(@F).log )
2832
2833	%.notest:
2834	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
2835	( \
2836	echo "take[4]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
2837	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
2838	"UNITDIR=$(@D)" \
2839	"UNITLIBNAME=$(@F:.notest=)" \
2840	"COVERAGE=0" \
2841	"ARB_PID=$(ARB_PID)_$(@F)" \
2842	"DEVELOPER=$(DEVELOPER)" \
2843	check_no_test; \
2844	echo "take[4]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'" \
2845	) >$(TEST_LOG_DIR)/$(@F).log 2>&1 )
2846
2847
2848	# tool test aliases (used to test one or multiple executable(s) in a single subdir):
2849	%.tooltests:
2850	$(error please define an explicit tooltest alias for $@)
2851
2852	AISC_MKPTPS/AISC_MKPTPS.tooltests : AISC_MKPTPS/mkptypes.test
2853	@echo "aliasing $@ -> $^"
2854	PERLTOOLS/PERLTOOLS.tooltests : PERLTOOLS/arb_proto_2_xsub.test
2855	@echo "aliasing $@ -> $^"
2856	PROBE_SET/PROBE_SET.tooltests : PROBE_SET/fb_test.test
2857	@echo "aliasing $@ -> $^"
2858	HELP_SOURCE/HELP_SOURCE.tooltests : HELP_SOURCE/arb_help2xml.test
2859	@echo "aliasing $@ -> $^"
2860	TOOLS/TOOLS.tooltests : TOOLS/arb_consensus_tree.test TOOLS/arb_probe.test TOOLS/arb_test.test
2861	@echo "aliasing $@ -> $^"
2862
2863	# aliases for tools w/o tests:
2864	READSEQ/READSEQ.tooltests:
2865	@echo "Note: no tests for $@"
2866
2867
2868	test_base: $(UNIT_TESTER_LIB:.a=.dummy) $(subst .test,.dummy,$(TEST_SANDBOXES))
2869
2870	clean_cov:
2871	find . $ -name ".gcda" -o -name ".gcov" -o -name "*.cov" $ -exec rm {} \;
2872
2873	clean_cov_all: clean_cov
2874	find . $ -name "*.gcno" $ -exec rm {} \;
2875
2876	cleanup_faked_arbpids:
2877	@rm ~/.arb_tmp/tmp/arb_pids_${USER}_${ARB_PID}_* \|\| true
2878
2879	cleanup_faked_arbpids_and_fail: cleanup_faked_arbpids
2880	@false
2881
2882	NOTESTS_IN_UNTESTED = $(subst .test,.notest,$(UNTESTED_UNITS))
2883
2884	run_tests_faked_arbpid:
2885	+@$(TEST_RUN_SUITE) init
2886	@echo "take[2]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2887	@$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(TESTED_UNITS) $(NOTESTS_IN_UNTESTED) \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2888	@echo "take[2]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2889	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2890	@$(MAKE) clean_cov >/dev/null
2891	@$(MAKE) cleanup_faked_arbpids
2892
2893	# @@@ instead of only running UNIT, this should as well run all tests this unit depends on? according to 'needs_libs'
2894	# @@@ '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
2895
2896	run_onetest_faked_arbpid:
2897	+@$(TEST_RUN_SUITE) init
2898	@echo "take[3]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2899	test -n "$(UNIT)" \|\| (echo "Error: UNIT has to be defined for target 'run_onetest_faked_arbpid'!"; false)
2900	$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(UNIT).test \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2901	@echo "take[3]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2902	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2903	@$(MAKE) clean_cov >/dev/null
2904	@$(MAKE) cleanup_faked_arbpids
2905
2906	run_tests: test_base clean_cov
2907	$(MAKE) "ARB_PID=UT_$$$$" run_tests_faked_arbpid list_undefined_units
2908
2909	run_oneunitstests: test_base
2910	$(MAKE) "ARB_PID=UT_$$$$" run_onetest_faked_arbpid
2911
2912
2913	ut:
2914	ifeq ($(UNIT_TESTS),1)
2915	@echo $(MAKE) run_tests
2916	@$(MAKE) run_tests
2917	else
2918	@echo "Not compiled with unit tests"
2919	endif
2920
2921
2922	aut:
2923	+@$(TEST_RUN_SUITE) unskip
2924	$(MAKE) ut
2925
2926	# --------------------------------------------------------------------------------
2927
2928	TIMELOG=$(ARBHOME)/arb_time.log
2929	TIMEARGS=--append --output=$(TIMELOG) --format=" * %E(%S+%U) %P [%C]"
2930	TIMECMD=$(TIME) $(TIMEARGS)
2931
2932	time_one:
2933	ifeq ($(ONE_TIMED_TARGET),)
2934	@echo "Error: You have to pass ONE_TIMED_TARGET to $@"
2935	false
2936	else
2937	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET)"
2938	@$(TIMECMD) $(MAKE) $(ONE_TIMED_TARGET)
2939	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET) [done]"
2940	endif
2941
2942	timed_target:
2943	ifeq ($(TIMED_TARGET),)
2944	@echo "Error: You have to pass TIMED_TARGET to $@"
2945	false
2946	else
2947	@echo "Build time:" > $(TIMELOG)
2948	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2949	@cat $(TIMELOG)
2950	@rm $(TIMELOG)
2951	endif
2952
2953	timed_target_tested:
2954	ifeq ($(TIMED_TARGET),)
2955	@echo "Error: You have to pass TIMED_TARGET to $@"
2956	false
2957	else
2958	@echo "Build time:" > $(TIMELOG)
2959	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2960	$(MAKE) "ONE_TIMED_TARGET=ut" time_one
2961	@cat $(TIMELOG)
2962	@rm $(TIMELOG)
2963	endif
2964
2965	clean_timed_target:
2966	ifeq ($(TIMED_TARGET),)
2967	@echo "Error: You have to pass TIMED_TARGET to $@"
2968	false
2969	else
2970	@echo "Build time:" > $(TIMELOG)
2971	$(MAKE) "ONE_TIMED_TARGET=clean" time_one
2972	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2973	@cat $(TIMELOG)
2974	@rm $(TIMELOG)
2975	endif
2976
2977	# --------------------------------------------------------------------------------
2978
2979	CHECKOUT_MODIFIED=0# set to 1 to temporarily skip test for modifications (do not check in if set to 1)
2980
2981	check_svn_does_not_contain_generated:
2982	ifeq ($(CHECKOUT_MODIFIED),0)
2983	@echo "Testing that build does not modify files in SVN"
2984	@test 0 = `svn status \| wc -l` \|\| ( \
2985	echo "The checkout is not/no longer clean:"; \
2986	svn status; \
2987	echo "- if this fails instantly, your checkout is not clean"; \
2988	echo "- if this fails after other targets, these targets modify checked in data"; \
2989	echo " (a common cause may be that depends are not up to date)"; \
2990	false)
2991	else
2992	grep -Hn 'CHECKOUT_MODIFIED' Makefile
2993	endif
2994
2995	check_svn_ignores_generated:
2996	@test 0 = `svn status \| grep '^\?' \| wc -l` \|\| ( \
2997	echo "There are svn-unignored files:"; \
2998	svn status \| grep '^\?'; \
2999	echo "(all generated files should be svn-ignored)"; \
3000	false)
3001
3002	check_svn_state: check_svn_does_not_contain_generated
3003	$(MAKE) check_svn_ignores_generated
3004	$(MAKE) savetest
3005
3006	things_that_always_should_work: depends proto
3007
3008	post_commit_check:
3009	@echo "---------------------------------------- [Initial]"
3010	$(MAKE) check_svn_state
3011
3012	$(MAKE) clean
3013	@echo "---------------------------------------- [After 'make clean']"
3014	$(MAKE) check_svn_state
3015
3016	$(MAKE) things_that_always_should_work
3017	@echo "---------------------------------------- [After 'make things_that_always_should_work']"
3018	$(MAKE) check_svn_state
3019
3020	$(MAKE) all
3021	@echo "---------------------------------------- [After 'make all']"
3022	$(MAKE) check_svn_state
3023
3024	$(MAKE) things_that_always_should_work
3025	@echo "---------------------------------------- [Final]"
3026	$(MAKE) check_svn_state
3027
3028	# --------------------------------------------------------------------------------
3029	# sanitize arb_ntree; also works for clients (arb_edit4, ...) started from there.
3030
3031	sanitize: all
3032	( \
3033	export "LSAN_OPTIONS=max_leaks=30:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp"; \
3034	echo "sake[1]: Entering directory \`$(ARBHOME)'"; \
3035	$(ARBHOME)/bin/arb_ntree --execute _logged ~/data/test.arb 2>&1 ; \
3036	echo "sake[1]: Leaving directory \`$(ARBHOME)'" \
3037	) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
3038
3039	# --------------------------------------------------------------------------------
3040	# build and test one unit:
3041
3042	build_oneunit:
3043	$(MAKE) "WITHPERL=1" $(UNIT).dummy
3044
3045	oneunit:
3046	ifndef UNIT
3047	@echo "Please define UNIT, e.g. using"
3048	@echo " make \"UNIT=ARBDB/libARBDB\" oneunit"
3049	@echo " make \"UNIT=SL/TREEDISP/TREEDISP\" oneunit"
3050	@echo "(Note: 1st is a shared library, 2nd isn't)"
3051	false
3052	else
3053	@echo "Build time" > $(TIMELOG)
3054	@echo "$(SEP) $(MAKE) build_oneunit"
3055	@$(TIMECMD) $(MAKE) build_oneunit
3056	ifeq ($(UNIT_TESTS),1)
3057	@echo "$(SEP) $(MAKE) run_oneunitstests"
3058	@$(TIMECMD) $(MAKE) run_oneunitstests
3059	endif
3060	@cat $(TIMELOG)
3061	@rm $(TIMELOG)
3062	endif
3063
3064	# --------------------------------------------------------------------------------
3065	# Main targets:
3066
3067	tarfile: rebuild
3068	$(MAKE) prepare_libdir
3069	util/arb_compress
3070
3071	tarfile_quick: all
3072	$(MAKE) prepare_libdir
3073	util/arb_compress
3074
3075	# -----------------------------------
3076
3077	build: arb
3078	$(MAKE) check_bin_dep preplib compile_compatibility fig_cure
3079
3080	all:
3081	@echo "Build time" > $(TIMELOG)
3082	# $(MAKE) clean_checked_vect # uncomment to rebuild sources where expected vectorization gets tested
3083	@echo "$(SEP) $(MAKE) all"
3084	@$(TIMECMD) $(MAKE) build
3085	@echo $(SEP)
3086	@echo "made 'all' with success."
3087	@echo "to start arb enter 'arb'"
3088	ifeq ($(UNIT_TESTS),1)
3089	@echo "$(SEP) $(MAKE) run_tests"
3090	@$(TIMECMD) $(MAKE) run_tests
3091	endif
3092	@echo "$(SEP) $(MAKE) all [done]"
3093	ifeq ($(DEBUG),1)
3094	@$(MAKE) save_test_no_error >/dev/null # just show hints
3095	endif
3096	@cat $(TIMELOG)
3097	@rm $(TIMELOG)
3098
3099	rebuild: clean
3100	$(MAKE) all
3101
3102	# --------------------------------------------------------------------------------
3103	# special targets showing obvious error at bottom
3104	# (intended to be used from automated builds)
3105
3106	BUILD_LOG=build.log
3107	SHELL=bash
3108	REDIRECT_KEEP_EXITCODE = tee $(BUILD_LOG) ; exit "$${PIPESTATUS[0]}"
3109	EXTRACT_ERROR_SUMMARY = (./SOURCE_TOOLS/short_error_summary.pl $(BUILD_LOG); false)
3110
3111	ALL:
3112	@(($(MAKE) all 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
3113
3114	REBUILD:
3115	@(($(MAKE) rebuild 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
3116
3117	TARFILE:
3118	@(($(MAKE) tarfile 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
3119
3120	TARFILE_QUICK:
3121	@(($(MAKE) tarfile_quick 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
3122

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