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Last change on this file was 19810, checked in by westram, 3 weeks ago
reintegrates 'unittest' into 'gcc' fixes #874 adds: log:branches/unittest@19744:19809
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 90.8 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	# [defined by make or env:]
14	#
15	# CC C compiler (cc)
16	# CXX C++ compiler (g++)
17	# AR Linker (ar)
18	#
19	# [defined by config.makefile:]
20	#
21	# DEVELOPER=name special compilation (values: ANY,RELEASE,your name)
22	# OPENGL=0/1 whether OPENGL is available
23	#
24	# -----------------------------------------------------
25	# Paths for several libraries may be set from config.makefile by using:
26	#
27	# export XLIBS=$(shell pkg-config --libs xpm xerces-c)
28	# export XINCLUDES=$(shell pkg-config --cflags x11)
29	# export XAW_LIBS=$(shell pkg-config --libs xaw7)
30	# export XML_INCLUDES=$(shell pkg-config --cflags xerces-c)
31	#
32	# You make have to explicitely point pkg-config to the *.pc files needed.
33	# For example, Xquartz X11 libraries on macOS can be located by adding
34	# the following line before those given above:
35	#
36	# export PKG_CONFIG_PATH=/usr/X11/lib/pkgconfig
37	#
38	# If you introduce a new variable that is handled as described above,
39	# please add to section .@InjectedEnvironment
40	#
41	# -----------------------------------------------------
42	# ARB Makefile and ARB source code are aware of the following defines:
43	#
44	# $(MACH) name of the machine (LINUX or DARWIN; see config.makefile)
45	# DEBUG compiles the DEBUG sections
46	# DEBUG_GRAPHICS all X-graphics are flushed immediately (for debugging)
47	# ARB_64=0/1 1=>compile 64 bit version
48	# UNIT_TESTS=0/1 1=>compile in unit tests and call them after build
49	# COVERAGE=0/1/2 compile in gcov support (useful together with UNIT_TESTS=1)
50	# 0=no, 1+2=compile in, 1=show
51	# STABS=0/1 force stabs format? (0 = "use default format")
52	# SANITIZE=0/#/all use Sanitizer? (defaults to 0,
53	# 1=AddressSanitizer+LeakSanitizer,
54	# 2=UndefinedBehaviorSanitizer,
55	# combine bit-values to activate multiple Sanitizers,
56	# specify 'all' to activate all)
57	# IGNORE_LEAKS=1 does not abort when leaks are detected (while using SANITIZE=1/all)
58	# SHOWTODO=0/1 activate TODO-warnings? (defaults to 0, except for ralf)
59	#
60	# -----------------------------------------------------
61	# The ARB source code is aware of the following defines:
62	#
63	# NDEBUG doesn't compile the DEBUG sections
64	# DEVEL_$(DEVELOPER) developer-dependent flag (enables you to have private sections in code)
65	# DEVELOPER='ANY' (default setting) will be ignored
66	# configurable in config.makefile
67	#
68	# -----------------------------------------------------
69
70	ifndef ARB_ORG_MAKEFLAGS
71	ARB_ORG_MAKEFLAGS=$(MAKEFLAGS)
72	else
73	ifeq ($(ARB_ORG_MAKEFLAGS),)
74	ARB_ORG_MAKEFLAGS=$(MAKEFLAGS)
75	endif
76	endif
77
78	# detect initial (i.e. non-recursive) call:
79	ifndef ARBBID
80	INITIAL_CALL:=yes
81	endif
82
83	# Read configuration
84	include config.makefile
85	CONFIG_MAKEFILE_FOUND=$(strip $(wildcard config.makefile))
86
87	# strip spaces from values defined in config.makefile
88	# (otherwise they easily have spaces appended)
89	ifdef DEVELOPER
90	DEVELOPER := $(strip $(DEVELOPER))
91	endif
92	ifdef OPENGL
93	OPENGL := $(strip $(OPENGL))
94	endif
95	ifdef ISINA
96	ISINA := $(strip $(ISINA))
97	endif
98	ifdef DEBUG
99	DEBUG := $(strip $(DEBUG))
100	endif
101	ifdef UNIT_TESTS
102	UNIT_TESTS := $(strip $(UNIT_TESTS))
103	endif
104	ifdef COVERAGE
105	COVERAGE := $(strip $(COVERAGE))
106	endif
107	ifdef SHOWTODO
108	SHOWTODO := $(strip $(SHOWTODO))
109	endif
110	ifdef STABS
111	STABS := $(strip $(STABS))
112	endif
113	ifdef TRACESYM
114	TRACESYM := $(strip $(TRACESYM))
115	endif
116	ifdef DEBUG_GRAPHICS
117	DEBUG_GRAPHICS := $(strip $(DEBUG_GRAPHICS))
118	endif
119
120	# set defaults for (or strip) variables commented out in config.makefile:
121	ifdef SANITIZE
122	SANITIZE := $(strip $(SANITIZE))
123	else
124	SANITIZE:=0
125	endif
126	ifdef IGNORE_LEAKS
127	IGNORE_LEAKS := $(strip $(IGNORE_LEAKS))
128	else
129	IGNORE_LEAKS:=0
130	endif
131	ifndef DARWIN
132	DARWIN:=0
133	else
134	DARWIN := $(strip $(DARWIN))
135	endif
136	ifndef LINUX
137	LINUX:=0
138	else
139	LINUX := $(strip $(LINUX))
140	endif
141	ifndef DEBIAN
142	DEBIAN:=0
143	else
144	DEBIAN := $(strip $(DEBIAN))
145	endif
146	ifndef ARB_64
147	ARB_64=1#default to 64bit
148	else
149	ARB_64 := $(strip $(ARB_64))
150	endif
151
152	# Variables allowed for injection [InjectedEnvironment]
153	# (alternatively initialize them with '?=', e.g. done for XLIBS and XINCLUDES)
154	# In both cases add them to SOURCE_TOOLS/export2sub
155	ifndef XML_INCLUDES
156	XML_INCLUDES=
157	endif
158	ifndef XAW_LIBS
159	XAW_LIBS=
160	endif
161
162
163	ifneq ($(CONFIG_MAKEFILE_FOUND),)
164	ifneq ($(DARWIN)$(LINUX),10)
165	ifneq ($(DARWIN)$(LINUX),01)
166	$(error exactly one of DARWIN=1 or LINUX=1 has to be defined (got:$(DARWIN)$(LINUX)))
167	endif
168	endif
169	endif
170
171	# compiler settings:
172	ifneq ($(CC),use__A_CC__instead_of__CC)
173	A_CC:=$(CC)# compile C
174	A_CXX:=$(CXX)# compile C++
175
176	# uncomment to ensure no submakefile uses CC and CXX directly
177	override CC:=use__A_CC__instead_of__CC
178	override CXX:=use__A_CXX__instead_of__CXX
179	endif
180
181	# unconditionally prepend $(ARBHOME)/lib to LD_LIBRARY_PATH if not found
182	ifeq ($(findstring $(ARBHOME)/lib,$(LD_LIBRARY_PATH)),)
183	LD_LIBRARY_PATH:=${ARBHOME}/lib:$(LD_LIBRARY_PATH)
184	endif
185
186	# store LD_LIBRARY_PATH to circumvent SIP restrictions:
187	ARBBUILD_LIBRARY_PATH:=$(LD_LIBRARY_PATH)
188
189	FORCEMASK = umask 002
190	NODIR=--no-print-directory
191
192	SED:=$(ARBHOME)/SH/arb_sed
193	READLINK:=$(ARBHOME)/SH/arb_readlink
194
195	# ---------------------- compiler version detection
196
197	# supported gcc versions:
198	ALLOWED_gcc_VERSIONS=\
199	4.4.3 4.4.5 4.4.6 4.4.7 \
200	4.5.2 \
201	4.6.1 4.6.2 4.6.3 4.6.4 \
202	4.7.1 4.7.2 4.7.3 4.7.4 \
203	4.8.0 4.8.1 4.8.2 4.8.3 4.8.4 4.8.5 \
204	4.9.0 4.9.1 4.9.2 4.9.3 4.9.4 \
205	5.1.0 5.2.0 5.3.0 5.4.0 5.5.0 \
206	6.1.0 6.2.0 6.3.0 6.4.0 6.5.0 \
207	7.1.0 7.2.0 7.3.0 7.4.0 7.5.0 \
208	8.1.0 8.2.0 8.3.0 8.4.0 8.5.0 \
209	9.1.0 9.2.0 9.3.0 9.4.0 9.5.0 \
210	10.1.0 10.2.0 10.3.0 10.4.0 10.5.0 \
211	11.3.0 \
212
213	# Note: starting with version 5, arb silently accepts any subversion number
214	# above zero. See SOURCE_TOOLS/arb_compiler_version.pl@acceptSubVersions
215	#
216	# This may cause problems when manually checking for compiler versions in code
217	# (GCC_VERSION_CODE is not affected, GCC_PATCHLEVEL_CODE may cause problems!)
218	# ----------------------
219
220	COMPILER_INFO:=$(shell SOURCE_TOOLS/arb_compiler_version.pl $(A_CXX))
221	COMPILER_NAME:=$(word 1,$(COMPILER_INFO))
222	COMPILER_VERSION:=$(word 2,$(COMPILER_INFO))
223
224	USE_CLANG:=0
225	ifneq ($(COMPILER_NAME),gcc)
226	ifeq ($(COMPILER_NAME),clang)
227	USE_CLANG:=1
228	else
229	ifeq ($(COMPILER_VERSION),4.6.4)
230	# gcc version 4.6.4 segfaults when dumping symbols for detection (silently accept as gcc)
231	COMPILER_NAME:=gcc
232	else
233	$(error failed to detect COMPILER_NAME (got '$(COMPILER_NAME)', expected 'clang' or 'gcc'))
234	endif
235	endif
236	endif
237
238	ifeq ($(USE_CLANG),1)
239	# accept all clang versions:
240	ALLOWED_COMPILER_VERSIONS=$(COMPILER_VERSION)
241	else
242	ALLOWED_COMPILER_VERSIONS=$(ALLOWED_gcc_VERSIONS)
243	endif
244
245	COMPILER_VERSION_ALLOWED=$(strip $(subst ___,,$(foreach version,$(ALLOWED_COMPILER_VERSIONS),$(findstring ___$(version)___,___$(COMPILER_VERSION)___))))
246
247	#---------------------- force no root
248
249	YOU_ARE_ROOT := $(strip $(shell bash -c 'echo $$((EUID == 0))'))
250	ifeq ($(YOU_ARE_ROOT),1)
251	$(error Building arb as root user is not recommended)
252	# To install a custom-compiled arb system-wide, build target 'tarfile' as "normal" user.
253	# Afterwards, use arb_install.sh as root.
254	endif
255
256	#---------------------- split gcc version
257
258	SPLITTED_VERSION:=$(subst ., ,$(COMPILER_VERSION))
259
260	USE_GCC_MAJOR:=$(word 1,$(SPLITTED_VERSION))
261	USE_GCC_MINOR:=$(word 2,$(SPLITTED_VERSION))
262	USE_GCC_PATCHLEVEL:=$(word 3,$(SPLITTED_VERSION))
263
264	USE_GCC_452_OR_HIGHER:=
265	USE_GCC_46_OR_HIGHER:=
266	USE_GCC_47_OR_HIGHER:=
267	USE_GCC_48_OR_HIGHER:=
268	USE_GCC_49_OR_HIGHER:=
269	USE_GCC_50_OR_HIGHER:=
270	USE_GCC_60_OR_HIGHER:=
271	USE_GCC_70_OR_HIGHER:=
272	USE_GCC_80_OR_HIGHER:=
273	USE_GCC_90_OR_HIGHER:=
274	USE_GCC_100_OR_HIGHER:=
275	USE_GCC_110_OR_HIGHER:=
276
277	ifeq ($(USE_CLANG),0)
278	ifeq ($(USE_GCC_MAJOR),4)
279	ifeq ($(USE_GCC_MINOR),5)
280	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),23456789)','')
281	USE_GCC_452_OR_HIGHER:=yes
282	endif
283	else
284	ifneq ('$(findstring $(USE_GCC_MINOR),6789)','')
285	USE_GCC_452_OR_HIGHER:=yes
286	USE_GCC_46_OR_HIGHER:=yes
287	ifneq ($(USE_GCC_MINOR),6)
288	USE_GCC_47_OR_HIGHER:=yes
289	ifneq ($(USE_GCC_MINOR),7)
290	USE_GCC_48_OR_HIGHER:=yes
291	ifneq ($(USE_GCC_MINOR),8)
292	USE_GCC_49_OR_HIGHER:=yes
293	endif
294	endif
295	endif
296	endif
297	endif
298	else
299	# gcc 5.x or higher
300	USE_GCC_452_OR_HIGHER:=yes
301	USE_GCC_46_OR_HIGHER:=yes
302	USE_GCC_47_OR_HIGHER:=yes
303	USE_GCC_48_OR_HIGHER:=yes
304	USE_GCC_49_OR_HIGHER:=yes
305	USE_GCC_50_OR_HIGHER:=yes
306	ifneq ($(USE_GCC_MAJOR),5)
307	# gcc 6.x or higher
308	USE_GCC_60_OR_HIGHER:=yes
309	ifneq ($(USE_GCC_MAJOR),6)
310	# gcc 7.x or higher
311	USE_GCC_70_OR_HIGHER:=yes
312	ifneq ($(USE_GCC_MAJOR),7)
313	# gcc 8.x or higher
314	USE_GCC_80_OR_HIGHER:=yes
315	ifneq ($(USE_GCC_MAJOR),8)
316	# gcc 9.x or higher
317	USE_GCC_90_OR_HIGHER:=yes
318	ifneq ($(USE_GCC_MAJOR),9)
319	# gcc 10.x or higher
320	USE_GCC_100_OR_HIGHER:=yes
321	ifneq ($(USE_GCC_MAJOR),10)
322	# gcc 11.x or higher
323	USE_GCC_110_OR_HIGHER:=yes
324	endif
325	endif
326	endif
327	endif
328	endif
329	endif
330	endif
331	endif
332
333	#---------------------- define special directories for non standard builds
334
335	ifeq ($(DARWIN),1)
336	OSX_FW:=/System/Library/Frameworks
337	OSX_FW_OPENGL:=$(OSX_FW)/OpenGL.framework/Versions/A/Libraries
338	OSX_FW_GLUT:=$(OSX_FW)/GLUT.framework/Versions/A/Libraries
339	OSX_FW_IMAGEIO:=$(OSX_FW)/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources
340	endif
341
342	#---------------------- SSE vectorization
343	# for details about vectorization checks see SOURCE_TOOLS/vectorize.README
344
345	DISABLE_VECTORIZE_CHECK:=0# set to 1 to completely disable vectorization checks
346	TRACE_MISSED_VECTORIZATIONS:=0# set to 1 to activate detailed output about failed vectorizations
347	# (does also show details about successful vectorized loops, which are not optimal)
348	VECTORIZATION_CHECK_CANDIDATES:=0# set to 1 to show vectorizations that may be checked
349	# (for yet unchecked files)
350	# Note: TRACE_MISSED_VECTORIZATIONS and VECTORIZATION_CHECK_CANDIDATES cannot be used together!
351
352	#---------------------- Support for OPENMP
353
354	USE_OPENMP:=1
355	ifeq ($(DARWIN),1)
356	USE_OPENMP:=0
357	endif
358
359	#----------------------
360
361	ifeq ($(DARWIN),1)
362	LINK_STATIC=1# link static
363	else
364	LINK_STATIC=0# link dynamically
365	# LINK_STATIC=1# link static (testing only)
366	endif
367
368	shared_cflags :=# flags for shared lib compilation
369	onlyC_flags :=# flags only suitable for C (not C++; see cxxflags).
370	clflags :=# linker flags (when passed through gcc, i.e. used to link binaries and shared libraries)
371	extended_warnings :=# warning flags for C and C++-compiler
372	extended_cpp_warnings :=# warning flags for C++-compiler only
373
374	ifeq ($(DEBUG),0)
375	dflags := -DNDEBUG# defines
376	ifeq ($(USE_CLANG),1)
377	cflags := -O3# compiler flags (C and C++)
378	else
379	clflags += -Wl,-O2# passthrough linker flags
380	# ------- standard optimization:
381	cflags := -O3# compiler flags (C and C++)
382	# ------- test changed optimization (DISABLE_VECTORIZE_CHECK for -O2 or lower):
383	# cflags := -O2# do not commit uncommented!
384	# DISABLE_VECTORIZE_CHECK:=1
385	endif
386	endif
387
388	ifeq ($(DEBIAN),1)
389	clflags += -Wl,-rpath=/usr/lib/arb/lib -Wl,-z,relro
390	endif
391
392	ifeq ($(DEBUG),1)
393	dflags := -DDEBUG
394
395	# [AFAI understand cc doc, the previous setting used here (-g -g3 -ggdb -ggdb3) was same as (-ggdb3)]
396	# GDB_COMMON := -g
397	# GDB_COMMON := -g3
398	GDB_COMMON := -ggdb3
399	# GDB_COMMON := -gdwarf -g3
400
401	DBGOPTI:=-O0
402	ifneq ('$(SANITIZE)','0')
403	# sanitizer report several bogus buffer-overflows when arb is build with -O0 (e.g. with gcc 7.5.0)
404	DBGOPTI:=-O1
405	endif
406	# DBGOPTI:=-O2 # use this for callgrind (to force inlining)
407
408	ifeq ($(STABS),1)
409	$(error STABS no longer supported)
410	endif
411
412	cflags := $(DBGOPTI) $(GDB_COMMON)
413	clflags += $(DBGOPTI) $(GDB_COMMON)
414
415	# to debug link problems uncomment next line:
416	# clflags += -Wl,--verbose
417
418	ifeq ($(DEBUG_GRAPHICS),1)
419	dflags += -DDEBUG_GRAPHICS
420	endif
421
422	endif # DEBUG only
423
424	# ------------------------------ POST_COMPILE - control how much you get spammed
425	# (please do not change default in SVN)
426	POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl
427
428	# POST_COMPILE += --original # dont modify compiler output
429	# POST_COMPILE += --hide-Noncopyable-advices
430	# POST_COMPILE += --show-useless-Weff++
431	# POST_COMPILE += --no-warnings
432	# POST_COMPILE += --only-first-error
433	# POST_COMPILE += --no-warnings --only-first-error
434
435	# always pass used compiler version to postcompile:
436	POST_COMPILE += --compiler=$(COMPILER_VERSION)
437
438	# ------------------------------
439
440	# Enable extra warnings
441	extended_warnings :=
442	extended_cpp_warnings :=
443
444	# C and C++
445	extended_warnings += -Wwrite-strings -Wunused -Wno-aggregate-return
446
447	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
448	# disable shadow warnings for gcc 4.8 (and lower)
449	# (does e.g. warn if a method-name is used as parameter in another method - even for derived classes. unusable!)
450	extended_warnings += -Wshadow
451	endif
452
453	# C++ only
454	extended_cpp_warnings += -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute
455	extended_cpp_warnings += -Wctor-dtor-privacy
456	# extended_cpp_warnings += -Wfloat-equal
457
458	extended_cpp_warnings += -Wmissing-noreturn
459	# extended_cpp_warnings += -Wold-style-cast# (warns about 28405 old-style casts)
460	extended_cpp_warnings += -Winit-self
461	extended_cpp_warnings += -Wstrict-aliasing
462	extended_cpp_warnings += -Wextra
463
464	# ------- above only warning-options already available in gcc 4.4.3
465
466	# -Weffc++ broken in 4.7.x series
467	# gcc 4.7.3 crashes on GenomeImport.cxx when -Weffc++ is active
468	# (bug reported https://gcc.gnu.org/bugzilla/show_bug.cgi?id=56923; apparently wont be fixed for 4.7-series)
469	# gcc 4.7.4 crashes on DBwriter.cxx when -Weffc++ is active
470	WEFFC_BROKEN:=0
471	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
472	ifneq ('$(USE_GCC_48_OR_HIGHER)','yes')
473	WEFFC_BROKEN:=1
474	endif
475	endif
476	ifeq ('$(WEFFC_BROKEN)','0')
477	extended_cpp_warnings += -Weffc++
478	endif
479
480	# turn off -Wmaybe-uninitialized in debug mode (gets activated with -Wextra). too many bogus warnings
481	ifeq ($(DEBUG),1)
482	ifeq ($(USE_CLANG),0)
483	extended_cpp_warnings += -Wno-maybe-uninitialized
484	endif
485	endif
486
487	SUGGEST_FINAL:=
488
489	ifeq ('$(USE_GCC_452_OR_HIGHER)','yes')
490	extended_cpp_warnings += -Wlogical-op# gcc 4.5.2
491	endif
492	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
493	extended_cpp_warnings += -Wzero-as-null-pointer-constant# gcc 4.7
494	endif
495	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
496	extended_cpp_warnings += -Wunused-local-typedefs# available since gcc 4.7 (but fails for each STATIC_ASSERT, so enable only for Cxx11)
497	endif
498	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
499	extended_cpp_warnings += -Wswitch-bool
500	extended_cpp_warnings += -Wlogical-not-parentheses
501	extended_cpp_warnings += -Wsizeof-array-argument
502	extended_cpp_warnings += -Wbool-compare
503
504	SUGGEST_FINAL:=yes
505	endif
506	ifeq ('$(USE_GCC_60_OR_HIGHER)','yes')
507	extended_cpp_warnings += -Wduplicated-cond
508	endif
509	ifeq ('$(USE_GCC_80_OR_HIGHER)','yes')
510	extended_cpp_warnings += -Wmultistatement-macros
511	endif
512
513	# switch off final suggestions for 8.3.0 and 8.4.0:
514	ifeq ('$(COMPILER_VERSION)','8.3.0')
515	SUGGEST_FINAL:=no
516	endif
517	ifeq ('$(COMPILER_VERSION)','8.4.0')
518	SUGGEST_FINAL:=no
519	endif
520
521	ifeq ($(DEVELOPER),RELEASE)
522	# switch off final suggestions in RELEASE:
523	SUGGEST_FINAL:=no
524	endif
525	# suggest final:
526	ifeq ('$(SUGGEST_FINAL)','yes')
527	extended_cpp_warnings += -Wsuggest-final-types
528	extended_cpp_warnings += -Wsuggest-final-methods
529	dflags += -DSUGGESTS_FINAL
530	endif
531
532	#---------------------- turn off clang bogus warnings
533
534	ifeq ($(USE_CLANG),1)
535	# -Wmismatched-tags warns about struct/class mismatch in forward declarations (which is explicitely allowed)
536	# -Wchar-subscripts reports too many bogus warnings for "array['x']" (when 'x' is known to be in range [0..128])
537	# -Wunused-private-field report too many false positives (currently ~ 2 of 3)
538	# -Wstring-plus-int warns about common ARB coding practice
539	# -Wgnu-static-float-init warns about accepted GNU extension
540	extended_cpp_warnings += -Wno-mismatched-tags -Wno-char-subscripts -Wno-unused-private-field -Wno-string-plus-int
541	ifeq ('$(COMPILER_VERSION)','4.2.1')
542	# jenkins build (doesn't know switch -Wno-gnu-static-float-init)
543	extended_cpp_warnings += -Wno-gnu
544	else
545	extended_cpp_warnings += -Wno-gnu-static-float-init
546	endif
547	endif
548
549	#---------------------- developer
550
551	ifneq ($(DEVELOPER),ANY) # ANY=default setting (skip all developer specific code)
552	dflags += -DDEVEL_$(DEVELOPER)# activate developer/release specific code
553	endif
554
555	#---------------------- activate TODO warnings?
556
557	ifndef SHOWTODO
558	ifeq ($(DEVELOPER),RALF)
559	SHOWTODO:=1
560	else
561	SHOWTODO:=0
562	endif
563	endif
564	ifeq ($(SHOWTODO),1)
565	dflags += -DWARN_TODO# activate "TODO" warnings
566	endif
567
568	#---------------------- be strict while building documentation?
569
570	STRICT_DOC:=0
571	ifeq ($(DEVELOPER),RALF)
572	STRICT_DOC:=1
573	endif
574
575	#---------------------- activate threads?
576	# only useful if compiler is able to compile Cxx11 or better
577
578	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
579	# see also ./TEMPLATES/cxxforward.h@USE_Cxx11
580	cflags += -pthread
581	clflags += -pthread
582	endif
583
584	#---------------------- activate Sanitizers?
585
586	ASAN_OPTIONS:=handle_segv=0:color=0
587	ifeq ($(IGNORE_LEAKS),1)
588	ASAN_OPTIONS+=:detect_leaks=0 # disable leak-detection
589	else
590	ASAN_OPTIONS+=:detect_leaks=1 # detect leaks (normal setting)
591	endif
592	ASAN_OPTIONS+=:check_initialization_order=1
593	# ASAN_OPTIONS+=:abort_on_error=1
594
595	# suppressions: SOURCE_TOOLS/arb.leaksan.supp
596	LSAN_OPTIONS:=max_leaks=3:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp
597
598	UBSAN_OPTIONS:=print_stacktrace=1
599
600	SANITIZE_ADDRESS:=0
601	SANITIZE_UNDEFINED:=0
602
603	ifneq ($(SANITIZE),0)
604	ifeq ($(SANITIZE),all)
605	SANITIZE:=3
606	endif
607
608	ifeq ($(SANITIZE),1)
609	SANITIZE_ADDRESS:=1
610	else
611	ifeq ($(SANITIZE),2)
612	SANITIZE_UNDEFINED:=1
613	else
614	ifeq ($(SANITIZE),3)
615	SANITIZE_ADDRESS:=1
616	SANITIZE_UNDEFINED:=1
617	else
618	$(error Unknown value '$(SANITIZE)' specified for SANITIZE in config.makefile)
619	endif
620	endif
621	endif
622	endif
623
624	ifeq ($(SANITIZE_ADDRESS),1)
625	ifneq ('$(USE_GCC_48_OR_HIGHER)','yes')
626	$(info AddressSanitizer not usable with gcc $(COMPILER_VERSION) - disabled)
627	SANITIZE_ADDRESS:=0
628	else
629	ifneq ('$(USE_GCC_49_OR_HIGHER)','yes')
630	$(info LeakSanitizer does not work with gcc $(COMPILER_VERSION) - disabled)
631	# need to disable AddressSanitizer (otherwise build fails; only affects gcc 4.8.x series)
632	SANITIZE_ADDRESS:=0
633	endif
634	endif
635	endif
636
637	ifeq ($(SANITIZE_UNDEFINED),1)
638	ifneq ('$(USE_GCC_49_OR_HIGHER)','yes')
639	$(info UndefinedBehaviorSanitizer not usable with gcc $(COMPILER_VERSION) - disabled)
640	SANITIZE_UNDEFINED:=0
641	endif
642	endif
643
644	SANITIZE_ANY:=0
645	ifeq ($(SANITIZE_ADDRESS),1)
646	SANITIZE_ANY:=1
647	endif
648	ifeq ($(SANITIZE_UNDEFINED),1)
649	SANITIZE_ANY:=1
650	endif
651
652	# vectorization fails if sanitizer active where it normally succeeds -> disable check
653	ifeq ($(SANITIZE_ANY),1)
654	$(info disabling vectorize checks. would fail with sanitized code)
655	DISABLE_VECTORIZE_CHECK:=1
656	else
657	$(info no sanitizer enabled. reset: SANITIZE=0)
658	SANITIZE:=0
659	endif
660
661	# deactivate some bogus warnings occurring when sanitizing NDEBUG version
662	# (do not disable for future gcc-version >= 8.x -> test again when available)
663	ifeq ($(SANITIZE_ANY),1)
664	ifeq ($(DEBUG),0)
665	ifneq ('$(USE_GCC_80_OR_HIGHER)','yes')
666	extended_cpp_warnings += -Wno-format-overflow
667	extended_cpp_warnings += -Wno-maybe-uninitialized
668	endif
669	endif
670	endif
671
672	#---------------------- 32 or 64 bit
673
674	cross_cflags:=
675	cross_lflags:=
676	cross_clflags:=
677
678	ifeq ($(ARB_64),1)
679	dflags += -DARB_64
680	shared_cflags += -fPIC
681	CROSS_LIB:=# empty => autodetect below
682	ifeq ($(DARWIN),1)
683	cross_cflags += -arch x86_64
684	cross_lflags += -arch x86_64
685	cross_clflags += -arch x86_64
686	endif
687	else
688	CROSS_LIB:=/lib
689	endif
690
691	cflags += $(cross_cflags)
692	clflags += $(cross_clflags)
693
694	ifeq ('$(CROSS_LIB)','')
695	# autodetect libdir
696	ifeq ($(ARB_64),1)
697	CROSS_LIB:=$(shell (test -d /lib64 && echo lib64) \|\| echo lib)
698	else
699	CROSS_LIB:=$(shell (test -d /lib32 && echo lib32) \|\| echo lib)
700	endif
701	endif
702
703	#---------------------- unit tests
704
705	ifndef UNIT_TESTS
706	UNIT_TESTS=0#default is "no tests"
707	endif
708	ifeq ($(UNIT_TESTS),1)
709	dflags += -DUNIT_TESTS
710	UNIT_TESTER_LIB=UNIT_TESTER/UNIT_TESTER.a
711	else
712	UNIT_TESTER_LIB=
713	endif
714
715	#---------------------- use gcov
716
717	ifndef COVERAGE
718	COVERAGE=0#default is "no"
719	endif
720	ifneq ($(COVERAGE),0)
721	GCOV_FLAGS=--coverage
722	$(info disabling vectorize checks. would fail with COVERAGE on)
723	DISABLE_VECTORIZE_CHECK:=1
724	else
725	GCOV_FLAGS=
726	endif
727
728	cflags += $(GCOV_FLAGS)
729	clflags += $(GCOV_FLAGS)
730	cross_lflags += $(GCOV_FLAGS)
731
732	#---------------------- disable vectorize checks atm
733
734	ifeq ('$(USE_GCC_110_OR_HIGHER)','yes')
735	ifdef INITIAL_CALL
736	$(warning Note: disabling vectorize checks. has to be fixed for gcc-11 and higher)
737	endif
738	DISABLE_VECTORIZE_CHECK:=1
739	endif
740
741	#---------------------- other flags
742
743	dflags += -D$(MACH) # define machine
744
745	ifeq ($(DARWIN),1)
746	shared_cflags += -fno-common
747	else
748	dflags += $(shell getconf LFS_CFLAGS)
749	endif
750
751	cflags += -pipe
752	cflags += -fmessage-length=0# dont wrap compiler output
753	cflags += -fshow-column# show columns
754	cflags += -funit-at-a-time
755	cflags += -fPIC
756	cflags += -fno-common# link all global data into one namespace
757	cflags += -fstrict-aliasing# gcc 3.4
758
759	onlyC_flags += -Werror-implicit-function-declaration
760
761	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
762	cflags += -fno-diagnostics-show-caret#gcc 4.8 (4.7.?)
763	endif
764	#cflags += -save-temps# uncomment to see preprocessor output
765
766	#---------------------- various sanitizers
767	# There are some disabled tests in CORE/arb_misc.cxx@sanitizers
768	# which trigger sanitizer reports.
769
770	ifeq ($(SANITIZE_ANY),1)
771	cflags += -ggdb3 -fno-omit-frame-pointer
772	endif
773
774	SANI_CFLAGS:=
775	SANI_CLFLAGS:=
776
777	# activate AddressSanitizer+LeakSanitizer?
778	ifeq ($(SANITIZE_ADDRESS),1)
779	SANI_CFLAGS += -fsanitize=address
780	SANI_CLFLAGS += -fsanitize=address
781	dflags += -DLEAKS_SANITIZED
782	endif
783
784	# activate UndefinedBehaviorSanitizer?
785	ifeq ($(SANITIZE_UNDEFINED),1)
786	SANI_CFLAGS += -fsanitize=undefined
787	SANI_CLFLAGS += -fsanitize=undefined
788	dflags += -DUNDEF_SANITIZED
789	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
790	# abort on runtime errors
791	SANI_CFLAGS += -fno-sanitize-recover=all
792	endif
793
794	cflags += $(SANI_CFLAGS)
795	clflags += $(SANI_CLFLAGS)
796
797	#
798	# Note: alignment-sanitizer is deactivated for ARBDB and PROBE!
799	ifeq ('$(DEBUG)','1')
800	ifeq ($(USE_GCC_MAJOR),4)
801	ifeq ($(USE_GCC_MINOR),9)
802	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),01)','')
803	# workaround https://gcc.gnu.org/bugzilla/show_bug.cgi?id=63531 for 4.9.0 + 4.9.1
804	# (problem is fixed in 4.9.2 release)
805	extended_cpp_warnings:=$(subst -Weffc++,,$(extended_cpp_warnings))
806	endif
807	endif
808	endif
809	endif
810	endif
811
812	#---------------------- X11 location
813
814	ifeq ($(DARWIN),1)
815	XHOME:=$(PREFIX)
816	else
817	ifeq ($(DEBIAN),1)
818	XHOME:=$(PREFIX)
819	else
820	XHOME:=/usr/X11R6
821	endif
822	endif
823
824	XINCLUDES ?= -I$(XHOME)/include
825	XLIBS ?= -L$(XHOME)/$(CROSS_LIB)
826	ifeq ($(DARWIN),1)
827	XINCLUDES += -I$(OSX_FW)/GLUT.framework/Headers -I$(OSX_FW)/OpenGL.framework/Headers -I$(OSX_SDK)/usr/include/krb5
828
829	XLIBS += -lXm -lpng -lz -lXt -lX11 -lXext -lXp -lXmu -lXi
830	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGL.dylib:$(OSX_FW_OPENGL)/libGL.dylib
831	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGLU.dylib:$(OSX_FW_OPENGL)/libGLU.dylib
832	else
833	XLIBS += -lXm -lXpm -lXt -lXext -lX11
834	endif
835
836	#---------------------- open GL
837
838	ifeq ($(OPENGL),1)
839	cflags += -DARB_OPENGL # activate OPENGL code
840	GL := gl # this is the name of the OPENGL base target
841	GL_LIB_SYS := -lGL -lGLU
842	GL_LIB_ARB := -L$(ARBHOME)/GL/glAW -lglAW
843
844	ifeq ($(DARWIN),1)
845	GL_LIB_SYS += -lpthread
846	endif
847
848	GL_PNGLIBS_ARB := -L$(ARBHOME)/GL/glpng -lglpng_arb
849	GL_PNGLIBS_SYS := -lpng
850
851	GLEWLIB := -lGLEW -lGLw
852	GLUTLIB := -lglut
853
854	GL_LIBS_SYS := $(GL_LIB_SYS) $(GL_PNGLIBS_SYS) $(GLEWLIB) $(GLUTLIB)
855	GL_LIBS_ARB := $(GL_LIB_ARB) $(GL_PNGLIBS_ARB)
856
857	RNA3D_LIB := RNA3D/RNA3D.a
858	else
859	GL_LIBS_SYS:=# no opengl -> no libs
860	GL_LIBS_ARB:=# no opengl -> no libs
861	GL:=# dont build ARB openGL libs
862
863	RNA3D_LIB :=
864	endif
865
866	RNA3D_LIB_4_DEPENDS := RNA3D/RNA3D.a
867
868	GL_LIBS:=$(GL_LIBS_ARB) $(GL_LIBS_SYS)
869
870	#---------------------- sina:
871
872	ifndef ISINA
873	# build sina delivered with arb?
874	ifeq ($(LINUX),1)
875	ifeq ('$(USE_GCC_70_OR_HIGHER)','yes')
876	ISINA := 1# default to 'yes' for linux with gcc>=7
877	endif
878	endif
879	ifndef ISINA
880	ISINA := 0# 'no' otherwise
881	endif
882	endif
883
884	#---------------------- tiff lib:
885
886	TIFFLIBS := -ltiff
887
888	#---------------------- XML lib:
889
890	XMLLIBS := -lxerces-c
891
892	#---------------------- glib:
893
894	ARB_NEEDED_GLIB=glib-2.0
895
896	ARB_GLIB_INCLUDE:=$(strip $(shell pkg-config --cflags $(ARB_NEEDED_GLIB)))
897	ARB_GLIB_LIBS:=$(strip $(shell pkg-config --libs $(ARB_NEEDED_GLIB)))
898
899	#---------------------- sunrpc lib:
900	# Note: sunrpc has been removed from glibc
901	# (e.g. in SuSE Leap 15.3 and Fedora 28)
902	# see https://fedoraproject.org/wiki/Changes/SunRPCRemoval
903	#
904	HAVE_LIBTIRPC=$(strip $(shell pkg-config --exists libtirpc && echo libtirpc))
905	ifeq ($(HAVE_LIBTIRPC),)
906	ARB_RPC_INCLUDE:=
907	ARB_RPC_LIBS:=
908	else
909	ARB_RPC_INCLUDE:=$(strip $(shell pkg-config --cflags $(HAVE_LIBTIRPC)))
910	ARB_RPC_LIBS:=$(strip $(shell pkg-config --libs $(HAVE_LIBTIRPC)))
911	endif
912
913	#---------------------- basic libs:
914
915	ARB_CORE_LIBS:=$(ARB_GLIB_LIBS) $(ARB_RPC_LIBS)
916
917	SYSLIBS:=
918	ifeq ($(DARWIN),1)
919	SYSLIBS += -lstdc++
920	else
921	SYSLIBS += -lm $(ARB_CORE_LIBS)
922	endif
923
924	#---------------------- system dependent commands
925
926	ifeq ($(DARWIN),1)
927	TIME:=gtime
928	else
929	TIME:=/usr/bin/time
930	endif
931
932	#---------------------- SSE vectorizer
933	# for details see SOURCE_TOOLS/vectorize.README
934
935	ifeq ($(DEBUG),0)
936	ifeq ($(USE_GCC_49_OR_HIGHER),yes)
937	ifeq ($(DISABLE_VECTORIZE_CHECK),0)
938	cflags += -fopt-info-vec
939	cflags += -fopt-info-vec-missed
940	ifeq ($(TRACE_MISSED_VECTORIZATIONS),1)
941	# Shows reasons for unsuccessful vectorization:
942	cflags += -ftree-vectorizer-verbose=10
943	POST_COMPILE += --dump-loop-optimization
944	ifeq ($(VECTORIZATION_CHECK_CANDIDATES),1)
945	$(error TRACE_MISSED_VECTORIZATIONS and VECTORIZATION_CHECK_CANDIDATES may not be used together!)
946	endif
947	endif
948	ifeq ($(VECTORIZATION_CHECK_CANDIDATES),1)
949	POST_COMPILE += --loop-optimization-candi
950	endif
951	POST_COMPILE += --check-loop-optimization
952	endif
953	else
954	ifeq ($(USE_GCC_48_OR_HIGHER),yes)
955	# no automatic vectorization-check for gcc<4.9.0
956	# -> uncomment the next 2 lines and grep the spam it will produce for 'vectorized.*loops'
957	# cflags += -fopt-info -fopt-info-vec-missed
958	# POST_COMPILE += --original
959	endif
960	endif
961	endif
962
963	#---------------------- stop early on broken flags/compiler combination
964
965	ifeq ($(DEBUG),0)
966	ifeq ($(SANITIZE_ANY),1)
967	ifeq ('$(COMPILER_VERSION)','4.9.1')
968	$(error compiling DEBUG=0 + SANITIZE!=0 crashes with gcc $(COMPILER_VERSION) (gcc 4.9.2 works))
969	endif
970	endif
971	endif
972
973	#---------------------- include symbols?
974
975	ifeq ($(TRACESYM),1)
976	ifeq ($(USE_CLANG),0)
977	cflags += -rdynamic
978	clflags += -rdynamic -Wl,--export-dynamic
979	endif
980	endif
981
982	#---------------------- warn about duplicate variable definitions
983
984	ifeq ($(DARWIN),1)
985	clflags += -Wl,-warn_commons
986	else
987	clflags += -Wl,--warn-common
988	endif
989
990	#---------------------- differences between linking executables and shared libs:
991
992	# executables:
993	ifeq ($(DARWIN),1)
994	blflags:=$(clflags)
995	else
996	blflags:=$(clflags) -Wl,--no-undefined
997	endif
998
999	# shared libraries
1000	llflags:=$(clflags)
1001
1002	# dont use clflags below
1003	clflags:=
1004
1005	# -------------------------------------------------------------------------
1006	# Don't put any machine/version/etc conditionals below!
1007	# (instead define variables above)
1008	# -------------------------------------------------------------------------
1009
1010	cflags += -W -Wall $(dflags) $(extended_warnings)
1011	cxxflags := $(extended_cpp_warnings)# flags only suitable for C++ (not C; see onlyC_flags).
1012
1013	# add CFLAGS + CPPFLAGS from environment for DEBIAN build
1014	ifeq ($(DEBIAN),1)
1015	cflags := $(CFLAGS) $(cflags)
1016	cxxflags += $(CPPFLAGS)
1017	endif
1018
1019	ifeq ('$(USE_CLANG)','1')
1020	# none of the following standards works with clang3.3 (under linux) => dont use standard (as done before r15516)
1021	# cxxflags += -std=gnu++11
1022	# cxxflags += -std=gnu++0x
1023	else
1024	# standard mostly supported by gcc version (according to https://gcc.gnu.org/projects/cxx-status.html)
1025	# C++20 with gcc>=12
1026	# C++23 with gcc>=15 (or 16 for reflection)
1027
1028	ifeq ('$(USE_GCC_80_OR_HIGHER)','yes')
1029	# C++17 mostly supported by gcc>=8
1030	cxxflags += -std=gnu++17 # see also TEMPLATES/cxxforward.h@USE_Cxx17
1031	else
1032	ifeq ('$(USE_GCC_60_OR_HIGHER)','yes')
1033	cxxflags += -std=gnu++14 # see also TEMPLATES/cxxforward.h@USE_Cxx14
1034	else
1035	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
1036	cxxflags += -std=gnu++11 # see also TEMPLATES/cxxforward.h@USE_Cxx11
1037	else
1038	# gcc versions between 4.3 (lowest supported) and <4.7
1039	cxxflags += -std=gnu++0x
1040	endif # 47
1041	endif # 60
1042	endif # 80
1043	endif # USE_CLANG
1044
1045	LINK_STATIC_LIB := $(AR) -csq# link static lib
1046	LINK_EXECUTABLE := $(A_CXX) $(blflags) -o# link executable (c++)
1047
1048	ifeq ($(LINK_STATIC),1)
1049	SHARED_LIB_SUFFIX = a# static lib suffix
1050	LINK_SHARED_LIB := $(LINK_STATIC_LIB)
1051	else
1052	SHARED_LIB_SUFFIX = so# shared lib suffix
1053	LINK_SHARED_LIB := $(A_CXX) $(llflags) -shared -o# link shared lib
1054	endif
1055
1056	ifeq ($(DARWIN),1)
1057	lflags4perl:=
1058	else
1059	lflags4perl:=$(cross_lflags) -shared
1060	endif
1061
1062	# delete variables unused below
1063	blflags:=
1064	llflags:=
1065
1066	# other used tools
1067	MAKEDEPEND_PLAIN = makedepend
1068	MAKEDEPEND = $(FORCEMASK);$(MAKEDEPEND_PLAIN)
1069
1070	SEPNODATE:=--------------------------------------------------------------------------------
1071	SEP=[`date +%M:%S.%N`] ------------------------------------------------
1072	# to analyse timings run
1073	# make -j9 clean; make -j9 all \| grep '^\[' \| sort
1074	# make -j9 "TIMED_TARGET=perl" clean_timed_target \| grep '^\[' \| sort
1075
1076	# ------------------------------------------------------------ DYNLIBDEFS
1077	# various dynamic library definitions for linking executables:
1078	#
1079	# SYSLIBS: system libraries needed by database lib
1080	# ARBDB_LIB: database lib
1081	# DBSYS_LIBS: executable using database (but no GUI)
1082	# GUI_LIBS: executable using database and GUI (arb gui uses database)
1083	#
1084	# Note: definitions exported to sub-makefiles are described in SOURCE_TOOLS/parent_make.txt
1085
1086	CORE_LIB=-lCORE
1087	ARBDB_LIB=-lARBDB $(CORE_LIB)
1088	DBSYS_LIBS = $(ARBDB_LIB) $(SYSLIBS)
1089
1090	GUI_LIBS_PREFIX:=
1091	ifeq ($(DARWIN),1)
1092	# this seem to be added at wrong place, since opengl is only needed to link EDIT4
1093	GUI_LIBS_PREFIX:=-framework GLUT -framework OpenGL
1094	endif
1095
1096	GUI_LIBS=$(GUI_LIBS_PREFIX) $(DBSYS_LIBS) -lWINDOW $(XLIBS)
1097
1098	LIBPATH = -L$(ARBHOME)/lib
1099
1100	DEST_LIB = lib
1101	DEST_BIN = bin
1102
1103	CC_INCLUDES := -I. -I$(ARBHOME)/INCLUDE $(XINCLUDES) $(ARB_GLIB_INCLUDE) $(ARB_RPC_INCLUDE)
1104	CXX_INCLUDES := $(CC_INCLUDES)
1105	MAKEDEPENDFLAGS := -- -DARB_OPENGL -DUNIT_TESTS -D__cplusplus -I. -Y$(ARBHOME)/INCLUDE
1106
1107	# ---------------------------------------
1108	# wrap main()
1109
1110	use_ARB_main=$(ARBHOME)/SOURCE_TOOLS/arb_main_cpp.o
1111	use_ARB_main_C=$(ARBHOME)/SOURCE_TOOLS/arb_main_c.o
1112
1113	# -----------------------------------------
1114	# generate unique IDs:
1115	#
1116	# 1) ARBBID
1117	# - different for different calls of make
1118	# - constant in recursive calls (submake)
1119	#
1120	ifndef ARBBID
1121	ARBBID:=$(shell SOURCE_TOOLS/uniqueID.sh)
1122	endif
1123
1124	# 2) ARBCID
1125	# - identical for multiple calls of make with same gcc and config
1126	# - uses DEBUG, UNIT_TESTS, OPENGL, DEVELOPER, gcc-version
1127
1128	ifndef ARBCID
1129	# Main purpuse is to simply generate filenames based on current config,
1130	# in order to log data and later compare between different versions.
1131	#
1132	# Note: change free at will (i.e. don't rely on content)
1133	ARBCID := $(if $(filter 1,$(DEBUG)),_DEBUG,NDEBUG)
1134	ARBCID := $(ARBCID)$(if $(filter 1,$(UNIT_TESTS)),__TESTS,_NTESTS)
1135	ARBCID := $(ARBCID)$(if $(filter 1,$(OPENGL)),__OPENGL,_NOPENGL)
1136	# ARBCID := $(ARBCID)_$(DEVELOPER)
1137	ARBCID := $(ARBCID)_$(COMPILER_NAME)_$(COMPILER_VERSION)
1138	# $(error ARBCID = $(ARBCID))
1139
1140	endif
1141
1142	# -----------------------------------------
1143	# export variables to submakefiles
1144
1145	include SOURCE_TOOLS/export2sub
1146
1147	# do not define (exported) variables below this point
1148
1149	# -------------------------
1150	# Main arb targets:
1151	# -------------------------
1152
1153	first_target:
1154	$(MAKE) checks
1155	@echo $(SEPNODATE)
1156	@echo 'Main targets:'
1157	@echo ''
1158	@echo ' all - Compile ARB + TOOLs + and copy shared libs + link foreign software'
1159	@echo ' (That is most likely the target you want)'
1160	@echo ''
1161	@echo ' clean - remove generated files ("SUBDIR/SUBDIR.clean" to clean only SUBDIR)'
1162	@echo ' rebuild - clean + all'
1163	@echo ' cleanlinked - remove all binaries'
1164	@echo ' relink - cleanlinked + all (=relink all from objects)'
1165	@echo ''
1166	@echo 'Targets for automated builds:'
1167	@echo ''
1168	@echo ' ALL, REBUILD, TARFILE + TARFILE_QUICK '
1169	@echo ' - same as all, rebuild, tarfile + tarfile_quick'
1170	@echo ' - if errors occur, they are extracted and listed at tail of output'
1171	@echo ''
1172	@echo $(SEPNODATE)
1173	@echo ''
1174	@echo 'Development targets:'
1175	@echo ''
1176	@echo ' depends - create or update dependencies ("SUBDIR/SUBDIR.depends" to update only SUBDIR)'
1177	@echo ' proto - create or update prototypes ("SUBDIR/SUBDIR.proto" to update only SUBDIR)'
1178	@echo ' tags - create tags for xemacs'
1179	@echo ' show - show available shortcuts (AKA subtargets)'
1180	@echo ' up - shortcut for depends+proto+tags'
1181	ifeq ($(UNIT_TESTS),1)
1182	@echo ' ut - only run tests'
1183	@echo ' "UNIT=..." oneunit - build one unit and run tests (see also UNIT_TESTER/Makefile.setup.local)'
1184	endif
1185	ifneq ($(SANITIZE),0)
1186	@echo ' sanitize - all + run arb_ntree with sanitizer (test.arb + execute _logged)'
1187	endif
1188	@echo ' modified - rebuild files modified in svn checkout (does touch)'
1189	@echo ' touch - touch files modified in svn checkout'
1190	@echo ''
1191	@echo 'Some often used sub targets:'
1192	@echo ''
1193	@echo ' arb - Just compile ARB (but none of the integrated tools)'
1194	@echo ' menus - create lib/gde/arb.menu from GDEHELP/ARB_GDEmenus.source'
1195	@echo ' perl - Compile the PERL XSUBS into lib/ARB.so and create links in lib to perl'
1196	@echo ' binlink - Create all links in the bin directory'
1197	@echo ''
1198	@echo 'Internal maintenance:'
1199	@echo ''
1200	@echo ' relinfo - show help on release targets'
1201	@echo ' tarfile - make rebuild and create arb version tarfile ("tarfile_quick" to skip rebuild)'
1202	@echo ' save - save all basic ARB sources into arbsrc_DATE ("savetest" to check filelist)'
1203	@echo ' patch - save svn diff to patchfile'
1204	@echo ' source_doc - create doxygen documentation'
1205	@echo ' relocated - rebuild partly (use when you have relocated ARBHOME)'
1206	@echo ' check_res - check resource usage'
1207	@echo ' dep_graph - Build dependency graphs'
1208	@echo ' clean_cov - Clean coverage results'
1209	@echo ''
1210	@echo ' clean_opengl_changed - clean after changing OPENGL setting in config.Makefile'
1211	@echo ' clean_checked_vect - clean units containing vectorization checks'
1212	@echo ' cleanRelinkable - similar to cleanlinked (but skips raxml8 to avoid rebuild)'
1213	@echo ''
1214	@echo ' post_commit_check - Checks whether'
1215	@echo ' * main make targets work,'
1216	@echo ' * dependencies and prototypes are up to date,'
1217	@echo ' * SVN-controlled files remain unaffected by called targets and'
1218	@echo ' * all generated files are ignored.'
1219	@echo ' (has to be called in a clean SVN checkout)'
1220	@echo $(SEPNODATE)
1221	@echo ''
1222
1223	relinfo:
1224	@echo ''
1225	@echo $(SEPNODATE)
1226	@echo 'Release targets:'
1227	@echo ''
1228	@echo ' inc_candi - increase RC candidate-number (only possible in "rc" branch, not needed for RC1)'
1229	@echo ' inc_patch - increase release patchlevel (only possible in "stable" branch)'
1230	@echo ' inc_minor - increase minor version number (only possible in "trunk")'
1231	@echo ' inc_major - increase MAJOR version number (only possible in "trunk")'
1232	@echo ''
1233	@echo ' show_version - show version tag'
1234	@echo ''
1235	@echo $(SEPNODATE)
1236	@echo ''
1237
1238	# auto-generate config.makefile:
1239
1240	config.makefile : config.makefile.template
1241	@echo --------------------------------------------------------------------------------
1242	ifeq ($(CONFIG_MAKEFILE_FOUND),)
1243	@cp $< $@
1244	@echo '$(ARBHOME)/$@:1: has been generated.'
1245	@echo 'Please edit $@ to configure your system!'
1246	@echo --------------------------------------------------------------------------------
1247	@false
1248	else
1249	@echo '$(ARBHOME)/$<:1: is more recent than'
1250	@echo '$(ARBHOME)/$@:1:'
1251	@ls -al config.makefile*
1252	@echo --------------------------------------------------------------------------------
1253	@echo "Updating $@ (if this fails, check manually)"
1254	SOURCE_TOOLS/update_config_makefile.pl
1255	@echo "Sucessfully updated $@"
1256	@echo --------------------------------------------------------------------------------
1257	@ls -al config.makefile*
1258	@echo --------------------------------------------------------------------------------
1259	@echo "Diff to your old config.makefile:"
1260	@echo --------------------------------------------------------------------------------
1261	-diff $@.bak $@
1262	@echo --------------------------------------------------------------------------------
1263	endif
1264
1265	# check if everything is configured correctly
1266
1267	check_DEVELOPER:
1268	ifndef DEVELOPER
1269	@echo 'config.makefile:1: DEVELOPER not defined'
1270	@false
1271	endif
1272
1273	check_DEBUG:
1274	ifndef dflags
1275	@echo 'config.makefile:1: DEBUG has to be defined. Valid values are 0 and 1'
1276	@false
1277	endif
1278
1279	check_ARB_64:
1280	ifndef ARB_64
1281	@echo 'config.makefile:1: ARB_64 has to be defined. Valid values are 0 and 1'
1282	@false
1283	endif
1284
1285	# ---------------------------------------- check gcc version
1286
1287	COMPILER_BROKEN:=0
1288
1289	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.6.4')
1290	COMPILER_BROKEN:=1
1291	endif
1292	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.8.0')
1293	COMPILER_BROKEN:=1
1294	endif
1295
1296	check_same_GCC_VERSION:
1297	$(ARBHOME)/SOURCE_TOOLS/check_same_compiler_version.pl $(COMPILER_NAME) $(COMPILER_VERSION_ALLOWED)
1298
1299	check_GCC_VERSION:
1300	@echo 'Compiler version check:'
1301	# see .@ALLOWED_gcc_VERSIONS
1302	ifeq ('$(COMPILER_VERSION_ALLOWED)', '')
1303	@echo " - Your compiler is '$(COMPILER_NAME)' version '$(COMPILER_VERSION)'"
1304	@echo ' This version is not in the list of supported $(COMPILER_NAME)-versions:'
1305	@$(foreach version,$(ALLOWED_COMPILER_VERSIONS),echo ' * $(version)';)
1306	@echo ' - You may either ..'
1307	@echo ' - add your version to ALLOWED_$(COMPILER_NAME)_VERSIONS in the Makefile and try it out or'
1308	@echo ' - switch to one of the allowed versions (see arb_README_gcc.txt for installing'
1309	@echo ' a different version of gcc)'
1310	$(error Unsupported compiler '$(COMPILER_NAME)' version '$(COMPILER_VERSION)')
1311	else
1312	ifeq ($(COMPILER_BROKEN),1)
1313	$(error compilation refused for $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)'. Refer to http://bugs.arb-home.de/wiki/GccVersionInfo for details.)
1314	else
1315	@echo " - Supported $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)' detected - fine!"
1316	@echo ''
1317	ifeq ($(USE_CLANG),1)
1318	@echo "Dump clang version:"
1319	$(A_CXX) -v
1320	endif
1321	$(MAKE) check_same_GCC_VERSION
1322	endif
1323	endif
1324
1325	#---------------------- check ARBHOME
1326
1327	# use arb_INSTALL.txt to determine whether ARBHOME points to correct directory
1328	ARB_INSTALL_FOUND=$(wildcard $(ARBHOME)/arb_INSTALL.txt)
1329
1330	check_ARBHOME:
1331	ifeq ($(strip $(ARB_INSTALL_FOUND)),)
1332	@echo ------------------------------------------------------------
1333	@echo "ARBHOME is set to '$(ARBHOME)'"
1334	@echo "The environment variable ARBHOME has to point to the top arb source directory."
1335	@echo "If you use bash enter:"
1336	@echo " export ARBHOME='`pwd`'"
1337	@echo ------------------------------------------------------------
1338	@false
1339	endif
1340
1341	ARB_PATH_SET=$(findstring $(ARBHOME)/bin,$(PATH))
1342
1343	check_PATH: check_ARBHOME
1344	ifeq ($(strip $(ARB_PATH_SET)),)
1345	@echo ------------------------------------------------------------
1346	@echo "The environment variable PATH has to contain $(ARBHOME)/bin"
1347	@echo "If you use bash enter:"
1348	@echo ' export PATH=$$ARBHOME/bin:$$PATH'
1349	@echo ------------------------------------------------------------
1350	@false
1351	endif
1352
1353	check_TOOLS:
1354	@util/arb_check_build_env.pl \
1355	"$(A_CC)" \
1356	"$(A_CXX)" \
1357	"$(LINK_SHARED_LIB)" \
1358
1359	have_makedepend:
1360	@util/arb_check_build_env.pl --check-only "$(MAKEDEPEND_PLAIN)"
1361
1362	check_ENVIRONMENT : check_PATH check_TOOLS
1363	@echo "-------------------- Environment [start]"
1364	@echo "ARBHOME='$(ARBHOME)'"
1365	@echo "PATH='$(PATH)'"
1366	@echo "LD_LIBRARY_PATH='$(LD_LIBRARY_PATH)'"
1367	@echo "-------------------- Environment [end]"
1368
1369	check_tabs: check_setup
1370	ifeq ($(DEBUG),1)
1371	@SOURCE_TOOLS/tabBrake.pl
1372	endif
1373
1374	force_tab_check:
1375	@touch -t 198001010000 SOURCE_TOOLS/stamp.tabBrake
1376	@$(MAKE) check_tabs
1377
1378
1379	# ---------------------
1380
1381	check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION
1382	@echo Your setup seems to be ok.
1383
1384	checks: check_setup check_tabs
1385	@rm -f SOURCE_TOOLS/postcompile.sav
1386
1387
1388	# end test section ------------------------------
1389
1390	# ---------------------------------------
1391	# List of standard top level directories
1392	#
1393	# sub-makefiles have to define the targets
1394	# - 'depends' and
1395	# - 'clean'
1396	#
1397	# when adding new libraries/subdirs here, also add a dependency vs 'links' or 'links_non_perl' in .@DD_links_non_perl
1398
1399	TL_ARCHIVES = \
1400	AISC/AISC.a \
1401	ARB_GDE/ARB_GDE.a \
1402	AWTC/AWTC.a \
1403	AWTI/AWTI.a \
1404	CONSENSUS_TREE/CONSENSUS_TREE.a \
1405	CONVERTALN/CONVERTALN.a \
1406	DBSERVER/DBSERVER.a \
1407	DIST/DIST.a \
1408	EDIT4/EDIT4.a \
1409	EISPACK/EISPACK.a \
1410	GENOM/GENOM.a \
1411	GENOM_IMPORT/GENOM_IMPORT.a \
1412	ISLAND_HOPPING/ISLAND_HOPPING.a \
1413	MERGE/MERGE.a \
1414	MULTI_PROBE/MULTI_PROBE.a \
1415	NALIGNER/NALIGNER.a \
1416	NAMES/NAMES.a \
1417	NAMES_COM/server.a \
1418	NTREE/NTREE.a \
1419	PARSIMONY/PARSIMONY.a \
1420	PHYLO/PHYLO.a \
1421	PRIMER_DESIGN/PRIMER_DESIGN.a \
1422	PROBE/PROBE.a \
1423	PROBE_COM/server.a \
1424	PROBE_DESIGN/PROBE_DESIGN.a \
1425	$(RNA3D_LIB) \
1426	RNACMA/RNACMA.a \
1427	SECEDIT/SECEDIT.a \
1428	SEQ_QUALITY/SEQ_QUALITY.a \
1429	SERVERCNTRL/SERVERCNTRL.a \
1430	STAT/STAT.a \
1431	TREEGEN/TREEGEN.a \
1432	WETC/WETC.a \
1433	XML/XML.a \
1434
1435	TL_SHARED_ARCHIVES = \
1436	ARBDB/libARBDB.so \
1437	CORE/libCORE.so \
1438	WINDOW/libWINDOW.so \
1439
1440	TL_ARCHIV_COLLECTIONS = \
1441	SL/SL.archColl \
1442
1443	TL_TOOLS_COLLECTIONS = \
1444	AISC_MKPTPS/AISC_MKPTPS.toolColl \
1445	TOOLS/TOOLS.toolColl \
1446	PERLTOOLS/PERLTOOLS.toolColl \
1447	PROBE_SET/PROBE_SET.toolColl \
1448	READSEQ/READSEQ.toolColl \
1449
1450	RECURSIVE_SUBS = \
1451	GDE/GDE.sub \
1452	UNIT_TESTER/UNIT_TESTER.sub \
1453
1454	SUBDIRS = \
1455	$(RECURSIVE_SUBS) \
1456	$(TL_ARCHIVES:.a=.sub) \
1457	$(TL_SHARED_ARCHIVES:.so=.sub) \
1458	$(TL_ARCHIV_COLLECTIONS:.archColl=.sub) \
1459	$(TL_TOOLS_COLLECTIONS:.toolColl=.sub) \
1460
1461	# sub directories inside TL_ARCHIV_COLLECTIONS
1462	CL_ARCH_DIRS = $(foreach coll,$(TL_ARCHIV_COLLECTIONS),$(shell find $(dir $(coll)) -maxdepth 1 -mindepth 1 -type d))
1463
1464	# archives inside CL_ARCH_DIRS:
1465	CL_ARCHIVES = $(foreach adir,$(CL_ARCH_DIRS),$(dir $(adir))$(notdir $(adir))/$(notdir $(adir)).a)
1466
1467	# -----------------------
1468	# library packets
1469
1470	ARCHS_CLIENT_PROBE = PROBE_COM/client.a
1471	ARCHS_CLIENT_NAMES = NAMES_COM/client.a
1472
1473	ARCHS_MAKEBIN = AISC_MKPTPS/AISC_MKPTPS.a AISC/AISC.a
1474
1475	# communication libs need aisc and aisc_mkpts:
1476
1477	AISC/AISC.dummy: proto_tools
1478
1479	comtools: AISC/AISC.dummy
1480
1481	ARCHS_SEQUENCE = \
1482	SL/SEQUENCE/SEQUENCE.a \
1483	SL/ALIVIEW/ALIVIEW.a \
1484	SL/PRONUC/PRONUC.a \
1485
1486	ARCHS_TREE = \
1487	SL/ARB_TREE/ARB_TREE.a \
1488	SL/FILTER/FILTER.a \
1489	$(ARCHS_SEQUENCE) \
1490
1491	# parsimony tree (used by NTREE, PARSIMONY, STAT(->EDIT4), DIST(obsolete!))
1492	ARCHS_AP_TREE = \
1493	SL/AP_TREE/AP_TREE.a \
1494	$(ARCHS_TREE) \
1495
1496	# --------------------------------------------------------------------------------
1497	# dependencies for linking shared libs
1498
1499	link_core: core
1500	link_db: db link_core
1501	link_aw: aw link_db
1502
1503	#***************************************************************************************
1504	# Individual_Programs_Section
1505	#***************************************************************************************
1506
1507	arbmainwrapper:
1508	$(MAKE) -C SOURCE_TOOLS -r mainwrapper
1509
1510
1511	#********************************* arb_ntree ************************************
1512	NTREE = bin/arb_ntree
1513	ARCHS_NTREE = \
1514	NTREE/NTREE.a \
1515	ARB_GDE/ARB_GDE.a \
1516	SL/SPECSEL/SPECSEL.a \
1517	SL/GROUP_SEARCH/GROUP_SEARCH.a \
1518	SL/SAICALC/SAICALC.a \
1519	SL/DB_UI/DB_UI.a \
1520	SL/ARB_SPEC/ARB_SPEC.a \
1521	SL/MASKS/MASKS.a \
1522	AWTC/AWTC.a \
1523	AWTI/AWTI.a \
1524	CONSENSUS_TREE/CONSENSUS_TREE.a \
1525	GENOM_IMPORT/GENOM_IMPORT.a \
1526	GENOM/GENOM.a \
1527	MERGE/MERGE.a \
1528	MULTI_PROBE/MULTI_PROBE.a \
1529	PRIMER_DESIGN/PRIMER_DESIGN.a \
1530	PROBE_DESIGN/PROBE_DESIGN.a \
1531	SEQ_QUALITY/SEQ_QUALITY.a \
1532	SERVERCNTRL/SERVERCNTRL.a \
1533	SL/ALILINK/ALILINK.a \
1534	SL/AW_NAME/AW_NAME.a \
1535	SL/APP/APP.a \
1536	SL/CONSENSUS/CONSENSUS.a \
1537	SL/CANVAS/CANVAS.a \
1538	SL/DB_SCANNER/DB_SCANNER.a \
1539	SL/DB_QUERY/DB_QUERY.a \
1540	SL/QUERY/QUERY.a \
1541	SL/SEQIO/SEQIO.a \
1542	STAT/STAT.a \
1543	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1544	SL/GUI_TK/GUI_TK.a \
1545	SL/HELIX/HELIX.a \
1546	SL/REGEXPR/REGEXPR.a \
1547	SL/REFENTRIES/REFENTRIES.a \
1548	SL/NDS/NDS.a \
1549	SL/ITEM_SHADER/ITEM_SHADER.a \
1550	SL/ITEMS/ITEMS.a \
1551	SL/INSDEL/INSDEL.a \
1552	SL/LOCATION/LOCATION.a \
1553	SL/MACROS/MACROS.a \
1554	SL/PVP/PVP.a \
1555	SL/TRANSLATE/TRANSLATE.a \
1556	SL/TREEDISP/TREEDISP.a \
1557	SL/TREE_ADMIN/TREE_ADMIN.a \
1558	SL/TREE_READ/TREE_READ.a \
1559	SL/TREE_WRITE/TREE_WRITE.a \
1560	SL/XFERGUI/XFERGUI.a \
1561	SL/XFERSET/XFERSET.a \
1562	XML/XML.a \
1563	$(ARCHS_AP_TREE) \
1564
1565	ARCHS_NTREE_ALL = $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(XMLLIBS)
1566
1567	$(NTREE): $(ARCHS_NTREE:.a=.dummy) link_aw
1568	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NTREE_ALL) \|\| ( \
1569	echo "$(SEP) Link $@"; \
1570	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE_ALL)" ; \
1571	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE_ALL) && \
1572	echo "$(SEP) Link $@ [done]"; \
1573	)
1574
1575	#********************************* arb_edit4 ************************************
1576	EDIT4 = bin/arb_edit4
1577
1578	ARCHS_EDIT4 := \
1579	EDIT4/EDIT4.a \
1580	ARB_GDE/ARB_GDE.a \
1581	SL/FAST_ALIGNER/FAST_ALIGNER.a \
1582	AWTC/AWTC.a \
1583	ISLAND_HOPPING/ISLAND_HOPPING.a \
1584	SECEDIT/SECEDIT.a \
1585	SERVERCNTRL/SERVERCNTRL.a \
1586	SL/APP/APP.a \
1587	SL/GUI_TK/GUI_TK.a \
1588	SL/ARB_SPEC/ARB_SPEC.a \
1589	SL/AW_HELIX/AW_HELIX.a \
1590	SL/AW_NAME/AW_NAME.a \
1591	SL/CONSENSUS/CONSENSUS.a \
1592	SL/CANVAS/CANVAS.a \
1593	SL/ITEMS/ITEMS.a \
1594	STAT/STAT.a \
1595	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1596	SL/HELIX/HELIX.a \
1597	SL/TRANSLATE/TRANSLATE.a \
1598	SL/MACROS/MACROS.a \
1599	SL/MAPKEY/MAPKEY.a \
1600	SL/NDS/NDS.a \
1601	$(ARCHS_AP_TREE) \
1602	XML/XML.a \
1603
1604	ifeq ($(OPENGL),1)
1605	ARCHS_EDIT4 += RNA3D/RNA3D.a
1606	endif
1607
1608	ARCHS_EDIT4_ALL = $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4)
1609
1610	LIBS_EDIT4 := $(GL_LIBS)
1611
1612	$(EDIT4): $(ARCHS_EDIT4:.a=.dummy) link_aw
1613	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_EDIT4_ALL) \|\| ( \
1614	echo "$(SEP) Link $@"; \
1615	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4_ALL)" ; \
1616	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4_ALL) && \
1617	echo "$(SEP) Link $@ [done]"; \
1618	)
1619
1620	#********************************* arb_rnacma ************************************
1621	RNACMA = bin/arb_rnacma
1622	ARCHS_RNACMA = \
1623	RNACMA/RNACMA.a \
1624
1625	ARCHS_RNACMA_ALL = $(ARCHS_RNACMA) $(DBSYS_LIBS)
1626
1627	$(RNACMA) : $(ARCHS_RNACMA:.a=.dummy) link_db
1628	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_RNACMA_ALL) \|\| ( \
1629	echo "$(SEP) Link $@"; \
1630	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_RNACMA_ALL)"; \
1631	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_RNACMA_ALL) && \
1632	echo "$(SEP) Link $@ [done]"; \
1633	)
1634
1635	#********************************* arb_wetc ************************************
1636	WETC = bin/arb_wetc
1637	ARCHS_WETC = \
1638	WETC/WETC.a \
1639	SL/APP/APP.a \
1640	SL/MACROS/MACROS.a \
1641	SL/GUI_TK/GUI_TK.a \
1642	SL/HELIX/HELIX.a \
1643	SL/FILTER/FILTER.a \
1644	XML/XML.a \
1645
1646	ARCHS_WETC_ALL = $(ARCHS_WETC) $(GUI_LIBS)
1647
1648	$(WETC): $(ARCHS_WETC:.a=.dummy) link_aw
1649	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_WETC_ALL) \|\| ( \
1650	echo "$(SEP) Link $@"; \
1651	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC_ALL)" ; \
1652	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC_ALL) && \
1653	echo "$(SEP) Link $@ [done]"; \
1654	)
1655
1656	#********************************* arb_dist ************************************
1657	DIST = bin/arb_dist
1658	ARCHS_DIST = \
1659	DIST/DIST.a \
1660	CONSENSUS_TREE/CONSENSUS_TREE.a \
1661	EISPACK/EISPACK.a \
1662	SERVERCNTRL/SERVERCNTRL.a \
1663	SL/APP/APP.a \
1664	SL/GUI_TK/GUI_TK.a \
1665	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1666	SL/HELIX/HELIX.a \
1667	SL/MATRIX/MATRIX.a \
1668	SL/MACROS/MACROS.a \
1669	SL/NDS/NDS.a \
1670	SL/ITEMS/ITEMS.a \
1671	SL/ARB_SPEC/ARB_SPEC.a \
1672	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.a \
1673	XML/XML.a \
1674	$(ARCHS_AP_TREE) \
1675
1676	ARCHS_DIST_ALL = $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS)
1677
1678	$(DIST): $(ARCHS_DIST:.a=.dummy) link_aw
1679	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_DIST_ALL) \|\| ( \
1680	echo "$(SEP) Link $@"; \
1681	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST_ALL)" ; \
1682	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST_ALL) && \
1683	echo "$(SEP) Link $@ [done]"; \
1684	)
1685
1686	#********************************* arb_pars ************************************
1687	PARSIMONY = bin/arb_pars
1688	ARCHS_PARSIMONY = \
1689	PARSIMONY/PARSIMONY.a \
1690	SERVERCNTRL/SERVERCNTRL.a \
1691	SL/APP/APP.a \
1692	SL/GUI_TK/GUI_TK.a \
1693	SL/AW_NAME/AW_NAME.a \
1694	SL/CANVAS/CANVAS.a \
1695	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1696	SL/HELIX/HELIX.a \
1697	SL/MACROS/MACROS.a \
1698	SL/NDS/NDS.a \
1699	SL/ITEMS/ITEMS.a \
1700	SL/TRANSLATE/TRANSLATE.a \
1701	SL/TREEDISP/TREEDISP.a \
1702	XML/XML.a \
1703	$(ARCHS_AP_TREE) \
1704
1705	ARCHS_PARSIMONY_ALL = $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS)
1706
1707	$(PARSIMONY): $(ARCHS_PARSIMONY:.a=.dummy) link_aw
1708	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_PARSIMONY_ALL) \|\| ( \
1709	echo "$(SEP) Link $@"; \
1710	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY_ALL)" ; \
1711	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY_ALL) && \
1712	echo "$(SEP) Link $@ [done]"; \
1713	)
1714
1715	#********************************* arb_convert_aln ************************************
1716	CONVERT_ALN = bin/arb_convert_aln
1717	ARCHS_CONVERT_ALN = \
1718	CONVERTALN/CONVERTALN.a \
1719
1720	ARCHS_CONVERT_ALN_ALL = $(ARCHS_CONVERT_ALN) $(DBSYS_LIBS)
1721
1722	$(CONVERT_ALN) : $(ARCHS_CONVERT_ALN:.a=.dummy) link_db
1723	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_CONVERT_ALN_ALL) \|\| ( \
1724	echo "$(SEP) Link $@"; \
1725	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN_ALL)"; \
1726	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN_ALL) && \
1727	echo "$(SEP) Link $@ [done]"; \
1728	)
1729
1730	#********************************* arb_treegen ************************************
1731
1732	TREEGEN = bin/arb_treegen
1733	ARCHS_TREEGEN = \
1734	TREEGEN/TREEGEN.a \
1735
1736	ARCHS_TREEGEN_ALL = $(ARCHS_TREEGEN)
1737
1738	$(TREEGEN) : $(ARCHS_TREEGEN:.a=.dummy)
1739	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main_C) $(ARCHS_TREEGEN_ALL) \|\| ( \
1740	echo "$(SEP) Link $@"; \
1741	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN_ALL)" ; \
1742	$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN_ALL) && \
1743	echo "$(SEP) Link $@ [done]"; \
1744	)
1745
1746	#********************************* arb_naligner ************************************
1747	NALIGNER = bin/arb_naligner
1748	ARCHS_NALIGNER = \
1749	NALIGNER/NALIGNER.a \
1750	SERVERCNTRL/SERVERCNTRL.a \
1751	SL/HELIX/HELIX.a \
1752
1753	ARCHS_NALIGNER_ALL = $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(DBSYS_LIBS)
1754
1755	$(NALIGNER): $(ARCHS_NALIGNER:.a=.dummy) link_db
1756	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NALIGNER_ALL) \|\| ( \
1757	echo "$(SEP) Link $@"; \
1758	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER_ALL)" ; \
1759	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER_ALL) && \
1760	echo "$(SEP) Link $@ [done]"; \
1761	)
1762
1763	#********************************* arb_phylo ************************************
1764	PHYLO = bin/arb_phylo
1765	ARCHS_PHYLO = \
1766	PHYLO/PHYLO.a \
1767	SL/APP/APP.a \
1768	SL/GUI_TK/GUI_TK.a \
1769	SL/HELIX/HELIX.a \
1770	SL/FILTER/FILTER.a \
1771	SL/MACROS/MACROS.a \
1772	XML/XML.a \
1773
1774	ARCHS_PHYLO_ALL = $(ARCHS_PHYLO) $(GUI_LIBS)
1775
1776	$(PHYLO): $(ARCHS_PHYLO:.a=.dummy) link_aw
1777	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_PHYLO_ALL) \|\| ( \
1778	echo "$(SEP) Link $@"; \
1779	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO_ALL)" ; \
1780	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO_ALL) && \
1781	echo "$(SEP) Link $@ [done]"; \
1782	)
1783
1784	#***************************************************************************************
1785	# SERVER SECTION
1786	#***************************************************************************************
1787
1788	#********************************* arb_db_server ************************************
1789	DBSERVER = bin/arb_db_server
1790	ARCHS_DBSERVER = \
1791	DBSERVER/DBSERVER.a \
1792	SERVERCNTRL/SERVERCNTRL.a \
1793
1794	ARCHS_DBSERVER_ALL = $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS)
1795
1796	$(DBSERVER): $(ARCHS_DBSERVER:.a=.dummy) link_db
1797	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_DBSERVER_ALL) \|\| ( \
1798	echo "$(SEP) Link $@"; \
1799	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER_ALL)" ; \
1800	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER_ALL) && \
1801	echo "$(SEP) Link $@ [done]"; \
1802	)
1803
1804	#********************************* arb_pt_server ************************************
1805	PROBE = bin/arb_pt_server
1806
1807	ARCHS_PROBE_DEPEND = \
1808	PROBE/PROBE.a \
1809	SL/PTCLEAN/PTCLEAN.a \
1810	SERVERCNTRL/SERVERCNTRL.a \
1811	SL/HELIX/HELIX.a \
1812
1813	ARCHS_PROBE_ALL = $(ARCHS_PROBE_DEPEND) $(ARCHS_CLIENT_PROBE) $(ARBDB_LIB) $(SYSLIBS)
1814
1815	$(PROBE): $(ARCHS_PROBE_DEPEND:.a=.dummy) link_db
1816	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) config.makefile $(ARCHS_PROBE_ALL) \|\| ( \
1817	echo "$(SEP) Link $@"; \
1818	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_ALL)" ; \
1819	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_ALL) && \
1820	echo "$(SEP) Link $@ [done]"; \
1821	)
1822
1823	#********************************* arb_name_server ************************************
1824	NAMES = bin/arb_name_server
1825	ARCHS_NAMES = \
1826	NAMES/NAMES.a \
1827	SERVERCNTRL/SERVERCNTRL.a \
1828
1829	ARCHS_NAMES_ALL = $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS)
1830
1831	$(NAMES): $(ARCHS_NAMES:.a=.dummy) link_db
1832	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NAMES_ALL) \|\| ( \
1833	echo "$(SEP) Link $@"; \
1834	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES_ALL)" ; \
1835	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES_ALL) && \
1836	echo "$(SEP) Link $@ [done]"; \
1837	)
1838
1839	#********************************* SHARED LIBRARIES SECTION ************************************
1840
1841	prepare_libdir: addlibs
1842
1843	addlibs:
1844	(perl $(ARBHOME)/SOURCE_TOOLS/provide_libs.pl \
1845	"arbhome=$(ARBHOME)" \
1846	"opengl=$(OPENGL)" \
1847	"link_static=$(LINK_STATIC)" \
1848	)
1849
1850	#***************************************************************************************
1851	# Recursive calls to sub-makefiles
1852	#***************************************************************************************
1853
1854	%.depends: have_makedepend
1855	@cp -p $(@D)/Makefile $(@D)/Makefile.old # save old Makefile
1856	@$(MAKE) -C $(@D) -r \
1857	"AUTODEPENDS=1" \
1858	"MAIN=nothing" \
1859	"cflags=noCflagsHere_use_MAKEDEPENDFLAGS" \
1860	"cxxflags=noCxxflagsHere_use_MAKEDEPENDFLAGS" \
1861	depends
1862	@grep "^# DO NOT DELETE" $(@D)/Makefile >/dev/null
1863	@cat $(@D)/Makefile \
1864	\| SOURCE_TOOLS/fix_depends.pl "(from main)" \
1865	>$(@D)/Makefile.2
1866	@mv $(@D)/Makefile.old $(@D)/Makefile # restore old Makefile
1867	@$(ARBHOME)/SOURCE_TOOLS/mv_if_diff $(@D)/Makefile.2 $(@D)/Makefile # update Makefile if changed
1868
1869	%.proto:
1870	@($(MAKE) -C $(@D) \
1871	"AUTODEPENDS=0" \
1872	"MAIN=nothing" \
1873	"cflags=noCflags" \
1874	"cxxflags=noCxxflags" \
1875	proto 2>&1 ) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
1876
1877	%.clean:
1878	@$(MAKE) -C $(@D) \
1879	"AUTODEPENDS=0" \
1880	"MAIN=nothing" \
1881	"cflags=noCflags" \
1882	"cxxflags=noCxxflags" \
1883	clean
1884
1885
1886	# stop wrong targets:
1887	target_is_missing_lib_prefix:
1888	@echo "Error: Denied to build shared library target with missing 'lib'-prefix"
1889	false
1890
1891	ARBDB/ARBDB.dummy: target_is_missing_lib_prefix
1892	CORE/CORE.dummy: target_is_missing_lib_prefix
1893	AWT/AWT.dummy: target_is_missing_lib_prefix
1894	WINDOW/WINDOW.dummy: target_is_missing_lib_prefix
1895
1896	# rule to generate main target (normally a library):
1897	# @@@ check effect of setting LANG=C below
1898	%.dummy:
1899	@( export ID=$$$$; LANG=C; \
1900	(( \
1901	echo "$(SEP) Make $(@D)"; \
1902	$(MAKE) -C $(@D) -r \
1903	"AUTODEPENDS=1" \
1904	"MAIN=$(@F:.dummy=.a)" \
1905	"cflags=$(cflags) -DIN_ARB_$(subst /,_,$(@D))" \
1906	&& \
1907	echo "$(SEP) Make $(@D) [done]"; \
1908	) >$(@D).$$ID.log 2>&1 && (cat $(@D).$$ID.log;rm $(@D).$$ID.log)) \|\| (cat $(@D).$$ID.log;rm $(@D).$$ID.log;false))
1909
1910	# Additional dependencies for subtargets:
1911
1912	PROBE_COM/PROBE_COM.dummy : comtools
1913	NAMES_COM/NAMES_COM.dummy : comtools
1914
1915	com: PROBE_COM/PROBE_COM.dummy NAMES_COM/NAMES_COM.dummy
1916
1917	# stop wrong more targets:
1918	PROBE_COM/server.dummy:
1919	@echo Unwanted request to make target $<
1920	false
1921
1922	PROBE_COM/client.dummy:
1923	@echo Unwanted request to make target $<
1924	false
1925
1926	NAMES_COM/server.dummy:
1927	@echo Unwanted request to make target $<
1928	false
1929
1930	NAMES_COM/client.dummy:
1931	@echo Unwanted request to make target $<
1932	false
1933
1934
1935	ARBDB/libARBDB.dummy: links
1936	CORE/libCORE.dummy: links
1937
1938	PERLTOOLS/PERLTOOLS.dummy: core db
1939
1940	# all subdirs perl not depends on go here (ADD_links_non_perl)
1941	AWTI/AWTI.dummy: links_non_perl
1942	CONSENSUS_TREE/CONSENSUS_TREE.dummy: links_non_perl
1943	CONVERTALN/CONVERTALN.dummy: links_non_perl
1944	DBSERVER/DBSERVER.dummy: links_non_perl
1945	DIST/DIST.dummy: links_non_perl
1946	EDIT4/EDIT4.dummy: links_non_perl com
1947	EISPACK/EISPACK.dummy: links_non_perl
1948	GDE/GDE.dummy: links_non_perl
1949	GENOM/GENOM.dummy: links_non_perl
1950	GENOM_IMPORT/GENOM_IMPORT.dummy: links_non_perl
1951	ISLAND_HOPPING/ISLAND_HOPPING.dummy: links_non_perl
1952	MERGE/MERGE.dummy: links_non_perl
1953	NTREE/NTREE.dummy: links_non_perl
1954	PARSIMONY/PARSIMONY.dummy: links_non_perl
1955	PHYLO/PHYLO.dummy: links_non_perl
1956	PRIMER_DESIGN/PRIMER_DESIGN.dummy: links_non_perl
1957	PROBE_SET/PROBE_SET.dummy: links_non_perl link_db
1958	READSEQ/READSEQ.dummy: links_non_perl
1959	RNACMA/RNACMA.dummy: links_non_perl header_libs
1960	SECEDIT/SECEDIT.dummy: links_non_perl
1961	SEQ_QUALITY/SEQ_QUALITY.dummy: links_non_perl
1962	SERVERCNTRL/SERVERCNTRL.dummy: links_non_perl com
1963	SL/ALILINK/ALILINK.dummy: links_non_perl
1964	SL/ALIVIEW/ALIVIEW.dummy: links_non_perl
1965	SL/AP_TREE/AP_TREE.dummy: links_non_perl
1966	SL/APP/APP.dummy: links_non_perl
1967	SL/ARB_SPEC/ARB_SPEC.dummy: links_non_perl
1968	SL/ARB_TREE/ARB_TREE.dummy: links_non_perl
1969	SL/AW_HELIX/AW_HELIX.dummy: links_non_perl
1970	SL/CONSENSUS/CONSENSUS.dummy: links_non_perl
1971	SL/CANVAS/CANVAS.dummy: links_non_perl
1972	SL/DB_QUERY/DB_QUERY.dummy: links_non_perl
1973	SL/DB_SCANNER/DB_SCANNER.dummy: links_non_perl
1974	SL/DB_UI/DB_UI.dummy: links_non_perl
1975	SL/FAST_ALIGNER/FAST_ALIGNER.dummy: links_non_perl
1976	SL/FILTER/FILTER.dummy: links_non_perl
1977	SL/FILTSEQEXP/FILTSEQEXP.dummy: links_non_perl
1978	SL/GROUP_SEARCH/GROUP_SEARCH.dummy: links_non_perl
1979	SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy: links_non_perl
1980	SL/GUI_TK/GUI_TK.dummy: links_non_perl
1981	SL/HEADERTESTS/HEADERTESTS.dummy: links_non_perl
1982	SL/HELIX/HELIX.dummy: links_non_perl
1983	SL/INSDEL/INSDEL.dummy: links_non_perl
1984	SL/ITEM_SHADER/ITEM_SHADER.dummy: links_non_perl
1985	SL/ITEMS/ITEMS.dummy: links_non_perl
1986	SL/LOCATION/LOCATION.dummy: links_non_perl
1987	SL/MACROS/MACROS.dummy: links_non_perl
1988	SL/MASKS/MASKS.dummy: links_non_perl
1989	SL/MATRIX/MATRIX.dummy: links_non_perl
1990	SL/MAPKEY/MAPKEY.dummy: links_non_perl
1991	SL/NDS/NDS.dummy: links_non_perl
1992	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.dummy: links_non_perl
1993	SL/PRONUC/PRONUC.dummy: links_non_perl
1994	SL/PTCLEAN/PTCLEAN.dummy: links_non_perl link_db
1995	SL/PVP/PVP.dummy: links_non_perl
1996	SL/QUERY/QUERY.dummy: links_non_perl link_db
1997	SL/REFENTRIES/REFENTRIES.dummy: links_non_perl
1998	SL/REGEXPR/REGEXPR.dummy: links_non_perl
1999	SL/SAICALC/SAICALC.dummy: links_non_perl
2000	SL/SPECSEL/SPECSEL.dummy: links_non_perl
2001	SL/SEQIO/SEQIO.dummy: links_non_perl
2002	SL/SEQUENCE/SEQUENCE.dummy: links_non_perl
2003	SL/TRANSLATE/TRANSLATE.dummy: links_non_perl
2004	SL/TREE_ADMIN/TREE_ADMIN.dummy: links_non_perl
2005	SL/TREE_READ/TREE_READ.dummy: links_non_perl
2006	SL/TREE_WRITE/TREE_WRITE.dummy: links_non_perl
2007	SL/TREEDISP/TREEDISP.dummy: links_non_perl
2008	SL/XFERGUI/XFERGUI.dummy: links_non_perl
2009	SL/XFERSET/XFERSET.dummy: links_non_perl
2010	STAT/STAT.dummy: links_non_perl
2011	TREEGEN/TREEGEN.dummy: links_non_perl
2012	WETC/WETC.dummy: links_non_perl
2013	WINDOW/libWINDOW.dummy: links_non_perl
2014	XML/XML.dummy: links_non_perl
2015
2016	ifeq ($(OPENGL),1)
2017	GL/glAW/glAW.dummy: links_non_perl
2018	GL/glpng/glpng.dummy: links_non_perl
2019	GL/GL.dummy: GL/glAW/glAW.dummy GL/glpng/glpng.dummy
2020	RNA3D/RNA3D.dummy: links_non_perl gl
2021	endif
2022
2023	UNIT_TESTER/UNIT_TESTER.dummy: link_db \
2024	SERVERCNTRL/SERVERCNTRL.dummy \
2025
2026	# see also TOOLS/Makefile@TOOLSLIBDEPENDS
2027	TOOLS/TOOLS.dummy : links_non_perl link_db com \
2028	CONSENSUS_TREE/CONSENSUS_TREE.dummy \
2029	SERVERCNTRL/SERVERCNTRL.dummy \
2030	SL/FILTER/FILTER.dummy \
2031	SL/FILTSEQEXP/FILTSEQEXP.dummy \
2032	SL/INSDEL/INSDEL.dummy \
2033	SL/PRONUC/PRONUC.dummy \
2034	SL/PVP/PVP.dummy \
2035	SL/REGEXPR/REGEXPR.dummy \
2036	SL/SEQIO/SEQIO.dummy \
2037	SL/TREE_READ/TREE_READ.dummy \
2038	SL/TREE_WRITE/TREE_WRITE.dummy \
2039	SL/XFERSET/XFERSET.dummy \
2040	XML/XML.dummy \
2041
2042	AWTC/AWTC.dummy : com
2043
2044	NAMES/NAMES.dummy : com
2045	SL/AW_NAME/AW_NAME.dummy : com
2046
2047	PROBE/PROBE.dummy : com
2048	MULTI_PROBE/MULTI_PROBE.dummy : com
2049	PROBE_DESIGN/PROBE_DESIGN.dummy : com
2050	NALIGNER/NALIGNER.dummy : com
2051
2052	ARB_GDE/ARB_GDE.dummy : proto_tools menus
2053
2054	compile_compatibility: SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.dummy
2055
2056	#***************************************************************************************
2057	# Short aliases to make targets
2058	#***************************************************************************************
2059
2060	show:
2061	@echo $(SEP)
2062	@echo 'Aliases for often needed targets:'
2063	@echo ''
2064	@echo ' executables:'
2065	@echo ''
2066	@echo ' nt arb_ntree'
2067	@echo ' e4 arb_edit4 (includes secedit)'
2068	@echo ' di arb_dist'
2069	@echo ' ph arb_phylo'
2070	@echo ' pa arb_parsimony'
2071	@echo ' tg arb_treegen'
2072	@echo ' ds arb_dbserver'
2073	@echo ' pt arb_pt_server'
2074	@echo ' na arb_name_server'
2075	@echo ''
2076	@echo ' libraries:'
2077	@echo ''
2078	@echo ' com communication libraries'
2079	@echo ' db ARB database'
2080	@echo ' aw GUI lib'
2081	@echo ' awt GUI toolkit'
2082	@echo ' awtc general purpose library'
2083	@echo ' awti import/export library'
2084	@echo ' mp multi probe library'
2085	@echo ' ge genome library'
2086	@echo ' pd probe design lib'
2087	@echo ' prd primer design lib'
2088	@echo ''
2089	@echo ' other targets:'
2090	@echo ''
2091	@echo ' help recompile help files'
2092	@echo ' tools make small tools used by arb'
2093	@echo ''
2094	@echo ' foreign targets:'
2095	@echo ''
2096	@echo ' gde GDE'
2097	@echo ' agde ARB_GDE'
2098	@echo ''
2099	@echo 'for other targets inspect $(ARBHOME)/Makefile'
2100	@echo ''
2101	@echo $(SEP)
2102
2103	source_doc:
2104	@echo "Remove some links (doxygen crashes otherwise):"
2105	find . $ -name "AISC" -o -name "C" -o -name "GDEHELP" $ -type l -exec rm {} \;
2106	doxygen 2>&1 1>/dev/null
2107	$(MAKE) forcelinks
2108
2109	dep_graph:
2110	@echo "Building some dependency graphs"
2111	SOURCE_TOOLS/dependency_graphs.pl
2112
2113	help: HELP_SOURCE/HELP_SOURCE.dummy
2114
2115	HELP_SOURCE/HELP_SOURCE.dummy: link_core xml menus
2116
2117	db: ARBDB/libARBDB.dummy
2118	core: CORE/libCORE.dummy
2119	aw: WINDOW/libWINDOW.dummy
2120	awtc: AWTC/AWTC.dummy
2121	awti: AWTI/AWTI.dummy
2122
2123	mp: MULTI_PROBE/MULTI_PROBE.dummy
2124	mg: MERGE/MERGE.dummy
2125	ge: GENOM/GENOM.dummy
2126	prd: PRIMER_DESIGN/PRIMER_DESIGN.dummy
2127
2128	nt: menus $(NTREE)
2129
2130	nal: $(NALIGNER)
2131
2132	di: $(DIST)
2133	ph: $(PHYLO)
2134	pa: $(PARSIMONY)
2135	tg: $(TREEGEN)
2136
2137	ifeq ($(OPENGL),1)
2138	3d: RNA3D/RNA3D.dummy
2139	gl: GL/GL.dummy
2140	else
2141	noopengl:
2142	@echo "invalid target for OPENGL=0"
2143	3d: noopengl
2144	gl: noopengl
2145	endif
2146
2147	SL/SL.dummy: com
2148
2149	ds: $(DBSERVER)
2150	pt: $(PROBE)
2151	pst: PROBE_SET/PROBE_SET.dummy
2152	pd: PROBE_DESIGN/PROBE_DESIGN.dummy
2153	na: $(NAMES)
2154	sq: SEQ_QUALITY/SEQ_QUALITY.dummy
2155	cma: $(RNACMA)
2156
2157	sec: SECEDIT/SECEDIT.dummy
2158
2159	e4: $(EDIT4) readseq menus
2160
2161	gi: GENOM_IMPORT/GENOM_IMPORT.dummy
2162	wetc: $(WETC)
2163
2164	xml: XML/XML.dummy
2165	stat: STAT/STAT.dummy $(NTREE) $(EDIT4)
2166	fa: SL/FAST_ALIGNER/FAST_ALIGNER.dummy
2167
2168	#********************************************************************************
2169
2170	up_by_remake: depends proto vectorize_checks
2171
2172	up: up_by_remake tags valgrind_update
2173
2174	#********************************************************************************
2175
2176	touch:
2177	SOURCE_TOOLS/touch_modified.pl
2178
2179	modified: touch
2180	$(MAKE) all
2181
2182	#********************************************************************************
2183
2184	libdepends:
2185	$(MAKE) -C "SOURCE_TOOLS" \
2186	"RNA3D_LIB=$(RNA3D_LIB_4_DEPENDS)" \
2187	libdepends
2188
2189	#********************************************************************************
2190
2191	# create generated headers:
2192	genheaders: TEMPLATES/TEMPLATES.dummy
2193
2194	clrdotdepends:
2195	rm PROBE_COM/.depends \|\| true
2196	rm NAMES_COM/.depends \|\| true
2197	rm PERL2ARB/.depends \|\| true
2198
2199	comdepends: comtools clrdotdepends have_makedepend
2200	@echo "$(SEP) Partially build com interface"
2201	$(MAKE) PROBE_COM/PROBE_COM.depends NAMES_COM/NAMES_COM.depends
2202	$(MAKE) PROBE_COM/server.depends NAMES_COM/server.depends
2203
2204	depends: genheaders comdepends vectorize_checks have_makedepend
2205	@echo "$(SEP) Updating other dependencies"
2206	$(MAKE) $(subst NAMES_COM/server.depends,,$(subst PROBE_COM/server.depends,,$(SUBDIRS:.sub=.depends))) \
2207	HELP_SOURCE/HELP_SOURCE.depends \
2208	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.depends \
2209
2210	$(MAKE) libdepends
2211
2212	depend: depends
2213
2214	# ------------------------------------------------------------
2215	# dependency generation tests for AISC code
2216	#(all should work w/o creating wrong dependencies;
2217	# neither in XXX_COM/Makefile nor in code using AISC interface)
2218	dependstest1: silent_clean
2219	$(MAKE) depends
2220	dependstest2: silent_clean
2221	$(MAKE) com
2222	dependstest3: silent_clean
2223	$(MAKE) aw
2224	dependstest4: silent_clean
2225	$(MAKE) pt
2226	dependstest5: silent_clean
2227	$(MAKE) na
2228	dependstest6: silent_clean
2229	$(MAKE) nt
2230	dependstest7: silent_clean
2231	$(MAKE) all
2232	# ------------------------------------------------------------
2233
2234	vectorize_checks:
2235	$(MAKE) -C SOURCE_TOOLS -r vectorize_checks
2236
2237	clean_checked_vect: lib/lib.clean
2238	SOURCE_TOOLS/clean_checked_vectorizations.sh
2239
2240	# ------------------------------------------------------------
2241
2242	AISC_MKPTPS/AISC_MKPTPS.dummy: links
2243
2244	proto_tools: AISC_MKPTPS/AISC_MKPTPS.dummy
2245
2246	proto: proto_tools
2247	@echo $(SEP) Updating prototypes
2248	$(MAKE) \
2249	ARBDB/ARBDB.proto \
2250	AISC_COM/AISC_COM.proto \
2251	ARB_GDE/ARB_GDE.proto \
2252	CORE/CORE.proto \
2253	CONVERTALN/CONVERTALN.proto \
2254	NTREE/NTREE.proto \
2255	MERGE/MERGE.proto \
2256	PROBE/PROBE.proto \
2257	SERVERCNTRL/SERVERCNTRL.proto \
2258	SL/SL.proto \
2259
2260	#********************************************************************************
2261
2262	valgrind_update: links
2263	@echo $(SEP) Updating for valgrind
2264	$(MAKE) -C SOURCE_TOOLS valgrind_update
2265
2266	#********************************************************************************
2267
2268	TAGFILE=TAGS
2269	UTAGS=TAGS.$(ARBBID)
2270	TAGFILE_TMP=$(UTAGS).tmp
2271
2272	TAG_SOURCE_HEADERS=$(UTAGS).headers.tmp
2273	TAG_SOURCE_CODE=$(UTAGS).codefiles.tmp
2274	TAG_SOURCE_LISTS=$(TAG_SOURCE_HEADERS) $(TAG_SOURCE_CODE)
2275
2276	ETAGS_IGNORE_LIST=SOURCE_TOOLS/etags_ignore.lst
2277
2278	ETAGS=ctags -e -I @$(ETAGS_IGNORE_LIST) --sort=no --if0=no --extra=q
2279	ETAGS_TYPES=--C-kinds=cgnsut --C++-kinds=cgnsut
2280	ETAGS_FUN =--C-kinds=fm --C++-kinds=fm
2281	ETAGS_REST =--C-kinds=dev --C++-kinds=dev
2282
2283	FILTER_TAGS_SOURCES= \
2284	$(SED) -e 's/^.\///g' \| \
2285	grep -Pvi '^HEADERLIBS/\|^GDE/\|^UNIT_TESTER/tests(?:\.slow)?/' \| \
2286	grep -Pvi '/GEN[CH]/'
2287
2288	$(TAG_SOURCE_HEADERS): links
2289	@find . $ -name '.hxx' -o -name ".h" $ -type f \| $(FILTER_TAGS_SOURCES) > $@
2290
2291	$(TAG_SOURCE_CODE): links
2292	@find . $ -name '.cxx' -o -name ".c" $ -type f \| $(FILTER_TAGS_SOURCES) > $@
2293
2294	$(UTAGS).1.tmp: $(TAG_SOURCE_HEADERS)
2295	@$(ETAGS) -f $@ $(ETAGS_TYPES) -L $<
2296	$(UTAGS).2.tmp: $(TAG_SOURCE_HEADERS)
2297	@$(ETAGS) -f $@ $(ETAGS_FUN) -L $<
2298	$(UTAGS).3.tmp: $(TAG_SOURCE_HEADERS)
2299	@$(ETAGS) -f $@ $(ETAGS_REST) -L $<
2300	$(UTAGS).4.tmp: $(TAG_SOURCE_CODE)
2301	@$(ETAGS) -f $@ $(ETAGS_TYPES) -L $<
2302	$(UTAGS).5.tmp: $(TAG_SOURCE_CODE)
2303	@$(ETAGS) -f $@ $(ETAGS_FUN) -L $<
2304	$(UTAGS).6.tmp: $(TAG_SOURCE_CODE)
2305	@$(ETAGS) -f $@ $(ETAGS_REST) -L $<
2306
2307	TAGS_ALL_PARTS=$(UTAGS).1.tmp $(UTAGS).2.tmp $(UTAGS).3.tmp $(UTAGS).4.tmp $(UTAGS).5.tmp $(UTAGS).6.tmp
2308
2309	$(TAGFILE_TMP) : $(TAGS_ALL_PARTS)
2310	@cat $(TAGS_ALL_PARTS) > $@
2311	@rm $(TAGS_ALL_PARTS) $(TAG_SOURCE_LISTS)
2312
2313	cleanOldTags:
2314	@find $(ARBHOME) -name 'TAGS.*.tmp' -ctime +2 -exec rm {} \;
2315
2316	tags: $(TAGFILE_TMP) cleanOldTags
2317	@mv_if_diff $(TAGFILE_TMP) $(TAGFILE)
2318
2319	#********************************************************************************
2320
2321	LINKSTAMP=SOURCE_TOOLS/stamp.generate_all_links
2322
2323	links: checks $(LINKSTAMP) arbmainwrapper
2324	links_no_checks: $(LINKSTAMP) arbmainwrapper
2325
2326	forcelinks:
2327	-rm $(LINKSTAMP)
2328	$(MAKE) links
2329
2330	$(LINKSTAMP): SOURCE_TOOLS/generate_all_links.sh genheaders
2331	+SOURCE_TOOLS/generate_all_links.sh
2332	touch $(LINKSTAMP)
2333
2334	clean_links:
2335	# avoid to delete linked pts, nas or arb_tcp.dat:
2336	find . -path './lib' -prune -o -type l -exec rm {} \;
2337	# removed obsolete file - refuses to disappear due to 'prune' above
2338	@rm -f lib/help/GDEHELP
2339	@rm -f $(LINKSTAMP) lib/inputMasks/format.readme
2340
2341	redo_links: clean_links
2342	$(MAKE) links_no_checks
2343
2344	#********************************************************************************
2345
2346	header_libs:
2347	@(( \
2348	echo "$(SEP) Make HEADERLIBS"; \
2349	$(MAKE) -C HEADERLIBS all && \
2350	echo "$(SEP) Make HEADERLIBS [done]"; \
2351	) > HEADERLIBS.log 2>&1 && (cat HEADERLIBS.log;rm HEADERLIBS.log)) \|\| (cat HEADERLIBS.log;rm HEADERLIBS.log;false)
2352
2353	#********************************************************************************
2354
2355	gde: GDE/GDE.dummy
2356	GDE: gde
2357	agde: ARB_GDE/ARB_GDE.dummy
2358	tools: TOOLS/TOOLS.dummy
2359	convert: $(CONVERT_ALN)
2360	readseq: READSEQ/READSEQ.dummy
2361
2362	#***************************************************************************************
2363	# Some user commands
2364	#***************************************************************************************
2365
2366	menus: binlink links
2367	@(( \
2368	echo "$(SEP) Make GDEHELP"; \
2369	$(MAKE) -C GDEHELP -r all && \
2370	echo "$(SEP) Make GDEHELP [done]"; \
2371	) > GDEHELP.log 2>&1 && (cat GDEHELP.log;rm GDEHELP.log)) \|\| (cat GDEHELP.log;rm GDEHELP.log;false)
2372
2373	ifeq ($(DEBUG),1)
2374	BIN_TARGET=develall
2375	else
2376	BIN_TARGET=all
2377	endif
2378
2379
2380	binlink:
2381	$(MAKE) -C bin $(BIN_TARGET)
2382
2383	check_bin_dep: binlink
2384	SOURCE_TOOLS/check_bin_dependencies.pl
2385
2386	fig_cure:
2387	SOURCE_TOOLS/sortfig.pl doit
2388
2389	preplib:
2390	(cd lib;$(MAKE) all)
2391
2392	# --------------------------------------------------------------------------------
2393	# This section is quite tricky:
2394	#
2395	# make 'perl' is a BIG target, so when it has to be made, it has to be started
2396	# as early as possible to reduce overall compile time. Since 'make' does not
2397	# provide any priorities, i force it to build all 'perl'-prerequisites early, by
2398	# adding artificial dependencies to these prerequisites
2399	#
2400	# That behavior is likely to be system-dependent.
2401	# My goal was only to make it work on my current development system,
2402	# where this saves about 20% of overall build time.
2403
2404	ifeq ($(WITHPERL),1)
2405	links_non_perl: PERLTOOLS/PERLTOOLS.dummy
2406	perltools: links_non_perl
2407	perl: realperl
2408	else
2409	links_non_perl: links
2410	perl: links
2411	$(MAKE) "WITHPERL=1" perl
2412	endif
2413
2414	# ---------------------------------------- perl
2415
2416	realperl: perltools
2417	(( \
2418	echo "$(SEP) Make PERL2ARB" ; \
2419	$(TIME) $(MAKE) -C PERL2ARB -r -f Makefile.main \
2420	"AUTODEPENDS=1" \
2421	"dflags=$(dflags)" \
2422	"cflags4perl=$(cflags) $(cxxflags) $(dflags)" \
2423	"lflags4perl=$(lflags4perl)" \
2424	"COMPILER_VERSION=$(COMPILER_VERSION)" \
2425	all && \
2426	$(MAKE) -C PERL_SCRIPTS/test test && \
2427	echo "$(SEP) Make PERL2ARB [done]" ; \
2428	) > PERL2ARB.log 2>&1 && (cat PERL2ARB.log;rm PERL2ARB.log)) \|\| (cat PERL2ARB.log;rm PERL2ARB.log;false)
2429
2430	perl_clean:
2431	@$(MAKE) -C PERL2ARB -r -f Makefile.main \
2432	"AUTODEPENDS=0" \
2433	clean
2434
2435	PERL2ARB/PERL2ARB.clean:
2436	$(MAKE) perl_clean
2437	$(MAKE) -C PERL_SCRIPTS/test clean
2438
2439	# ---------------------------------------- bindings to script languages
2440
2441	bindings: lib/libCORE.so lib/libARBDB.so
2442	$(MAKE) -C BINDINGS all ARBDEPENDS="$(^:%=../%)" DFLAGS="$(dflags)"
2443
2444	bindings_clean:
2445	$(MAKE) -C BINDINGS clean
2446
2447	# ---------------------------------------- check resources
2448
2449	check_res:
2450	$(ARBHOME)/SOURCE_TOOLS/check_resources.pl
2451
2452	# ---------------------------------------- cleaning
2453
2454	rmbak:
2455	@echo "[cleanup backup/core files]"
2456	@find . \( -name '*%' \
2457	-o -name '*.bak' \
2458	-o -name '*~' \) \
2459	-o $ -name 'core' -a \! -type d $ \
2460	-exec rm -v {} \; \|\| \
2461	echo "Warning: target 'rmbak' reported problems when removing misc. backup files (ignored)"
2462	@echo "[cleanup done]"
2463
2464	bin_reinit:
2465	$(MAKE) bin/bin.clean
2466	$(MAKE) -C "bin" all
2467
2468	clean_directories:
2469	-rm -rf \
2470	$(ARBHOME)/PROBE_SET/bin \
2471	$(ARBHOME)/INCLUDE \
2472
2473	libclean:
2474	-find $(ARBHOME) -type f $ -name '*.a' ! -type l $ -exec rm -f {} \;
2475	-find $(ARBHOME) -type f $ -name 'lib*.so' ! -type l $ -exec rm -f {} \;
2476
2477	objclean:
2478	-find $(ARBHOME) -type f $ -name '*.o' ! -type l $ -exec rm -f {} \;
2479
2480	# bin.clean and HELP_SOURCE.clean interfere
2481	clean3:
2482	$(MAKE) bin/bin.clean
2483	$(MAKE) HELP_SOURCE/HELP_SOURCE.clean
2484
2485
2486	# delete all binaries (similar to 'cleanlinked')
2487	cleanRelinkable: libclean UNIT_TESTER/UNIT_TESTER.clean
2488	$(MAKE) -C bin cleanbinariesRelinkable
2489	$(MAKE) -C PROBE_SET cleanLinked
2490
2491
2492	clean2: $(SUBDIRS:.sub=.clean) \
2493	clean3 \
2494	rmbak \
2495	libclean \
2496	objclean \
2497	lib/lib.clean \
2498	GDEHELP/GDEHELP.clean \
2499	HEADERLIBS/HEADERLIBS.clean \
2500	SOURCE_TOOLS/SOURCE_TOOLS.clean \
2501	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.clean \
2502	UNIT_TESTER/UNIT_TESTER.clean \
2503	TEMPLATES/TEMPLATES.clean \
2504	perl_clean \
2505
2506	rm -f .last_gcc .last_compiler config.makefile.bak
2507	$(MAKE) clean_directories
2508
2509	# links are needed for cleanup
2510	clean: redo_links motif_xpm_hack_clean
2511	$(MAKE) clean2
2512	$(MAKE) clean_cov_all clean_links
2513
2514	silent_clean:
2515	$(MAKE) clean >/dev/null
2516
2517	# 'relocated' is about 50% faster than 'rebuild'
2518	reloc_clean: links
2519	@echo "---------------------------------------- Relocation cleanup"
2520	$(MAKE) \
2521	perl_clean \
2522	GDEHELP/GDEHELP.clean \
2523	HELP_SOURCE/genhelp/genhelp.clean \
2524	bin/bin.clean \
2525	libclean \
2526	objclean
2527
2528	relocated: links
2529	$(MAKE) reloc_clean
2530	@echo "---------------------------------------- and remake"
2531	$(MAKE) build
2532
2533	# -----------------------------------
2534	# some stress tests
2535	# (helpful to reveal race conditions with -j)
2536
2537	rebuild4ever: rebuild
2538	$(MAKE) rebuild4ever
2539
2540	build4ever: build
2541	$(MAKE) build4ever
2542
2543	clean4ever: clean
2544	$(MAKE) clean4ever
2545
2546	test4ever: ut
2547	$(MAKE) test4ever
2548
2549	perl4ever: clean
2550	$(MAKE) links
2551	$(MAKE) perl
2552	$(MAKE) perl4ever
2553
2554	help4ever: clean
2555	$(MAKE) help
2556	$(MAKE) help4ever
2557
2558	# -----------------------------------
2559
2560	cleanlinked: bin/bin.clean libclean
2561
2562	relink: cleanlinked
2563	$(MAKE) all
2564
2565	# --------------------------------------------------------------------------------
2566	# source related targets
2567
2568	CLOC=cloc
2569	CLOCFLAGS=--no3 --quiet --progress-rate=0
2570	CLOCARB=--exclude-dir=GDE .
2571	CLOCEXT=GDE
2572	CLOCCODE=--force-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.code.def
2573	CLOCREST=--force-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.rest.def
2574	CLOCFILT=tail --lines=+4
2575
2576	cloc:
2577	@echo 'Arb code:'
2578	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCARB) \| $(CLOCFILT)
2579	@echo 'Arb rest:'
2580	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCARB) \| $(CLOCFILT)
2581	@echo 'External code:'
2582	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCEXT) \| $(CLOCFILT)
2583	@echo 'External rest:'
2584	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCEXT) \| $(CLOCFILT)
2585
2586
2587	# patch generation
2588	patch:
2589	SOURCE_TOOLS/arb_create_patch.sh arbPatch --svn
2590
2591	# source tarball generation
2592	save: sourcetarfile
2593
2594	sourcetarfile: rmbak
2595	util/arb_save
2596
2597	# test early whether save will work
2598	savetest:
2599	@util/arb_srclst.pl >/dev/null
2600
2601	testsave: savetest
2602
2603	save2: rmbak
2604	util/arb_save ignore
2605
2606	save_test: rmbak
2607	@echo "Testing source list.."
2608	@util/arb_srclst.pl > /dev/null
2609
2610	save_test_no_error:
2611	@-$(MAKE) save_test
2612
2613	# --------------------------------------------------------------------------------
2614	# version management
2615
2616	inc_candi:
2617	touch SOURCE_TOOLS/inc_candi.stamp
2618	$(MAKE) do_version_update
2619
2620	inc_patch:
2621	touch SOURCE_TOOLS/inc_patch.stamp
2622	$(MAKE) do_version_update
2623
2624	inc_minor:
2625	touch SOURCE_TOOLS/inc_minor.stamp
2626	$(MAKE) do_version_update
2627
2628	inc_major:
2629	touch SOURCE_TOOLS/inc_major.stamp
2630	$(MAKE) do_version_update
2631
2632	do_version_update:
2633	@echo Incrementing version information
2634	$(MAKE) savetest
2635	$(MAKE) genheaders # auto upgrades version early
2636
2637	show_version:
2638	$(MAKE) genheaders # updates version info
2639	@echo "$(SEP) ARB version info"
2640	@grep ARB_VERSION TEMPLATES/arb_build.h
2641	@echo "$(SEP)"
2642
2643	# --------------------------------------------------------------------------------
2644	# special cleanups
2645
2646	clean_opengl_changed: RNA3D/RNA3D.clean EDIT4/EDIT4.clean WINDOW/WINDOW.clean GL/GL.clean
2647
2648	# --------------------------------------------------------------------------------
2649
2650	arbapplications: nt pa e4 wetc pt na nal di ph ds wetc cma
2651
2652	arb_external: convert tools gde readseq tg pst
2653
2654	arb_no_perl: arbapplications help arb_external
2655
2656	arb: motif_xpm_hack
2657	$(MAKE) "WITHPERL=1" perl arb_no_perl
2658
2659	motif_xpm_hack:
2660	$(MAKE) -r -C "lib/motifHack" all
2661
2662	motif_xpm_hack_clean:
2663	$(MAKE) -r -C "lib/motifHack" clean
2664
2665	# --------------------------------------------------------------------------------
2666	# special targets for SOURCE_TOOLS/remake_after_change.pl
2667
2668	rac_arb_dist: di
2669	rac_arb_edit4: e4
2670	rac_arb_ntree: nt
2671	rac_arb_pars: pa
2672	rac_arb_phylo: ph
2673	rac_arb_wetc: wetc
2674	rac_arb_naligner: nal
2675	rac_arb_pt_server: pt
2676	rac_arb_db_server: ds
2677	rac_arb_name_server: na
2678	rac_arb_convert_aln: convert
2679	rac_arb_treegen: tg
2680	rac_arb_rnacma: cma
2681	rac_arb_help2xml: help
2682
2683	rac_arb_a2ps: tools
2684	rac_arb_consensus_tree: tools
2685	rac_arb_dnarates: tools
2686	rac_arb_export_rates: tools
2687	rac_arb_export_tree: tools
2688	rac_arb_gene_probe: tools
2689	rac_arb_message: tools
2690	rac_arb_primer: tools
2691	rac_arb_probe: tools
2692	rac_arb_read_tree: tools
2693
2694	# --------------------------------------------------------------------------------
2695	# unit testing
2696	# @@@ work in progress
2697	#
2698	# goal is to automatically test all libraries/executables using TESTED_UNITS_AUTO
2699	# currently not all test executables link w/o error.
2700	# therefor units are organized in three sets:
2701	#
2702	# TESTED_UNITS = testable and contain tests
2703	# UNTESTED_UNITS = testable, but no tests written yet
2704	# UNTESTABLE_UNITS = not testable
2705
2706	# always define OPENGL units manually:
2707	OPENGL_TESTS :=
2708	ifeq ($(OPENGL),1)
2709	# this section defines RNA3D.test
2710	OPENGL_TESTS += \
2711	$(subst .a,.test,$(RNA3D_LIB)) \
2712	GL/glAW/libglAW.test \
2713	GL/glpng/libglpng_arb.test \
2714
2715	endif
2716
2717	UNITS_NOT_AUTODETECTED = \
2718	HELP_SOURCE/HELP_SOURCE.tooltests
2719
2720	TESTED_UNITS_AUTO = \
2721	$(OPENGL_TESTS) \
2722	$(TL_ARCHIVES:.a=.test) \
2723	$(TL_SHARED_ARCHIVES:.so=.test) \
2724	$(CL_ARCHIVES:.a=.test) \
2725	$(TL_TOOLS_COLLECTIONS:.toolColl=.tooltests) \
2726	$(UNITS_NOT_AUTODETECTED) \
2727
2728	UNTESTED_UNITS = \
2729	$(OPENGL_TESTS) \
2730	EISPACK/EISPACK.test \
2731	GENOM/GENOM.test \
2732	ISLAND_HOPPING/ISLAND_HOPPING.test \
2733	NALIGNER/NALIGNER.test \
2734	NAMES/NAMES.test \
2735	PHYLO/PHYLO.test \
2736	PRIMER_DESIGN/PRIMER_DESIGN.test \
2737	READSEQ/READSEQ.tooltests \
2738	SECEDIT/SECEDIT.test \
2739	SEQ_QUALITY/SEQ_QUALITY.test \
2740	SERVERCNTRL/SERVERCNTRL.test \
2741	SL/ALIVIEW/ALIVIEW.test \
2742	SL/AP_TREE/AP_TREE.test \
2743	SL/ARB_SPEC/ARB_SPEC.test \
2744	SL/ARB_TREE/ARB_TREE.test \
2745	SL/AW_HELIX/AW_HELIX.test \
2746	SL/AW_NAME/AW_NAME.test \
2747	SL/CANVAS/CANVAS.test \
2748	SL/DB_SCANNER/DB_SCANNER.test \
2749	SL/DB_UI/DB_UI.test \
2750	SL/GUI_ALIVIEW/GUI_ALIVIEW.test \
2751	SL/GUI_TK/GUI_TK.test \
2752	SL/HELIX/HELIX.test \
2753	SL/MASKS/MASKS.test \
2754	SL/MAPKEY/MAPKEY.test \
2755	SL/QUERY/QUERY.test \
2756	SL/REFENTRIES/REFENTRIES.test \
2757	SL/SEQUENCE/SEQUENCE.test \
2758	SL/TREE_ADMIN/TREE_ADMIN.test \
2759	SL/TREE_WRITE/TREE_WRITE.test \
2760	SL/XFERGUI/XFERGUI.test \
2761	STAT/STAT.test \
2762	TREEGEN/TREEGEN.test \
2763	WETC/WETC.test \
2764	XML/XML.test \
2765
2766	# untestable units
2767
2768	UNTESTABLE_UNITS = \
2769	AISC/AISC.test \
2770	NAMES_COM/server.test \
2771	PROBE_COM/server.test \
2772
2773	# --------------------
2774	# put all units containing tests into the following 4 sections (see also TESTED_UNITS below)
2775
2776	# recent development
2777	UNITS_TESTED_FIRST = \
2778	SL/SPECSEL/SPECSEL.test \
2779	SL/MATRIX/MATRIX.test \
2780	AWTI/AWTI.test \
2781	SL/FILTSEQEXP/FILTSEQEXP.test \
2782	SL/GROUP_SEARCH/GROUP_SEARCH.test \
2783	SL/PVP/PVP.test \
2784	SL/SAICALC/SAICALC.test \
2785	SL/TRANSLATE/TRANSLATE.test \
2786	SL/XFERSET/XFERSET.test \
2787
2788	# start units with long duration early
2789	UNITS_RUNNING_LONG = \
2790	ARBDB/libARBDB.test \
2791	AWTC/AWTC.test \
2792	TOOLS/TOOLS.tooltests \
2793
2794	# plain test-libaries that are not linked anywhere
2795	TEST_SANDBOXES = \
2796	SL/CB/CB.test \
2797	SL/HEADERTESTS/HEADERTESTS.test \
2798
2799	UNITS_TESTED = \
2800	AISC_MKPTPS/AISC_MKPTPS.tooltests \
2801	ARB_GDE/ARB_GDE.test \
2802	CONSENSUS_TREE/CONSENSUS_TREE.test \
2803	CONVERTALN/CONVERTALN.test \
2804	CORE/libCORE.test \
2805	DBSERVER/DBSERVER.test \
2806	DIST/DIST.test \
2807	EDIT4/EDIT4.test \
2808	GENOM_IMPORT/GENOM_IMPORT.test \
2809	HELP_SOURCE/HELP_SOURCE.tooltests \
2810	MERGE/MERGE.test \
2811	MULTI_PROBE/MULTI_PROBE.test \
2812	NTREE/NTREE.test \
2813	PARSIMONY/PARSIMONY.test \
2814	PERLTOOLS/PERLTOOLS.tooltests \
2815	PROBE/PROBE.test \
2816	PROBE_DESIGN/PROBE_DESIGN.test \
2817	PROBE_SET/PROBE_SET.tooltests \
2818	RNACMA/RNACMA.test \
2819	SL/ALILINK/ALILINK.test \
2820	SL/APP/APP.test \
2821	SL/CONSENSUS/CONSENSUS.test \
2822	SL/DB_QUERY/DB_QUERY.test \
2823	SL/FAST_ALIGNER/FAST_ALIGNER.test \
2824	SL/FILTER/FILTER.test \
2825	SL/INSDEL/INSDEL.test \
2826	SL/ITEM_SHADER/ITEM_SHADER.test \
2827	SL/ITEMS/ITEMS.test \
2828	SL/LOCATION/LOCATION.test \
2829	SL/MACROS/MACROS.test \
2830	SL/NDS/NDS.test \
2831	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.test \
2832	SL/PRONUC/PRONUC.test \
2833	SL/PTCLEAN/PTCLEAN.test \
2834	SL/REGEXPR/REGEXPR.test \
2835	SL/SEQIO/SEQIO.test \
2836	SL/TREE_READ/TREE_READ.test \
2837	SL/TREEDISP/TREEDISP.test \
2838	WINDOW/libWINDOW.test \
2839
2840	TESTED_UNITS = \
2841	$(UNITS_TESTED_FIRST) \
2842	$(UNITS_RUNNING_LONG) \
2843	$(TEST_SANDBOXES) \
2844	$(UNITS_TESTED) \
2845
2846	# ----------------------------------------
2847
2848	ifeq ($(DEVELOPER),RALF)
2849
2850	DEFINED_TEST_UNITS = \
2851	$(TESTED_UNITS) \
2852	$(UNTESTED_UNITS) \
2853	$(UNTESTABLE_UNITS) \
2854
2855	list_undefined_units:
2856	@UNIT_TESTER/list_undefined_units.pl $(DEFINED_TEST_UNITS) -- $(TESTED_UNITS_AUTO)
2857
2858	else
2859
2860	list_undefined_units:
2861
2862	endif
2863
2864	# ----------------------------------------
2865
2866	TEST_LOG_DIR = UNIT_TESTER/logs
2867	TEST_RUN_SUITE=$(MAKE) $(NODIR) -C UNIT_TESTER -f Makefile.suite -r
2868	# -> UNIT_TESTER/Makefile.suite
2869	TEST_MAKE_FLAGS=
2870	TEST_POST_CLEAN=
2871	ifeq ($(COVERAGE),1)
2872	TEST_POST_CLEAN=$(MAKE) clean_cov
2873	TEST_MAKE_FLAGS+=-j1
2874	endif
2875
2876
2877	%.test:
2878	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
2879	( \
2880	echo "take[1]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
2881	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
2882	"UNITDIR=$(@D)" \
2883	"UNITLIBNAME=$(@F:.test=)" \
2884	"COVERAGE=$(COVERAGE)" \
2885	"ARB_PID=$(ARB_PID)_$(@F)" \
2886	"DEVELOPER=$(DEVELOPER)" \
2887	runtest; \
2888	echo "take[1]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"; \
2889	$(TEST_POST_CLEAN) \
2890	) >$(TEST_LOG_DIR)/$(@F).log 2>&1; \
2891	UNIT_TESTER/log_result.pl $(TEST_LOG_DIR)/$(@F).log )
2892
2893	%.notest:
2894	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
2895	( \
2896	echo "take[4]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
2897	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
2898	"UNITDIR=$(@D)" \
2899	"UNITLIBNAME=$(@F:.notest=)" \
2900	"COVERAGE=0" \
2901	"ARB_PID=$(ARB_PID)_$(@F)" \
2902	"DEVELOPER=$(DEVELOPER)" \
2903	check_no_test; \
2904	echo "take[4]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'" \
2905	) >$(TEST_LOG_DIR)/$(@F).log 2>&1 )
2906
2907
2908	# tool test aliases (used to test one or multiple executable(s) in a single subdir):
2909	%.tooltests:
2910	$(error please define an explicit tooltest alias for $@)
2911
2912	AISC_MKPTPS/AISC_MKPTPS.tooltests : AISC_MKPTPS/mkptypes.test
2913	@echo "aliasing $@ -> $^"
2914	PERLTOOLS/PERLTOOLS.tooltests : PERLTOOLS/arb_proto_2_xsub.test
2915	@echo "aliasing $@ -> $^"
2916	PROBE_SET/PROBE_SET.tooltests : PROBE_SET/fb_test.test
2917	@echo "aliasing $@ -> $^"
2918	HELP_SOURCE/HELP_SOURCE.tooltests : HELP_SOURCE/arb_help2xml.test
2919	@echo "aliasing $@ -> $^"
2920	TOOLS/TOOLS.tooltests : TOOLS/arb_consensus_tree.test TOOLS/arb_probe.test TOOLS/arb_test.test
2921	@echo "aliasing $@ -> $^"
2922
2923	# aliases for tools w/o tests:
2924	READSEQ/READSEQ.tooltests:
2925	@echo "Note: no tests for $@"
2926
2927
2928	test_base: $(UNIT_TESTER_LIB:.a=.dummy) $(subst .test,.dummy,$(TEST_SANDBOXES))
2929
2930	clean_cov:
2931	find . $ -name ".gcda" -o -name ".gcov" -o -name "*.cov" $ -exec rm {} \;
2932
2933	clean_cov_all: clean_cov
2934	find . $ -name "*.gcno" $ -exec rm {} \;
2935
2936	cleanup_faked_arbpids:
2937	@rm ~/.arb_tmp/tmp/arb_pids_${USER}_${ARB_PID}_* \|\| true
2938
2939	cleanup_faked_arbpids_and_fail: cleanup_faked_arbpids
2940	@false
2941
2942	NOTESTS_IN_UNTESTED = $(subst .test,.notest,$(UNTESTED_UNITS))
2943
2944	run_tests_faked_arbpid:
2945	+@$(TEST_RUN_SUITE) init
2946	@echo "take[2]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2947	@$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(TESTED_UNITS) $(NOTESTS_IN_UNTESTED) \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2948	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2949	@echo "take[2]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2950	@$(MAKE) clean_cov >/dev/null
2951	@$(MAKE) cleanup_faked_arbpids
2952
2953	# @@@ instead of only running UNIT, this should as well run all tests this unit depends on? according to 'needs_libs'
2954	# @@@ '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
2955
2956	run_onetest_faked_arbpid:
2957	+@$(TEST_RUN_SUITE) init
2958	@echo "take[3]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2959	@test -n "$(UNIT)" \|\| (echo "Error: UNIT has to be defined for target 'run_onetest_faked_arbpid'!"; false)
2960	$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(UNIT).test \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2961	@echo "take[3]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2962	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2963	@$(MAKE) clean_cov >/dev/null
2964	@$(MAKE) cleanup_faked_arbpids
2965
2966	run_tests: test_base clean_cov
2967	$(MAKE) "ARB_PID=UT_$$$$" run_tests_faked_arbpid list_undefined_units
2968
2969	run_oneunitstests: test_base
2970	$(MAKE) "ARB_PID=UT_$$$$" run_onetest_faked_arbpid
2971
2972
2973	ut:
2974	ifeq ($(UNIT_TESTS),1)
2975	@echo $(MAKE) run_tests
2976	@$(MAKE) run_tests
2977	else
2978	@echo "Not compiled with unit tests"
2979	endif
2980
2981
2982	aut:
2983	+@$(TEST_RUN_SUITE) unskip
2984	$(MAKE) ut
2985
2986	# --------------------------------------------------------------------------------
2987
2988	TIMELOG=$(ARBHOME)/arb_time.log
2989	TIMEARGS=--append --output=$(TIMELOG) --format=" * %E(%S+%U) %P [%C]"
2990	TIMECMD=$(TIME) $(TIMEARGS)
2991
2992	time_one:
2993	ifeq ($(ONE_TIMED_TARGET),)
2994	@echo "Error: You have to pass ONE_TIMED_TARGET to $@"
2995	false
2996	else
2997	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET)"
2998	@$(TIMECMD) $(MAKE) $(ONE_TIMED_TARGET)
2999	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET) [done]"
3000	endif
3001
3002	timed_target:
3003	ifeq ($(TIMED_TARGET),)
3004	@echo "Error: You have to pass TIMED_TARGET to $@"
3005	false
3006	else
3007	@echo "Build time:" > $(TIMELOG)
3008	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
3009	@cat $(TIMELOG)
3010	@rm $(TIMELOG)
3011	endif
3012
3013	timed_target_tested:
3014	ifeq ($(TIMED_TARGET),)
3015	@echo "Error: You have to pass TIMED_TARGET to $@"
3016	false
3017	else
3018	@echo "Build time:" > $(TIMELOG)
3019	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
3020	$(MAKE) "ONE_TIMED_TARGET=ut" time_one
3021	@cat $(TIMELOG)
3022	@rm $(TIMELOG)
3023	endif
3024
3025	clean_timed_target:
3026	ifeq ($(TIMED_TARGET),)
3027	@echo "Error: You have to pass TIMED_TARGET to $@"
3028	false
3029	else
3030	@echo "Build time:" > $(TIMELOG)
3031	$(MAKE) "ONE_TIMED_TARGET=clean" time_one
3032	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
3033	@cat $(TIMELOG)
3034	@rm $(TIMELOG)
3035	endif
3036
3037	# --------------------------------------------------------------------------------
3038
3039	CHECKOUT_MODIFIED=0# set to 1 to temporarily skip test for modifications (do not check in if set to 1)
3040
3041	check_svn_does_not_contain_generated:
3042	ifeq ($(CHECKOUT_MODIFIED),0)
3043	@echo "Testing that build does not modify files in SVN"
3044	@test 0 = `svn status \| wc -l` \|\| ( \
3045	echo "The checkout is not/no longer clean:"; \
3046	svn status; \
3047	echo "- if this fails instantly, your checkout is not clean"; \
3048	echo "- if this fails after other targets, these targets modify checked in data"; \
3049	echo " (a common cause may be that depends are not up to date)"; \
3050	false)
3051	else
3052	grep -Hn 'CHECKOUT_MODIFIED' Makefile
3053	endif
3054
3055	check_svn_ignores_generated:
3056	@test 0 = `svn status \| grep '^\?' \| wc -l` \|\| ( \
3057	echo "There are svn-unignored files:"; \
3058	svn status \| grep '^\?'; \
3059	echo "(all generated files should be svn-ignored)"; \
3060	false)
3061
3062	check_svn_state: check_svn_does_not_contain_generated
3063	$(MAKE) check_svn_ignores_generated
3064	$(MAKE) savetest
3065
3066	things_that_always_should_work: depends proto
3067
3068	post_commit_check:
3069	@echo "---------------------------------------- [Initial]"
3070	$(MAKE) check_svn_state
3071
3072	$(MAKE) clean
3073	@echo "---------------------------------------- [After 'make clean']"
3074	$(MAKE) check_svn_state
3075
3076	$(MAKE) things_that_always_should_work
3077	@echo "---------------------------------------- [After 'make things_that_always_should_work']"
3078	$(MAKE) check_svn_state
3079
3080	$(MAKE) all
3081	@echo "---------------------------------------- [After 'make all']"
3082	$(MAKE) check_svn_state
3083
3084	$(MAKE) things_that_always_should_work
3085	@echo "---------------------------------------- [Final]"
3086	$(MAKE) check_svn_state
3087
3088	# --------------------------------------------------------------------------------
3089	# sanitize arb_ntree; also works for clients (arb_edit4, ...) started from there.
3090
3091	sanitize: all
3092	( \
3093	export "LSAN_OPTIONS=max_leaks=30:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp"; \
3094	echo "sake[1]: Entering directory \`$(ARBHOME)'"; \
3095	$(ARBHOME)/bin/arb_ntree --execute _logged ~/data/test.arb 2>&1 ; \
3096	echo "sake[1]: Leaving directory \`$(ARBHOME)'" \
3097	) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
3098
3099	# --------------------------------------------------------------------------------
3100	# build and test one unit:
3101
3102	build_oneunit:
3103	$(MAKE) "WITHPERL=1" $(UNIT).dummy
3104
3105	oneunit:
3106	ifndef UNIT
3107	@echo "Please define UNIT, e.g. using"
3108	@echo " make \"UNIT=ARBDB/libARBDB\" oneunit"
3109	@echo " make \"UNIT=SL/TREEDISP/TREEDISP\" oneunit"
3110	@echo "(Note: 1st is a shared library, 2nd isn't)"
3111	false
3112	else
3113	@echo "Build time" > $(TIMELOG)
3114	@echo "$(SEP) $(MAKE) build_oneunit"
3115	@$(TIMECMD) $(MAKE) build_oneunit
3116	ifeq ($(UNIT_TESTS),1)
3117	@echo "$(SEP) $(MAKE) run_oneunitstests"
3118	@$(TIMECMD) $(MAKE) run_oneunitstests
3119	endif
3120	@cat $(TIMELOG)
3121	@rm $(TIMELOG)
3122	endif
3123
3124	# --------------------------------------------------------------------------------
3125	# Main targets:
3126
3127	tarfile: rebuild
3128	$(MAKE) prepare_libdir
3129	util/arb_compress
3130
3131	tarfile_quick: all
3132	$(MAKE) prepare_libdir
3133	util/arb_compress
3134
3135	# -----------------------------------
3136
3137	build: arb
3138	$(MAKE) check_bin_dep preplib compile_compatibility fig_cure
3139
3140	all:
3141	@echo "Build time" > $(TIMELOG)
3142	# $(MAKE) clean_checked_vect # uncomment to rebuild sources where expected vectorization gets tested
3143	@echo "$(SEP) $(MAKE) all"
3144	@$(TIMECMD) $(MAKE) build
3145	@echo $(SEP)
3146	@echo "made 'all' with success."
3147	@echo "to start arb enter 'arb'"
3148	ifeq ($(UNIT_TESTS),1)
3149	@echo "$(SEP) $(MAKE) run_tests"
3150	@$(TIMECMD) $(MAKE) run_tests
3151	endif
3152	@echo "$(SEP) $(MAKE) all [done]"
3153	ifeq ($(DEBUG),1)
3154	@$(MAKE) save_test_no_error >/dev/null # just show hints
3155	endif
3156	@cat $(TIMELOG)
3157	@rm $(TIMELOG)
3158
3159	rebuild: clean
3160	$(MAKE) all
3161
3162	# --------------------------------------------------------------------------------
3163	# special targets showing obvious error at bottom
3164	# (intended to be used from automated builds)
3165
3166	BUILD_LOG=build.log
3167	SHELL=bash
3168	REDIRECT_KEEP_EXITCODE = tee $(BUILD_LOG) ; exit "$${PIPESTATUS[0]}"
3169	EXTRACT_ERROR_SUMMARY = (./SOURCE_TOOLS/short_error_summary.pl $(BUILD_LOG); false)
3170
3171	REEXTRACT:
3172	@echo "Note: Re-extracting errors from $(BUILD_LOG):"
3173	@$(EXTRACT_ERROR_SUMMARY)
3174
3175	ALL:
3176	@(($(MAKE) all 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
3177
3178	REBUILD:
3179	@(($(MAKE) rebuild 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
3180
3181	TARFILE:
3182	@(($(MAKE) tarfile 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
3183
3184	TARFILE_QUICK:
3185	@(($(MAKE) tarfile_quick 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
3186

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