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Last change on this file was 15228, checked in by westram, 8 years ago
tested arb with gcc 6.2.0 also disabled vectorization (produces broken code; see #700)
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 73.9 KB

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1	# =============================================================== #
2	# #
3	# File : Makefile #
4	# #
5	# Institute of Microbiology (Technical University Munich) #
6	# http://www.arb-home.de/ #
7	# #
8	# =============================================================== #
9
10	# -----------------------------------------------------
11	# The ARB Makefile is aware of the following defines:
12	#
13	# CC C compiler (should be defined by OS)
14	# CXX C++ compiler (should be defined by OS)
15	#
16	# BUILDHOST_64=0/1 1=>compile on 64 bit platform (defaults to ARB_64)
17	# DEVELOPER=name special compilation (values: ANY,RELEASE,your name)
18	# OPENGL=0/1 whether OPENGL is available
19	#
20	# -----------------------------------------------------
21	# Paths for several libraries may be set from config.makefile by using:
22	#
23	# export XLIBS=$(shell pkg-config --libs xpm xerces-c)
24	# export XAW_LIBS=$(shell pkg-config --libs xaw7)
25	# export XML_INCLUDES=$(shell pkg-config --cflags xerces-c)
26	#
27	# -----------------------------------------------------
28	# ARB Makefile and ARB source code are aware of the following defines:
29	#
30	# $(MACH) name of the machine (LINUX or DARWIN; see config.makefile)
31	# DEBUG compiles the DEBUG sections
32	# DEBUG_GRAPHICS all X-graphics are flushed immediately (for debugging)
33	# ARB_64=0/1 1=>compile 64 bit version
34	# UNIT_TESTS=0/1 1=>compile in unit tests and call them after build
35	# COVERAGE=0/1/2 compile in gcov support (useful together with UNIT_TESTS=1)
36	# 0=no, 1+2=compile in, 1=show
37	# STABS=0/1 force stabs format? (0 = "use default format")
38	# SANITIZE=0/#/all use Sanitizer? (defaults to 0,
39	# 1=AddressSanitizer+LeakSanitizer,
40	# 2=UndefinedBehaviorSanitizer,
41	# combine bit-values to activate multiple Sanitizers,
42	# specify 'all' to activate all)
43	# SHOWTODO=0/1 activate TODO-warnings? (defaults to 0, except for ralf)
44	#
45	# -----------------------------------------------------
46	# The ARB source code is aware of the following defines:
47	#
48	# NDEBUG doesn't compile the DEBUG sections
49	# DEVEL_$(DEVELOPER) developer-dependent flag (enables you to have private sections in code)
50	# DEVELOPER='ANY' (default setting) will be ignored
51	# configurable in config.makefile
52	#
53	# -----------------------------------------------------
54	# Read configuration
55	include config.makefile
56
57	# set defaults for variables commented out in config.makefile:
58	ifndef DARWIN
59	DARWIN:=0
60	endif
61	ifndef LINUX
62	LINUX:=0
63	endif
64	ifndef DEBIAN
65	DEBIAN:=0
66	endif
67	ifndef REDHAT
68	REDHAT:=0
69	endif
70	ifndef ARB_64
71	ARB_64=1#default to 64bit
72	endif
73
74	# compiler settings:
75	ifneq ($(CC),use__A_CC__instead_of__CC)
76
77	A_CC:=$(CC)# compile C
78	A_CXX:=$(CXX)# compile C++
79
80	# uncomment to ensure no submakefile uses CC and CXX directly
81	override CC:=use__A_CC__instead_of__CC
82	override CXX:=use__A_CXX__instead_of__CXX
83
84	endif
85
86	export CC CXX A_CC A_CXX
87
88	# unconditionally prepend $(ARBHOME)/lib to LD_LIBRARY_PATH if not found
89	ifeq ($(findstring $(ARBHOME)/lib,$(LD_LIBRARY_PATH)),)
90	LD_LIBRARY_PATH:=${ARBHOME}/lib:$(LD_LIBRARY_PATH)
91	endif
92
93	# store LD_LIBRARY_PATH to circumvent SIP restrictions:
94	ARBBUILD_LIBRARY_PATH:=$(LD_LIBRARY_PATH)
95
96	FORCEMASK = umask 002
97	NODIR=--no-print-directory
98
99	SED:=$(ARBHOME)/SH/arb_sed
100	READLINK:=$(ARBHOME)/SH/arb_readlink
101
102	# ---------------------- compiler version detection
103
104	# supported gcc versions:
105	ALLOWED_gcc_VERSIONS=\
106	4.3.1 4.3.2 4.3.3 4.3.4 \
107	4.4.1 4.4.3 4.4.5 4.4.6 4.4.7 \
108	4.5.2 \
109	4.6.1 4.6.2 4.6.3 4.6.4 \
110	4.7.1 4.7.2 4.7.3 4.7.4 \
111	4.8.0 4.8.1 4.8.2 4.8.3 4.8.4 4.8.5 \
112	4.9.0 4.9.1 4.9.2 4.9.3 4.9.4 \
113	5.1.0 5.2.0 5.3.0 5.3.1 5.4.0 \
114	6.1.0 6.2.0 \
115
116
117	# ----------------------
118
119	COMPILER_INFO:=$(shell SOURCE_TOOLS/arb_compiler_version.pl $(A_CXX))
120	COMPILER_NAME:=$(word 1,$(COMPILER_INFO))
121	COMPILER_VERSION:=$(word 2,$(COMPILER_INFO))
122
123	USE_CLANG:=0
124	ifneq ($(COMPILER_NAME),gcc)
125	ifeq ($(COMPILER_NAME),clang)
126	USE_CLANG:=1
127	else
128	$(error failed to detect COMPILER_NAME (got '$(COMPILER_NAME)', expected 'clang' or 'gcc'))
129	endif
130	endif
131
132	ifeq ($(USE_CLANG),1)
133	# accept all clang versions:
134	ALLOWED_COMPILER_VERSIONS=$(COMPILER_VERSION)
135	else
136	ALLOWED_COMPILER_VERSIONS=$(ALLOWED_gcc_VERSIONS)
137	endif
138
139	COMPILER_VERSION_ALLOWED=$(strip $(subst ___,,$(foreach version,$(ALLOWED_COMPILER_VERSIONS),$(findstring ___$(version)___,___$(COMPILER_VERSION)___))))
140
141	#---------------------- split gcc version
142
143	SPLITTED_VERSION:=$(subst ., ,$(COMPILER_VERSION))
144
145	USE_GCC_MAJOR:=$(word 1,$(SPLITTED_VERSION))
146	USE_GCC_MINOR:=$(word 2,$(SPLITTED_VERSION))
147	USE_GCC_PATCHLEVEL:=$(word 3,$(SPLITTED_VERSION))
148
149	USE_GCC_452_OR_HIGHER:=
150	USE_GCC_46_OR_HIGHER:=
151	USE_GCC_47_OR_HIGHER:=
152	USE_GCC_48_OR_HIGHER:=
153	USE_GCC_49_OR_HIGHER:=
154	USE_GCC_50_OR_HIGHER:=
155
156	ifeq ($(USE_CLANG),0)
157	ifeq ($(USE_GCC_MAJOR),4)
158	ifeq ($(USE_GCC_MINOR),5)
159	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),23456789)','')
160	USE_GCC_452_OR_HIGHER:=yes
161	endif
162	else
163	ifneq ('$(findstring $(USE_GCC_MINOR),6789)','')
164	USE_GCC_452_OR_HIGHER:=yes
165	USE_GCC_46_OR_HIGHER:=yes
166	ifneq ($(USE_GCC_MINOR),6)
167	USE_GCC_47_OR_HIGHER:=yes
168	ifneq ($(USE_GCC_MINOR),7)
169	USE_GCC_48_OR_HIGHER:=yes
170	ifneq ($(USE_GCC_MINOR),8)
171	USE_GCC_49_OR_HIGHER:=yes
172	endif
173	endif
174	endif
175	endif
176	endif
177	else
178	USE_GCC_452_OR_HIGHER:=yes
179	USE_GCC_46_OR_HIGHER:=yes
180	USE_GCC_47_OR_HIGHER:=yes
181	USE_GCC_48_OR_HIGHER:=yes
182	USE_GCC_49_OR_HIGHER:=yes
183	USE_GCC_50_OR_HIGHER:=yes
184	endif
185	endif
186
187	#---------------------- define special directories for non standard builds
188
189	ifeq ($(DARWIN),1)
190	OSX_FW:=/System/Library/Frameworks
191	OSX_FW_OPENGL:=$(OSX_FW)/OpenGL.framework/Versions/A/Libraries
192	OSX_FW_GLUT:=$(OSX_FW)/GLUT.framework/Versions/A/Libraries
193	OSX_FW_IMAGEIO:=$(OSX_FW)/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources
194	endif
195
196	#----------------------
197
198	ifeq ($(DARWIN),1)
199	LINK_STATIC=1# link static
200	else
201	LINK_STATIC=0# link dynamically
202	# LINK_STATIC=1# link static (testing only)
203	endif
204
205	shared_cflags :=# flags for shared lib compilation
206	clflags :=# linker flags (when passed through gcc)
207	extended_warnings :=# warning flags for C and C++-compiler
208	extended_cpp_warnings :=# warning flags for C++-compiler only
209
210	DISABLE_VECTORIZE_CHECK:=0
211
212	ifeq ($(DEBUG),0)
213	dflags := -DNDEBUG# defines
214	ifeq ($(USE_CLANG),1)
215	cflags := -O3# compiler flags (C and C++)
216	else
217	clflags += -Wl,-O2# passthrough linker flags
218	# ------- standard optimization:
219	cflags := -O3# compiler flags (C and C++)
220	# ------- test changed optimization (DISABLE_VECTORIZE_CHECK for -O2 or lower):
221	# cflags := -O2# do not commit uncommented!
222	# DISABLE_VECTORIZE_CHECK:=1
223	endif
224	endif
225
226	ifeq ($(DEBIAN),1)
227	clflags += -Wl,-rpath=/usr/lib/arb/lib -Wl,-z,relro
228	endif
229
230	ifeq ($(DEBUG),1)
231	dflags := -DDEBUG
232
233	gdb_common := -g -g3 -ggdb -ggdb3
234
235	DBGOPTI:=-O0
236	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
237	DBGOPTI:=-Og
238	endif
239
240	ifeq ($(STABS),1)
241	cflags := $(DBGOPTI) $(gdb_common) -gstabs+ # using stabs+ (enable this for bigger debug session: debugs inlines, quick var inspect, BUT valgrind stops working :/)
242	else
243	cflags := $(DBGOPTI) $(gdb_common) # (using dwarf - cant debug inlines here, incredible slow on showing variable content)
244	endif
245
246	# cflags := $(DBGOPTI) $(gdb_common) -gdwarf-3 # (specify explicit dwarf format)
247	# cflags := $(DBGOPTI) $(gdb_common) -gstabs # using stabs (same here IIRC)
248	# cflags := -O2 $(gdb_common) # use this for callgrind (force inlining)
249
250	ifeq ($(DARWIN),0)
251	clflags += -Wl,-g
252
253	# Note:
254	# Previously '-Wl,-noinhibit-exec' was added to 'clflags' here,
255	# to fix some issues with launchpad binutils (see [12972]).
256	# But that change also caused 'undefined symbols' NOT to be reported as errors
257	# at link time, producing executables that fail at runtime :/
258
259	endif
260
261	ifeq ($(DEBUG_GRAPHICS),1)
262	dflags += -DDEBUG_GRAPHICS
263	endif
264
265	endif # DEBUG only
266
267	# control how much you get spammed
268	# (please do not change default in SVN, use developer specific setting as below)
269	POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl
270	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --original# dont modify compiler output
271	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --loop-optimization-candi# show candidates for vectorization check
272	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --dump-loop-optimization# useful while optimizing code for vectorization
273	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --hide-Noncopyable-advices
274	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --show-useless-Weff++
275	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --no-warnings
276	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --only-first-error
277	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --no-warnings --only-first-error
278	ifeq ($(DEVELOPER),ELMAR)
279	POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --only-first-error
280	endif
281
282	# Enable extra warnings
283	extended_warnings :=
284	extended_cpp_warnings :=
285
286	# C and C++
287	extended_warnings += -Wwrite-strings -Wunused -Wno-aggregate-return -Wshadow
288
289	# C++ only
290	extended_cpp_warnings += -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute
291	extended_cpp_warnings += -Wctor-dtor-privacy# < gcc 3
292	# extended_cpp_warnings += -Wfloat-equal# gcc 3.0
293
294	# ------- above only warnings available in 3.0
295
296	WEFFC_BROKEN:=0
297	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
298	ifneq ('$(USE_GCC_48_OR_HIGHER)','yes')
299	# -Weffc++ broken in 4.7.x series
300	# gcc 4.7.3 crashes on GenomeImport.cxx when -Weffc++ is active
301	# (bug reported https://gcc.gnu.org/bugzilla/show_bug.cgi?id=56923; apparently wont be fixed for 4.7-series)
302	# gcc 4.7.4 crashes on DBwriter.cxx when -Weffc++ is active
303	WEFFC_BROKEN:=1
304	endif
305	endif
306	ifeq ('$(WEFFC_BROKEN)','0')
307	extended_cpp_warnings += -Weffc++# gcc 3.0.1
308	endif
309	extended_cpp_warnings += -Wmissing-noreturn# gcc 3.0.2
310	# extended_cpp_warnings += -Wold-style-cast# gcc 3.0.4 (warn about 28405 old-style casts)
311	extended_cpp_warnings += -Winit-self# gcc 3.4.0
312	extended_cpp_warnings += -Wstrict-aliasing# gcc 3.4
313	extended_cpp_warnings += -Wextra# gcc 3.4.0
314	ifeq ($(DEBUG),1)
315	ifeq ($(USE_CLANG),0)
316	# turn off -Wmaybe-uninitialized in debug mode (gets activated with -Wextra). too many bogus warnings
317	extended_cpp_warnings += -Wno-maybe-uninitialized
318	endif
319	endif
320	ifeq ('$(USE_GCC_452_OR_HIGHER)','yes')
321	extended_cpp_warnings += -Wlogical-op# gcc 4.5.2
322	endif
323	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
324	# extended_cpp_warnings += -Wunused-local-typedefs# gcc 4.7 (fails for each STATIC_ASSERT, enable only for Cxx11)
325	# extended_cpp_warnings += -Wzero-as-null-pointer-constant# gcc 4.7 #@@@ activate
326	endif
327	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
328	extended_cpp_warnings += -Wunused-local-typedefs# available since gcc 4.7 (but fails for each STATIC_ASSERT, so enable only for Cxx11)
329	endif
330
331	#---------------------- turn off clang bogus warnings
332
333	ifeq ($(USE_CLANG),1)
334	# -Wmismatched-tags warns about struct/class mismatch in forward declarations (which is explicitely allowed)
335	# -Wchar-subscripts reports too many bogus warnings for "array['x']" (when 'x' is known to be in range [0..128])
336	# -Wunused-private-field report too many false positives (currently ~ 2 of 3)
337	# -Wstring-plus-int warns about common ARB coding practice
338	# -Wgnu-static-float-init warns about accepted GNU extension
339	extended_cpp_warnings += -Wno-mismatched-tags -Wno-char-subscripts -Wno-unused-private-field -Wno-string-plus-int -Wno-gnu-static-float-init
340	endif
341
342	#---------------------- developer
343
344	ifneq ($(DEVELOPER),ANY) # ANY=default setting (skip all developer specific code)
345	dflags += -DDEVEL_$(DEVELOPER)# activate developer/release specific code
346	endif
347
348	#---------------------- activate TODO warnings?
349
350	ifndef SHOWTODO
351	ifeq ($(DEVELOPER),RALF)
352	SHOWTODO:=1
353	else
354	SHOWTODO:=0
355	endif
356	endif
357	ifeq ($(SHOWTODO),1)
358	dflags += -DWARN_TODO# activate "TODO" warnings
359	endif
360
361	#---------------------- activate Sanitizers?
362
363	ASAN_OPTIONS:=handle_segv=0:color=0
364	ASAN_OPTIONS+=:detect_leaks=1 # comment-out to disable leak-detection
365	ASAN_OPTIONS+=:check_initialization_order=1
366	# ASAN_OPTIONS+=:abort_on_error=1
367
368	# suppressions: SOURCE_TOOLS/arb.leaksan.supp
369	LSAN_OPTIONS:=max_leaks=3:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp
370
371
372	ifndef SANITIZE
373	SANITIZE:=0
374	endif
375
376	SANITIZE_ADDRESS:=0
377	SANITIZE_UNDEFINED:=0
378
379	ifneq ($(SANITIZE),0)
380	ifeq ($(SANITIZE),all)
381	SANITIZE:=3
382	endif
383
384	ifeq ($(SANITIZE),1)
385	SANITIZE_ADDRESS:=1
386	else
387	ifeq ($(SANITIZE),2)
388	SANITIZE_UNDEFINED:=1
389	else
390	ifeq ($(SANITIZE),3)
391	SANITIZE_ADDRESS:=1
392	SANITIZE_UNDEFINED:=1
393	else
394	$(error Unknown value '$(SANITIZE)' specified for SANITIZE in config.makefile)
395	endif
396	endif
397	endif
398	endif
399
400	ifeq ($(SANITIZE_ADDRESS),1)
401	ifneq ('$(USE_GCC_48_OR_HIGHER)','yes')
402	$(info AddressSanitizer not usable with gcc $(COMPILER_VERSION) - disabled)
403	SANITIZE_ADDRESS:=0
404	else
405	ifneq ('$(USE_GCC_49_OR_HIGHER)','yes')
406	$(warning note that LeakSanitizer does not work with gcc $(COMPILER_VERSION))
407	endif
408	endif
409	endif
410
411	ifeq ($(SANITIZE_UNDEFINED),1)
412	ifneq ('$(USE_GCC_49_OR_HIGHER)','yes')
413	$(info UndefinedBehaviorSanitizer not usable with gcc $(COMPILER_VERSION) - disabled)
414	SANITIZE_UNDEFINED:=0
415	endif
416	endif
417
418	SANITIZE_ANY:=0
419	ifeq ($(SANITIZE_ADDRESS),1)
420	SANITIZE_ANY:=1
421	endif
422	ifeq ($(SANITIZE_UNDEFINED),1)
423	SANITIZE_ANY:=1
424	endif
425
426	ifeq ($(SANITIZE_ANY),1)
427	DISABLE_VECTORIZE_CHECK:=1
428	endif
429
430	#---------------------- 32 or 64 bit
431
432	ifndef BUILDHOST_64
433	BUILDHOST_64:=$(ARB_64)# assume build host is same as version (see config.makefile)
434	endif
435
436	cross_cflags:=
437	cross_lflags:=
438	cross_clflags:=
439
440	ifeq ($(ARB_64),1)
441	dflags += -DARB_64 #-fPIC
442	shared_cflags += -fPIC
443
444	ifeq ($(BUILDHOST_64),1)
445	# build 64-bit ARB version on 64-bit host
446	CROSS_LIB:=# empty = autodetect below
447	ifeq ($(DARWIN),1)
448	cross_cflags += -arch x86_64
449	cross_lflags += -arch x86_64
450	cross_clflags += -arch x86_64
451	endif
452	else
453	# build 64-bit ARB version on 32-bit host
454	CROSS_LIB:=/lib64
455	cross_cflags += -m64
456	cross_lflags += -m64 -m elf_x86_64
457	cross_clflags += -m64 -Wl,-m64,-m,elf_x86_64
458	endif
459	else
460	ifeq ($(BUILDHOST_64),1)
461	# build 32-bit ARB version on 64-bit host
462	CROSS_LIB:=# empty = autodetect below
463	cross_cflags += -m32
464	cross_lflags += -m32 -m elf_i386
465	cross_clflags += -m32 -Wl,-m32,-m,elf_i386
466	else
467	# build 32-bit ARB version on 32-bit host
468	CROSS_LIB:=/lib
469	endif
470	endif
471
472	cflags += $(cross_cflags)
473	clflags += $(cross_clflags)
474
475	ifeq ('$(CROSS_LIB)','')
476	# autodetect libdir
477	ifeq ($(ARB_64),1)
478	CROSS_LIB:=$(shell (test -d /lib64 && echo lib64) \|\| echo lib)
479	else
480	CROSS_LIB:=$(shell (test -d /lib32 && echo lib32) \|\| echo lib)
481	endif
482	endif
483
484	#---------------------- unit tests
485
486	ifndef UNIT_TESTS
487	UNIT_TESTS=0#default is "no tests"
488	endif
489	ifeq ($(UNIT_TESTS),1)
490	dflags += -DUNIT_TESTS
491	UNIT_TESTER_LIB=UNIT_TESTER/UNIT_TESTER.a
492	else
493	UNIT_TESTER_LIB=
494	endif
495
496	#---------------------- use gcov
497
498	ifndef COVERAGE
499	COVERAGE=0#default is "no"
500	endif
501	ifneq ($(COVERAGE),0)
502	GCOVFLAGS=-ftest-coverage -fprofile-arcs
503	cflags += $(GCOVFLAGS)
504	EXECLIBS=-lgcov
505	else
506	GCOVFLAGS=
507	EXECLIBS=
508	endif
509
510	#---------------------- other flags
511
512	dflags += -D$(MACH) # define machine
513
514	ifeq ($(DARWIN),1)
515	shared_cflags += -fno-common
516	else
517	dflags += $(shell getconf LFS_CFLAGS)
518	endif
519
520	cflags += -pipe
521	cflags += -fmessage-length=0# don't wrap compiler output
522	cflags += -fshow-column# show columns
523	cflags += -funit-at-a-time
524	cflags += -fPIC
525	cflags += -fno-common# link all global data into one namespace
526	cflags += -fstrict-aliasing# gcc 3.4
527	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
528	cflags += -fno-diagnostics-show-caret#gcc 4.8 (4.7.?)
529	endif
530	#cflags += -save-temps# uncomment to see preprocessor output
531
532	#---------------------- various sanitizers
533
534	COMMON_SANITIZE_FLAGS:=-ggdb3 -fno-omit-frame-pointer
535
536	# activate AddressSanitizer+LeakSanitizer?
537	ifeq ($(SANITIZE_ADDRESS),1)
538	cflags += $(COMMON_SANITIZE_FLAGS) -fsanitize=address
539	dflags += -DLEAKS_SANITIZED
540	EXECLIBS += -lasan
541	# EXECLIBS += -static-libasan
542	endif
543
544	# activate UndefinedBehaviorSanitizer?
545	ifeq ($(SANITIZE_UNDEFINED),1)
546	cflags += $(COMMON_SANITIZE_FLAGS) -fsanitize=undefined
547	# uncomment next line to abort on runtime errors (needs 'rebuild')
548	#cflags += -fno-sanitize-recover
549	# Note: alignment-sanitizer is deactivated for ARBDB and PROBE!
550	ifeq ('$(DEBUG)','1')
551	ifeq ($(USE_GCC_MAJOR),4)
552	ifeq ($(USE_GCC_MINOR),9)
553	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),01)','')
554	# workaround https://gcc.gnu.org/bugzilla/show_bug.cgi?id=63531 for 4.9.0 + 4.9.1
555	# (problem is fixed in 4.9.2 release)
556	extended_cpp_warnings:=$(subst -Weffc++,,$(extended_cpp_warnings))
557	endif
558	endif
559	endif
560	endif
561	EXECLIBS += -lubsan
562	endif
563
564	#---------------------- X11 location
565
566	ifeq ($(DARWIN),1)
567	XHOME:=$(PREFIX)
568	else
569	ifeq ($(DEBIAN),1)
570	XHOME:=$(PREFIX)
571	else
572	XHOME:=/usr/X11R6
573	endif
574	endif
575
576	XINCLUDES ?= -I$(XHOME)/include
577	XLIBS ?= -L$(XHOME)/$(CROSS_LIB)
578	ifeq ($(DARWIN),1)
579	XINCLUDES += -I$(OSX_FW)/GLUT.framework/Headers -I$(OSX_FW)/OpenGL.framework/Headers -I$(OSX_SDK)/usr/include/krb5
580
581	XLIBS += -lXm -lpng -lz -lXt -lX11 -lXext -lXp -lXmu -lXi
582	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGL.dylib:$(OSX_FW_OPENGL)/libGL.dylib
583	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGLU.dylib:$(OSX_FW_OPENGL)/libGLU.dylib
584	else
585	XLIBS += -lXm -lXpm -lXt -lXext -lX11
586	endif
587
588	dflags += -DARB_MOTIF
589
590	#---------------------- open GL
591
592	ifeq ($(OPENGL),1)
593	cflags += -DARB_OPENGL # activate OPENGL code
594	GL := gl # this is the name of the OPENGL base target
595	GL_LIB_SYS := -lGL -lGLU
596	GL_LIB_ARB := -L$(ARBHOME)/GL/glAW -lglAW
597
598	ifeq ($(DARWIN),1)
599	GL_LIB_SYS += -lpthread
600	endif
601
602	GL_PNGLIBS_ARB := -L$(ARBHOME)/GL/glpng -lglpng_arb
603	GL_PNGLIBS_SYS := -lpng
604
605	GLEWLIB := -lGLEW -lGLw
606	ifeq ($(DARWIN),1)
607	GLUTLIB := -glut
608	else
609	GLUTLIB := -lglut
610	endif
611
612	GL_LIBS_SYS := $(GL_LIB_SYS) $(GL_PNGLIBS_SYS) $(GLEWLIB) $(GLUTLIB)
613	GL_LIBS_ARB := $(GL_LIB_ARB) $(GL_PNGLIBS_ARB)
614
615	RNA3D_LIB := RNA3D/RNA3D.a
616
617	else
618
619	GL_LIBS_ARB:=# no opengl -> no libs
620	GL_LIBS_SYS:=# no opengl -> no libs
621	GL:=# don't build ARB openGL libs
622
623	RNA3D_LIB :=
624
625	endif
626
627	RNA3D_LIB_4_DEPENDS := RNA3D/RNA3D.a
628
629	GL_LIBS:=$(GL_LIBS_ARB) $(GL_LIBS_SYS)
630
631	#---------------------- tiff lib:
632
633	TIFFLIBS := -ltiff
634
635	#---------------------- XML lib:
636
637	XMLLIBS := -lxerces-c
638
639	#---------------------- glib:
640
641	ARB_NEEDED_GLIB=glib-2.0
642
643	ARB_GLIB_INCLUDE:=$(strip $(shell pkg-config --cflags $(ARB_NEEDED_GLIB)))
644	ARB_GLIB_LIBS:=$(strip $(shell pkg-config --libs $(ARB_NEEDED_GLIB)))
645
646	#---------------------- basic libs:
647
648	SYSLIBS:=
649
650	ifeq ($(DARWIN),1)
651	SYSLIBS += -lstdc++
652	else
653	SYSLIBS += -lm $(ARB_GLIB_LIBS)
654	endif
655
656	#---------------------- include symbols?
657
658	ifeq ($(TRACESYM),1)
659	ifeq ($(USE_CLANG),0)
660	cflags += -rdynamic
661	clflags += -rdynamic -Wl,--export-dynamic
662	endif
663	endif
664
665	#---------------------- system dependent commands
666
667	ifeq ($(DARWIN),1)
668	TIME:=gtime
669	else
670	TIME:=/usr/bin/time
671	endif
672
673	#---------------------- SSE vectorizer
674
675	BROKEN_VECTORIZATION:=0
676	ifeq ('$(COMPILER_VERSION)','6.1.0')
677	BROKEN_VECTORIZATION:=1
678	endif
679	ifeq ('$(COMPILER_VERSION)','6.2.0')
680	BROKEN_VECTORIZATION:=1
681	endif
682
683	ifeq ('$(BROKEN_VECTORIZATION)','1')
684	# see http://bugs.arb-home.de/ticket/700
685	cflags += -fno-tree-loop-vectorize
686	DISABLE_VECTORIZE_CHECK:=1
687	endif
688
689	ifeq ($(DEBUG),0)
690	ifeq ($(USE_GCC_49_OR_HIGHER),yes)
691	ifeq ($(DISABLE_VECTORIZE_CHECK),0)
692	# cflags += -fopt-info
693	cflags += -fopt-info-vec
694
695	# Shows reasons for unsuccessful vectorization:
696	# cflags += -fopt-info-vec-missed
697
698	POST_COMPILE += --check-loop-optimization
699	endif
700	else
701	ifeq ($(USE_GCC_48_OR_HIGHER),yes)
702	# no automatic vectorization-check for gcc<4.9.0
703	# -> uncomment the next 2 lines and grep the spam it will produce for 'vectorized.*loops'
704	# cflags += -fopt-info -fopt-info-vec-missed
705	# POST_COMPILE += --original
706	endif
707	endif
708	endif
709
710	#---------------------- stop early on broken flags/compiler combination
711
712	ifeq ($(DEBUG),0)
713	ifeq ($(SANITIZE_ANY),1)
714	ifeq ('$(COMPILER_VERSION)','4.9.1')
715	$(error compiling DEBUG=0 + SANITIZE!=0 crashes with gcc $(COMPILER_VERSION) (gcc 4.9.2 works))
716	endif
717	endif
718	endif
719
720	#---------------------- differences between linking executables and shared libs:
721
722	# executables:
723	ifeq ($(DARWIN),1)
724	blflags:=$(clflags)
725	else
726	blflags:=$(clflags) -Wl,--no-undefined
727	endif
728
729	# shared libraries
730	llflags:=$(clflags)
731
732	# dont use clflags below
733	clflags:=
734
735	# -------------------------------------------------------------------------
736	# Don't put any machine/version/etc conditionals below!
737	# (instead define variables above)
738	# -------------------------------------------------------------------------
739
740	cflags += -W -Wall $(dflags) $(extended_warnings)
741	cxxflags := $(extended_cpp_warnings)
742
743	# add CFLAGS + CPPFLAGS from environment for DEBIAN build
744	ifeq ($(DEBIAN),1)
745	cflags := $(CFLAGS) $(cflags)
746	cxxflags += $(CPPFLAGS)
747	endif
748
749	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
750	cxxflags += -std=gnu++11# see also TEMPLATES/cxxforward.h@USE_Cxx11
751	else
752	# only use for gcc versions between 4.3 and <4.7 (4.7++ adds -Wc++11-compat above)
753	HAVE_GNUPP0X=`SOURCE_TOOLS/requireVersion.pl 4.3 $(COMPILER_VERSION)`
754	ifeq ($(HAVE_GNUPP0X),1)
755	# ensure compatibility with upcoming C++ standard
756	cxxflags += -std=gnu++0x
757	endif
758	endif
759
760	LINK_STATIC_LIB := ar -csq# link static lib
761	LINK_EXECUTABLE := $(A_CXX) $(blflags) -o# link executable (c++)
762
763	ifeq ($(LINK_STATIC),1)
764	SHARED_LIB_SUFFIX = a# static lib suffix
765	LINK_SHARED_LIB := $(LINK_STATIC_LIB)
766	else
767	SHARED_LIB_SUFFIX = so# shared lib suffix
768	LINK_SHARED_LIB := $(A_CXX) $(llflags) -shared $(GCOVFLAGS) -o# link shared lib
769	endif
770
771	ifeq ($(DARWIN),1)
772	lflags4perl:=
773	else
774	lflags4perl:=$(cross_lflags) -shared
775	endif
776
777	# delete variables unused below
778	blflags:=
779	llflags:=
780
781	# other used tools
782	MAKEDEPEND_PLAIN = makedepend
783	MAKEDEPEND = $(FORCEMASK);$(MAKEDEPEND_PLAIN)
784
785	#SEP:=--------------------------------------------------------------------------------
786	SEP=[`date +%M:%S.%N`] ------------------------------------------------
787	# to analyse timings run
788	# make -j9 clean; make -j9 all \| grep '^\[' \| sort
789	# make -j9 "TIMED_TARGET=perl" clean_timed_target \| grep '^\[' \| sort
790
791	CORE_LIB=-lCORE
792	ARBDB_LIB=-lARBDB $(CORE_LIB)
793	LIBS = $(ARBDB_LIB) $(SYSLIBS)
794
795	GUI_LIBS_PREFIX:=
796	ifeq ($(DARWIN),1)
797	# this seem to be added at wrong place, since opengl is only needed to link EDIT4
798	GUI_LIBS_PREFIX:=-framework GLUT -framework OpenGL
799	endif
800
801	GUI_LIBS=$(GUI_LIBS_PREFIX) $(LIBS) -lAWT -lWINDOW
802	GUI_LIBS+=$(XLIBS)
803
804	LIBPATH = -L$(ARBHOME)/lib
805
806	DEST_LIB = lib
807	DEST_BIN = bin
808
809	CC_INCLUDES := -I. -I$(ARBHOME)/INCLUDE $(XINCLUDES) $(ARB_GLIB_INCLUDE)
810	CXX_INCLUDES := $(CC_INCLUDES)
811	MAKEDEPENDFLAGS := -- -DARB_OPENGL -DUNIT_TESTS -D__cplusplus -I. -Y$(ARBHOME)/INCLUDE
812
813	# -------------------------------
814	# old PTSERVER or PTPAN?
815
816	ifeq ($(PTPAN),1)
817	# PTPAN only libs
818	ARCHS_PT_SERVER = \
819	ptpan/PROBE.a
820	else
821	ifeq ($(PTPAN),2)
822	# special mode to compile both servers (developers only!)
823	ARCHS_PT_SERVER = \
824	ptpan/PROBE.a \
825	PROBE/PROBE.a
826	ARCHS_PT_SERVER_LINK = PROBE/PROBE.a# default to old ptserver
827	else
828	# PT-server only libs
829	ARCHS_PT_SERVER = \
830	PROBE/PROBE.a
831	endif
832	endif
833
834	ifndef ARCHS_PT_SERVER_LINK
835	ARCHS_PT_SERVER_LINK = $(ARCHS_PT_SERVER)
836	endif
837
838	# ---------------------------------------
839	# wrap main()
840
841	use_ARB_main=$(ARBHOME)/SOURCE_TOOLS/arb_main_cpp.o
842	use_ARB_main_C=$(ARBHOME)/SOURCE_TOOLS/arb_main_c.o
843
844	# -----------------------------------------
845	# export variables to submakefiles
846
847	include SOURCE_TOOLS/export2sub
848
849	# do not define (exported) variables below this point
850
851	# -------------------------
852	# Main arb targets:
853	# -------------------------
854
855	first_target:
856	$(MAKE) checks
857	@echo $(SEP)
858	@echo 'Main targets:'
859	@echo ''
860	@echo ' all - Compile ARB + TOOLs + and copy shared libs + link foreign software'
861	@echo ' (That is most likely the target you want)'
862	@echo ''
863	@echo ' clean - remove generated files ("SUBDIR/SUBDIR.clean" to clean only SUBDIR)'
864	@echo ' rebuild - clean + all'
865	@echo ' cleanlinked - remove all binaries'
866	@echo ' relink - cleanlinked + all (=relink all from objects)'
867	@echo ''
868	@echo 'Some often used sub targets (make all makes them all):'
869	@echo ''
870	@echo ' arb - Just compile ARB (but none of the integrated tools)'
871	@echo ' menus - create lib/gde/arb.menu from GDEHELP/ARB_GDEmenus.source'
872	@echo ' perl - Compile the PERL XSUBS into lib/ARB.so and create links in lib to perl'
873	@echo ' binlink - Create all links in the bin directory'
874	@echo ''
875	@echo 'Development targets:'
876	@echo ''
877	@echo ' depends - create or update dependencies ("SUBDIR/SUBDIR.depends" to update only SUBDIR)'
878	@echo ' proto - create or update prototypes ("SUBDIR/SUBDIR.proto" to update only SUBDIR)'
879	@echo ' tags - create tags for xemacs'
880	@echo ' show - show available shortcuts (AKA subtargets)'
881	@echo ' up - shortcut for depends+proto+tags'
882	ifeq ($(UNIT_TESTS),1)
883	@echo ' ut - only run tests'
884	endif
885	ifneq ($(SANITIZE),0)
886	@echo ' sanitize - all + run arb_ntree with sanitizer (test.arb + execute _logged)'
887	endif
888	@echo ' modified - rebuild files modified in svn checkout (does touch)'
889	@echo ' touch - touch files modified in svn checkout'
890	@echo ''
891	@echo 'Internal maintenance:'
892	@echo ''
893	@echo ' relinfo - show help on release targets'
894	@echo ' tarfile - make rebuild and create arb version tarfile ("tarfile_quick" to skip rebuild)'
895	@echo ' save - save all basic ARB sources into arbsrc_DATE ("savetest" to check filelist)'
896	@echo ' patch - save svn diff to patchfile'
897	@echo ' source_doc - create doxygen documentation'
898	@echo ' relocated - rebuild partly (use when you have relocated ARBHOME)'
899	@echo ' check_res - check resource usage'
900	@echo ' dep_graph - Build dependency graphs'
901	@echo ' clean_cov - Clean coverage results'
902	@echo ''
903	@echo ' post_commit_check - Checks whether'
904	@echo ' * main make targets work,'
905	@echo ' * dependencies and prototypes are up to date,'
906	@echo ' * SVN-controlled files remain unaffected by called targets and'
907	@echo ' * all generated files are ignored.'
908	@echo ' (has to be called in a clean SVN checkout)'
909	@echo $(SEP)
910	@echo ''
911
912	relinfo:
913	@echo ''
914	@echo $(SEP)
915	@echo 'Release targets:'
916	@echo ''
917	@echo ' inc_candi - increase RC candidate-number (only possible in "rc" branch, not needed for RC1)'
918	@echo ' inc_patch - increase release patchlevel (only possible in "stable" branch)'
919	@echo ' inc_minor - increase minor version number (only possible in "trunk")'
920	@echo ' inc_major - increase MAJOR version number (only possible in "trunk")'
921	@echo ''
922	@echo ' show_version - show version tag'
923	@echo ''
924	@echo $(SEP)
925	@echo ''
926
927	# auto-generate config.makefile:
928
929	CONFIG_MAKEFILE_FOUND=$(wildcard config.makefile)
930
931	config.makefile : config.makefile.template
932	@echo --------------------------------------------------------------------------------
933	ifeq ($(strip $(CONFIG_MAKEFILE_FOUND)),)
934	@cp $< $@
935	@echo '$(ARBHOME)/$@:1: has been generated.'
936	@echo 'Please edit $@ to configure your system!'
937	@echo --------------------------------------------------------------------------------
938	@false
939	else
940	@echo '$(ARBHOME)/$<:1: is more recent than'
941	@echo '$(ARBHOME)/$@:1:'
942	@ls -al config.makefile*
943	@echo --------------------------------------------------------------------------------
944	@echo "Updating $@ (if this fails, check manually)"
945	SOURCE_TOOLS/update_config_makefile.pl
946	@echo "Sucessfully updated $@"
947	@echo --------------------------------------------------------------------------------
948	@ls -al config.makefile*
949	@echo --------------------------------------------------------------------------------
950	@echo "Diff to your old config.makefile:"
951	@echo --------------------------------------------------------------------------------
952	-diff $@.bak $@
953	@echo --------------------------------------------------------------------------------
954	endif
955
956	# check if everything is configured correctly
957
958	check_DEVELOPER:
959	ifndef DEVELOPER
960	@echo 'config.makefile:1: DEVELOPER not defined'
961	@false
962	endif
963
964	check_DEBUG:
965	ifndef dflags
966	@echo 'config.makefile:1: DEBUG has to be defined. Valid values are 0 and 1'
967	@false
968	endif
969
970	check_ARB_64:
971	ifndef ARB_64
972	@echo 'config.makefile:1: ARB_64 has to be defined. Valid values are 0 and 1'
973	@false
974	endif
975
976	# ---------------------------------------- check gcc version
977
978	COMPILER_BROKEN:=0
979
980	# gcc 4.8.0 produces invalid code (see #617)
981	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.8.0')
982	COMPILER_BROKEN:=1
983	endif
984
985	check_same_GCC_VERSION:
986	$(ARBHOME)/SOURCE_TOOLS/check_same_compiler_version.pl $(COMPILER_NAME) $(COMPILER_VERSION_ALLOWED)
987
988	check_GCC_VERSION:
989	@echo 'Compiler version check:'
990	# see .@ALLOWED_gcc_VERSIONS
991	ifeq ('$(COMPILER_VERSION_ALLOWED)', '')
992	@echo " - Your compiler is '$(COMPILER_NAME)' version '$(COMPILER_VERSION)'"
993	@echo ' This version is not in the list of supported $(COMPILER_NAME)-versions:'
994	@$(foreach version,$(ALLOWED_COMPILER_VERSIONS),echo ' * $(version)';)
995	@echo ' - You may either ..'
996	@echo ' - add your version to ALLOWED_$(COMPILER_NAME)_VERSIONS in the Makefile and try it out or'
997	@echo ' - switch to one of the allowed versions (see arb_README_gcc.txt for installing'
998	@echo ' a different version of gcc)'
999	$(error Unsupported compiler '$(COMPILER_NAME)' version '$(COMPILER_VERSION)')
1000	else
1001	ifeq ($(COMPILER_BROKEN),1)
1002	$(error $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)' would build a broken ARB version. Compilation refused)
1003	else
1004	@echo " - Supported $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)' detected - fine!"
1005	@echo ''
1006	$(MAKE) check_same_GCC_VERSION
1007	endif
1008	endif
1009
1010	#---------------------- check ARBHOME
1011
1012	# use arb_INSTALL.txt to determine whether ARBHOME points to correct directory
1013	ARB_INSTALL_FOUND=$(wildcard $(ARBHOME)/arb_INSTALL.txt)
1014
1015	check_ARBHOME:
1016	ifeq ($(strip $(ARB_INSTALL_FOUND)),)
1017	@echo ------------------------------------------------------------
1018	@echo "ARBHOME is set to '$(ARBHOME)'"
1019	@echo "The environment variable ARBHOME has to point to the top arb source directory."
1020	@echo "If you use bash enter:"
1021	@echo " export ARBHOME='`pwd`'"
1022	@echo ------------------------------------------------------------
1023	@false
1024	endif
1025
1026	ARB_PATH_SET=$(findstring $(ARBHOME)/bin,$(PATH))
1027
1028	check_PATH: check_ARBHOME
1029	ifeq ($(strip $(ARB_PATH_SET)),)
1030	@echo ------------------------------------------------------------
1031	@echo "The environment variable PATH has to contain $(ARBHOME)/bin"
1032	@echo "If you use bash enter:"
1033	@echo ' export PATH=$$ARBHOME/bin:$$PATH'
1034	@echo ------------------------------------------------------------
1035	@false
1036	endif
1037
1038	check_TOOLS:
1039	@util/arb_check_build_env.pl \
1040	"$(A_CC)" \
1041	"$(A_CXX)" \
1042	"$(MAKEDEPEND_PLAIN)" \
1043	"$(LINK_SHARED_LIB)" \
1044	"$(LINK_SHARED_LIB)" \
1045
1046	check_ENVIRONMENT : check_PATH check_TOOLS
1047	@echo "-------------------- Environment [start]"
1048	@echo "ARBHOME='$(ARBHOME)'"
1049	@echo "PATH='$(PATH)'"
1050	@echo "LD_LIBRARY_PATH='$(LD_LIBRARY_PATH)'"
1051	@echo "-------------------- Environment [end]"
1052
1053	check_tabs: check_setup
1054	ifeq ($(DEBUG),1)
1055	@SOURCE_TOOLS/tabBrake.pl
1056	endif
1057
1058	force_tab_check:
1059	@touch -t 198001010000 SOURCE_TOOLS/stamp.tabBrake
1060	@$(MAKE) check_tabs
1061
1062
1063	# ---------------------
1064
1065	check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION
1066	@echo Your setup seems to be ok.
1067
1068	checks: check_setup check_tabs
1069	@rm -f SOURCE_TOOLS/postcompile.sav
1070
1071
1072	# end test section ------------------------------
1073
1074	# ---------------------------------------
1075	# List of standard top level directories
1076	#
1077	# sub-makefiles have to define the targets
1078	# - 'depends' and
1079	# - 'clean'
1080	#
1081	# when adding new libs here, also add a dependency vs 'links' or 'links_non_perl' in .@DD_links_non_perl
1082
1083	ARCHS = \
1084	$(ARCHS_PT_SERVER) \
1085	AISC/AISC.a \
1086	AISC_MKPTPS/AISC_MKPTPS.a \
1087	ARBDB/libARBDB.a \
1088	CORE/libCORE.a \
1089	ARB_GDE/ARB_GDE.a \
1090	AWT/libAWT.a \
1091	AWTC/AWTC.a \
1092	AWTI/AWTI.a \
1093	CONSENSUS_TREE/CONSENSUS_TREE.a \
1094	CONVERTALN/CONVERTALN.a \
1095	DBSERVER/DBSERVER.a \
1096	DIST/DIST.a \
1097	EDIT4/EDIT4.a \
1098	EISPACK/EISPACK.a \
1099	GDE/GDE.a \
1100	GENOM/GENOM.a \
1101	GENOM_IMPORT/GENOM_IMPORT.a \
1102	GL/GL.a \
1103	ISLAND_HOPPING/ISLAND_HOPPING.a \
1104	MERGE/MERGE.a \
1105	MULTI_PROBE/MULTI_PROBE.a \
1106	NALIGNER/NALIGNER.a \
1107	NAMES/NAMES.a \
1108	NAMES_COM/server.a \
1109	NTREE/NTREE.a \
1110	PARSIMONY/PARSIMONY.a \
1111	PERLTOOLS/PERLTOOLS.a \
1112	PHYLO/PHYLO.a \
1113	PRIMER_DESIGN/PRIMER_DESIGN.a \
1114	PROBE_COM/server.a \
1115	PROBE_DESIGN/PROBE_DESIGN.a \
1116	PROBE_SET/PROBE_SET.a \
1117	READSEQ/READSEQ.a \
1118	RNA3D/RNA3D.a \
1119	RNACMA/RNACMA.a \
1120	SECEDIT/SECEDIT.a \
1121	SEQ_QUALITY/SEQ_QUALITY.a \
1122	SERVERCNTRL/SERVERCNTRL.a \
1123	SL/SL.a \
1124	STAT/STAT.a \
1125	TOOLS/TOOLS.a \
1126	TREEGEN/TREEGEN.a \
1127	UNIT_TESTER/UNIT_TESTER.a \
1128	WETC/WETC.a \
1129	WINDOW/libWINDOW.a \
1130	XML/XML.a \
1131
1132	# -----------------------
1133	# library packets
1134
1135	ARCHS_CLIENT_PROBE = PROBE_COM/client.a
1136	ARCHS_CLIENT_NAMES = NAMES_COM/client.a
1137
1138	ARCHS_MAKEBIN = AISC_MKPTPS/AISC_MKPTPS.a AISC/AISC.a
1139
1140	# communication libs need aisc and aisc_mkpts:
1141
1142	AISC/AISC.dummy: proto_tools
1143
1144	comtools: AISC/AISC.dummy
1145
1146	ARCHS_SEQUENCE = \
1147	SL/SEQUENCE/SEQUENCE.a \
1148	SL/ALIVIEW/ALIVIEW.a \
1149	SL/PRONUC/PRONUC.a \
1150
1151	ARCHS_TREE = \
1152	SL/ARB_TREE/ARB_TREE.a \
1153	SL/FILTER/FILTER.a \
1154	$(ARCHS_SEQUENCE) \
1155
1156	# parsimony tree (used by NTREE, PARSIMONY, STAT(->EDIT4), DIST(obsolete!))
1157	ARCHS_AP_TREE = \
1158	SL/AP_TREE/AP_TREE.a \
1159	$(ARCHS_TREE) \
1160
1161	# --------------------------------------------------------------------------------
1162	# dependencies for linking shared libs
1163
1164	link_core: core
1165	link_db: db link_core
1166	link_aw: aw link_db
1167	link_awt: awt link_aw
1168
1169	#***************************************************************************************
1170	# Individual_Programs_Section
1171	#***************************************************************************************
1172
1173	arbmainwrapper:
1174	$(MAKE) -C SOURCE_TOOLS -r mainwrapper
1175
1176
1177	#********************************* arb_ntree ************************************
1178	NTREE = bin/arb_ntree
1179	ARCHS_NTREE = \
1180	NTREE/NTREE.a \
1181	$(ARCHS_AP_TREE) \
1182	ARB_GDE/ARB_GDE.a \
1183	SL/DB_UI/DB_UI.a \
1184	AWTC/AWTC.a \
1185	AWTI/AWTI.a \
1186	CONSENSUS_TREE/CONSENSUS_TREE.a \
1187	GENOM_IMPORT/GENOM_IMPORT.a \
1188	GENOM/GENOM.a \
1189	MERGE/MERGE.a \
1190	MULTI_PROBE/MULTI_PROBE.a \
1191	PRIMER_DESIGN/PRIMER_DESIGN.a \
1192	PROBE_DESIGN/PROBE_DESIGN.a \
1193	SEQ_QUALITY/SEQ_QUALITY.a \
1194	SERVERCNTRL/SERVERCNTRL.a \
1195	SL/ALILINK/ALILINK.a \
1196	SL/AW_NAME/AW_NAME.a \
1197	SL/CONSENSUS/CONSENSUS.a \
1198	SL/DB_SCANNER/DB_SCANNER.a \
1199	SL/DB_QUERY/DB_QUERY.a \
1200	SL/SEQIO/SEQIO.a \
1201	STAT/STAT.a \
1202	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1203	SL/HELIX/HELIX.a \
1204	SL/REGEXPR/REGEXPR.a \
1205	SL/REFENTRIES/REFENTRIES.a \
1206	SL/NDS/NDS.a \
1207	SL/ITEM_SHADER/ITEM_SHADER.a \
1208	SL/ITEMS/ITEMS.a \
1209	SL/INSDEL/INSDEL.a \
1210	SL/LOCATION/LOCATION.a \
1211	SL/MACROS/MACROS.a \
1212	SL/TRANSLATE/TRANSLATE.a \
1213	SL/TREEDISP/TREEDISP.a \
1214	SL/TREE_ADMIN/TREE_ADMIN.a \
1215	SL/TREE_READ/TREE_READ.a \
1216	SL/TREE_WRITE/TREE_WRITE.a \
1217	XML/XML.a \
1218
1219	$(NTREE): $(ARCHS_NTREE:.a=.dummy) link_awt
1220	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NTREE) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1221	echo "$(SEP) Link $@"; \
1222	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(XMLLIBS)" ; \
1223	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(XMLLIBS) && \
1224	echo "$(SEP) Link $@ [done]"; \
1225	)
1226
1227	#********************************* arb_edit4 ************************************
1228	EDIT4 = bin/arb_edit4
1229
1230	ARCHS_EDIT4 := \
1231	EDIT4/EDIT4.a \
1232	ARB_GDE/ARB_GDE.a \
1233	SL/FAST_ALIGNER/FAST_ALIGNER.a \
1234	AWTC/AWTC.a \
1235	ISLAND_HOPPING/ISLAND_HOPPING.a \
1236	SECEDIT/SECEDIT.a \
1237	SERVERCNTRL/SERVERCNTRL.a \
1238	SL/AW_HELIX/AW_HELIX.a \
1239	SL/AW_NAME/AW_NAME.a \
1240	SL/CONSENSUS/CONSENSUS.a \
1241	SL/ITEMS/ITEMS.a \
1242	STAT/STAT.a \
1243	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1244	SL/HELIX/HELIX.a \
1245	SL/TRANSLATE/TRANSLATE.a \
1246	SL/MACROS/MACROS.a \
1247	SL/NDS/NDS.a \
1248	$(ARCHS_AP_TREE) \
1249	XML/XML.a \
1250
1251	ifeq ($(OPENGL),1)
1252	ARCHS_EDIT4 += RNA3D/RNA3D.a
1253	endif
1254
1255	LIBS_EDIT4 := $(GL_LIBS)
1256
1257	$(EDIT4): $(ARCHS_EDIT4:.a=.dummy) link_awt
1258	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_EDIT4) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1259	echo "$(SEP) Link $@"; \
1260	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4)" ; \
1261	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4) && \
1262	echo "$(SEP) Link $@ [done]"; \
1263	)
1264
1265	#********************************* arb_rnacma ************************************
1266	RNACMA = bin/arb_rnacma
1267	ARCHS_RNACMA = \
1268	RNACMA/RNACMA.a \
1269
1270	$(RNACMA) : $(ARCHS_RNACMA:.a=.dummy) link_db
1271	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_RNACMA) \|\| ( \
1272	echo "$(SEP) Link $@"; \
1273	echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_RNACMA) $(LIBS) $(EXECLIBS)"; \
1274	$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_RNACMA) $(LIBS) $(EXECLIBS) && \
1275	echo "$(SEP) Link $@ [done]"; \
1276	)
1277
1278	#********************************* arb_wetc ************************************
1279	WETC = bin/arb_wetc
1280	ARCHS_WETC = \
1281	WETC/WETC.a \
1282	SL/HELIX/HELIX.a \
1283	SL/FILTER/FILTER.a \
1284	XML/XML.a \
1285
1286	$(WETC): $(ARCHS_WETC:.a=.dummy) link_awt
1287	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_WETC) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1288	echo "$(SEP) Link $@"; \
1289	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_WETC) $(GUI_LIBS)" ; \
1290	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_WETC) $(GUI_LIBS) && \
1291	echo "$(SEP) Link $@ [done]"; \
1292	)
1293
1294	#********************************* arb_dist ************************************
1295	DIST = bin/arb_dist
1296	ARCHS_DIST = \
1297	DIST/DIST.a \
1298	CONSENSUS_TREE/CONSENSUS_TREE.a \
1299	EISPACK/EISPACK.a \
1300	SERVERCNTRL/SERVERCNTRL.a \
1301	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1302	SL/HELIX/HELIX.a \
1303	SL/MATRIX/MATRIX.a \
1304	SL/MACROS/MACROS.a \
1305	SL/NDS/NDS.a \
1306	SL/ITEMS/ITEMS.a \
1307	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.a \
1308	XML/XML.a \
1309	$(ARCHS_AP_TREE) \
1310
1311	$(DIST): $(ARCHS_DIST:.a=.dummy) link_awt
1312	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_DIST) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1313	echo "$(SEP) Link $@"; \
1314	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS)" ; \
1315	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) && \
1316	echo "$(SEP) Link $@ [done]"; \
1317	)
1318
1319	#********************************* arb_pars ************************************
1320	PARSIMONY = bin/arb_pars
1321	ARCHS_PARSIMONY = \
1322	PARSIMONY/PARSIMONY.a \
1323	SERVERCNTRL/SERVERCNTRL.a \
1324	SL/AW_NAME/AW_NAME.a \
1325	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1326	SL/HELIX/HELIX.a \
1327	SL/MACROS/MACROS.a \
1328	SL/NDS/NDS.a \
1329	SL/ITEMS/ITEMS.a \
1330	SL/TRANSLATE/TRANSLATE.a \
1331	SL/TREEDISP/TREEDISP.a \
1332	XML/XML.a \
1333	$(ARCHS_AP_TREE) \
1334
1335	$(PARSIMONY): $(ARCHS_PARSIMONY:.a=.dummy) link_awt
1336	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PARSIMONY) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1337	echo "$(SEP) Link $@"; \
1338	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS)" ; \
1339	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) && \
1340	echo "$(SEP) Link $@ [done]"; \
1341	)
1342
1343	#********************************* arb_convert_aln ************************************
1344	CONVERT_ALN = bin/arb_convert_aln
1345	ARCHS_CONVERT_ALN = \
1346	CONVERTALN/CONVERTALN.a \
1347
1348	$(CONVERT_ALN) : $(ARCHS_CONVERT_ALN:.a=.dummy) link_db
1349	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_CONVERT_ALN) $(use_ARB_main) \|\| ( \
1350	echo "$(SEP) Link $@"; \
1351	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_CONVERT_ALN) $(LIBS)"; \
1352	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_CONVERT_ALN) $(LIBS) && \
1353	echo "$(SEP) Link $@ [done]"; \
1354	)
1355
1356	#********************************* arb_treegen ************************************
1357
1358	TREEGEN = bin/arb_treegen
1359	ARCHS_TREEGEN = \
1360	TREEGEN/TREEGEN.a \
1361
1362	$(TREEGEN) : $(ARCHS_TREEGEN:.a=.dummy)
1363	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_TREEGEN) $(use_ARB_main_C) \|\| ( \
1364	echo "$(SEP) Link $@"; \
1365	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(EXECLIBS) $(ARCHS_TREEGEN)" ; \
1366	$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(EXECLIBS) $(ARCHS_TREEGEN) && \
1367	echo "$(SEP) Link $@ [done]"; \
1368	)
1369
1370	#********************************* arb_naligner ************************************
1371	NALIGNER = bin/arb_naligner
1372	ARCHS_NALIGNER = \
1373	NALIGNER/NALIGNER.a \
1374	SERVERCNTRL/SERVERCNTRL.a \
1375	SL/HELIX/HELIX.a \
1376
1377	$(NALIGNER): $(ARCHS_NALIGNER:.a=.dummy) link_db
1378	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NALIGNER) $(use_ARB_main) \|\| ( \
1379	echo "$(SEP) Link $@"; \
1380	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(LIBS)" ; \
1381	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(LIBS) && \
1382	echo "$(SEP) Link $@ [done]"; \
1383	)
1384
1385	#********************************* arb_phylo ************************************
1386	PHYLO = bin/arb_phylo
1387	ARCHS_PHYLO = \
1388	PHYLO/PHYLO.a \
1389	SL/HELIX/HELIX.a \
1390	SL/FILTER/FILTER.a \
1391	SL/MACROS/MACROS.a \
1392	XML/XML.a \
1393
1394	$(PHYLO): $(ARCHS_PHYLO:.a=.dummy) link_awt
1395	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PHYLO) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1396	echo "$(SEP) Link $@"; \
1397	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_PHYLO) $(GUI_LIBS)" ; \
1398	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_PHYLO) $(GUI_LIBS) && \
1399	echo "$(SEP) Link $@ [done]"; \
1400	)
1401
1402	#***************************************************************************************
1403	# SERVER SECTION
1404	#***************************************************************************************
1405
1406	#********************************* arb_db_server ************************************
1407	DBSERVER = bin/arb_db_server
1408	ARCHS_DBSERVER = \
1409	DBSERVER/DBSERVER.a \
1410	SERVERCNTRL/SERVERCNTRL.a \
1411
1412	$(DBSERVER): $(ARCHS_DBSERVER:.a=.dummy) link_db
1413	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_DBSERVER) $(ARBDB_LIB) $(use_ARB_main) \|\| ( \
1414	echo "$(SEP) Link $@"; \
1415	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS)" ; \
1416	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS) && \
1417	echo "$(SEP) Link $@ [done]"; \
1418	)
1419
1420	#********************************* arb_pt_server ************************************
1421	PROBE = bin/arb_pt_server
1422	ARCHS_PROBE_COMMON = \
1423	SL/PTCLEAN/PTCLEAN.a \
1424	SERVERCNTRL/SERVERCNTRL.a \
1425	SL/HELIX/HELIX.a \
1426
1427	ARCHS_PROBE_LINK = \
1428	$(ARCHS_PT_SERVER_LINK) \
1429	$(ARCHS_PROBE_COMMON) \
1430
1431	ARCHS_PROBE_DEPEND = \
1432	$(ARCHS_PT_SERVER) \
1433	$(ARCHS_PROBE_COMMON) \
1434
1435	$(PROBE): $(ARCHS_PROBE_DEPEND:.a=.dummy) link_db
1436	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_SERVER_PROBE) config.makefile $(use_ARB_main) \|\| ( \
1437	echo "$(SEP) Link $@"; \
1438	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_PROBE_LINK) $(ARCHS_CLIENT_PROBE) $(ARBDB_LIB) $(SYSLIBS)" ; \
1439	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_PROBE_LINK) $(ARCHS_CLIENT_PROBE) $(ARBDB_LIB) $(SYSLIBS) && \
1440	echo "$(SEP) Link $@ [done]"; \
1441	)
1442
1443	#********************************* arb_name_server ************************************
1444	NAMES = bin/arb_name_server
1445	ARCHS_NAMES = \
1446	NAMES/NAMES.a \
1447	SERVERCNTRL/SERVERCNTRL.a \
1448
1449	$(NAMES): $(ARCHS_NAMES:.a=.dummy) link_db
1450	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) $(use_ARB_main) \|\| ( \
1451	echo "$(SEP) Link $@"; \
1452	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS)" ; \
1453	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS) && \
1454	echo "$(SEP) Link $@ [done]"; \
1455	)
1456
1457	#********************************* SHARED LIBRARIES SECTION ************************************
1458
1459	prepare_libdir: addlibs
1460
1461	addlibs:
1462	(perl $(ARBHOME)/SOURCE_TOOLS/provide_libs.pl \
1463	"arbhome=$(ARBHOME)" \
1464	"opengl=$(OPENGL)" \
1465	"link_static=$(LINK_STATIC)" \
1466	)
1467
1468	#***************************************************************************************
1469	# Recursive calls to sub-makefiles
1470	#***************************************************************************************
1471
1472	%.depends:
1473	@cp -p $(@D)/Makefile $(@D)/Makefile.old # save old Makefile
1474	@$(MAKE) -C $(@D) -r \
1475	"AUTODEPENDS=1" \
1476	"MAIN=nothing" \
1477	"cflags=noCflagsHere_use_MAKEDEPENDFLAGS" \
1478	"cxxflags=noCxxflagsHere_use_MAKEDEPENDFLAGS" \
1479	depends
1480	@grep "^# DO NOT DELETE" $(@D)/Makefile >/dev/null
1481	@cat $(@D)/Makefile \
1482	\| SOURCE_TOOLS/fix_depends.pl "(from main)" \
1483	>$(@D)/Makefile.2
1484	@mv $(@D)/Makefile.old $(@D)/Makefile # restore old Makefile
1485	@$(ARBHOME)/SOURCE_TOOLS/mv_if_diff $(@D)/Makefile.2 $(@D)/Makefile # update Makefile if changed
1486
1487	%.proto:
1488	@($(MAKE) -C $(@D) \
1489	"AUTODEPENDS=0" \
1490	"MAIN=nothing" \
1491	"cflags=noCflags" \
1492	"cxxflags=noCxxflags" \
1493	proto 2>&1 ) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
1494
1495	%.clean:
1496	@$(MAKE) -C $(@D) \
1497	"AUTODEPENDS=0" \
1498	"MAIN=nothing" \
1499	"cflags=noCflags" \
1500	"cxxflags=noCxxflags" \
1501	clean
1502
1503
1504	# stop wrong targets
1505	target_is_missing_lib_prefix:
1506	@echo "Error: Denied to build shared library target with missing 'lib'-prefix"
1507	false
1508
1509	ARBDB/ARBDB.dummy: target_is_missing_lib_prefix
1510	CORE/CORE.dummy: target_is_missing_lib_prefix
1511	AWT/AWT.dummy: target_is_missing_lib_prefix
1512	WINDOW/WINDOW.dummy: target_is_missing_lib_prefix
1513
1514	# rule to generate main target (normally a library):
1515	# @@@ check effect of setting LANG=C below
1516	%.dummy:
1517	@( export ID=$$$$; LANG=C; \
1518	(( \
1519	echo "$(SEP) Make $(@D)"; \
1520	$(MAKE) -C $(@D) -r \
1521	"AUTODEPENDS=1" \
1522	"MAIN=$(@F:.dummy=.a)" \
1523	"cflags=$(cflags) -DIN_ARB_$(subst /,_,$(@D))" \
1524	&& \
1525	echo "$(SEP) Make $(@D) [done]"; \
1526	) >$(@D).$$ID.log 2>&1 && (cat $(@D).$$ID.log;rm $(@D).$$ID.log)) \|\| (cat $(@D).$$ID.log;rm $(@D).$$ID.log;false))
1527
1528	# Additional dependencies for subtargets:
1529
1530	PROBE_COM/PROBE_COM.dummy : comtools
1531	NAMES_COM/NAMES_COM.dummy : comtools
1532
1533	com: PROBE_COM/PROBE_COM.dummy NAMES_COM/NAMES_COM.dummy
1534
1535	PROBE_COM/server.dummy:
1536	@echo Unwanted request to make target $<
1537	false
1538
1539	PROBE_COM/client.dummy:
1540	@echo Unwanted request to make target $<
1541	false
1542
1543	NAMES_COM/server.dummy:
1544	@echo Unwanted request to make target $<
1545	false
1546
1547	NAMES_COM/client.dummy:
1548	@echo Unwanted request to make target $<
1549	false
1550
1551
1552	ARBDB/libARBDB.dummy: links
1553	CORE/libCORE.dummy: links
1554
1555	PERLTOOLS/PERLTOOLS.dummy: core db
1556
1557	# all subdirs perl not depends on go here (ADD_links_non_perl)
1558	AWT/libAWT.dummy: links_non_perl
1559	AWTI/AWTI.dummy: links_non_perl
1560	CONSENSUS_TREE/CONSENSUS_TREE.dummy: links_non_perl
1561	CONVERTALN/CONVERTALN.dummy: links_non_perl
1562	DBSERVER/DBSERVER.dummy: links_non_perl
1563	DIST/DIST.dummy: links_non_perl
1564	EDIT4/EDIT4.dummy: links_non_perl com
1565	EISPACK/EISPACK.dummy: links_non_perl
1566	GDE/GDE.dummy: links_non_perl
1567	GENOM/GENOM.dummy: links_non_perl
1568	GENOM_IMPORT/GENOM_IMPORT.dummy: links_non_perl
1569	ISLAND_HOPPING/ISLAND_HOPPING.dummy: links_non_perl
1570	MERGE/MERGE.dummy: links_non_perl
1571	NTREE/NTREE.dummy: links_non_perl
1572	PARSIMONY/PARSIMONY.dummy: links_non_perl
1573	PHYLO/PHYLO.dummy: links_non_perl
1574	PRIMER_DESIGN/PRIMER_DESIGN.dummy: links_non_perl
1575	PROBE_SET/PROBE_SET.dummy: links_non_perl link_db
1576	READSEQ/READSEQ.dummy: links_non_perl
1577	RNACMA/RNACMA.dummy: links_non_perl header_libs
1578	SECEDIT/SECEDIT.dummy: links_non_perl
1579	SEQ_QUALITY/SEQ_QUALITY.dummy: links_non_perl
1580	SERVERCNTRL/SERVERCNTRL.dummy: links_non_perl com
1581	SL/ALILINK/ALILINK.dummy: links_non_perl
1582	SL/ALIVIEW/ALIVIEW.dummy: links_non_perl
1583	SL/AP_TREE/AP_TREE.dummy: links_non_perl
1584	SL/ARB_TREE/ARB_TREE.dummy: links_non_perl
1585	SL/AW_HELIX/AW_HELIX.dummy: links_non_perl
1586	SL/CONSENSUS/CONSENSUS.dummy: links_non_perl
1587	SL/DB_QUERY/DB_QUERY.dummy: links_non_perl
1588	SL/DB_SCANNER/DB_SCANNER.dummy: links_non_perl
1589	SL/DB_UI/DB_UI.dummy: links_non_perl
1590	SL/FAST_ALIGNER/FAST_ALIGNER.dummy: links_non_perl
1591	SL/FILTER/FILTER.dummy: links_non_perl
1592	SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy: links_non_perl
1593	SL/HELIX/HELIX.dummy: links_non_perl
1594	SL/INSDEL/INSDEL.dummy: links_non_perl
1595	SL/ITEMS/ITEMS.dummy: links_non_perl
1596	SL/ITEM_SHADER/ITEM_SHADER.dummy: links_non_perl
1597	SL/LOCATION/LOCATION.dummy: links_non_perl
1598	SL/MACROS/MACROS.dummy: links_non_perl
1599	SL/MATRIX/MATRIX.dummy: links_non_perl
1600	SL/NDS/NDS.dummy: links_non_perl
1601	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.dummy: links_non_perl
1602	SL/PRONUC/PRONUC.dummy: links_non_perl
1603	SL/PTCLEAN/PTCLEAN.dummy: links_non_perl link_db
1604	SL/REFENTRIES/REFENTRIES.dummy: links_non_perl
1605	SL/REGEXPR/REGEXPR.dummy: links_non_perl
1606	SL/SEQIO/SEQIO.dummy: links_non_perl
1607	SL/SEQUENCE/SEQUENCE.dummy: links_non_perl
1608	SL/TRANSLATE/TRANSLATE.dummy: links_non_perl
1609	SL/TREE_ADMIN/TREE_ADMIN.dummy: links_non_perl
1610	SL/TREE_READ/TREE_READ.dummy: links_non_perl
1611	SL/TREE_WRITE/TREE_WRITE.dummy: links_non_perl
1612	SL/TREEDISP/TREEDISP.dummy: links_non_perl
1613	STAT/STAT.dummy: links_non_perl
1614	TREEGEN/TREEGEN.dummy: links_non_perl
1615	WETC/WETC.dummy: links_non_perl
1616	WINDOW/libWINDOW.dummy: links_non_perl
1617	XML/XML.dummy: links_non_perl
1618
1619	ifeq ($(OPENGL),1)
1620	GL/glAW/glAW.dummy: links_non_perl
1621	GL/glpng/glpng.dummy: links_non_perl
1622	GL/GL.dummy: GL/glAW/glAW.dummy GL/glpng/glpng.dummy
1623	RNA3D/RNA3D.dummy: links_non_perl gl
1624	endif
1625
1626	UNIT_TESTER/UNIT_TESTER.dummy: link_db \
1627	SERVERCNTRL/SERVERCNTRL.dummy \
1628
1629	# see also TOOLS/Makefile@TOOLSLIBDEPENDS
1630	TOOLS/TOOLS.dummy : links_non_perl link_db \
1631	CONSENSUS_TREE/CONSENSUS_TREE.dummy \
1632	SERVERCNTRL/SERVERCNTRL.dummy \
1633	SL/FILTER/FILTER.dummy \
1634	SL/INSDEL/INSDEL.dummy \
1635	SL/REGEXPR/REGEXPR.dummy \
1636	SL/SEQIO/SEQIO.dummy \
1637	SL/TREE_READ/TREE_READ.dummy \
1638	SL/TREE_WRITE/TREE_WRITE.dummy \
1639	XML/XML.dummy \
1640
1641	AWTC/AWTC.dummy : com
1642
1643	NAMES/NAMES.dummy : com
1644	SL/AW_NAME/AW_NAME.dummy : com
1645
1646	PROBE/PROBE.dummy : com
1647	ptpan/PROBE.dummy : com
1648	MULTI_PROBE/MULTI_PROBE.dummy : com
1649	PROBE_DESIGN/PROBE_DESIGN.dummy : com
1650	NALIGNER/NALIGNER.dummy : com
1651
1652	ARB_GDE/ARB_GDE.dummy : proto_tools
1653
1654	compile_compatibility: SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.dummy
1655
1656	#***************************************************************************************
1657	# Short aliases to make targets
1658	#***************************************************************************************
1659
1660	show:
1661	@echo $(SEP)
1662	@echo 'Aliases for often needed targets:'
1663	@echo ''
1664	@echo ' executables:'
1665	@echo ''
1666	@echo ' nt arb_ntree'
1667	@echo ' e4 arb_edit4 (includes secedit)'
1668	@echo ' di arb_dist'
1669	@echo ' ph arb_phylo'
1670	@echo ' pa arb_parsimony'
1671	@echo ' tg arb_treegen'
1672	@echo ' ds arb_dbserver'
1673	@echo ' pt arb_pt_server'
1674	@echo ' na arb_name_server'
1675	@echo ''
1676	@echo ' libraries:'
1677	@echo ''
1678	@echo ' com communication libraries'
1679	@echo ' db ARB database'
1680	@echo ' aw GUI lib'
1681	@echo ' awt GUI toolkit'
1682	@echo ' awtc general purpose library'
1683	@echo ' awti import/export library'
1684	@echo ' mp multi probe library'
1685	@echo ' ge genome library'
1686	@echo ' pd probe design lib'
1687	@echo ' prd primer design lib'
1688	@echo ''
1689	@echo ' other targets:'
1690	@echo ''
1691	@echo ' help recompile help files'
1692	@echo ' tools make small tools used by arb'
1693	@echo ''
1694	@echo ' foreign targets:'
1695	@echo ''
1696	@echo ' gde GDE'
1697	@echo ' agde ARB_GDE'
1698	@echo ''
1699	@echo 'for other targets inspect $(ARBHOME)/Makefile'
1700	@echo ''
1701	@echo $(SEP)
1702
1703	source_doc:
1704	@echo "Remove some links (doxygen crashes otherwise):"
1705	find . \( -name "AISC" -o -name "C" -o -name "GDEHELP" \) -type l -exec rm {} \;
1706	doxygen 2>&1 1>/dev/null
1707	$(MAKE) forcelinks
1708
1709	dep_graph:
1710	@echo "Building some dependency graphs"
1711	SOURCE_TOOLS/dependency_graphs.pl
1712
1713	help: HELP_SOURCE/HELP_SOURCE.dummy
1714
1715	HELP_SOURCE/HELP_SOURCE.dummy: link_core xml menus
1716
1717	db: ARBDB/libARBDB.dummy
1718	core: CORE/libCORE.dummy
1719	aw: WINDOW/libWINDOW.dummy
1720	awt: AWT/libAWT.dummy
1721	awtc: AWTC/AWTC.dummy
1722	awti: AWTI/AWTI.dummy
1723
1724	mp: MULTI_PROBE/MULTI_PROBE.dummy
1725	mg: MERGE/MERGE.dummy
1726	ge: GENOM/GENOM.dummy
1727	prd: PRIMER_DESIGN/PRIMER_DESIGN.dummy
1728
1729	nt: menus $(NTREE)
1730
1731	nal: $(NALIGNER)
1732
1733	di: $(DIST)
1734	ph: $(PHYLO)
1735	pa: $(PARSIMONY)
1736	tg: $(TREEGEN)
1737
1738	ifeq ($(OPENGL),1)
1739	3d: RNA3D/RNA3D.dummy
1740	gl: GL/GL.dummy
1741	else
1742	noopengl:
1743	@echo "invalid target for OPENGL=0"
1744	3d: noopengl
1745	gl: noopengl
1746	endif
1747
1748	SL/SL.dummy: com
1749
1750	ds: $(DBSERVER)
1751	pt: $(PROBE)
1752	pst: PROBE_SET/PROBE_SET.dummy
1753	pd: PROBE_DESIGN/PROBE_DESIGN.dummy
1754	na: $(NAMES)
1755	sq: SEQ_QUALITY/SEQ_QUALITY.dummy
1756	cma: $(RNACMA)
1757
1758	sec: SECEDIT/SECEDIT.dummy
1759
1760	e4: $(EDIT4) readseq menus
1761
1762	gi: GENOM_IMPORT/GENOM_IMPORT.dummy
1763	wetc: $(WETC)
1764
1765	xml: XML/XML.dummy
1766	xmlin: XML_IMPORT/XML_IMPORT.dummy# broken
1767	stat: STAT/STAT.dummy $(NTREE) $(EDIT4)
1768	fa: SL/FAST_ALIGNER/FAST_ALIGNER.dummy
1769
1770	#********************************************************************************
1771
1772	up_by_remake: depends proto vectorize_checks
1773
1774	up: up_by_remake tags valgrind_update
1775
1776	#********************************************************************************
1777
1778	touch:
1779	SOURCE_TOOLS/touch_modified.pl
1780
1781	modified: touch
1782	$(MAKE) all
1783
1784	#********************************************************************************
1785
1786	libdepends:
1787	$(MAKE) -C "SOURCE_TOOLS" \
1788	"RNA3D_LIB=$(RNA3D_LIB_4_DEPENDS)" \
1789	libdepends
1790
1791	#********************************************************************************
1792
1793	# create generated headers:
1794	genheaders: TEMPLATES/TEMPLATES.dummy
1795
1796	clrdotdepends:
1797	rm PROBE_COM/.depends \|\| true
1798	rm NAMES_COM/.depends \|\| true
1799	rm PERL2ARB/.depends \|\| true
1800
1801	comdepends: comtools clrdotdepends
1802	@echo "$(SEP) Partially build com interface"
1803	$(MAKE) PROBE_COM/PROBE_COM.depends NAMES_COM/NAMES_COM.depends
1804	$(MAKE) PROBE_COM/server.depends NAMES_COM/server.depends
1805
1806	depends: genheaders comdepends vectorize_checks
1807	@echo "$(SEP) Updating other dependencies"
1808	$(MAKE) $(subst NAMES_COM/server.depends,,$(subst PROBE_COM/server.depends,,$(ARCHS:.a=.depends))) \
1809	HELP_SOURCE/HELP_SOURCE.depends \
1810	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.depends \
1811
1812	$(MAKE) libdepends
1813
1814	depend: depends
1815
1816	# ------------------------------------------------------------
1817	# dependency generation tests for AISC code
1818	#(all should work w/o creating wrong dependencies;
1819	# neither in XXX_COM/Makefile nor in code using AISC interface)
1820	dependstest1: silent_clean
1821	$(MAKE) depends
1822	dependstest2: silent_clean
1823	$(MAKE) com
1824	dependstest3: silent_clean
1825	$(MAKE) aw
1826	dependstest4: silent_clean
1827	$(MAKE) pt
1828	dependstest5: silent_clean
1829	$(MAKE) na
1830	dependstest6: silent_clean
1831	$(MAKE) nt
1832	dependstest7: silent_clean
1833	$(MAKE) all
1834	# ------------------------------------------------------------
1835
1836	vectorize_checks:
1837	$(MAKE) -C SOURCE_TOOLS -r vectorize_checks
1838
1839	# ------------------------------------------------------------
1840
1841	AISC_MKPTPS/AISC_MKPTPS.dummy: links
1842
1843	proto_tools: AISC_MKPTPS/AISC_MKPTPS.dummy
1844
1845	proto: proto_tools
1846	@echo $(SEP) Updating prototypes
1847	$(MAKE) \
1848	ARBDB/ARBDB.proto \
1849	AISC_COM/AISC_COM.proto \
1850	ARB_GDE/ARB_GDE.proto \
1851	CORE/CORE.proto \
1852	CONVERTALN/CONVERTALN.proto \
1853	NTREE/NTREE.proto \
1854	MERGE/MERGE.proto \
1855	$(ARCHS_PT_SERVER:.a=.proto) \
1856	SERVERCNTRL/SERVERCNTRL.proto \
1857	SL/SL.proto \
1858
1859	#********************************************************************************
1860
1861	valgrind_update: links
1862	@echo $(SEP) Updating for valgrind
1863	$(MAKE) -C SOURCE_TOOLS valgrind_update
1864
1865	#********************************************************************************
1866
1867	TAGFILE=TAGS
1868	TAGFILE_TMP=TAGS.tmp
1869
1870	TAG_SOURCE_HEADERS=TAGS.headers
1871	TAG_SOURCE_CODE=TAGS.codefiles
1872	TAG_SOURCE_LISTS=$(TAG_SOURCE_HEADERS) $(TAG_SOURCE_CODE)
1873
1874	ETAGS=ctags -e -f $(TAGFILE_TMP) --sort=no --if0=no --extra=q
1875	ETAGS_TYPES=--C-kinds=cgnsut --C++-kinds=cgnsut
1876	ETAGS_FUN =--C-kinds=fm --C++-kinds=fm
1877	ETAGS_REST =--C-kinds=dev --C++-kinds=dev
1878
1879	FILTER_TAGS_SOURCES= \
1880	$(SED) -e 's/^.\///g' \| \
1881	grep -P -v -i '^HEADERLIBS\|^GDE/\|/GEN[CH]/'
1882
1883	$(TAG_SOURCE_HEADERS): links
1884	find . \( -name '.hxx' -o -name ".h" \) -type f \| $(FILTER_TAGS_SOURCES) > $@
1885
1886	$(TAG_SOURCE_CODE): links
1887	find . \( -name '.cxx' -o -name ".c" \) -type f \| $(FILTER_TAGS_SOURCES) > $@
1888
1889	tags: $(TAG_SOURCE_LISTS)
1890	$(ETAGS) $(ETAGS_TYPES) -L $(TAG_SOURCE_HEADERS)
1891	$(ETAGS) -a $(ETAGS_FUN) -L $(TAG_SOURCE_HEADERS)
1892	$(ETAGS) -a $(ETAGS_REST) -L $(TAG_SOURCE_HEADERS)
1893	$(ETAGS) -a $(ETAGS_TYPES) -L $(TAG_SOURCE_CODE)
1894	$(ETAGS) -a $(ETAGS_FUN) -L $(TAG_SOURCE_CODE)
1895	$(ETAGS) -a $(ETAGS_REST) -L $(TAG_SOURCE_CODE)
1896	mv_if_diff $(TAGFILE_TMP) $(TAGFILE)
1897	rm $(TAG_SOURCE_LISTS)
1898
1899	#********************************************************************************
1900
1901	LINKSTAMP=SOURCE_TOOLS/stamp.generate_all_links
1902
1903	links: checks $(LINKSTAMP) arbmainwrapper
1904	links_no_checks: $(LINKSTAMP) arbmainwrapper
1905
1906	forcelinks:
1907	-rm $(LINKSTAMP)
1908	$(MAKE) links
1909
1910	$(LINKSTAMP): SOURCE_TOOLS/generate_all_links.sh genheaders
1911	+SOURCE_TOOLS/generate_all_links.sh
1912	touch $(LINKSTAMP)
1913
1914	clean_links:
1915	# avoid to delete linked pts, nas or arb_tcp.dat:
1916	find . -path './lib' -prune -o -type l -exec rm {} \;
1917	# removed obsolete file - refuses to disappear due to 'prune' above
1918	@rm -f lib/help/GDEHELP
1919	@rm -f $(LINKSTAMP) lib/inputMasks/format.readme
1920
1921	redo_links: clean_links
1922	$(MAKE) links_no_checks
1923
1924	#********************************************************************************
1925
1926	header_libs:
1927	$(MAKE) -C HEADERLIBS all
1928
1929	#********************************************************************************
1930
1931	gde: GDE/GDE.dummy
1932	GDE: gde
1933	agde: ARB_GDE/ARB_GDE.dummy
1934
1935	tools: TOOLS/TOOLS.dummy
1936
1937	convert: $(CONVERT_ALN)
1938	readseq: READSEQ/READSEQ.dummy
1939
1940	#***************************************************************************************
1941	# Some user commands
1942	#***************************************************************************************
1943
1944	menus: binlink links
1945	@(( \
1946	echo "$(SEP) Make GDEHELP"; \
1947	$(MAKE) -C GDEHELP -r all && \
1948	echo "$(SEP) Make GDEHELP [done]"; \
1949	) > GDEHELP.log 2>&1 && (cat GDEHELP.log;rm GDEHELP.log)) \|\| (cat GDEHELP.log;rm GDEHELP.log;false)
1950
1951	ifeq ($(DEBUG),1)
1952	BIN_TARGET=develall
1953	else
1954	BIN_TARGET=all
1955	endif
1956
1957
1958	binlink:
1959	$(MAKE) -C bin $(BIN_TARGET)
1960
1961	preplib:
1962	(cd lib;$(MAKE) all)
1963
1964	# --------------------------------------------------------------------------------
1965	# This section is quite tricky:
1966	#
1967	# make 'perl' is a BIG target, so when it has to be made, it has to be started
1968	# as early as possible to reduce overall compile time. Since 'make' does not
1969	# provide any priotities, i force it to build all 'perl'-prerequisites early, by
1970	# adding artificial dependencies to these prerequisites
1971	#
1972	# That behavior is likely to be system-dependent.
1973	# My goal was only to make it work on my current development system,
1974	# where this saves about 20% of overall build time.
1975
1976	ifeq ($(WITHPERL),1)
1977	links_non_perl: PERLTOOLS/PERLTOOLS.dummy
1978	perltools: links_non_perl
1979	perl: realperl
1980	else
1981	links_non_perl: links
1982	perl:
1983	$(MAKE) "WITHPERL=1" perl
1984	endif
1985
1986	# ---------------------------------------- perl
1987
1988	ifeq ($(ARB_64),$(BUILDHOST_64))
1989	TEST_PERL_SCRIPTS=$(MAKE) -C PERL_SCRIPTS/test test
1990	else
1991	TEST_PERL_SCRIPTS=echo "skipping perl script compilation (when cross-compiling)"
1992	endif
1993
1994	realperl: perltools
1995	(( \
1996	echo "$(SEP) Make PERL2ARB" ; \
1997	$(TIME) $(MAKE) -C PERL2ARB -r -f Makefile.main \
1998	"AUTODEPENDS=1" \
1999	"dflags=$(dflags)" \
2000	"cflags4perl=$(cflags) $(cxxflags) $(dflags)" \
2001	"lflags4perl=$(lflags4perl)" \
2002	"COMPILER_VERSION=$(COMPILER_VERSION)" \
2003	all && \
2004	$(TEST_PERL_SCRIPTS) && \
2005	echo "$(SEP) Make PERL2ARB [done]" ; \
2006	) > PERL2ARB.log 2>&1 && (cat PERL2ARB.log;rm PERL2ARB.log)) \|\| (cat PERL2ARB.log;rm PERL2ARB.log;false)
2007
2008	perl_clean:
2009	@$(MAKE) -C PERL2ARB -r -f Makefile.main \
2010	"AUTODEPENDS=0" \
2011	clean
2012
2013	PERL2ARB/PERL2ARB.clean:
2014	$(MAKE) perl_clean
2015	$(MAKE) -C PERL_SCRIPTS/test clean
2016
2017	# ---------------------------------------- bindings to script languages
2018
2019	bindings: lib/libCORE.so lib/libARBDB.so
2020	$(MAKE) -C BINDINGS all ARBDEPENDS="$(^:%=../%)" DFLAGS="$(dflags)"
2021
2022	bindings_clean:
2023	$(MAKE) -C BINDINGS clean
2024
2025	# ----------------------------------------
2026
2027	CLOC=cloc-1.08.pl
2028	CLOCFLAGS=--no3 --quiet --progress-rate=0
2029	CLOCARB=--exclude-dir=GDE .
2030	CLOCEXT=GDE
2031	CLOCCODE=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.code.def
2032	CLOCREST=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.rest.def
2033	CLOCFILT=tail --lines=+4
2034
2035	cloc:
2036	@echo 'Arb code:'
2037	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCARB) \| $(CLOCFILT)
2038	@echo 'Arb rest:'
2039	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCARB) \| $(CLOCFILT)
2040	@echo 'External code:'
2041	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCEXT) \| $(CLOCFILT)
2042	@echo 'External rest:'
2043	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCEXT) \| $(CLOCFILT)
2044
2045	# ---------------------------------------- check resources
2046
2047	check_res:
2048	$(ARBHOME)/SOURCE_TOOLS/check_resources.pl
2049
2050	# ---------------------------------------- cleaning
2051
2052	rmbak:
2053	@echo "Cleanup:"
2054	@find . \( -name '*%' \
2055	-o -name '*.bak' \
2056	-o -name '*~' \) \
2057	-o \( -name 'core' -a \! -type d \) \
2058	-exec rm -v {} \;
2059
2060	bin_reinit:
2061	$(MAKE) bin/bin.clean
2062	$(MAKE) -C "bin" all
2063
2064	clean_directories:
2065	-rm -rf \
2066	$(ARBHOME)/PROBE_SET/bin \
2067	$(ARBHOME)/INCLUDE \
2068
2069	libclean:
2070	-find $(ARBHOME) -type f \( -name '*.a' ! -type l \) -exec rm -f {} \;
2071
2072	objclean:
2073	-find $(ARBHOME) -type f \( -name '*.o' ! -type l \) -exec rm -f {} \;
2074
2075	# bin.clean and HELP_SOURCE.clean interfere
2076	clean3:
2077	$(MAKE) bin/bin.clean
2078	$(MAKE) HELP_SOURCE/HELP_SOURCE.clean
2079
2080	clean2: $(ARCHS:.a=.clean) \
2081	clean3 \
2082	rmbak \
2083	libclean \
2084	objclean \
2085	lib/lib.clean \
2086	GDEHELP/GDEHELP.clean \
2087	HEADERLIBS/HEADERLIBS.clean \
2088	SOURCE_TOOLS/SOURCE_TOOLS.clean \
2089	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.clean \
2090	UNIT_TESTER/UNIT_TESTER.clean \
2091	TEMPLATES/TEMPLATES.clean \
2092	perl_clean \
2093	clean_directories \
2094
2095	rm -f .last_gcc .last_compiler config.makefile.bak
2096
2097	# links are needed for cleanup
2098	clean: redo_links motif_xpm_hack_clean
2099	$(MAKE) clean2
2100	$(MAKE) clean_cov_all clean_links
2101
2102	silent_clean:
2103	$(MAKE) clean >/dev/null
2104
2105	# 'relocated' is about 50% faster than 'rebuild'
2106	reloc_clean: links
2107	@echo "---------------------------------------- Relocation cleanup"
2108	$(MAKE) \
2109	perl_clean \
2110	GDEHELP/GDEHELP.clean \
2111	HELP_SOURCE/genhelp/genhelp.clean \
2112	bin/bin.clean \
2113	libclean \
2114	objclean
2115
2116	relocated: links
2117	$(MAKE) reloc_clean
2118	@echo "---------------------------------------- and remake"
2119	$(MAKE) build
2120
2121	# -----------------------------------
2122	# some stress tests
2123	# (helpful to reveal race conditions with -j)
2124
2125	rebuild4ever: rebuild
2126	$(MAKE) rebuild4ever
2127
2128	build4ever: build
2129	$(MAKE) build4ever
2130
2131	clean4ever: clean
2132	$(MAKE) clean4ever
2133
2134	test4ever: ut
2135	$(MAKE) test4ever
2136
2137	perl4ever: clean
2138	$(MAKE) links
2139	$(MAKE) perl
2140	$(MAKE) perl4ever
2141
2142	help4ever: clean
2143	$(MAKE) help
2144	$(MAKE) help4ever
2145
2146	# -----------------------------------
2147
2148	rebuild: clean
2149	$(MAKE) all
2150
2151	cleanlinked: bin/bin.clean libclean
2152
2153	relink: cleanlinked
2154	$(MAKE) all
2155
2156	tarfile: rebuild
2157	$(MAKE) prepare_libdir
2158	util/arb_compress
2159
2160	tarfile_quick: build
2161	$(MAKE) prepare_libdir
2162	util/arb_compress
2163
2164	save: sourcetarfile
2165
2166	patch:
2167	SOURCE_TOOLS/arb_create_patch.sh arbPatch
2168
2169	# test early whether save will work
2170	savetest:
2171	@util/arb_srclst.pl >/dev/null
2172
2173	testsave: savetest
2174
2175	sourcetarfile: rmbak
2176	util/arb_save
2177
2178	save2: rmbak
2179	util/arb_save ignore
2180
2181	save_test: rmbak
2182	@echo "Testing source list.."
2183	@util/arb_srclst.pl > /dev/null
2184
2185	save_test_no_error:
2186	@-$(MAKE) save_test
2187
2188	inc_candi:
2189	touch SOURCE_TOOLS/inc_candi.stamp
2190	$(MAKE) do_version_update
2191
2192	inc_patch:
2193	touch SOURCE_TOOLS/inc_patch.stamp
2194	$(MAKE) do_version_update
2195
2196	inc_minor:
2197	touch SOURCE_TOOLS/inc_minor.stamp
2198	$(MAKE) do_version_update
2199
2200	inc_major:
2201	touch SOURCE_TOOLS/inc_major.stamp
2202	$(MAKE) do_version_update
2203
2204	do_version_update:
2205	@echo Incrementing version information
2206	$(MAKE) testsave
2207	$(MAKE) genheaders # auto upgrades version early
2208
2209	show_version:
2210	$(MAKE) genheaders # updates version info
2211	@echo "$(SEP) ARB version info"
2212	@grep ARB_VERSION TEMPLATES/arb_build.h
2213	@echo "$(SEP)"
2214
2215	release_quick:
2216	-rm arb.tgz arbsrc.tgz
2217	$(MAKE) tarfile_quick
2218	$(MAKE) sourcetarfile
2219
2220	# --------------------------------------------------------------------------------
2221
2222	MAKE_IF_COMMITTED=$(MAKE) -C SOURCE_TOOLS -f Makefile.commitbuild
2223
2224	build_CTARGET:
2225	+$(MAKE_IF_COMMITTED) "CTARGET=$(CTARGET)" build_CTARGET
2226
2227	reset_committed_build:
2228	+$(MAKE_IF_COMMITTED) reset
2229
2230	# --------------------------------------------------------------------------------
2231
2232	arbapplications: nt pa e4 wetc pt na nal di ph ds wetc cma
2233
2234	arb_external: convert tools gde readseq tg pst xmlin
2235
2236	arb_no_perl: arbapplications help arb_external
2237
2238	arb: motif_xpm_hack
2239	$(MAKE) "WITHPERL=1" perl arb_no_perl
2240
2241	motif_xpm_hack:
2242	$(MAKE) -r -C "lib/motifHack" all
2243
2244	motif_xpm_hack_clean:
2245	$(MAKE) -r -C "lib/motifHack" clean
2246
2247	# --------------------------------------------------------------------------------
2248	# special targets for SOURCE_TOOLS/remake_after_change.pl
2249
2250	rac_arb_dist: di
2251	rac_arb_edit4: e4
2252	rac_arb_ntree: nt
2253	rac_arb_pars: pa
2254	rac_arb_phylo: ph
2255	rac_arb_wetc: wetc
2256	rac_arb_naligner: nal
2257	rac_arb_pt_server: pt
2258	rac_arb_db_server: ds
2259	rac_arb_name_server: na
2260	rac_arb_convert_aln: convert
2261	rac_arb_treegen: tg
2262	rac_arb_rnacma: cma
2263	rac_arb_help2xml: help
2264
2265	rac_arb_a2ps: tools
2266	rac_arb_consensus_tree: tools
2267	rac_arb_dnarates: tools
2268	rac_arb_export_rates: tools
2269	rac_arb_export_tree: tools
2270	rac_arb_gene_probe: tools
2271	rac_arb_message: tools
2272	rac_arb_notify: tools
2273	rac_arb_primer: tools
2274	rac_arb_probe: tools
2275	rac_arb_read_tree: tools
2276
2277	# --------------------------------------------------------------------------------
2278	# unit testing
2279	# @@@ work in progress
2280	#
2281	# goal is to automatically test all libraries/executables using TESTED_UNITS_AUTO
2282	#
2283	# currently not all test executables link w/o error
2284	# (see UNITS_WORKING, UNITS_UNTESTABLE_ATM and UNITS_NEED_FIX)
2285
2286	# define RNA3D/RNA3D.test
2287	RNA3D_TEST := $(subst .a,.test,$(RNA3D_LIB))
2288
2289	TESTED_UNITS_AUTO = $(ARCHS:.a=.test)
2290
2291	UNITS_WORKING = \
2292	$(RNA3D_TEST) \
2293	AWTI/AWTI.test \
2294	EISPACK/EISPACK.test \
2295	GENOM/GENOM.test \
2296	GL/glAW/libglAW.test \
2297	GL/glpng/libglpng_arb.test \
2298	ISLAND_HOPPING/ISLAND_HOPPING.test \
2299	NALIGNER/NALIGNER.test \
2300	NAMES/NAMES.test \
2301	PHYLO/PHYLO.test \
2302	PRIMER_DESIGN/PRIMER_DESIGN.test \
2303	PROBE_DESIGN/PROBE_DESIGN.test \
2304	SECEDIT/SECEDIT.test \
2305	SEQ_QUALITY/SEQ_QUALITY.test \
2306	SERVERCNTRL/SERVERCNTRL.test \
2307	SL/ALIVIEW/ALIVIEW.test \
2308	SL/AP_TREE/AP_TREE.test \
2309	SL/ARB_TREE/ARB_TREE.test \
2310	SL/AW_HELIX/AW_HELIX.test \
2311	SL/AW_NAME/AW_NAME.test \
2312	SL/DB_SCANNER/DB_SCANNER.test \
2313	SL/GUI_ALIVIEW/GUI_ALIVIEW.test \
2314	SL/HELIX/HELIX.test \
2315	SL/LOCATION/LOCATION.test \
2316	SL/MATRIX/MATRIX.test \
2317	SL/REFENTRIES/REFENTRIES.test \
2318	SL/SEQUENCE/SEQUENCE.test \
2319	SL/TRANSLATE/TRANSLATE.test \
2320	SL/TREE_ADMIN/TREE_ADMIN.test \
2321	SL/TREE_WRITE/TREE_WRITE.test \
2322	STAT/STAT.test \
2323	TREEGEN/TREEGEN.test \
2324	WETC/WETC.test \
2325	XML/XML.test \
2326
2327	# untestable units
2328
2329	UNITS_NEED_FIX = \
2330	ptpan/PROBE.test \
2331
2332	UNITS_UNTESTABLE_ATM = \
2333	XML_IMPORT/XML_IMPORT.test \
2334
2335	# for the moment, put all units containing tests into UNITS_TESTED or UNITS_TESTED_FIRST
2336
2337	UNITS_TESTED_FIRST = \
2338	SL/ITEM_SHADER/ITEM_SHADER.test \
2339	PROBE_SET/fb_test.test \
2340	SL/ITEMS/ITEMS.test \
2341	SL/CONSENSUS/CONSENSUS.test \
2342	DIST/DIST.test \
2343	PARSIMONY/PARSIMONY.test \
2344	EDIT4/EDIT4.test \
2345	NTREE/NTREE.test \
2346	MULTI_PROBE/MULTI_PROBE.test \
2347
2348	# plain test-libaries not linked anywhere
2349	TEST_SANDBOXES = \
2350	SL/CB/CB.test \
2351
2352	UNITS_TESTED = \
2353	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.test \
2354	SL/NDS/NDS.test \
2355	ARB_GDE/ARB_GDE.test \
2356	GENOM_IMPORT/GENOM_IMPORT.test \
2357	SL/MACROS/MACROS.test \
2358	SL/REGEXPR/REGEXPR.test \
2359	SL/FILTER/FILTER.test \
2360	ARBDB/libARBDB.test \
2361	CONSENSUS_TREE/CONSENSUS_TREE.test \
2362	TOOLS/arb_consensus_tree.test \
2363	TOOLS/arb_test.test \
2364	TOOLS/arb_probe.test \
2365	PERLTOOLS/arb_proto_2_xsub.test \
2366	AWTC/AWTC.test \
2367	SL/ALILINK/ALILINK.test \
2368	SL/TREE_READ/TREE_READ.test \
2369	DBSERVER/DBSERVER.test \
2370	AWT/libAWT.test \
2371	CORE/libCORE.test \
2372	SL/INSDEL/INSDEL.test \
2373	SL/TREEDISP/TREEDISP.test \
2374	AISC_MKPTPS/mkptypes.test \
2375	MERGE/MERGE.test \
2376	SERVERCNTRL/SERVERCNTRL.test \
2377	SL/FAST_ALIGNER/FAST_ALIGNER.test \
2378	SL/PRONUC/PRONUC.test \
2379	WINDOW/libWINDOW.test \
2380	HELP_SOURCE/arb_help2xml.test \
2381	CONVERTALN/CONVERTALN.test \
2382	SL/SEQIO/SEQIO.test \
2383	SL/PTCLEAN/PTCLEAN.test \
2384	PROBE/PROBE.test \
2385	SL/DB_QUERY/DB_QUERY.test \
2386
2387	TESTED_UNITS_MANUAL = \
2388	$(TEST_SANDBOXES) \
2389	$(UNITS_TESTED_FIRST) \
2390	$(UNITS_TESTED) \
2391
2392	# $(UNITS_WORKING)
2393
2394	# see UNIT_TESTER/sym2testcode.pl@disableErrorOnUnitsWithoutTests
2395
2396	#TESTED_UNITS = $(TESTED_UNITS_AUTO)
2397	TESTED_UNITS = $(TESTED_UNITS_MANUAL)
2398
2399	# ----------------------------------------
2400
2401	TEST_LOG_DIR = UNIT_TESTER/logs
2402	TEST_RUN_SUITE=$(MAKE) $(NODIR) -C UNIT_TESTER -f Makefile.suite -r
2403	TEST_MAKE_FLAGS=
2404	TEST_POST_CLEAN=
2405	ifeq ($(COVERAGE),1)
2406	TEST_POST_CLEAN=$(MAKE) clean_cov
2407	TEST_MAKE_FLAGS+=-j1
2408	endif
2409
2410
2411	%.test:
2412	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
2413	( \
2414	echo "fake[1]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
2415	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
2416	"UNITDIR=$(@D)" \
2417	"UNITLIBNAME=$(@F:.test=)" \
2418	"COVERAGE=$(COVERAGE)" \
2419	"ARB_PID=$(ARB_PID)_$(@F)" \
2420	runtest; \
2421	echo "fake[1]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"; \
2422	$(TEST_POST_CLEAN) \
2423	) >$(TEST_LOG_DIR)/$(@F).log 2>&1; \
2424	UNIT_TESTER/log_result.pl $(TEST_LOG_DIR)/$(@F).log )
2425
2426
2427	test_base: $(UNIT_TESTER_LIB:.a=.dummy) $(subst .test,.dummy,$(TEST_SANDBOXES))
2428
2429	clean_cov:
2430	find . \( -name ".gcda" -o -name ".gcov" -o -name "*.cov" \) -exec rm {} \;
2431
2432	clean_cov_all: clean_cov
2433	find . \( -name "*.gcno" \) -exec rm {} \;
2434
2435	run_tests: test_base clean_cov
2436	$(MAKE) "ARB_PID=UT_$$$$" run_tests_faked_arbpid
2437
2438	cleanup_faked_arbpids:
2439	@rm ~/.arb_tmp/tmp/arb_pids_${USER}_${ARB_PID}_* \|\| true
2440
2441	cleanup_faked_arbpids_and_fail: cleanup_faked_arbpids
2442	@false
2443
2444	run_tests_faked_arbpid:
2445	+@$(TEST_RUN_SUITE) init
2446	@echo "fake[2]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2447	$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(TESTED_UNITS) \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2448	@echo "fake[2]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2449	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2450	@$(MAKE) clean_cov >/dev/null
2451	@$(MAKE) cleanup_faked_arbpids
2452
2453	ut:
2454	ifeq ($(UNIT_TESTS),1)
2455	@echo $(MAKE) run_tests
2456	@$(MAKE) run_tests
2457	else
2458	@echo "Not compiled with unit tests"
2459	endif
2460
2461
2462	aut:
2463	+@$(TEST_RUN_SUITE) unskip
2464	$(MAKE) ut
2465
2466	# --------------------------------------------------------------------------------
2467
2468	TIMELOG=$(ARBHOME)/arb_time.log
2469	TIMEARGS=--append --output=$(TIMELOG) --format=" %E(%S+%U) %P [%C]"
2470	TIMECMD=$(TIME) $(TIMEARGS)
2471
2472	time_one:
2473	ifeq ($(ONE_TIMED_TARGET),)
2474	@echo "Error: You have to pass ONE_TIMED_TARGET to $@"
2475	false
2476	else
2477	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET)"
2478	@$(TIMECMD) $(MAKE) $(ONE_TIMED_TARGET)
2479	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET) [done]"
2480	endif
2481
2482	timed_target:
2483	ifeq ($(TIMED_TARGET),)
2484	@echo "Error: You have to pass TIMED_TARGET to $@"
2485	false
2486	else
2487	@echo "Build time:" > $(TIMELOG)
2488	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2489	@cat $(TIMELOG)
2490	@rm $(TIMELOG)
2491	endif
2492
2493	timed_target_tested:
2494	ifeq ($(TIMED_TARGET),)
2495	@echo "Error: You have to pass TIMED_TARGET to $@"
2496	false
2497	else
2498	@echo "Build time:" > $(TIMELOG)
2499	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2500	$(MAKE) "ONE_TIMED_TARGET=ut" time_one
2501	@cat $(TIMELOG)
2502	@rm $(TIMELOG)
2503	endif
2504
2505	clean_timed_target:
2506	ifeq ($(TIMED_TARGET),)
2507	@echo "Error: You have to pass TIMED_TARGET to $@"
2508	false
2509	else
2510	@echo "Build time:" > $(TIMELOG)
2511	$(MAKE) "ONE_TIMED_TARGET=clean" time_one
2512	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2513	@cat $(TIMELOG)
2514	@rm $(TIMELOG)
2515	endif
2516
2517	# --------------------------------------------------------------------------------
2518
2519	CHECKOUT_MODIFIED=0# set to 1 to temporarily skip test for modifications (do not check in if set to 1)
2520
2521	check_svn_does_not_contain_generated:
2522	ifeq ($(CHECKOUT_MODIFIED),0)
2523	@echo "Testing that build does not modify files in SVN"
2524	@test 0 = `svn status \| wc -l` \|\| ( \
2525	echo "The checkout is not/no longer clean:"; \
2526	svn status; \
2527	echo "- if this fails instantly, your checkout is not clean"; \
2528	echo "- if this fails after other targets, these targets modify checked in data"; \
2529	echo " (a common cause may be that depends are not up to date)"; \
2530	false)
2531	else
2532	grep -Hn 'CHECKOUT_MODIFIED' Makefile
2533	endif
2534
2535	check_svn_ignores_generated:
2536	@test 0 = `svn status \| grep '^\?' \| wc -l` \|\| ( \
2537	echo "There are svn-unignored files:"; \
2538	svn status \| grep '^\?'; \
2539	echo "(all generated files should be svn-ignored)"; \
2540	false)
2541
2542	check_svn_state: check_svn_does_not_contain_generated
2543	$(MAKE) check_svn_ignores_generated
2544	$(MAKE) savetest
2545
2546	things_that_always_should_work: depends proto
2547
2548	post_commit_check:
2549	@echo "---------------------------------------- [Initial]"
2550	$(MAKE) check_svn_state
2551
2552	$(MAKE) clean
2553	@echo "---------------------------------------- [After 'make clean']"
2554	$(MAKE) check_svn_state
2555
2556	$(MAKE) things_that_always_should_work
2557	@echo "---------------------------------------- [After 'make things_that_always_should_work']"
2558	$(MAKE) check_svn_state
2559
2560	$(MAKE) all
2561	@echo "---------------------------------------- [After 'make all']"
2562	$(MAKE) check_svn_state
2563
2564	$(MAKE) things_that_always_should_work
2565	@echo "---------------------------------------- [Final]"
2566	$(MAKE) check_svn_state
2567
2568	# --------------------------------------------------------------------------------
2569	# sanitize arb_ntree; also works for clients (arb_edit4, ...) started from there.
2570
2571	sanitize: all
2572	( \
2573	export "LSAN_OPTIONS=max_leaks=30:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp"; \
2574	echo "sake[1]: Entering directory \`$(ARBHOME)'"; \
2575	$(ARBHOME)/bin/arb_ntree --execute _logged ~/data/test.arb 2>&1 ; \
2576	echo "sake[1]: Leaving directory \`$(ARBHOME)'" \
2577	) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
2578
2579	# --------------------------------------------------------------------------------
2580
2581	build: arb
2582	$(MAKE) binlink preplib compile_compatibility
2583
2584	all:
2585	@echo "Build time" > $(TIMELOG)
2586	@echo "$(SEP) $(MAKE) build"
2587	@$(TIMECMD) $(MAKE) build
2588	@echo $(SEP)
2589	@echo "made 'all' with success."
2590	@echo "to start arb enter 'arb'"
2591	ifeq ($(UNIT_TESTS),1)
2592	@echo $(MAKE) run_tests
2593	@$(TIMECMD) $(MAKE) run_tests
2594	endif
2595	@echo "$(SEP) $(MAKE) build [done]"
2596	ifeq ($(DEBUG),1)
2597	@$(MAKE) save_test_no_error >/dev/null # just show hints
2598	endif
2599	@cat $(TIMELOG)
2600	@rm $(TIMELOG)
2601

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