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Last change on this file was 15458, checked in by westram, 7 years ago
adds gcc 6.3.0
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 74.0 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:=$(ARBHOME)/SH/arb_readlink
101
102	# ---------------------- compiler version detection
103
104	# supported gcc versions:
105	ALLOWED_gcc_VERSIONS=\
106	4.3.1 4.3.2 4.3.3 4.3.4 \
107	4.4.1 4.4.3 4.4.5 4.4.6 4.4.7 \
108	4.5.2 \
109	4.6.1 4.6.2 4.6.3 4.6.4 \
110	4.7.1 4.7.2 4.7.3 4.7.4 \
111	4.8.0 4.8.1 4.8.2 4.8.3 4.8.4 4.8.5 \
112	4.9.0 4.9.1 4.9.2 4.9.3 4.9.4 \
113	5.1.0 5.2.0 5.3.0 5.3.1 5.4.0 \
114	6.1.0 6.2.0 6.3.0 \
115
116
117	# ----------------------
118
119	COMPILER_INFO:=$(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	# There are some disabled tests in CORE/arb_misc.cxx@sanitizers
534	# which trigger sanitizer reports.
535
536	ifeq ($(SANITIZE_ANY),1)
537	cflags += -ggdb3 -fno-omit-frame-pointer
538	endif
539
540	# activate AddressSanitizer+LeakSanitizer?
541	ifeq ($(SANITIZE_ADDRESS),1)
542	cflags += -fsanitize=address
543	clflags += -fsanitize=address
544	dflags += -DLEAKS_SANITIZED
545	endif
546
547	# activate UndefinedBehaviorSanitizer?
548	ifeq ($(SANITIZE_UNDEFINED),1)
549	cflags += -fsanitize=undefined
550	clflags += -fsanitize=undefined
551	dflags += -DUNDEF_SANITIZED
552	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
553	# abort on runtime errors
554	cflags += -fno-sanitize-recover=all
555	endif
556	#
557	# Note: alignment-sanitizer is deactivated for ARBDB and PROBE!
558	ifeq ('$(DEBUG)','1')
559	ifeq ($(USE_GCC_MAJOR),4)
560	ifeq ($(USE_GCC_MINOR),9)
561	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),01)','')
562	# workaround https://gcc.gnu.org/bugzilla/show_bug.cgi?id=63531 for 4.9.0 + 4.9.1
563	# (problem is fixed in 4.9.2 release)
564	extended_cpp_warnings:=$(subst -Weffc++,,$(extended_cpp_warnings))
565	endif
566	endif
567	endif
568	endif
569	endif
570
571	#---------------------- X11 location
572
573	ifeq ($(DARWIN),1)
574	XHOME:=$(PREFIX)
575	else
576	ifeq ($(DEBIAN),1)
577	XHOME:=$(PREFIX)
578	else
579	XHOME:=/usr/X11R6
580	endif
581	endif
582
583	XINCLUDES ?= -I$(XHOME)/include
584	XLIBS ?= -L$(XHOME)/$(CROSS_LIB)
585	ifeq ($(DARWIN),1)
586	XINCLUDES += -I$(OSX_FW)/GLUT.framework/Headers -I$(OSX_FW)/OpenGL.framework/Headers -I$(OSX_SDK)/usr/include/krb5
587
588	XLIBS += -lXm -lpng -lz -lXt -lX11 -lXext -lXp -lXmu -lXi
589	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGL.dylib:$(OSX_FW_OPENGL)/libGL.dylib
590	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGLU.dylib:$(OSX_FW_OPENGL)/libGLU.dylib
591	else
592	XLIBS += -lXm -lXpm -lXt -lXext -lX11
593	endif
594
595	dflags += -DARB_MOTIF
596
597	#---------------------- open GL
598
599	ifeq ($(OPENGL),1)
600	cflags += -DARB_OPENGL # activate OPENGL code
601	GL := gl # this is the name of the OPENGL base target
602	GL_LIB_SYS := -lGL -lGLU
603	GL_LIB_ARB := -L$(ARBHOME)/GL/glAW -lglAW
604
605	ifeq ($(DARWIN),1)
606	GL_LIB_SYS += -lpthread
607	endif
608
609	GL_PNGLIBS_ARB := -L$(ARBHOME)/GL/glpng -lglpng_arb
610	GL_PNGLIBS_SYS := -lpng
611
612	GLEWLIB := -lGLEW -lGLw
613	ifeq ($(DARWIN),1)
614	GLUTLIB := -glut
615	else
616	GLUTLIB := -lglut
617	endif
618
619	GL_LIBS_SYS := $(GL_LIB_SYS) $(GL_PNGLIBS_SYS) $(GLEWLIB) $(GLUTLIB)
620	GL_LIBS_ARB := $(GL_LIB_ARB) $(GL_PNGLIBS_ARB)
621
622	RNA3D_LIB := RNA3D/RNA3D.a
623
624	else
625
626	GL_LIBS_ARB:=# no opengl -> no libs
627	GL_LIBS_SYS:=# no opengl -> no libs
628	GL:=# don't build ARB openGL libs
629
630	RNA3D_LIB :=
631
632	endif
633
634	RNA3D_LIB_4_DEPENDS := RNA3D/RNA3D.a
635
636	GL_LIBS:=$(GL_LIBS_ARB) $(GL_LIBS_SYS)
637
638	#---------------------- tiff lib:
639
640	TIFFLIBS := -ltiff
641
642	#---------------------- XML lib:
643
644	XMLLIBS := -lxerces-c
645
646	#---------------------- glib:
647
648	ARB_NEEDED_GLIB=glib-2.0
649
650	ARB_GLIB_INCLUDE:=$(strip $(shell pkg-config --cflags $(ARB_NEEDED_GLIB)))
651	ARB_GLIB_LIBS:=$(strip $(shell pkg-config --libs $(ARB_NEEDED_GLIB)))
652
653	#---------------------- basic libs:
654
655	SYSLIBS:=
656
657	ifeq ($(DARWIN),1)
658	SYSLIBS += -lstdc++
659	else
660	SYSLIBS += -lm $(ARB_GLIB_LIBS)
661	endif
662
663	#---------------------- include symbols?
664
665	ifeq ($(TRACESYM),1)
666	ifeq ($(USE_CLANG),0)
667	cflags += -rdynamic
668	clflags += -rdynamic -Wl,--export-dynamic
669	endif
670	endif
671
672	#---------------------- system dependent commands
673
674	ifeq ($(DARWIN),1)
675	TIME:=gtime
676	else
677	TIME:=/usr/bin/time
678	endif
679
680	#---------------------- SSE vectorizer
681
682	BROKEN_VECTORIZATION:=0
683	ifeq ('$(COMPILER_VERSION)','6.1.0')
684	BROKEN_VECTORIZATION:=1
685	endif
686	ifeq ('$(COMPILER_VERSION)','6.2.0')
687	BROKEN_VECTORIZATION:=1
688	endif
689
690	ifeq ('$(BROKEN_VECTORIZATION)','1')
691	# see http://bugs.arb-home.de/ticket/700
692	cflags += -fno-tree-loop-vectorize
693	DISABLE_VECTORIZE_CHECK:=1
694	endif
695
696	ifeq ($(DEBUG),0)
697	ifeq ($(USE_GCC_49_OR_HIGHER),yes)
698	ifeq ($(DISABLE_VECTORIZE_CHECK),0)
699	# cflags += -fopt-info
700	cflags += -fopt-info-vec
701
702	# Shows reasons for unsuccessful vectorization:
703	# cflags += -fopt-info-vec-missed
704
705	POST_COMPILE += --check-loop-optimization
706	endif
707	else
708	ifeq ($(USE_GCC_48_OR_HIGHER),yes)
709	# no automatic vectorization-check for gcc<4.9.0
710	# -> uncomment the next 2 lines and grep the spam it will produce for 'vectorized.*loops'
711	# cflags += -fopt-info -fopt-info-vec-missed
712	# POST_COMPILE += --original
713	endif
714	endif
715	endif
716
717	#---------------------- stop early on broken flags/compiler combination
718
719	ifeq ($(DEBUG),0)
720	ifeq ($(SANITIZE_ANY),1)
721	ifeq ('$(COMPILER_VERSION)','4.9.1')
722	$(error compiling DEBUG=0 + SANITIZE!=0 crashes with gcc $(COMPILER_VERSION) (gcc 4.9.2 works))
723	endif
724	endif
725	endif
726
727	#---------------------- differences between linking executables and shared libs:
728
729	# executables:
730	ifeq ($(DARWIN),1)
731	blflags:=$(clflags)
732	else
733	blflags:=$(clflags) -Wl,--no-undefined
734	endif
735
736	# shared libraries
737	llflags:=$(clflags)
738
739	# dont use clflags below
740	clflags:=
741
742	# -------------------------------------------------------------------------
743	# Don't put any machine/version/etc conditionals below!
744	# (instead define variables above)
745	# -------------------------------------------------------------------------
746
747	cflags += -W -Wall $(dflags) $(extended_warnings)
748	cxxflags := $(extended_cpp_warnings)
749
750	# add CFLAGS + CPPFLAGS from environment for DEBIAN build
751	ifeq ($(DEBIAN),1)
752	cflags := $(CFLAGS) $(cflags)
753	cxxflags += $(CPPFLAGS)
754	endif
755
756	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
757	cxxflags += -std=gnu++11# see also TEMPLATES/cxxforward.h@USE_Cxx11
758	else
759	# only use for gcc versions between 4.3 and <4.7 (4.7++ adds -Wc++11-compat above)
760	HAVE_GNUPP0X=`SOURCE_TOOLS/requireVersion.pl 4.3 $(COMPILER_VERSION)`
761	ifeq ($(HAVE_GNUPP0X),1)
762	# ensure compatibility with upcoming C++ standard
763	cxxflags += -std=gnu++0x
764	endif
765	endif
766
767	LINK_STATIC_LIB := ar -csq# link static lib
768	LINK_EXECUTABLE := $(A_CXX) $(blflags) -o# link executable (c++)
769
770	ifeq ($(LINK_STATIC),1)
771	SHARED_LIB_SUFFIX = a# static lib suffix
772	LINK_SHARED_LIB := $(LINK_STATIC_LIB)
773	else
774	SHARED_LIB_SUFFIX = so# shared lib suffix
775	LINK_SHARED_LIB := $(A_CXX) $(llflags) -shared $(GCOVFLAGS) -o# link shared lib
776	endif
777
778	ifeq ($(DARWIN),1)
779	lflags4perl:=
780	else
781	lflags4perl:=$(cross_lflags) -shared
782	endif
783
784	# delete variables unused below
785	blflags:=
786	llflags:=
787
788	# other used tools
789	MAKEDEPEND_PLAIN = makedepend
790	MAKEDEPEND = $(FORCEMASK);$(MAKEDEPEND_PLAIN)
791
792	#SEP:=--------------------------------------------------------------------------------
793	SEP=[`date +%M:%S.%N`] ------------------------------------------------
794	# to analyse timings run
795	# make -j9 clean; make -j9 all \| grep '^\[' \| sort
796	# make -j9 "TIMED_TARGET=perl" clean_timed_target \| grep '^\[' \| sort
797
798	CORE_LIB=-lCORE
799	ARBDB_LIB=-lARBDB $(CORE_LIB)
800	LIBS = $(ARBDB_LIB) $(SYSLIBS)
801
802	GUI_LIBS_PREFIX:=
803	ifeq ($(DARWIN),1)
804	# this seem to be added at wrong place, since opengl is only needed to link EDIT4
805	GUI_LIBS_PREFIX:=-framework GLUT -framework OpenGL
806	endif
807
808	GUI_LIBS=$(GUI_LIBS_PREFIX) $(LIBS) -lAWT -lWINDOW
809	GUI_LIBS+=$(XLIBS)
810
811	LIBPATH = -L$(ARBHOME)/lib
812
813	DEST_LIB = lib
814	DEST_BIN = bin
815
816	CC_INCLUDES := -I. -I$(ARBHOME)/INCLUDE $(XINCLUDES) $(ARB_GLIB_INCLUDE)
817	CXX_INCLUDES := $(CC_INCLUDES)
818	MAKEDEPENDFLAGS := -- -DARB_OPENGL -DUNIT_TESTS -D__cplusplus -I. -Y$(ARBHOME)/INCLUDE
819
820	# -------------------------------
821	# old PTSERVER or PTPAN?
822
823	ifeq ($(PTPAN),1)
824	# PTPAN only libs
825	ARCHS_PT_SERVER = \
826	ptpan/PROBE.a
827	else
828	ifeq ($(PTPAN),2)
829	# special mode to compile both servers (developers only!)
830	ARCHS_PT_SERVER = \
831	ptpan/PROBE.a \
832	PROBE/PROBE.a
833	ARCHS_PT_SERVER_LINK = PROBE/PROBE.a# default to old ptserver
834	else
835	# PT-server only libs
836	ARCHS_PT_SERVER = \
837	PROBE/PROBE.a
838	endif
839	endif
840
841	ifndef ARCHS_PT_SERVER_LINK
842	ARCHS_PT_SERVER_LINK = $(ARCHS_PT_SERVER)
843	endif
844
845	# ---------------------------------------
846	# wrap main()
847
848	use_ARB_main=$(ARBHOME)/SOURCE_TOOLS/arb_main_cpp.o
849	use_ARB_main_C=$(ARBHOME)/SOURCE_TOOLS/arb_main_c.o
850
851	# -----------------------------------------
852	# export variables to submakefiles
853
854	include SOURCE_TOOLS/export2sub
855
856	# do not define (exported) variables below this point
857
858	# -------------------------
859	# Main arb targets:
860	# -------------------------
861
862	first_target:
863	$(MAKE) checks
864	@echo $(SEP)
865	@echo 'Main targets:'
866	@echo ''
867	@echo ' all - Compile ARB + TOOLs + and copy shared libs + link foreign software'
868	@echo ' (That is most likely the target you want)'
869	@echo ''
870	@echo ' clean - remove generated files ("SUBDIR/SUBDIR.clean" to clean only SUBDIR)'
871	@echo ' rebuild - clean + all'
872	@echo ' cleanlinked - remove all binaries'
873	@echo ' relink - cleanlinked + all (=relink all from objects)'
874	@echo ''
875	@echo 'Some often used sub targets (make all makes them all):'
876	@echo ''
877	@echo ' arb - Just compile ARB (but none of the integrated tools)'
878	@echo ' menus - create lib/gde/arb.menu from GDEHELP/ARB_GDEmenus.source'
879	@echo ' perl - Compile the PERL XSUBS into lib/ARB.so and create links in lib to perl'
880	@echo ' binlink - Create all links in the bin directory'
881	@echo ''
882	@echo 'Development targets:'
883	@echo ''
884	@echo ' depends - create or update dependencies ("SUBDIR/SUBDIR.depends" to update only SUBDIR)'
885	@echo ' proto - create or update prototypes ("SUBDIR/SUBDIR.proto" to update only SUBDIR)'
886	@echo ' tags - create tags for xemacs'
887	@echo ' show - show available shortcuts (AKA subtargets)'
888	@echo ' up - shortcut for depends+proto+tags'
889	ifeq ($(UNIT_TESTS),1)
890	@echo ' ut - only run tests'
891	endif
892	ifneq ($(SANITIZE),0)
893	@echo ' sanitize - all + run arb_ntree with sanitizer (test.arb + execute _logged)'
894	endif
895	@echo ' modified - rebuild files modified in svn checkout (does touch)'
896	@echo ' touch - touch files modified in svn checkout'
897	@echo ''
898	@echo 'Internal maintenance:'
899	@echo ''
900	@echo ' relinfo - show help on release targets'
901	@echo ' tarfile - make rebuild and create arb version tarfile ("tarfile_quick" to skip rebuild)'
902	@echo ' save - save all basic ARB sources into arbsrc_DATE ("savetest" to check filelist)'
903	@echo ' patch - save svn diff to patchfile'
904	@echo ' source_doc - create doxygen documentation'
905	@echo ' relocated - rebuild partly (use when you have relocated ARBHOME)'
906	@echo ' check_res - check resource usage'
907	@echo ' dep_graph - Build dependency graphs'
908	@echo ' clean_cov - Clean coverage results'
909	@echo ''
910	@echo ' post_commit_check - Checks whether'
911	@echo ' * main make targets work,'
912	@echo ' * dependencies and prototypes are up to date,'
913	@echo ' * SVN-controlled files remain unaffected by called targets and'
914	@echo ' * all generated files are ignored.'
915	@echo ' (has to be called in a clean SVN checkout)'
916	@echo $(SEP)
917	@echo ''
918
919	relinfo:
920	@echo ''
921	@echo $(SEP)
922	@echo 'Release targets:'
923	@echo ''
924	@echo ' inc_candi - increase RC candidate-number (only possible in "rc" branch, not needed for RC1)'
925	@echo ' inc_patch - increase release patchlevel (only possible in "stable" branch)'
926	@echo ' inc_minor - increase minor version number (only possible in "trunk")'
927	@echo ' inc_major - increase MAJOR version number (only possible in "trunk")'
928	@echo ''
929	@echo ' show_version - show version tag'
930	@echo ''
931	@echo $(SEP)
932	@echo ''
933
934	# auto-generate config.makefile:
935
936	CONFIG_MAKEFILE_FOUND=$(wildcard config.makefile)
937
938	config.makefile : config.makefile.template
939	@echo --------------------------------------------------------------------------------
940	ifeq ($(strip $(CONFIG_MAKEFILE_FOUND)),)
941	@cp $< $@
942	@echo '$(ARBHOME)/$@:1: has been generated.'
943	@echo 'Please edit $@ to configure your system!'
944	@echo --------------------------------------------------------------------------------
945	@false
946	else
947	@echo '$(ARBHOME)/$<:1: is more recent than'
948	@echo '$(ARBHOME)/$@:1:'
949	@ls -al config.makefile*
950	@echo --------------------------------------------------------------------------------
951	@echo "Updating $@ (if this fails, check manually)"
952	SOURCE_TOOLS/update_config_makefile.pl
953	@echo "Sucessfully updated $@"
954	@echo --------------------------------------------------------------------------------
955	@ls -al config.makefile*
956	@echo --------------------------------------------------------------------------------
957	@echo "Diff to your old config.makefile:"
958	@echo --------------------------------------------------------------------------------
959	-diff $@.bak $@
960	@echo --------------------------------------------------------------------------------
961	endif
962
963	# check if everything is configured correctly
964
965	check_DEVELOPER:
966	ifndef DEVELOPER
967	@echo 'config.makefile:1: DEVELOPER not defined'
968	@false
969	endif
970
971	check_DEBUG:
972	ifndef dflags
973	@echo 'config.makefile:1: DEBUG has to be defined. Valid values are 0 and 1'
974	@false
975	endif
976
977	check_ARB_64:
978	ifndef ARB_64
979	@echo 'config.makefile:1: ARB_64 has to be defined. Valid values are 0 and 1'
980	@false
981	endif
982
983	# ---------------------------------------- check gcc version
984
985	COMPILER_BROKEN:=0
986
987	# gcc 4.8.0 produces invalid code (see #617)
988	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.8.0')
989	COMPILER_BROKEN:=1
990	endif
991
992	check_same_GCC_VERSION:
993	$(ARBHOME)/SOURCE_TOOLS/check_same_compiler_version.pl $(COMPILER_NAME) $(COMPILER_VERSION_ALLOWED)
994
995	check_GCC_VERSION:
996	@echo 'Compiler version check:'
997	# see .@ALLOWED_gcc_VERSIONS
998	ifeq ('$(COMPILER_VERSION_ALLOWED)', '')
999	@echo " - Your compiler is '$(COMPILER_NAME)' version '$(COMPILER_VERSION)'"
1000	@echo ' This version is not in the list of supported $(COMPILER_NAME)-versions:'
1001	@$(foreach version,$(ALLOWED_COMPILER_VERSIONS),echo ' * $(version)';)
1002	@echo ' - You may either ..'
1003	@echo ' - add your version to ALLOWED_$(COMPILER_NAME)_VERSIONS in the Makefile and try it out or'
1004	@echo ' - switch to one of the allowed versions (see arb_README_gcc.txt for installing'
1005	@echo ' a different version of gcc)'
1006	$(error Unsupported compiler '$(COMPILER_NAME)' version '$(COMPILER_VERSION)')
1007	else
1008	ifeq ($(COMPILER_BROKEN),1)
1009	$(error $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)' would build a broken ARB version. Compilation refused)
1010	else
1011	@echo " - Supported $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)' detected - fine!"
1012	@echo ''
1013	$(MAKE) check_same_GCC_VERSION
1014	endif
1015	endif
1016
1017	#---------------------- check ARBHOME
1018
1019	# use arb_INSTALL.txt to determine whether ARBHOME points to correct directory
1020	ARB_INSTALL_FOUND=$(wildcard $(ARBHOME)/arb_INSTALL.txt)
1021
1022	check_ARBHOME:
1023	ifeq ($(strip $(ARB_INSTALL_FOUND)),)
1024	@echo ------------------------------------------------------------
1025	@echo "ARBHOME is set to '$(ARBHOME)'"
1026	@echo "The environment variable ARBHOME has to point to the top arb source directory."
1027	@echo "If you use bash enter:"
1028	@echo " export ARBHOME='`pwd`'"
1029	@echo ------------------------------------------------------------
1030	@false
1031	endif
1032
1033	ARB_PATH_SET=$(findstring $(ARBHOME)/bin,$(PATH))
1034
1035	check_PATH: check_ARBHOME
1036	ifeq ($(strip $(ARB_PATH_SET)),)
1037	@echo ------------------------------------------------------------
1038	@echo "The environment variable PATH has to contain $(ARBHOME)/bin"
1039	@echo "If you use bash enter:"
1040	@echo ' export PATH=$$ARBHOME/bin:$$PATH'
1041	@echo ------------------------------------------------------------
1042	@false
1043	endif
1044
1045	check_TOOLS:
1046	@util/arb_check_build_env.pl \
1047	"$(A_CC)" \
1048	"$(A_CXX)" \
1049	"$(MAKEDEPEND_PLAIN)" \
1050	"$(LINK_SHARED_LIB)" \
1051	"$(LINK_SHARED_LIB)" \
1052
1053	check_ENVIRONMENT : check_PATH check_TOOLS
1054	@echo "-------------------- Environment [start]"
1055	@echo "ARBHOME='$(ARBHOME)'"
1056	@echo "PATH='$(PATH)'"
1057	@echo "LD_LIBRARY_PATH='$(LD_LIBRARY_PATH)'"
1058	@echo "-------------------- Environment [end]"
1059
1060	check_tabs: check_setup
1061	ifeq ($(DEBUG),1)
1062	@SOURCE_TOOLS/tabBrake.pl
1063	endif
1064
1065	force_tab_check:
1066	@touch -t 198001010000 SOURCE_TOOLS/stamp.tabBrake
1067	@$(MAKE) check_tabs
1068
1069
1070	# ---------------------
1071
1072	check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION
1073	@echo Your setup seems to be ok.
1074
1075	checks: check_setup check_tabs
1076	@rm -f SOURCE_TOOLS/postcompile.sav
1077
1078
1079	# end test section ------------------------------
1080
1081	# ---------------------------------------
1082	# List of standard top level directories
1083	#
1084	# sub-makefiles have to define the targets
1085	# - 'depends' and
1086	# - 'clean'
1087	#
1088	# when adding new libs here, also add a dependency vs 'links' or 'links_non_perl' in .@DD_links_non_perl
1089
1090	ARCHS = \
1091	$(ARCHS_PT_SERVER) \
1092	AISC/AISC.a \
1093	AISC_MKPTPS/AISC_MKPTPS.a \
1094	ARBDB/libARBDB.a \
1095	CORE/libCORE.a \
1096	ARB_GDE/ARB_GDE.a \
1097	AWT/libAWT.a \
1098	AWTC/AWTC.a \
1099	AWTI/AWTI.a \
1100	CONSENSUS_TREE/CONSENSUS_TREE.a \
1101	CONVERTALN/CONVERTALN.a \
1102	DBSERVER/DBSERVER.a \
1103	DIST/DIST.a \
1104	EDIT4/EDIT4.a \
1105	EISPACK/EISPACK.a \
1106	GDE/GDE.a \
1107	GENOM/GENOM.a \
1108	GENOM_IMPORT/GENOM_IMPORT.a \
1109	GL/GL.a \
1110	ISLAND_HOPPING/ISLAND_HOPPING.a \
1111	MERGE/MERGE.a \
1112	MULTI_PROBE/MULTI_PROBE.a \
1113	NALIGNER/NALIGNER.a \
1114	NAMES/NAMES.a \
1115	NAMES_COM/server.a \
1116	NTREE/NTREE.a \
1117	PARSIMONY/PARSIMONY.a \
1118	PERLTOOLS/PERLTOOLS.a \
1119	PHYLO/PHYLO.a \
1120	PRIMER_DESIGN/PRIMER_DESIGN.a \
1121	PROBE_COM/server.a \
1122	PROBE_DESIGN/PROBE_DESIGN.a \
1123	PROBE_SET/PROBE_SET.a \
1124	READSEQ/READSEQ.a \
1125	RNA3D/RNA3D.a \
1126	RNACMA/RNACMA.a \
1127	SECEDIT/SECEDIT.a \
1128	SEQ_QUALITY/SEQ_QUALITY.a \
1129	SERVERCNTRL/SERVERCNTRL.a \
1130	SL/SL.a \
1131	STAT/STAT.a \
1132	TOOLS/TOOLS.a \
1133	TREEGEN/TREEGEN.a \
1134	UNIT_TESTER/UNIT_TESTER.a \
1135	WETC/WETC.a \
1136	WINDOW/libWINDOW.a \
1137	XML/XML.a \
1138
1139	# -----------------------
1140	# library packets
1141
1142	ARCHS_CLIENT_PROBE = PROBE_COM/client.a
1143	ARCHS_CLIENT_NAMES = NAMES_COM/client.a
1144
1145	ARCHS_MAKEBIN = AISC_MKPTPS/AISC_MKPTPS.a AISC/AISC.a
1146
1147	# communication libs need aisc and aisc_mkpts:
1148
1149	AISC/AISC.dummy: proto_tools
1150
1151	comtools: AISC/AISC.dummy
1152
1153	ARCHS_SEQUENCE = \
1154	SL/SEQUENCE/SEQUENCE.a \
1155	SL/ALIVIEW/ALIVIEW.a \
1156	SL/PRONUC/PRONUC.a \
1157
1158	ARCHS_TREE = \
1159	SL/ARB_TREE/ARB_TREE.a \
1160	SL/FILTER/FILTER.a \
1161	$(ARCHS_SEQUENCE) \
1162
1163	# parsimony tree (used by NTREE, PARSIMONY, STAT(->EDIT4), DIST(obsolete!))
1164	ARCHS_AP_TREE = \
1165	SL/AP_TREE/AP_TREE.a \
1166	$(ARCHS_TREE) \
1167
1168	# --------------------------------------------------------------------------------
1169	# dependencies for linking shared libs
1170
1171	link_core: core
1172	link_db: db link_core
1173	link_aw: aw link_db
1174	link_awt: awt link_aw
1175
1176	#***************************************************************************************
1177	# Individual_Programs_Section
1178	#***************************************************************************************
1179
1180	arbmainwrapper:
1181	$(MAKE) -C SOURCE_TOOLS -r mainwrapper
1182
1183
1184	#********************************* arb_ntree ************************************
1185	NTREE = bin/arb_ntree
1186	ARCHS_NTREE = \
1187	NTREE/NTREE.a \
1188	$(ARCHS_AP_TREE) \
1189	ARB_GDE/ARB_GDE.a \
1190	SL/DB_UI/DB_UI.a \
1191	AWTC/AWTC.a \
1192	AWTI/AWTI.a \
1193	CONSENSUS_TREE/CONSENSUS_TREE.a \
1194	GENOM_IMPORT/GENOM_IMPORT.a \
1195	GENOM/GENOM.a \
1196	MERGE/MERGE.a \
1197	MULTI_PROBE/MULTI_PROBE.a \
1198	PRIMER_DESIGN/PRIMER_DESIGN.a \
1199	PROBE_DESIGN/PROBE_DESIGN.a \
1200	SEQ_QUALITY/SEQ_QUALITY.a \
1201	SERVERCNTRL/SERVERCNTRL.a \
1202	SL/ALILINK/ALILINK.a \
1203	SL/AW_NAME/AW_NAME.a \
1204	SL/CONSENSUS/CONSENSUS.a \
1205	SL/DB_SCANNER/DB_SCANNER.a \
1206	SL/DB_QUERY/DB_QUERY.a \
1207	SL/SEQIO/SEQIO.a \
1208	STAT/STAT.a \
1209	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1210	SL/HELIX/HELIX.a \
1211	SL/REGEXPR/REGEXPR.a \
1212	SL/REFENTRIES/REFENTRIES.a \
1213	SL/NDS/NDS.a \
1214	SL/ITEM_SHADER/ITEM_SHADER.a \
1215	SL/ITEMS/ITEMS.a \
1216	SL/INSDEL/INSDEL.a \
1217	SL/LOCATION/LOCATION.a \
1218	SL/MACROS/MACROS.a \
1219	SL/TRANSLATE/TRANSLATE.a \
1220	SL/TREEDISP/TREEDISP.a \
1221	SL/TREE_ADMIN/TREE_ADMIN.a \
1222	SL/TREE_READ/TREE_READ.a \
1223	SL/TREE_WRITE/TREE_WRITE.a \
1224	XML/XML.a \
1225
1226	$(NTREE): $(ARCHS_NTREE:.a=.dummy) link_awt
1227	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NTREE) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1228	echo "$(SEP) Link $@"; \
1229	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(XMLLIBS)" ; \
1230	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(XMLLIBS) && \
1231	echo "$(SEP) Link $@ [done]"; \
1232	)
1233
1234	#********************************* arb_edit4 ************************************
1235	EDIT4 = bin/arb_edit4
1236
1237	ARCHS_EDIT4 := \
1238	EDIT4/EDIT4.a \
1239	ARB_GDE/ARB_GDE.a \
1240	SL/FAST_ALIGNER/FAST_ALIGNER.a \
1241	AWTC/AWTC.a \
1242	ISLAND_HOPPING/ISLAND_HOPPING.a \
1243	SECEDIT/SECEDIT.a \
1244	SERVERCNTRL/SERVERCNTRL.a \
1245	SL/AW_HELIX/AW_HELIX.a \
1246	SL/AW_NAME/AW_NAME.a \
1247	SL/CONSENSUS/CONSENSUS.a \
1248	SL/ITEMS/ITEMS.a \
1249	STAT/STAT.a \
1250	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1251	SL/HELIX/HELIX.a \
1252	SL/TRANSLATE/TRANSLATE.a \
1253	SL/MACROS/MACROS.a \
1254	SL/NDS/NDS.a \
1255	$(ARCHS_AP_TREE) \
1256	XML/XML.a \
1257
1258	ifeq ($(OPENGL),1)
1259	ARCHS_EDIT4 += RNA3D/RNA3D.a
1260	endif
1261
1262	LIBS_EDIT4 := $(GL_LIBS)
1263
1264	$(EDIT4): $(ARCHS_EDIT4:.a=.dummy) link_awt
1265	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_EDIT4) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1266	echo "$(SEP) Link $@"; \
1267	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4)" ; \
1268	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4) && \
1269	echo "$(SEP) Link $@ [done]"; \
1270	)
1271
1272	#********************************* arb_rnacma ************************************
1273	RNACMA = bin/arb_rnacma
1274	ARCHS_RNACMA = \
1275	RNACMA/RNACMA.a \
1276
1277	$(RNACMA) : $(ARCHS_RNACMA:.a=.dummy) link_db
1278	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_RNACMA) \|\| ( \
1279	echo "$(SEP) Link $@"; \
1280	echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_RNACMA) $(LIBS) $(EXECLIBS)"; \
1281	$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_RNACMA) $(LIBS) $(EXECLIBS) && \
1282	echo "$(SEP) Link $@ [done]"; \
1283	)
1284
1285	#********************************* arb_wetc ************************************
1286	WETC = bin/arb_wetc
1287	ARCHS_WETC = \
1288	WETC/WETC.a \
1289	SL/HELIX/HELIX.a \
1290	SL/FILTER/FILTER.a \
1291	XML/XML.a \
1292
1293	$(WETC): $(ARCHS_WETC:.a=.dummy) link_awt
1294	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_WETC) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1295	echo "$(SEP) Link $@"; \
1296	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_WETC) $(GUI_LIBS)" ; \
1297	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_WETC) $(GUI_LIBS) && \
1298	echo "$(SEP) Link $@ [done]"; \
1299	)
1300
1301	#********************************* arb_dist ************************************
1302	DIST = bin/arb_dist
1303	ARCHS_DIST = \
1304	DIST/DIST.a \
1305	CONSENSUS_TREE/CONSENSUS_TREE.a \
1306	EISPACK/EISPACK.a \
1307	SERVERCNTRL/SERVERCNTRL.a \
1308	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1309	SL/HELIX/HELIX.a \
1310	SL/MATRIX/MATRIX.a \
1311	SL/MACROS/MACROS.a \
1312	SL/NDS/NDS.a \
1313	SL/ITEMS/ITEMS.a \
1314	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.a \
1315	XML/XML.a \
1316	$(ARCHS_AP_TREE) \
1317
1318	$(DIST): $(ARCHS_DIST:.a=.dummy) link_awt
1319	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_DIST) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1320	echo "$(SEP) Link $@"; \
1321	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS)" ; \
1322	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) && \
1323	echo "$(SEP) Link $@ [done]"; \
1324	)
1325
1326	#********************************* arb_pars ************************************
1327	PARSIMONY = bin/arb_pars
1328	ARCHS_PARSIMONY = \
1329	PARSIMONY/PARSIMONY.a \
1330	SERVERCNTRL/SERVERCNTRL.a \
1331	SL/AW_NAME/AW_NAME.a \
1332	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1333	SL/HELIX/HELIX.a \
1334	SL/MACROS/MACROS.a \
1335	SL/NDS/NDS.a \
1336	SL/ITEMS/ITEMS.a \
1337	SL/TRANSLATE/TRANSLATE.a \
1338	SL/TREEDISP/TREEDISP.a \
1339	XML/XML.a \
1340	$(ARCHS_AP_TREE) \
1341
1342	$(PARSIMONY): $(ARCHS_PARSIMONY:.a=.dummy) link_awt
1343	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PARSIMONY) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1344	echo "$(SEP) Link $@"; \
1345	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS)" ; \
1346	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) && \
1347	echo "$(SEP) Link $@ [done]"; \
1348	)
1349
1350	#********************************* arb_convert_aln ************************************
1351	CONVERT_ALN = bin/arb_convert_aln
1352	ARCHS_CONVERT_ALN = \
1353	CONVERTALN/CONVERTALN.a \
1354
1355	$(CONVERT_ALN) : $(ARCHS_CONVERT_ALN:.a=.dummy) link_db
1356	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_CONVERT_ALN) $(use_ARB_main) \|\| ( \
1357	echo "$(SEP) Link $@"; \
1358	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_CONVERT_ALN) $(LIBS)"; \
1359	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_CONVERT_ALN) $(LIBS) && \
1360	echo "$(SEP) Link $@ [done]"; \
1361	)
1362
1363	#********************************* arb_treegen ************************************
1364
1365	TREEGEN = bin/arb_treegen
1366	ARCHS_TREEGEN = \
1367	TREEGEN/TREEGEN.a \
1368
1369	$(TREEGEN) : $(ARCHS_TREEGEN:.a=.dummy)
1370	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_TREEGEN) $(use_ARB_main_C) \|\| ( \
1371	echo "$(SEP) Link $@"; \
1372	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(EXECLIBS) $(ARCHS_TREEGEN)" ; \
1373	$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(EXECLIBS) $(ARCHS_TREEGEN) && \
1374	echo "$(SEP) Link $@ [done]"; \
1375	)
1376
1377	#********************************* arb_naligner ************************************
1378	NALIGNER = bin/arb_naligner
1379	ARCHS_NALIGNER = \
1380	NALIGNER/NALIGNER.a \
1381	SERVERCNTRL/SERVERCNTRL.a \
1382	SL/HELIX/HELIX.a \
1383
1384	$(NALIGNER): $(ARCHS_NALIGNER:.a=.dummy) link_db
1385	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NALIGNER) $(use_ARB_main) \|\| ( \
1386	echo "$(SEP) Link $@"; \
1387	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(LIBS)" ; \
1388	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(LIBS) && \
1389	echo "$(SEP) Link $@ [done]"; \
1390	)
1391
1392	#********************************* arb_phylo ************************************
1393	PHYLO = bin/arb_phylo
1394	ARCHS_PHYLO = \
1395	PHYLO/PHYLO.a \
1396	SL/HELIX/HELIX.a \
1397	SL/FILTER/FILTER.a \
1398	SL/MACROS/MACROS.a \
1399	XML/XML.a \
1400
1401	$(PHYLO): $(ARCHS_PHYLO:.a=.dummy) link_awt
1402	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PHYLO) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1403	echo "$(SEP) Link $@"; \
1404	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_PHYLO) $(GUI_LIBS)" ; \
1405	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_PHYLO) $(GUI_LIBS) && \
1406	echo "$(SEP) Link $@ [done]"; \
1407	)
1408
1409	#***************************************************************************************
1410	# SERVER SECTION
1411	#***************************************************************************************
1412
1413	#********************************* arb_db_server ************************************
1414	DBSERVER = bin/arb_db_server
1415	ARCHS_DBSERVER = \
1416	DBSERVER/DBSERVER.a \
1417	SERVERCNTRL/SERVERCNTRL.a \
1418
1419	$(DBSERVER): $(ARCHS_DBSERVER:.a=.dummy) link_db
1420	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_DBSERVER) $(ARBDB_LIB) $(use_ARB_main) \|\| ( \
1421	echo "$(SEP) Link $@"; \
1422	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS)" ; \
1423	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS) && \
1424	echo "$(SEP) Link $@ [done]"; \
1425	)
1426
1427	#********************************* arb_pt_server ************************************
1428	PROBE = bin/arb_pt_server
1429	ARCHS_PROBE_COMMON = \
1430	SL/PTCLEAN/PTCLEAN.a \
1431	SERVERCNTRL/SERVERCNTRL.a \
1432	SL/HELIX/HELIX.a \
1433
1434	ARCHS_PROBE_LINK = \
1435	$(ARCHS_PT_SERVER_LINK) \
1436	$(ARCHS_PROBE_COMMON) \
1437
1438	ARCHS_PROBE_DEPEND = \
1439	$(ARCHS_PT_SERVER) \
1440	$(ARCHS_PROBE_COMMON) \
1441
1442	$(PROBE): $(ARCHS_PROBE_DEPEND:.a=.dummy) link_db
1443	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_SERVER_PROBE) config.makefile $(use_ARB_main) \|\| ( \
1444	echo "$(SEP) Link $@"; \
1445	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_PROBE_LINK) $(ARCHS_CLIENT_PROBE) $(ARBDB_LIB) $(SYSLIBS)" ; \
1446	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_PROBE_LINK) $(ARCHS_CLIENT_PROBE) $(ARBDB_LIB) $(SYSLIBS) && \
1447	echo "$(SEP) Link $@ [done]"; \
1448	)
1449
1450	#********************************* arb_name_server ************************************
1451	NAMES = bin/arb_name_server
1452	ARCHS_NAMES = \
1453	NAMES/NAMES.a \
1454	SERVERCNTRL/SERVERCNTRL.a \
1455
1456	$(NAMES): $(ARCHS_NAMES:.a=.dummy) link_db
1457	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) $(use_ARB_main) \|\| ( \
1458	echo "$(SEP) Link $@"; \
1459	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS)" ; \
1460	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS) && \
1461	echo "$(SEP) Link $@ [done]"; \
1462	)
1463
1464	#********************************* SHARED LIBRARIES SECTION ************************************
1465
1466	prepare_libdir: addlibs
1467
1468	addlibs:
1469	(perl $(ARBHOME)/SOURCE_TOOLS/provide_libs.pl \
1470	"arbhome=$(ARBHOME)" \
1471	"opengl=$(OPENGL)" \
1472	"link_static=$(LINK_STATIC)" \
1473	)
1474
1475	#***************************************************************************************
1476	# Recursive calls to sub-makefiles
1477	#***************************************************************************************
1478
1479	%.depends:
1480	@cp -p $(@D)/Makefile $(@D)/Makefile.old # save old Makefile
1481	@$(MAKE) -C $(@D) -r \
1482	"AUTODEPENDS=1" \
1483	"MAIN=nothing" \
1484	"cflags=noCflagsHere_use_MAKEDEPENDFLAGS" \
1485	"cxxflags=noCxxflagsHere_use_MAKEDEPENDFLAGS" \
1486	depends
1487	@grep "^# DO NOT DELETE" $(@D)/Makefile >/dev/null
1488	@cat $(@D)/Makefile \
1489	\| SOURCE_TOOLS/fix_depends.pl "(from main)" \
1490	>$(@D)/Makefile.2
1491	@mv $(@D)/Makefile.old $(@D)/Makefile # restore old Makefile
1492	@$(ARBHOME)/SOURCE_TOOLS/mv_if_diff $(@D)/Makefile.2 $(@D)/Makefile # update Makefile if changed
1493
1494	%.proto:
1495	@($(MAKE) -C $(@D) \
1496	"AUTODEPENDS=0" \
1497	"MAIN=nothing" \
1498	"cflags=noCflags" \
1499	"cxxflags=noCxxflags" \
1500	proto 2>&1 ) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
1501
1502	%.clean:
1503	@$(MAKE) -C $(@D) \
1504	"AUTODEPENDS=0" \
1505	"MAIN=nothing" \
1506	"cflags=noCflags" \
1507	"cxxflags=noCxxflags" \
1508	clean
1509
1510
1511	# stop wrong targets
1512	target_is_missing_lib_prefix:
1513	@echo "Error: Denied to build shared library target with missing 'lib'-prefix"
1514	false
1515
1516	ARBDB/ARBDB.dummy: target_is_missing_lib_prefix
1517	CORE/CORE.dummy: target_is_missing_lib_prefix
1518	AWT/AWT.dummy: target_is_missing_lib_prefix
1519	WINDOW/WINDOW.dummy: target_is_missing_lib_prefix
1520
1521	# rule to generate main target (normally a library):
1522	# @@@ check effect of setting LANG=C below
1523	%.dummy:
1524	@( export ID=$$$$; LANG=C; \
1525	(( \
1526	echo "$(SEP) Make $(@D)"; \
1527	$(MAKE) -C $(@D) -r \
1528	"AUTODEPENDS=1" \
1529	"MAIN=$(@F:.dummy=.a)" \
1530	"cflags=$(cflags) -DIN_ARB_$(subst /,_,$(@D))" \
1531	&& \
1532	echo "$(SEP) Make $(@D) [done]"; \
1533	) >$(@D).$$ID.log 2>&1 && (cat $(@D).$$ID.log;rm $(@D).$$ID.log)) \|\| (cat $(@D).$$ID.log;rm $(@D).$$ID.log;false))
1534
1535	# Additional dependencies for subtargets:
1536
1537	PROBE_COM/PROBE_COM.dummy : comtools
1538	NAMES_COM/NAMES_COM.dummy : comtools
1539
1540	com: PROBE_COM/PROBE_COM.dummy NAMES_COM/NAMES_COM.dummy
1541
1542	PROBE_COM/server.dummy:
1543	@echo Unwanted request to make target $<
1544	false
1545
1546	PROBE_COM/client.dummy:
1547	@echo Unwanted request to make target $<
1548	false
1549
1550	NAMES_COM/server.dummy:
1551	@echo Unwanted request to make target $<
1552	false
1553
1554	NAMES_COM/client.dummy:
1555	@echo Unwanted request to make target $<
1556	false
1557
1558
1559	ARBDB/libARBDB.dummy: links
1560	CORE/libCORE.dummy: links
1561
1562	PERLTOOLS/PERLTOOLS.dummy: core db
1563
1564	# all subdirs perl not depends on go here (ADD_links_non_perl)
1565	AWT/libAWT.dummy: links_non_perl
1566	AWTI/AWTI.dummy: links_non_perl
1567	CONSENSUS_TREE/CONSENSUS_TREE.dummy: links_non_perl
1568	CONVERTALN/CONVERTALN.dummy: links_non_perl
1569	DBSERVER/DBSERVER.dummy: links_non_perl
1570	DIST/DIST.dummy: links_non_perl
1571	EDIT4/EDIT4.dummy: links_non_perl com
1572	EISPACK/EISPACK.dummy: links_non_perl
1573	GDE/GDE.dummy: links_non_perl
1574	GENOM/GENOM.dummy: links_non_perl
1575	GENOM_IMPORT/GENOM_IMPORT.dummy: links_non_perl
1576	ISLAND_HOPPING/ISLAND_HOPPING.dummy: links_non_perl
1577	MERGE/MERGE.dummy: links_non_perl
1578	NTREE/NTREE.dummy: links_non_perl
1579	PARSIMONY/PARSIMONY.dummy: links_non_perl
1580	PHYLO/PHYLO.dummy: links_non_perl
1581	PRIMER_DESIGN/PRIMER_DESIGN.dummy: links_non_perl
1582	PROBE_SET/PROBE_SET.dummy: links_non_perl link_db
1583	READSEQ/READSEQ.dummy: links_non_perl
1584	RNACMA/RNACMA.dummy: links_non_perl header_libs
1585	SECEDIT/SECEDIT.dummy: links_non_perl
1586	SEQ_QUALITY/SEQ_QUALITY.dummy: links_non_perl
1587	SERVERCNTRL/SERVERCNTRL.dummy: links_non_perl com
1588	SL/ALILINK/ALILINK.dummy: links_non_perl
1589	SL/ALIVIEW/ALIVIEW.dummy: links_non_perl
1590	SL/AP_TREE/AP_TREE.dummy: links_non_perl
1591	SL/ARB_TREE/ARB_TREE.dummy: links_non_perl
1592	SL/AW_HELIX/AW_HELIX.dummy: links_non_perl
1593	SL/CONSENSUS/CONSENSUS.dummy: links_non_perl
1594	SL/DB_QUERY/DB_QUERY.dummy: links_non_perl
1595	SL/DB_SCANNER/DB_SCANNER.dummy: links_non_perl
1596	SL/DB_UI/DB_UI.dummy: links_non_perl
1597	SL/FAST_ALIGNER/FAST_ALIGNER.dummy: links_non_perl
1598	SL/FILTER/FILTER.dummy: links_non_perl
1599	SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy: links_non_perl
1600	SL/HELIX/HELIX.dummy: links_non_perl
1601	SL/INSDEL/INSDEL.dummy: links_non_perl
1602	SL/ITEMS/ITEMS.dummy: links_non_perl
1603	SL/ITEM_SHADER/ITEM_SHADER.dummy: links_non_perl
1604	SL/LOCATION/LOCATION.dummy: links_non_perl
1605	SL/MACROS/MACROS.dummy: links_non_perl
1606	SL/MATRIX/MATRIX.dummy: links_non_perl
1607	SL/NDS/NDS.dummy: links_non_perl
1608	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.dummy: links_non_perl
1609	SL/PRONUC/PRONUC.dummy: links_non_perl
1610	SL/PTCLEAN/PTCLEAN.dummy: links_non_perl link_db
1611	SL/REFENTRIES/REFENTRIES.dummy: links_non_perl
1612	SL/REGEXPR/REGEXPR.dummy: links_non_perl
1613	SL/SEQIO/SEQIO.dummy: links_non_perl
1614	SL/SEQUENCE/SEQUENCE.dummy: links_non_perl
1615	SL/TRANSLATE/TRANSLATE.dummy: links_non_perl
1616	SL/TREE_ADMIN/TREE_ADMIN.dummy: links_non_perl
1617	SL/TREE_READ/TREE_READ.dummy: links_non_perl
1618	SL/TREE_WRITE/TREE_WRITE.dummy: links_non_perl
1619	SL/TREEDISP/TREEDISP.dummy: links_non_perl
1620	STAT/STAT.dummy: links_non_perl
1621	TREEGEN/TREEGEN.dummy: links_non_perl
1622	WETC/WETC.dummy: links_non_perl
1623	WINDOW/libWINDOW.dummy: links_non_perl
1624	XML/XML.dummy: links_non_perl
1625
1626	ifeq ($(OPENGL),1)
1627	GL/glAW/glAW.dummy: links_non_perl
1628	GL/glpng/glpng.dummy: links_non_perl
1629	GL/GL.dummy: GL/glAW/glAW.dummy GL/glpng/glpng.dummy
1630	RNA3D/RNA3D.dummy: links_non_perl gl
1631	endif
1632
1633	UNIT_TESTER/UNIT_TESTER.dummy: link_db \
1634	SERVERCNTRL/SERVERCNTRL.dummy \
1635
1636	# see also TOOLS/Makefile@TOOLSLIBDEPENDS
1637	TOOLS/TOOLS.dummy : links_non_perl link_db \
1638	CONSENSUS_TREE/CONSENSUS_TREE.dummy \
1639	SERVERCNTRL/SERVERCNTRL.dummy \
1640	SL/FILTER/FILTER.dummy \
1641	SL/INSDEL/INSDEL.dummy \
1642	SL/REGEXPR/REGEXPR.dummy \
1643	SL/SEQIO/SEQIO.dummy \
1644	SL/TREE_READ/TREE_READ.dummy \
1645	SL/TREE_WRITE/TREE_WRITE.dummy \
1646	XML/XML.dummy \
1647
1648	AWTC/AWTC.dummy : com
1649
1650	NAMES/NAMES.dummy : com
1651	SL/AW_NAME/AW_NAME.dummy : com
1652
1653	PROBE/PROBE.dummy : com
1654	ptpan/PROBE.dummy : com
1655	MULTI_PROBE/MULTI_PROBE.dummy : com
1656	PROBE_DESIGN/PROBE_DESIGN.dummy : com
1657	NALIGNER/NALIGNER.dummy : com
1658
1659	ARB_GDE/ARB_GDE.dummy : proto_tools
1660
1661	compile_compatibility: SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.dummy
1662
1663	#***************************************************************************************
1664	# Short aliases to make targets
1665	#***************************************************************************************
1666
1667	show:
1668	@echo $(SEP)
1669	@echo 'Aliases for often needed targets:'
1670	@echo ''
1671	@echo ' executables:'
1672	@echo ''
1673	@echo ' nt arb_ntree'
1674	@echo ' e4 arb_edit4 (includes secedit)'
1675	@echo ' di arb_dist'
1676	@echo ' ph arb_phylo'
1677	@echo ' pa arb_parsimony'
1678	@echo ' tg arb_treegen'
1679	@echo ' ds arb_dbserver'
1680	@echo ' pt arb_pt_server'
1681	@echo ' na arb_name_server'
1682	@echo ''
1683	@echo ' libraries:'
1684	@echo ''
1685	@echo ' com communication libraries'
1686	@echo ' db ARB database'
1687	@echo ' aw GUI lib'
1688	@echo ' awt GUI toolkit'
1689	@echo ' awtc general purpose library'
1690	@echo ' awti import/export library'
1691	@echo ' mp multi probe library'
1692	@echo ' ge genome library'
1693	@echo ' pd probe design lib'
1694	@echo ' prd primer design lib'
1695	@echo ''
1696	@echo ' other targets:'
1697	@echo ''
1698	@echo ' help recompile help files'
1699	@echo ' tools make small tools used by arb'
1700	@echo ''
1701	@echo ' foreign targets:'
1702	@echo ''
1703	@echo ' gde GDE'
1704	@echo ' agde ARB_GDE'
1705	@echo ''
1706	@echo 'for other targets inspect $(ARBHOME)/Makefile'
1707	@echo ''
1708	@echo $(SEP)
1709
1710	source_doc:
1711	@echo "Remove some links (doxygen crashes otherwise):"
1712	find . \( -name "AISC" -o -name "C" -o -name "GDEHELP" \) -type l -exec rm {} \;
1713	doxygen 2>&1 1>/dev/null
1714	$(MAKE) forcelinks
1715
1716	dep_graph:
1717	@echo "Building some dependency graphs"
1718	SOURCE_TOOLS/dependency_graphs.pl
1719
1720	help: HELP_SOURCE/HELP_SOURCE.dummy
1721
1722	HELP_SOURCE/HELP_SOURCE.dummy: link_core xml menus
1723
1724	db: ARBDB/libARBDB.dummy
1725	core: CORE/libCORE.dummy
1726	aw: WINDOW/libWINDOW.dummy
1727	awt: AWT/libAWT.dummy
1728	awtc: AWTC/AWTC.dummy
1729	awti: AWTI/AWTI.dummy
1730
1731	mp: MULTI_PROBE/MULTI_PROBE.dummy
1732	mg: MERGE/MERGE.dummy
1733	ge: GENOM/GENOM.dummy
1734	prd: PRIMER_DESIGN/PRIMER_DESIGN.dummy
1735
1736	nt: menus $(NTREE)
1737
1738	nal: $(NALIGNER)
1739
1740	di: $(DIST)
1741	ph: $(PHYLO)
1742	pa: $(PARSIMONY)
1743	tg: $(TREEGEN)
1744
1745	ifeq ($(OPENGL),1)
1746	3d: RNA3D/RNA3D.dummy
1747	gl: GL/GL.dummy
1748	else
1749	noopengl:
1750	@echo "invalid target for OPENGL=0"
1751	3d: noopengl
1752	gl: noopengl
1753	endif
1754
1755	SL/SL.dummy: com
1756
1757	ds: $(DBSERVER)
1758	pt: $(PROBE)
1759	pst: PROBE_SET/PROBE_SET.dummy
1760	pd: PROBE_DESIGN/PROBE_DESIGN.dummy
1761	na: $(NAMES)
1762	sq: SEQ_QUALITY/SEQ_QUALITY.dummy
1763	cma: $(RNACMA)
1764
1765	sec: SECEDIT/SECEDIT.dummy
1766
1767	e4: $(EDIT4) readseq menus
1768
1769	gi: GENOM_IMPORT/GENOM_IMPORT.dummy
1770	wetc: $(WETC)
1771
1772	xml: XML/XML.dummy
1773	xmlin: XML_IMPORT/XML_IMPORT.dummy# broken
1774	stat: STAT/STAT.dummy $(NTREE) $(EDIT4)
1775	fa: SL/FAST_ALIGNER/FAST_ALIGNER.dummy
1776
1777	#********************************************************************************
1778
1779	up_by_remake: depends proto vectorize_checks
1780
1781	up: up_by_remake tags valgrind_update
1782
1783	#********************************************************************************
1784
1785	touch:
1786	SOURCE_TOOLS/touch_modified.pl
1787
1788	modified: touch
1789	$(MAKE) all
1790
1791	#********************************************************************************
1792
1793	libdepends:
1794	$(MAKE) -C "SOURCE_TOOLS" \
1795	"RNA3D_LIB=$(RNA3D_LIB_4_DEPENDS)" \
1796	libdepends
1797
1798	#********************************************************************************
1799
1800	# create generated headers:
1801	genheaders: TEMPLATES/TEMPLATES.dummy
1802
1803	clrdotdepends:
1804	rm PROBE_COM/.depends \|\| true
1805	rm NAMES_COM/.depends \|\| true
1806	rm PERL2ARB/.depends \|\| true
1807
1808	comdepends: comtools clrdotdepends
1809	@echo "$(SEP) Partially build com interface"
1810	$(MAKE) PROBE_COM/PROBE_COM.depends NAMES_COM/NAMES_COM.depends
1811	$(MAKE) PROBE_COM/server.depends NAMES_COM/server.depends
1812
1813	depends: genheaders comdepends vectorize_checks
1814	@echo "$(SEP) Updating other dependencies"
1815	$(MAKE) $(subst NAMES_COM/server.depends,,$(subst PROBE_COM/server.depends,,$(ARCHS:.a=.depends))) \
1816	HELP_SOURCE/HELP_SOURCE.depends \
1817	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.depends \
1818
1819	$(MAKE) libdepends
1820
1821	depend: depends
1822
1823	# ------------------------------------------------------------
1824	# dependency generation tests for AISC code
1825	#(all should work w/o creating wrong dependencies;
1826	# neither in XXX_COM/Makefile nor in code using AISC interface)
1827	dependstest1: silent_clean
1828	$(MAKE) depends
1829	dependstest2: silent_clean
1830	$(MAKE) com
1831	dependstest3: silent_clean
1832	$(MAKE) aw
1833	dependstest4: silent_clean
1834	$(MAKE) pt
1835	dependstest5: silent_clean
1836	$(MAKE) na
1837	dependstest6: silent_clean
1838	$(MAKE) nt
1839	dependstest7: silent_clean
1840	$(MAKE) all
1841	# ------------------------------------------------------------
1842
1843	vectorize_checks:
1844	$(MAKE) -C SOURCE_TOOLS -r vectorize_checks
1845
1846	# ------------------------------------------------------------
1847
1848	AISC_MKPTPS/AISC_MKPTPS.dummy: links
1849
1850	proto_tools: AISC_MKPTPS/AISC_MKPTPS.dummy
1851
1852	proto: proto_tools
1853	@echo $(SEP) Updating prototypes
1854	$(MAKE) \
1855	ARBDB/ARBDB.proto \
1856	AISC_COM/AISC_COM.proto \
1857	ARB_GDE/ARB_GDE.proto \
1858	CORE/CORE.proto \
1859	CONVERTALN/CONVERTALN.proto \
1860	NTREE/NTREE.proto \
1861	MERGE/MERGE.proto \
1862	$(ARCHS_PT_SERVER:.a=.proto) \
1863	SERVERCNTRL/SERVERCNTRL.proto \
1864	SL/SL.proto \
1865
1866	#********************************************************************************
1867
1868	valgrind_update: links
1869	@echo $(SEP) Updating for valgrind
1870	$(MAKE) -C SOURCE_TOOLS valgrind_update
1871
1872	#********************************************************************************
1873
1874	TAGFILE=TAGS
1875	TAGFILE_TMP=TAGS.tmp
1876
1877	TAG_SOURCE_HEADERS=TAGS.headers
1878	TAG_SOURCE_CODE=TAGS.codefiles
1879	TAG_SOURCE_LISTS=$(TAG_SOURCE_HEADERS) $(TAG_SOURCE_CODE)
1880
1881	ETAGS=ctags -e -f $(TAGFILE_TMP) --sort=no --if0=no --extra=q
1882	ETAGS_TYPES=--C-kinds=cgnsut --C++-kinds=cgnsut
1883	ETAGS_FUN =--C-kinds=fm --C++-kinds=fm
1884	ETAGS_REST =--C-kinds=dev --C++-kinds=dev
1885
1886	FILTER_TAGS_SOURCES= \
1887	$(SED) -e 's/^.\///g' \| \
1888	grep -P -v -i '^HEADERLIBS\|^GDE/\|/GEN[CH]/'
1889
1890	$(TAG_SOURCE_HEADERS): links
1891	find . \( -name '.hxx' -o -name ".h" \) -type f \| $(FILTER_TAGS_SOURCES) > $@
1892
1893	$(TAG_SOURCE_CODE): links
1894	find . \( -name '.cxx' -o -name ".c" \) -type f \| $(FILTER_TAGS_SOURCES) > $@
1895
1896	tags: $(TAG_SOURCE_LISTS)
1897	$(ETAGS) $(ETAGS_TYPES) -L $(TAG_SOURCE_HEADERS)
1898	$(ETAGS) -a $(ETAGS_FUN) -L $(TAG_SOURCE_HEADERS)
1899	$(ETAGS) -a $(ETAGS_REST) -L $(TAG_SOURCE_HEADERS)
1900	$(ETAGS) -a $(ETAGS_TYPES) -L $(TAG_SOURCE_CODE)
1901	$(ETAGS) -a $(ETAGS_FUN) -L $(TAG_SOURCE_CODE)
1902	$(ETAGS) -a $(ETAGS_REST) -L $(TAG_SOURCE_CODE)
1903	mv_if_diff $(TAGFILE_TMP) $(TAGFILE)
1904	rm $(TAG_SOURCE_LISTS)
1905
1906	#********************************************************************************
1907
1908	LINKSTAMP=SOURCE_TOOLS/stamp.generate_all_links
1909
1910	links: checks $(LINKSTAMP) arbmainwrapper
1911	links_no_checks: $(LINKSTAMP) arbmainwrapper
1912
1913	forcelinks:
1914	-rm $(LINKSTAMP)
1915	$(MAKE) links
1916
1917	$(LINKSTAMP): SOURCE_TOOLS/generate_all_links.sh genheaders
1918	+SOURCE_TOOLS/generate_all_links.sh
1919	touch $(LINKSTAMP)
1920
1921	clean_links:
1922	# avoid to delete linked pts, nas or arb_tcp.dat:
1923	find . -path './lib' -prune -o -type l -exec rm {} \;
1924	# removed obsolete file - refuses to disappear due to 'prune' above
1925	@rm -f lib/help/GDEHELP
1926	@rm -f $(LINKSTAMP) lib/inputMasks/format.readme
1927
1928	redo_links: clean_links
1929	$(MAKE) links_no_checks
1930
1931	#********************************************************************************
1932
1933	header_libs:
1934	$(MAKE) -C HEADERLIBS all
1935
1936	#********************************************************************************
1937
1938	gde: GDE/GDE.dummy
1939	GDE: gde
1940	agde: ARB_GDE/ARB_GDE.dummy
1941
1942	tools: TOOLS/TOOLS.dummy
1943
1944	convert: $(CONVERT_ALN)
1945	readseq: READSEQ/READSEQ.dummy
1946
1947	#***************************************************************************************
1948	# Some user commands
1949	#***************************************************************************************
1950
1951	menus: binlink links
1952	@(( \
1953	echo "$(SEP) Make GDEHELP"; \
1954	$(MAKE) -C GDEHELP -r all && \
1955	echo "$(SEP) Make GDEHELP [done]"; \
1956	) > GDEHELP.log 2>&1 && (cat GDEHELP.log;rm GDEHELP.log)) \|\| (cat GDEHELP.log;rm GDEHELP.log;false)
1957
1958	ifeq ($(DEBUG),1)
1959	BIN_TARGET=develall
1960	else
1961	BIN_TARGET=all
1962	endif
1963
1964
1965	binlink:
1966	$(MAKE) -C bin $(BIN_TARGET)
1967
1968	preplib:
1969	(cd lib;$(MAKE) all)
1970
1971	# --------------------------------------------------------------------------------
1972	# This section is quite tricky:
1973	#
1974	# make 'perl' is a BIG target, so when it has to be made, it has to be started
1975	# as early as possible to reduce overall compile time. Since 'make' does not
1976	# provide any priotities, i force it to build all 'perl'-prerequisites early, by
1977	# adding artificial dependencies to these prerequisites
1978	#
1979	# That behavior is likely to be system-dependent.
1980	# My goal was only to make it work on my current development system,
1981	# where this saves about 20% of overall build time.
1982
1983	ifeq ($(WITHPERL),1)
1984	links_non_perl: PERLTOOLS/PERLTOOLS.dummy
1985	perltools: links_non_perl
1986	perl: realperl
1987	else
1988	links_non_perl: links
1989	perl:
1990	$(MAKE) "WITHPERL=1" perl
1991	endif
1992
1993	# ---------------------------------------- perl
1994
1995	ifeq ($(ARB_64),$(BUILDHOST_64))
1996	TEST_PERL_SCRIPTS=$(MAKE) -C PERL_SCRIPTS/test test
1997	else
1998	TEST_PERL_SCRIPTS=echo "skipping perl script compilation (when cross-compiling)"
1999	endif
2000
2001	realperl: perltools
2002	(( \
2003	echo "$(SEP) Make PERL2ARB" ; \
2004	$(TIME) $(MAKE) -C PERL2ARB -r -f Makefile.main \
2005	"AUTODEPENDS=1" \
2006	"dflags=$(dflags)" \
2007	"cflags4perl=$(cflags) $(cxxflags) $(dflags)" \
2008	"lflags4perl=$(lflags4perl)" \
2009	"COMPILER_VERSION=$(COMPILER_VERSION)" \
2010	all && \
2011	$(TEST_PERL_SCRIPTS) && \
2012	echo "$(SEP) Make PERL2ARB [done]" ; \
2013	) > PERL2ARB.log 2>&1 && (cat PERL2ARB.log;rm PERL2ARB.log)) \|\| (cat PERL2ARB.log;rm PERL2ARB.log;false)
2014
2015	perl_clean:
2016	@$(MAKE) -C PERL2ARB -r -f Makefile.main \
2017	"AUTODEPENDS=0" \
2018	clean
2019
2020	PERL2ARB/PERL2ARB.clean:
2021	$(MAKE) perl_clean
2022	$(MAKE) -C PERL_SCRIPTS/test clean
2023
2024	# ---------------------------------------- bindings to script languages
2025
2026	bindings: lib/libCORE.so lib/libARBDB.so
2027	$(MAKE) -C BINDINGS all ARBDEPENDS="$(^:%=../%)" DFLAGS="$(dflags)"
2028
2029	bindings_clean:
2030	$(MAKE) -C BINDINGS clean
2031
2032	# ----------------------------------------
2033
2034	CLOC=cloc-1.08.pl
2035	CLOCFLAGS=--no3 --quiet --progress-rate=0
2036	CLOCARB=--exclude-dir=GDE .
2037	CLOCEXT=GDE
2038	CLOCCODE=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.code.def
2039	CLOCREST=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.rest.def
2040	CLOCFILT=tail --lines=+4
2041
2042	cloc:
2043	@echo 'Arb code:'
2044	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCARB) \| $(CLOCFILT)
2045	@echo 'Arb rest:'
2046	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCARB) \| $(CLOCFILT)
2047	@echo 'External code:'
2048	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCEXT) \| $(CLOCFILT)
2049	@echo 'External rest:'
2050	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCEXT) \| $(CLOCFILT)
2051
2052	# ---------------------------------------- check resources
2053
2054	check_res:
2055	$(ARBHOME)/SOURCE_TOOLS/check_resources.pl
2056
2057	# ---------------------------------------- cleaning
2058
2059	rmbak:
2060	@echo "Cleanup:"
2061	@find . \( -name '*%' \
2062	-o -name '*.bak' \
2063	-o -name '*~' \) \
2064	-o \( -name 'core' -a \! -type d \) \
2065	-exec rm -v {} \;
2066
2067	bin_reinit:
2068	$(MAKE) bin/bin.clean
2069	$(MAKE) -C "bin" all
2070
2071	clean_directories:
2072	-rm -rf \
2073	$(ARBHOME)/PROBE_SET/bin \
2074	$(ARBHOME)/INCLUDE \
2075
2076	libclean:
2077	-find $(ARBHOME) -type f \( -name '*.a' ! -type l \) -exec rm -f {} \;
2078
2079	objclean:
2080	-find $(ARBHOME) -type f \( -name '*.o' ! -type l \) -exec rm -f {} \;
2081
2082	# bin.clean and HELP_SOURCE.clean interfere
2083	clean3:
2084	$(MAKE) bin/bin.clean
2085	$(MAKE) HELP_SOURCE/HELP_SOURCE.clean
2086
2087	clean2: $(ARCHS:.a=.clean) \
2088	clean3 \
2089	rmbak \
2090	libclean \
2091	objclean \
2092	lib/lib.clean \
2093	GDEHELP/GDEHELP.clean \
2094	HEADERLIBS/HEADERLIBS.clean \
2095	SOURCE_TOOLS/SOURCE_TOOLS.clean \
2096	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.clean \
2097	UNIT_TESTER/UNIT_TESTER.clean \
2098	TEMPLATES/TEMPLATES.clean \
2099	perl_clean \
2100	clean_directories \
2101
2102	rm -f .last_gcc .last_compiler config.makefile.bak
2103
2104	# links are needed for cleanup
2105	clean: redo_links motif_xpm_hack_clean
2106	$(MAKE) clean2
2107	$(MAKE) clean_cov_all clean_links
2108
2109	silent_clean:
2110	$(MAKE) clean >/dev/null
2111
2112	# 'relocated' is about 50% faster than 'rebuild'
2113	reloc_clean: links
2114	@echo "---------------------------------------- Relocation cleanup"
2115	$(MAKE) \
2116	perl_clean \
2117	GDEHELP/GDEHELP.clean \
2118	HELP_SOURCE/genhelp/genhelp.clean \
2119	bin/bin.clean \
2120	libclean \
2121	objclean
2122
2123	relocated: links
2124	$(MAKE) reloc_clean
2125	@echo "---------------------------------------- and remake"
2126	$(MAKE) build
2127
2128	# -----------------------------------
2129	# some stress tests
2130	# (helpful to reveal race conditions with -j)
2131
2132	rebuild4ever: rebuild
2133	$(MAKE) rebuild4ever
2134
2135	build4ever: build
2136	$(MAKE) build4ever
2137
2138	clean4ever: clean
2139	$(MAKE) clean4ever
2140
2141	test4ever: ut
2142	$(MAKE) test4ever
2143
2144	perl4ever: clean
2145	$(MAKE) links
2146	$(MAKE) perl
2147	$(MAKE) perl4ever
2148
2149	help4ever: clean
2150	$(MAKE) help
2151	$(MAKE) help4ever
2152
2153	# -----------------------------------
2154
2155	rebuild: clean
2156	$(MAKE) all
2157
2158	cleanlinked: bin/bin.clean libclean
2159
2160	relink: cleanlinked
2161	$(MAKE) all
2162
2163	tarfile: rebuild
2164	$(MAKE) prepare_libdir
2165	util/arb_compress
2166
2167	tarfile_quick: build
2168	$(MAKE) prepare_libdir
2169	util/arb_compress
2170
2171	save: sourcetarfile
2172
2173	patch:
2174	SOURCE_TOOLS/arb_create_patch.sh arbPatch
2175
2176	# test early whether save will work
2177	savetest:
2178	@util/arb_srclst.pl >/dev/null
2179
2180	testsave: savetest
2181
2182	sourcetarfile: rmbak
2183	util/arb_save
2184
2185	save2: rmbak
2186	util/arb_save ignore
2187
2188	save_test: rmbak
2189	@echo "Testing source list.."
2190	@util/arb_srclst.pl > /dev/null
2191
2192	save_test_no_error:
2193	@-$(MAKE) save_test
2194
2195	inc_candi:
2196	touch SOURCE_TOOLS/inc_candi.stamp
2197	$(MAKE) do_version_update
2198
2199	inc_patch:
2200	touch SOURCE_TOOLS/inc_patch.stamp
2201	$(MAKE) do_version_update
2202
2203	inc_minor:
2204	touch SOURCE_TOOLS/inc_minor.stamp
2205	$(MAKE) do_version_update
2206
2207	inc_major:
2208	touch SOURCE_TOOLS/inc_major.stamp
2209	$(MAKE) do_version_update
2210
2211	do_version_update:
2212	@echo Incrementing version information
2213	$(MAKE) testsave
2214	$(MAKE) genheaders # auto upgrades version early
2215
2216	show_version:
2217	$(MAKE) genheaders # updates version info
2218	@echo "$(SEP) ARB version info"
2219	@grep ARB_VERSION TEMPLATES/arb_build.h
2220	@echo "$(SEP)"
2221
2222	release_quick:
2223	-rm arb.tgz arbsrc.tgz
2224	$(MAKE) tarfile_quick
2225	$(MAKE) sourcetarfile
2226
2227	# --------------------------------------------------------------------------------
2228
2229	MAKE_IF_COMMITTED=$(MAKE) -C SOURCE_TOOLS -f Makefile.commitbuild
2230
2231	build_CTARGET:
2232	+$(MAKE_IF_COMMITTED) "CTARGET=$(CTARGET)" build_CTARGET
2233
2234	reset_committed_build:
2235	+$(MAKE_IF_COMMITTED) reset
2236
2237	# --------------------------------------------------------------------------------
2238
2239	arbapplications: nt pa e4 wetc pt na nal di ph ds wetc cma
2240
2241	arb_external: convert tools gde readseq tg pst xmlin
2242
2243	arb_no_perl: arbapplications help arb_external
2244
2245	arb: motif_xpm_hack
2246	$(MAKE) "WITHPERL=1" perl arb_no_perl
2247
2248	motif_xpm_hack:
2249	$(MAKE) -r -C "lib/motifHack" all
2250
2251	motif_xpm_hack_clean:
2252	$(MAKE) -r -C "lib/motifHack" clean
2253
2254	# --------------------------------------------------------------------------------
2255	# special targets for SOURCE_TOOLS/remake_after_change.pl
2256
2257	rac_arb_dist: di
2258	rac_arb_edit4: e4
2259	rac_arb_ntree: nt
2260	rac_arb_pars: pa
2261	rac_arb_phylo: ph
2262	rac_arb_wetc: wetc
2263	rac_arb_naligner: nal
2264	rac_arb_pt_server: pt
2265	rac_arb_db_server: ds
2266	rac_arb_name_server: na
2267	rac_arb_convert_aln: convert
2268	rac_arb_treegen: tg
2269	rac_arb_rnacma: cma
2270	rac_arb_help2xml: help
2271
2272	rac_arb_a2ps: tools
2273	rac_arb_consensus_tree: tools
2274	rac_arb_dnarates: tools
2275	rac_arb_export_rates: tools
2276	rac_arb_export_tree: tools
2277	rac_arb_gene_probe: tools
2278	rac_arb_message: tools
2279	rac_arb_notify: tools
2280	rac_arb_primer: tools
2281	rac_arb_probe: tools
2282	rac_arb_read_tree: tools
2283
2284	# --------------------------------------------------------------------------------
2285	# unit testing
2286	# @@@ work in progress
2287	#
2288	# goal is to automatically test all libraries/executables using TESTED_UNITS_AUTO
2289	#
2290	# currently not all test executables link w/o error
2291	# (see UNITS_WORKING, UNITS_UNTESTABLE_ATM and UNITS_NEED_FIX)
2292
2293	# define RNA3D/RNA3D.test
2294	RNA3D_TEST := $(subst .a,.test,$(RNA3D_LIB))
2295
2296	TESTED_UNITS_AUTO = $(ARCHS:.a=.test)
2297
2298	UNITS_WORKING = \
2299	$(RNA3D_TEST) \
2300	AWTI/AWTI.test \
2301	EISPACK/EISPACK.test \
2302	GENOM/GENOM.test \
2303	GL/glAW/libglAW.test \
2304	GL/glpng/libglpng_arb.test \
2305	ISLAND_HOPPING/ISLAND_HOPPING.test \
2306	NALIGNER/NALIGNER.test \
2307	NAMES/NAMES.test \
2308	PHYLO/PHYLO.test \
2309	PRIMER_DESIGN/PRIMER_DESIGN.test \
2310	PROBE_DESIGN/PROBE_DESIGN.test \
2311	SECEDIT/SECEDIT.test \
2312	SEQ_QUALITY/SEQ_QUALITY.test \
2313	SERVERCNTRL/SERVERCNTRL.test \
2314	SL/ALIVIEW/ALIVIEW.test \
2315	SL/AP_TREE/AP_TREE.test \
2316	SL/ARB_TREE/ARB_TREE.test \
2317	SL/AW_HELIX/AW_HELIX.test \
2318	SL/AW_NAME/AW_NAME.test \
2319	SL/DB_SCANNER/DB_SCANNER.test \
2320	SL/GUI_ALIVIEW/GUI_ALIVIEW.test \
2321	SL/HELIX/HELIX.test \
2322	SL/LOCATION/LOCATION.test \
2323	SL/MATRIX/MATRIX.test \
2324	SL/REFENTRIES/REFENTRIES.test \
2325	SL/SEQUENCE/SEQUENCE.test \
2326	SL/TRANSLATE/TRANSLATE.test \
2327	SL/TREE_ADMIN/TREE_ADMIN.test \
2328	SL/TREE_WRITE/TREE_WRITE.test \
2329	STAT/STAT.test \
2330	TREEGEN/TREEGEN.test \
2331	WETC/WETC.test \
2332	XML/XML.test \
2333
2334	# untestable units
2335
2336	UNITS_NEED_FIX = \
2337	ptpan/PROBE.test \
2338
2339	UNITS_UNTESTABLE_ATM = \
2340	XML_IMPORT/XML_IMPORT.test \
2341
2342	# for the moment, put all units containing tests into UNITS_TESTED or UNITS_TESTED_FIRST
2343
2344	UNITS_TESTED_FIRST = \
2345	SL/ITEM_SHADER/ITEM_SHADER.test \
2346	PROBE_SET/fb_test.test \
2347	SL/ITEMS/ITEMS.test \
2348	SL/CONSENSUS/CONSENSUS.test \
2349	DIST/DIST.test \
2350	PARSIMONY/PARSIMONY.test \
2351	EDIT4/EDIT4.test \
2352	NTREE/NTREE.test \
2353	MULTI_PROBE/MULTI_PROBE.test \
2354
2355	# plain test-libaries not linked anywhere
2356	TEST_SANDBOXES = \
2357	SL/CB/CB.test \
2358
2359	UNITS_TESTED = \
2360	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.test \
2361	SL/NDS/NDS.test \
2362	ARB_GDE/ARB_GDE.test \
2363	GENOM_IMPORT/GENOM_IMPORT.test \
2364	SL/MACROS/MACROS.test \
2365	SL/REGEXPR/REGEXPR.test \
2366	SL/FILTER/FILTER.test \
2367	ARBDB/libARBDB.test \
2368	CONSENSUS_TREE/CONSENSUS_TREE.test \
2369	TOOLS/arb_consensus_tree.test \
2370	TOOLS/arb_test.test \
2371	TOOLS/arb_probe.test \
2372	PERLTOOLS/arb_proto_2_xsub.test \
2373	AWTC/AWTC.test \
2374	SL/ALILINK/ALILINK.test \
2375	SL/TREE_READ/TREE_READ.test \
2376	DBSERVER/DBSERVER.test \
2377	AWT/libAWT.test \
2378	CORE/libCORE.test \
2379	SL/INSDEL/INSDEL.test \
2380	SL/TREEDISP/TREEDISP.test \
2381	AISC_MKPTPS/mkptypes.test \
2382	MERGE/MERGE.test \
2383	SERVERCNTRL/SERVERCNTRL.test \
2384	SL/FAST_ALIGNER/FAST_ALIGNER.test \
2385	SL/PRONUC/PRONUC.test \
2386	WINDOW/libWINDOW.test \
2387	HELP_SOURCE/arb_help2xml.test \
2388	CONVERTALN/CONVERTALN.test \
2389	SL/SEQIO/SEQIO.test \
2390	SL/PTCLEAN/PTCLEAN.test \
2391	PROBE/PROBE.test \
2392	SL/DB_QUERY/DB_QUERY.test \
2393
2394	TESTED_UNITS_MANUAL = \
2395	$(TEST_SANDBOXES) \
2396	$(UNITS_TESTED_FIRST) \
2397	$(UNITS_TESTED) \
2398
2399	# $(UNITS_WORKING)
2400
2401	# see UNIT_TESTER/sym2testcode.pl@disableErrorOnUnitsWithoutTests
2402
2403	#TESTED_UNITS = $(TESTED_UNITS_AUTO)
2404	TESTED_UNITS = $(TESTED_UNITS_MANUAL)
2405
2406	# ----------------------------------------
2407
2408	TEST_LOG_DIR = UNIT_TESTER/logs
2409	TEST_RUN_SUITE=$(MAKE) $(NODIR) -C UNIT_TESTER -f Makefile.suite -r
2410	TEST_MAKE_FLAGS=
2411	TEST_POST_CLEAN=
2412	ifeq ($(COVERAGE),1)
2413	TEST_POST_CLEAN=$(MAKE) clean_cov
2414	TEST_MAKE_FLAGS+=-j1
2415	endif
2416
2417
2418	%.test:
2419	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
2420	( \
2421	echo "fake[1]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
2422	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
2423	"UNITDIR=$(@D)" \
2424	"UNITLIBNAME=$(@F:.test=)" \
2425	"COVERAGE=$(COVERAGE)" \
2426	"ARB_PID=$(ARB_PID)_$(@F)" \
2427	runtest; \
2428	echo "fake[1]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"; \
2429	$(TEST_POST_CLEAN) \
2430	) >$(TEST_LOG_DIR)/$(@F).log 2>&1; \
2431	UNIT_TESTER/log_result.pl $(TEST_LOG_DIR)/$(@F).log )
2432
2433
2434	test_base: $(UNIT_TESTER_LIB:.a=.dummy) $(subst .test,.dummy,$(TEST_SANDBOXES))
2435
2436	clean_cov:
2437	find . \( -name ".gcda" -o -name ".gcov" -o -name "*.cov" \) -exec rm {} \;
2438
2439	clean_cov_all: clean_cov
2440	find . \( -name "*.gcno" \) -exec rm {} \;
2441
2442	run_tests: test_base clean_cov
2443	$(MAKE) "ARB_PID=UT_$$$$" run_tests_faked_arbpid
2444
2445	cleanup_faked_arbpids:
2446	@rm ~/.arb_tmp/tmp/arb_pids_${USER}_${ARB_PID}_* \|\| true
2447
2448	cleanup_faked_arbpids_and_fail: cleanup_faked_arbpids
2449	@false
2450
2451	run_tests_faked_arbpid:
2452	+@$(TEST_RUN_SUITE) init
2453	@echo "fake[2]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2454	$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(TESTED_UNITS) \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2455	@echo "fake[2]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2456	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2457	@$(MAKE) clean_cov >/dev/null
2458	@$(MAKE) cleanup_faked_arbpids
2459
2460	ut:
2461	ifeq ($(UNIT_TESTS),1)
2462	@echo $(MAKE) run_tests
2463	@$(MAKE) run_tests
2464	else
2465	@echo "Not compiled with unit tests"
2466	endif
2467
2468
2469	aut:
2470	+@$(TEST_RUN_SUITE) unskip
2471	$(MAKE) ut
2472
2473	# --------------------------------------------------------------------------------
2474
2475	TIMELOG=$(ARBHOME)/arb_time.log
2476	TIMEARGS=--append --output=$(TIMELOG) --format=" %E(%S+%U) %P [%C]"
2477	TIMECMD=$(TIME) $(TIMEARGS)
2478
2479	time_one:
2480	ifeq ($(ONE_TIMED_TARGET),)
2481	@echo "Error: You have to pass ONE_TIMED_TARGET to $@"
2482	false
2483	else
2484	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET)"
2485	@$(TIMECMD) $(MAKE) $(ONE_TIMED_TARGET)
2486	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET) [done]"
2487	endif
2488
2489	timed_target:
2490	ifeq ($(TIMED_TARGET),)
2491	@echo "Error: You have to pass TIMED_TARGET to $@"
2492	false
2493	else
2494	@echo "Build time:" > $(TIMELOG)
2495	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2496	@cat $(TIMELOG)
2497	@rm $(TIMELOG)
2498	endif
2499
2500	timed_target_tested:
2501	ifeq ($(TIMED_TARGET),)
2502	@echo "Error: You have to pass TIMED_TARGET to $@"
2503	false
2504	else
2505	@echo "Build time:" > $(TIMELOG)
2506	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2507	$(MAKE) "ONE_TIMED_TARGET=ut" time_one
2508	@cat $(TIMELOG)
2509	@rm $(TIMELOG)
2510	endif
2511
2512	clean_timed_target:
2513	ifeq ($(TIMED_TARGET),)
2514	@echo "Error: You have to pass TIMED_TARGET to $@"
2515	false
2516	else
2517	@echo "Build time:" > $(TIMELOG)
2518	$(MAKE) "ONE_TIMED_TARGET=clean" time_one
2519	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2520	@cat $(TIMELOG)
2521	@rm $(TIMELOG)
2522	endif
2523
2524	# --------------------------------------------------------------------------------
2525
2526	CHECKOUT_MODIFIED=0# set to 1 to temporarily skip test for modifications (do not check in if set to 1)
2527
2528	check_svn_does_not_contain_generated:
2529	ifeq ($(CHECKOUT_MODIFIED),0)
2530	@echo "Testing that build does not modify files in SVN"
2531	@test 0 = `svn status \| wc -l` \|\| ( \
2532	echo "The checkout is not/no longer clean:"; \
2533	svn status; \
2534	echo "- if this fails instantly, your checkout is not clean"; \
2535	echo "- if this fails after other targets, these targets modify checked in data"; \
2536	echo " (a common cause may be that depends are not up to date)"; \
2537	false)
2538	else
2539	grep -Hn 'CHECKOUT_MODIFIED' Makefile
2540	endif
2541
2542	check_svn_ignores_generated:
2543	@test 0 = `svn status \| grep '^\?' \| wc -l` \|\| ( \
2544	echo "There are svn-unignored files:"; \
2545	svn status \| grep '^\?'; \
2546	echo "(all generated files should be svn-ignored)"; \
2547	false)
2548
2549	check_svn_state: check_svn_does_not_contain_generated
2550	$(MAKE) check_svn_ignores_generated
2551	$(MAKE) savetest
2552
2553	things_that_always_should_work: depends proto
2554
2555	post_commit_check:
2556	@echo "---------------------------------------- [Initial]"
2557	$(MAKE) check_svn_state
2558
2559	$(MAKE) clean
2560	@echo "---------------------------------------- [After 'make clean']"
2561	$(MAKE) check_svn_state
2562
2563	$(MAKE) things_that_always_should_work
2564	@echo "---------------------------------------- [After 'make things_that_always_should_work']"
2565	$(MAKE) check_svn_state
2566
2567	$(MAKE) all
2568	@echo "---------------------------------------- [After 'make all']"
2569	$(MAKE) check_svn_state
2570
2571	$(MAKE) things_that_always_should_work
2572	@echo "---------------------------------------- [Final]"
2573	$(MAKE) check_svn_state
2574
2575	# --------------------------------------------------------------------------------
2576	# sanitize arb_ntree; also works for clients (arb_edit4, ...) started from there.
2577
2578	sanitize: all
2579	( \
2580	export "LSAN_OPTIONS=max_leaks=30:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp"; \
2581	echo "sake[1]: Entering directory \`$(ARBHOME)'"; \
2582	$(ARBHOME)/bin/arb_ntree --execute _logged ~/data/test.arb 2>&1 ; \
2583	echo "sake[1]: Leaving directory \`$(ARBHOME)'" \
2584	) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
2585
2586	# --------------------------------------------------------------------------------
2587
2588	build: arb
2589	$(MAKE) binlink preplib compile_compatibility
2590
2591	all:
2592	@echo "Build time" > $(TIMELOG)
2593	@echo "$(SEP) $(MAKE) build"
2594	@$(TIMECMD) $(MAKE) build
2595	@echo $(SEP)
2596	@echo "made 'all' with success."
2597	@echo "to start arb enter 'arb'"
2598	ifeq ($(UNIT_TESTS),1)
2599	@echo $(MAKE) run_tests
2600	@$(TIMECMD) $(MAKE) run_tests
2601	endif
2602	@echo "$(SEP) $(MAKE) build [done]"
2603	ifeq ($(DEBUG),1)
2604	@$(MAKE) save_test_no_error >/dev/null # just show hints
2605	endif
2606	@cat $(TIMELOG)
2607	@rm $(TIMELOG)
2608

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