Context Navigation

source: tags/ms_r16q2/Makefile

Visit:

Last change on this file was 14968, checked in by westram, 8 years ago
added `MutableBoundItemSel::get_any_item()` fixed link-order of ITEMS and ITEM_SHADER
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 73.6 KB

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

Note: See TracBrowser for help on using the repository browser.

Download in other formats: