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Last change on this file since 13131 was 13131, checked in by westram, 10 years ago
partial update from 'trunk' into 'pars' adds: log:trunk@13079,13081:13130
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 69.9 KB

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1	# =============================================================== #
2	# #
3	# File : Makefile #
4	# #
5	# Institute of Microbiology (Technical University Munich) #
6	# http://www.arb-home.de/ #
7	# #
8	# =============================================================== #
9
10	# -----------------------------------------------------
11	# The ARB Makefile is aware of the following defines:
12	#
13	# CC C compiler (should be defined by OS)
14	# CXX C++ compiler (should be defined by OS)
15	#
16	# BUILDHOST_64=0/1 1=>compile on 64 bit platform (defaults to ARB_64)
17	# DEVELOPER=name special compilation (values: ANY,RELEASE,your name)
18	# OPENGL=0/1 whether OPENGL is available
19	#
20	# -----------------------------------------------------
21	# ARB Makefile and ARB source code are aware of the following defines:
22	#
23	# $(MACH) name of the machine (LINUX or DARWIN; see config.makefile)
24	# DEBUG compiles the DEBUG sections
25	# DEBUG_GRAPHICS all X-graphics are flushed immediately (for debugging)
26	# ARB_64=0/1 1=>compile 64 bit version
27	# UNIT_TESTS=0/1 1=>compile in unit tests and call them after build
28	# COVERAGE=0/1/2 compile in gcov support (useful together with UNIT_TESTS=1)
29	# 0=no, 1+2=compile in, 1=show
30	# STABS=0/1 force stabs format? (0 = "use default format")
31	# SANITIZE=0/#/all use Sanitizer? (defaults to 0,
32	# 1=AddressSanitizer+LeakSanitizer,
33	# 2=UndefinedBehaviorSanitizer,
34	# combine bit-values to activate multiple Sanitizers,
35	# specify 'all' to activate all)
36	# SHOWTODO=0/1 activate TODO-warnings? (defaults to 0, except for ralf)
37	#
38	# -----------------------------------------------------
39	# The ARB source code is aware of the following defines:
40	#
41	# NDEBUG doesn't compile the DEBUG sections
42	# DEVEL_$(DEVELOPER) developer-dependent flag (enables you to have private sections in code)
43	# DEVELOPER='ANY' (default setting) will be ignored
44	# configurable in config.makefile
45	#
46	# -----------------------------------------------------
47	# Read configuration
48	include config.makefile
49
50	# set defaults for variables commented out in config.makefile:
51	ifndef DARWIN
52	DARWIN:=0
53	endif
54	ifndef LINUX
55	LINUX:=0
56	endif
57	ifndef DEBIAN
58	DEBIAN:=0
59	endif
60	ifndef REDHAT
61	REDHAT:=0
62	endif
63	ifndef ARB_64
64	ARB_64=1#default to 64bit
65	endif
66
67	# compiler settings:
68	ifneq ($(CC),use__A_CC__instead_of__CC)
69
70	A_CC:=$(CC)# compile C
71	A_CXX:=$(CXX)# compile C++
72
73	# uncomment to ensure no submakefile uses CC and CXX directly
74	override CC:=use__A_CC__instead_of__CC
75	override CXX:=use__A_CXX__instead_of__CXX
76
77	endif
78
79	export CC CXX A_CC A_CXX
80
81	# unconditionally prepend $(ARBHOME)/lib to LD_LIBRARY_PATH if not found
82	ifeq ($(findstring $(ARBHOME)/lib,$(LD_LIBRARY_PATH)),)
83	LD_LIBRARY_PATH:=${ARBHOME}/lib:$(LD_LIBRARY_PATH)
84	endif
85
86	FORCEMASK = umask 002
87	NODIR=--no-print-directory
88
89	SED:=$(ARBHOME)/SH/arb_sed
90	READLINK:=$(ARBHOME)/SH/arb_readlink
91
92	# ---------------------- compiler version detection
93
94	# supported gcc versions:
95	ALLOWED_gcc_VERSIONS=\
96	4.3.1 4.3.2 4.3.3 4.3.4 \
97	4.4.1 4.4.3 4.4.5 4.4.6 4.4.7 \
98	4.5.2 \
99	4.6.1 4.6.2 4.6.3 \
100	4.7.1 4.7.2 4.7.3 4.7.4 \
101	4.8.0 4.8.1 4.8.2 4.8.3 \
102	4.9.0 4.9.1 4.9.2 \
103
104	# supported clang versions:
105	ALLOWED_clang_VERSIONS=\
106	4.2.1 \
107
108	# ----------------------
109
110	COMPILER_INFO:=$(shell SOURCE_TOOLS/arb_compiler_version.pl $(A_CXX))
111	COMPILER_NAME:=$(word 1,$(COMPILER_INFO))
112	COMPILER_VERSION:=$(word 2,$(COMPILER_INFO))
113
114	USE_CLANG:=0
115	ifneq ($(COMPILER_NAME),gcc)
116	ifeq ($(COMPILER_NAME),clang)
117	USE_CLANG:=1
118	else
119	$(error failed to detect COMPILER_NAME (got '$(COMPILER_NAME)', expected 'clang' or 'gcc'))
120	endif
121	endif
122
123	ifeq ($(USE_CLANG),1)
124	ALLOWED_COMPILER_VERSIONS=$(ALLOWED_clang_VERSIONS)
125	else
126	ALLOWED_COMPILER_VERSIONS=$(ALLOWED_gcc_VERSIONS)
127	endif
128
129	COMPILER_VERSION_ALLOWED=$(strip $(subst ___,,$(foreach version,$(ALLOWED_COMPILER_VERSIONS),$(findstring ___$(version)___,___$(COMPILER_VERSION)___))))
130
131	#---------------------- split gcc version
132
133	SPLITTED_VERSION:=$(subst ., ,$(COMPILER_VERSION))
134
135	USE_GCC_MAJOR:=$(word 1,$(SPLITTED_VERSION))
136	USE_GCC_MINOR:=$(word 2,$(SPLITTED_VERSION))
137	USE_GCC_PATCHLEVEL:=$(word 3,$(SPLITTED_VERSION))
138
139	USE_GCC_452_OR_HIGHER:=
140	USE_GCC_46_OR_HIGHER:=
141	USE_GCC_47_OR_HIGHER:=
142	USE_GCC_48_OR_HIGHER:=
143	USE_GCC_49_OR_HIGHER:=
144
145	ifeq ($(USE_GCC_MAJOR),4)
146	ifeq ($(USE_GCC_MINOR),5)
147	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),23456789)','')
148	USE_GCC_452_OR_HIGHER:=yes
149	endif
150	else
151	ifneq ('$(findstring $(USE_GCC_MINOR),6789)','')
152	USE_GCC_452_OR_HIGHER:=yes
153	USE_GCC_46_OR_HIGHER:=yes
154	ifneq ($(USE_GCC_MINOR),6)
155	USE_GCC_47_OR_HIGHER:=yes
156	ifneq ($(USE_GCC_MINOR),7)
157	USE_GCC_48_OR_HIGHER:=yes
158	ifneq ($(USE_GCC_MINOR),8)
159	USE_GCC_49_OR_HIGHER:=yes
160	endif
161	endif
162	endif
163	endif
164	endif
165	else
166	USE_GCC_452_OR_HIGHER:=yes
167	USE_GCC_46_OR_HIGHER:=yes
168	USE_GCC_47_OR_HIGHER:=yes
169	USE_GCC_48_OR_HIGHER:=yes
170	USE_GCC_49_OR_HIGHER:=yes
171	endif
172
173	#---------------------- define special directories for non standard builds
174
175	ifeq ($(DARWIN),1)
176	OSX_FW:=/System/Library/Frameworks
177	OSX_FW_OPENGL:=$(OSX_FW)/OpenGL.framework/Versions/A/Libraries
178	OSX_FW_GLUT:=$(OSX_FW)/GLUT.framework/Versions/A/Libraries
179	OSX_FW_IMAGEIO:=$(OSX_FW)/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources
180	endif
181
182	#----------------------
183
184	ifeq ($(DARWIN),1)
185	LINK_STATIC=1# link static
186	else
187	LINK_STATIC=0# link dynamically
188	# LINK_STATIC=1# link static (testing only)
189	endif
190
191	shared_cflags :=# flags for shared lib compilation
192	lflags :=# linker flags
193	clflags :=# linker flags (when passed through gcc)
194	extended_warnings :=# warning flags for C and C++-compiler
195	extended_cpp_warnings :=# warning flags for C++-compiler only
196
197	# TEMPORARY WORKAROUND for linker issues with launchpad binutils
198	# code was added to ld to check for overlapping FDEs. Since ARB
199	# worked before, we want this not to fail for the moment.
200	# FIXME: remove this!
201	clflags += -Wl,-noinhibit-exec
202
203
204	ifeq ($(DEBUG),0)
205	dflags := -DNDEBUG# defines
206	ifeq ($(USE_CLANG),1)
207	cflags := -O3# compiler flags (C and C++)
208	else
209	cflags := -O4# compiler flags (C and C++)
210	lflags += -O2# linker flags
211	clflags += -Wl,-O2# passthrough linker flags
212	endif
213	endif
214
215	ifeq ($(DEBIAN),1)
216	lflags += -rpath=/usr/lib/arb/lib -z relro
217	clflags += -Wl,-rpath=/usr/lib/arb/lib -Wl,-z,relro
218	endif
219
220	ifeq ($(DEBUG),1)
221	dflags := -DDEBUG
222
223	gdb_common := -g -g3 -ggdb -ggdb3
224
225	DBGOPTI:=-O0
226	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
227	DBGOPTI:=-Og
228	endif
229
230	ifeq ($(STABS),1)
231	cflags := $(DBGOPTI) $(gdb_common) -gstabs+ # using stabs+ (enable this for bigger debug session: debugs inlines, quick var inspect, BUT valgrind stops working :/)
232	else
233	cflags := $(DBGOPTI) $(gdb_common) # (using dwarf - cant debug inlines here, incredible slow on showing variable content)
234	endif
235
236	# cflags := $(DBGOPTI) $(gdb_common) -gdwarf-3 # (specify explicit dwarf format)
237	# cflags := $(DBGOPTI) $(gdb_common) -gstabs # using stabs (same here IIRC)
238	# cflags := -O2 $(gdb_common) # use this for callgrind (force inlining)
239
240	ifeq ($(DARWIN),0)
241	lflags += -g
242	clflags += -Wl,-g
243	endif
244
245	# control how much you get spammed
246	# (please do not change default in SVN, use developer specific setting as below)
247	POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl
248	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --original# dont modify compiler output
249	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --hide-Noncopyable-advices
250	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --show-useless-Weff++
251	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --no-warnings
252	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --only-first-error
253	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --no-warnings --only-first-error
254	ifeq ($(DEVELOPER),ELMAR)
255	POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --only-first-error
256	endif
257
258
259	# Enable extra warnings
260	extended_warnings :=
261	extended_cpp_warnings :=
262
263	# C and C++
264	extended_warnings += -Wwrite-strings -Wunused -Wno-aggregate-return -Wshadow
265
266	# C++ only
267	extended_cpp_warnings += -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute
268	extended_cpp_warnings += -Wctor-dtor-privacy# < gcc 3
269	# extended_cpp_warnings += -Wfloat-equal# gcc 3.0
270
271	# ------- above only warnings available in 3.0
272
273	WEFFC_BROKEN:=0
274	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
275	ifneq ('$(USE_GCC_48_OR_HIGHER)','yes')
276	# -Weffc++ broken in 4.7.x series
277	# gcc 4.7.3 crashes on GenomeImport.cxx when -Weffc++ is active
278	# (bug reported https://gcc.gnu.org/bugzilla/show_bug.cgi?id=56923; apparently wont be fixed for 4.7-series)
279	# gcc 4.7.4 crashes on DBwriter.cxx when -Weffc++ is active
280	WEFFC_BROKEN:=1
281	endif
282	endif
283	ifeq ('$(WEFFC_BROKEN)','0')
284	extended_cpp_warnings += -Weffc++# gcc 3.0.1
285	endif
286	extended_cpp_warnings += -Wmissing-noreturn# gcc 3.0.2
287	# extended_cpp_warnings += -Wold-style-cast# gcc 3.0.4 (warn about 28405 old-style casts)
288	extended_cpp_warnings += -Winit-self# gcc 3.4.0
289	extended_cpp_warnings += -Wstrict-aliasing# gcc 3.4
290	extended_cpp_warnings += -Wextra# gcc 3.4.0
291	ifeq ('$(USE_GCC_452_OR_HIGHER)','yes')
292	extended_cpp_warnings += -Wlogical-op# gcc 4.5.2
293	endif
294	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
295	# extended_cpp_warnings += -Wunused-local-typedefs# gcc 4.7 (fails for each STATIC_ASSERT, enable only for Cxx11)
296	# extended_cpp_warnings += -Wzero-as-null-pointer-constant# gcc 4.7 #@@@ activate
297	endif
298	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
299	extended_cpp_warnings += -Wunused-local-typedefs# available since gcc 4.7 (but fails for each STATIC_ASSERT, so enable only for Cxx11)
300	endif
301
302	ifeq ($(DEBUG_GRAPHICS),1)
303	dflags += -DDEBUG_GRAPHICS
304	endif
305	endif
306
307	#---------------------- turn off clang bogus warnings
308
309	ifeq ($(USE_CLANG),1)
310	# -Wmismatched-tags warns about struct/class mismatch in forward declarations (which is explicitely allowed)
311	# -Wchar-subscripts reports too many bogus warnings for "array['x']" (when 'x' is known to be in range [0..128])
312	# -Wunused-private-field report too many false positives (currently ~ 2 of 3)
313	# -Wstring-plus-int warns about common ARB coding practice
314	# -Wgnu-static-float-init warns about accepted GNU extension
315	extended_cpp_warnings += -Wno-mismatched-tags -Wno-char-subscripts -Wno-unused-private-field -Wno-string-plus-int -Wno-gnu-static-float-init
316	endif
317
318	#---------------------- developer
319
320	ifneq ($(DEVELOPER),ANY) # ANY=default setting (skip all developer specific code)
321	dflags += -DDEVEL_$(DEVELOPER)# activate developer/release specific code
322	endif
323
324	#---------------------- activate TODO warnings?
325
326	ifndef SHOWTODO
327	ifeq ($(DEVELOPER),RALF)
328	SHOWTODO:=1
329	else
330	SHOWTODO:=0
331	endif
332	endif
333	ifeq ($(SHOWTODO),1)
334	dflags += -DWARN_TODO# activate "TODO" warnings
335	endif
336
337	#---------------------- activate Sanitizers?
338
339	ASAN_OPTIONS:=handle_segv=0:color=0
340	ASAN_OPTIONS+=:detect_leaks=1 # comment-out to disable leak-detection
341	ASAN_OPTIONS+=:check_initialization_order=1
342
343	# suppressions: SOURCE_TOOLS/arb.leaksan.supp
344	LSAN_OPTIONS:=max_leaks=3:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp
345
346
347	ifndef SANITIZE
348	SANITIZE:=0
349	endif
350
351	SANITIZE_ADDRESS:=0
352	SANITIZE_UNDEFINED:=0
353
354	ifneq ($(SANITIZE),0)
355	ifeq ($(SANITIZE),all)
356	SANITIZE:=3
357	endif
358
359	ifeq ($(SANITIZE),1)
360	SANITIZE_ADDRESS:=1
361	else
362	ifeq ($(SANITIZE),2)
363	SANITIZE_UNDEFINED:=1
364	else
365	ifeq ($(SANITIZE),3)
366	SANITIZE_ADDRESS:=1
367	SANITIZE_UNDEFINED:=1
368	else
369	$(error Unknown value '$(SANITIZE)' specified for SANITIZE in config.makefile)
370	endif
371	endif
372	endif
373	endif
374
375	ifeq ($(SANITIZE_ADDRESS),1)
376	ifneq ('$(USE_GCC_48_OR_HIGHER)','yes')
377	$(info AddressSanitizer not usable with gcc $(COMPILER_VERSION) - disabled)
378	SANITIZE_ADDRESS:=0
379	else
380	ifneq ('$(USE_GCC_49_OR_HIGHER)','yes')
381	$(warning note that LeakSanitizer does not work with gcc $(COMPILER_VERSION))
382	endif
383	endif
384	endif
385
386	ifeq ($(SANITIZE_UNDEFINED),1)
387	ifneq ('$(USE_GCC_49_OR_HIGHER)','yes')
388	$(info UndefinedBehaviorSanitizer not usable with gcc $(COMPILER_VERSION) - disabled)
389	SANITIZE_UNDEFINED:=0
390	endif
391	endif
392
393	#---------------------- 32 or 64 bit
394
395	ifndef BUILDHOST_64
396	BUILDHOST_64:=$(ARB_64)# assume build host is same as version (see config.makefile)
397	endif
398
399	cross_cflags:=
400	cross_lflags:=
401	cross_clflags:=
402
403	ifeq ($(ARB_64),1)
404	dflags += -DARB_64 #-fPIC
405	shared_cflags += -fPIC
406
407	ifeq ($(BUILDHOST_64),1)
408	# build 64-bit ARB version on 64-bit host
409	CROSS_LIB:=# empty = autodetect below
410	ifeq ($(DARWIN),1)
411	cross_cflags += -arch x86_64
412	cross_lflags += -arch x86_64
413	cross_clflags += -arch x86_64
414	endif
415	else
416	# build 64-bit ARB version on 32-bit host
417	CROSS_LIB:=/lib64
418	cross_cflags += -m64
419	cross_lflags += -m64 -m elf_x86_64
420	cross_clflags += -m64 -Wl,-m64,-m,elf_x86_64
421	endif
422	else
423	ifeq ($(BUILDHOST_64),1)
424	# build 32-bit ARB version on 64-bit host
425	CROSS_LIB:=# empty = autodetect below
426	cross_cflags += -m32
427	cross_lflags += -m32 -m elf_i386
428	cross_clflags += -m32 -Wl,-m32,-m,elf_i386
429	else
430	# build 32-bit ARB version on 32-bit host
431	CROSS_LIB:=/lib
432	endif
433	endif
434
435	cflags += $(cross_cflags)
436	lflags += $(cross_lflags)
437	clflags += $(cross_clflags)
438
439	ifeq ('$(CROSS_LIB)','')
440	# autodetect libdir
441	ifeq ($(ARB_64),1)
442	CROSS_LIB:=$(shell (test -d /lib64 && echo lib64) \|\| echo lib)
443	else
444	CROSS_LIB:=$(shell (test -d /lib32 && echo lib32) \|\| echo lib)
445	endif
446	endif
447
448	#---------------------- unit tests
449
450	ifndef UNIT_TESTS
451	UNIT_TESTS=0#default is "no tests"
452	endif
453	ifeq ($(UNIT_TESTS),1)
454	dflags += -DUNIT_TESTS
455	UNIT_TESTER_LIB=UNIT_TESTER/UNIT_TESTER.a
456	else
457	UNIT_TESTER_LIB=
458	endif
459
460	#---------------------- use gcov
461
462	ifndef COVERAGE
463	COVERAGE=0#default is "no"
464	endif
465	ifneq ($(COVERAGE),0)
466	GCOVFLAGS=-ftest-coverage -fprofile-arcs
467	cflags += $(GCOVFLAGS)
468	EXECLIBS=-lgcov
469	else
470	GCOVFLAGS=
471	EXECLIBS=
472	endif
473
474	#---------------------- other flags
475
476	dflags += -D$(MACH) # define machine
477
478	ifeq ($(DARWIN),1)
479	shared_cflags += -fno-common
480	else
481	dflags += $(shell getconf LFS_CFLAGS)
482	endif
483
484	cflags += -pipe
485	cflags += -fmessage-length=0# don't wrap compiler output
486	cflags += -fshow-column# show columns
487	cflags += -funit-at-a-time
488	cflags += -fPIC
489	cflags += -fno-common# link all global data into one namespace
490	cflags += -fstrict-aliasing# gcc 3.4
491	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
492	cflags += -fno-diagnostics-show-caret#gcc 4.8 (4.7.?)
493	endif
494	#cflags += -save-temps# uncomment to see preprocessor output
495
496	#---------------------- various sanitizers
497
498	COMMON_SANITIZE_FLAGS:=-ggdb3 -fno-omit-frame-pointer
499
500	# activate AddressSanitizer+LeakSanitizer?
501	ifeq ($(SANITIZE_ADDRESS),1)
502	cflags += $(COMMON_SANITIZE_FLAGS) -fsanitize=address
503	EXECLIBS += -lasan
504	# EXECLIBS += -static-libasan
505	endif
506
507	# activate UndefinedBehaviorSanitizer?
508	ifeq ($(SANITIZE_UNDEFINED),1)
509	cflags += $(COMMON_SANITIZE_FLAGS) -fsanitize=undefined
510	ifeq ('$(DEBUG)','1')
511	ifeq ($(USE_GCC_MAJOR),4)
512	ifeq ($(USE_GCC_MINOR),9)
513	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),01)','')
514	# workaround https://gcc.gnu.org/bugzilla/show_bug.cgi?id=63531 for 4.9.0 + 4.9.1
515	# (problem is fixed in 4.9.2 release)
516	extended_cpp_warnings:=$(subst -Weffc++,,$(extended_cpp_warnings))
517	endif
518	endif
519	endif
520	endif
521	EXECLIBS += -lubsan
522	endif
523
524	#---------------------- X11 location
525
526	ifeq ($(DARWIN),1)
527	XHOME:=$(PREFIX)
528	else
529	ifeq ($(DEBIAN),1)
530	XHOME:=$(PREFIX)
531	else
532	XHOME:=/usr/X11R6
533	endif
534	endif
535
536	XINCLUDES:=-I$(XHOME)/include
537	ifeq ($(DARWIN),1)
538	XINCLUDES += -I$(OSX_FW)/GLUT.framework/Headers -I$(OSX_FW)/OpenGL.framework/Headers -I$(OSX_SDK)/usr/include/krb5
539
540	XLIBS := -L$(XHOME)/lib -lXm -lpng -lz -lXt -lX11 -lXext -lXp -lXmu -lXi
541	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGL.dylib:$(OSX_FW_OPENGL)/libGL.dylib
542	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGLU.dylib:$(OSX_FW_OPENGL)/libGLU.dylib
543	else
544	XLIBS:=-L$(XHOME)/$(CROSS_LIB) -lXm -lXpm -lXt -lXext -lX11
545	endif
546
547	dflags += -DARB_MOTIF
548
549	#---------------------- open GL
550
551	ifeq ($(OPENGL),1)
552	cflags += -DARB_OPENGL # activate OPENGL code
553	GL := gl # this is the name of the OPENGL base target
554	GL_LIB_SYS := -lGL -lGLU
555	GL_LIB_ARB := -L$(ARBHOME)/GL/glAW -lglAW
556
557	ifeq ($(DARWIN),1)
558	GL_LIB_SYS += -lpthread
559	endif
560
561	GL_PNGLIBS_ARB := -L$(ARBHOME)/GL/glpng -lglpng_arb
562	GL_PNGLIBS_SYS := -lpng
563
564	GLEWLIB := -lGLEW -lGLw
565	ifeq ($(DARWIN),1)
566	GLUTLIB := -glut
567	else
568	GLUTLIB := -lglut
569	endif
570
571	GL_LIBS_SYS := $(GL_LIB_SYS) $(GL_PNGLIBS_SYS) $(GLEWLIB) $(GLUTLIB)
572	GL_LIBS_ARB := $(GL_LIB_ARB) $(GL_PNGLIBS_ARB)
573
574	RNA3D_LIB := RNA3D/RNA3D.a
575
576	else
577
578	GL_LIBS_ARB:=# no opengl -> no libs
579	GL_LIBS_SYS:=# no opengl -> no libs
580	GL:=# don't build ARB openGL libs
581
582	RNA3D_LIB :=
583
584	endif
585
586	RNA3D_LIB_4_DEPENDS := RNA3D/RNA3D.a
587
588	GL_LIBS:=$(GL_LIBS_ARB) $(GL_LIBS_SYS)
589
590	#---------------------- tiff lib:
591
592	TIFFLIBS := -ltiff
593
594	#---------------------- glib:
595
596	ARB_NEEDED_GLIB=glib-2.0
597
598	ARB_GLIB_INCLUDE:=$(strip $(shell pkg-config --cflags $(ARB_NEEDED_GLIB)))
599	ARB_GLIB_LIBS:=$(strip $(shell pkg-config --libs $(ARB_NEEDED_GLIB)))
600
601	#---------------------- basic libs:
602
603	SYSLIBS:=
604
605	ifeq ($(DARWIN),1)
606	SYSLIBS += -lstdc++
607	else
608	SYSLIBS += -lm $(ARB_GLIB_LIBS)
609	endif
610
611	#---------------------- include symbols?
612
613	ifeq ($(TRACESYM),1)
614	ifeq ($(USE_CLANG),0)
615	cflags += -rdynamic
616	lflags += --export-dynamic
617	clflags += -rdynamic -Wl,--export-dynamic
618	endif
619	endif
620
621	#---------------------- system dependent commands
622
623	ifeq ($(DARWIN),1)
624	TIME:=gtime
625	else
626	TIME:=/usr/bin/time
627	endif
628
629	# -------------------------------------------------------------------------
630	# Don't put any machine/version/etc conditionals below!
631	# (instead define variables above)
632	# -------------------------------------------------------------------------
633
634	cflags += -W -Wall $(dflags) $(extended_warnings)
635	cxxflags := $(extended_cpp_warnings)
636
637	# add CFLAGS + CPPFLAGS from environment for DEBIAN build
638	ifeq ($(DEBIAN),1)
639	cflags := $(CFLAGS) $(cflags)
640	cxxflags += $(CPPFLAGS)
641	endif
642
643	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
644	cxxflags += -std=gnu++11# see also TEMPLATES/cxxforward.h@USE_Cxx11
645	else
646	# only use for gcc versions between 4.3 and <4.7 (4.7++ adds -Wc++11-compat above)
647	HAVE_GNUPP0X=`SOURCE_TOOLS/requireVersion.pl 4.3 $(COMPILER_VERSION)`
648	ifeq ($(HAVE_GNUPP0X),1)
649	# ensure compatibility with upcoming C++ standard
650	cxxflags += -std=gnu++0x
651	endif
652	endif
653
654	LINK_STATIC_LIB := ld $(lflags) -r -o# link static lib
655	LINK_EXECUTABLE := $(A_CXX) $(clflags) -o# link executable (c++)
656
657	ifeq ($(LINK_STATIC),1)
658	SHARED_LIB_SUFFIX = a# static lib suffix
659	LINK_SHARED_LIB := $(LINK_STATIC_LIB)
660	else
661	SHARED_LIB_SUFFIX = so# shared lib suffix
662	LINK_SHARED_LIB := $(A_CXX) $(clflags) -shared $(GCOVFLAGS) -o# link shared lib
663	endif
664
665	# delete variables unused below
666	lflags:=
667	clflags:=
668
669	# other used tools
670	MAKEDEPEND_PLAIN = makedepend
671	MAKEDEPEND = $(FORCEMASK);$(MAKEDEPEND_PLAIN)
672
673	#SEP:=--------------------------------------------------------------------------------
674	SEP=[`date +%M:%S.%N`] ------------------------------------------------
675	# to analyse timings run
676	# make -j9 clean; make -j9 all \| grep '^\[' \| sort
677	# make -j9 "TIMED_TARGET=perl" clean_timed_target \| grep '^\[' \| sort
678
679	CORE_LIB=-lCORE
680	ARBDB_LIB=-lARBDB $(CORE_LIB)
681	LIBS = $(ARBDB_LIB) $(SYSLIBS)
682
683	GUI_LIBS_PREFIX:=
684	ifeq ($(DARWIN),1)
685	# this seem to be added at wrong place, since opengl is only needed to link EDIT4
686	GUI_LIBS_PREFIX:=-framework GLUT -framework OpenGL
687	endif
688
689	GUI_LIBS=$(GUI_LIBS_PREFIX) $(LIBS) -lAWT -lWINDOW
690	GUI_LIBS+=$(XLIBS)
691
692	LIBPATH = -L$(ARBHOME)/lib
693
694	DEST_LIB = lib
695	DEST_BIN = bin
696
697	CC_INCLUDES := -I. -I$(ARBHOME)/INCLUDE $(XINCLUDES) $(ARB_GLIB_INCLUDE)
698	CXX_INCLUDES := $(CC_INCLUDES)
699	MAKEDEPENDFLAGS := -- -DARB_OPENGL -DUNIT_TESTS -D__cplusplus -I. -Y$(ARBHOME)/INCLUDE
700
701	# -------------------------------
702	# old PTSERVER or PTPAN?
703
704	ifeq ($(PTPAN),1)
705	# PTPAN only libs
706	ARCHS_PT_SERVER = \
707	ptpan/PROBE.a
708	else
709	ifeq ($(PTPAN),2)
710	# special mode to compile both servers (developers only!)
711	ARCHS_PT_SERVER = \
712	ptpan/PROBE.a \
713	PROBE/PROBE.a
714	ARCHS_PT_SERVER_LINK = PROBE/PROBE.a# default to old ptserver
715	else
716	# PT-server only libs
717	ARCHS_PT_SERVER = \
718	PROBE/PROBE.a
719	endif
720	endif
721
722	ifndef ARCHS_PT_SERVER_LINK
723	ARCHS_PT_SERVER_LINK = $(ARCHS_PT_SERVER)
724	endif
725
726	# ---------------------------------------
727	# wrap main()
728
729	use_ARB_main=$(ARBHOME)/SOURCE_TOOLS/arb_main_cpp.o
730	use_ARB_main_C=$(ARBHOME)/SOURCE_TOOLS/arb_main_c.o
731
732	# -----------------------------------------
733	# export variables to submakefiles
734
735	include SOURCE_TOOLS/export2sub
736
737	# do not define (exported) variables below this point
738
739	# -------------------------
740	# Main arb targets:
741	# -------------------------
742
743	first_target:
744	$(MAKE) checks
745	@echo $(SEP)
746	@echo 'Main targets:'
747	@echo ''
748	@echo ' all - Compile ARB + TOOLs + and copy shared libs + link foreign software'
749	@echo ' (That is most likely the target you want)'
750	@echo ''
751	@echo ' clean - remove generated files ("SUBDIR/SUBDIR.clean" to clean only SUBDIR)'
752	@echo ' rebuild - clean + all'
753	@echo ' relink - remove all binaries and relink them from objects'
754	@echo ''
755	@echo 'Some often used sub targets (make all makes them all):'
756	@echo ''
757	@echo ' arb - Just compile ARB (but none of the integrated tools)'
758	@echo ' menus - create lib/gde/arb.menu from GDEHELP/ARB_GDEmenus.source'
759	@echo ' perl - Compile the PERL XSUBS into lib/ARB.so and create links in lib to perl'
760	@echo ' binlink - Create all links in the bin directory'
761	@echo ''
762	@echo 'Development targets:'
763	@echo ''
764	@echo ' depends - create or update dependencies ("SUBDIR/SUBDIR.depends" to update only SUBDIR)'
765	@echo ' proto - create or update prototypes ("SUBDIR/SUBDIR.proto" to update only SUBDIR)'
766	@echo ' tags - create tags for xemacs'
767	@echo ' show - show available shortcuts (AKA subtargets)'
768	@echo ' up - shortcut for depends+proto+tags'
769	ifeq ($(UNIT_TESTS),1)
770	@echo ' ut - only run tests'
771	endif
772	@echo ' modified - rebuild files modified in svn checkout (does touch)'
773	@echo ' touch - touch files modified in svn checkout'
774	@echo ''
775	@echo 'Internal maintenance:'
776	@echo ''
777	@echo ' relinfo - show help on release targets'
778	@echo ' tarfile - make rebuild and create arb version tarfile ("tarfile_quick" to skip rebuild)'
779	@echo ' save - save all basic ARB sources into arbsrc_DATE ("savetest" to check filelist)'
780	@echo ' patch - save svn diff to patchfile'
781	@echo ' source_doc - create doxygen documentation'
782	@echo ' relocated - rebuild partly (use when you have relocated ARBHOME)'
783	@echo ' check_res - check ressource usage'
784	@echo ' dep_graph - Build dependency graphs'
785	@echo ' clean_cov - Clean coverage results'
786	@echo ''
787	@echo ' post_commit_check - Checks whether'
788	@echo ' * main make targets work,'
789	@echo ' * dependencies and prototypes are up to date,'
790	@echo ' * SVN-controlled files remain unaffected by called targets and'
791	@echo ' * all generated files are ignored.'
792	@echo ' (has to be called in a clean SVN checkout)'
793	@echo $(SEP)
794	@echo ''
795
796	relinfo:
797	@echo ''
798	@echo $(SEP)
799	@echo 'Release targets:'
800	@echo ''
801	@echo ' inc_candi - increase RC candidate-number (only possible in "rc" branch, not needed for RC1)'
802	@echo ' inc_patch - increase release patchlevel (only possible in "stable" branch)'
803	@echo ' inc_minor - increase minor version number (only possible in "trunk")'
804	@echo ' inc_major - increase MAJOR version number (only possible in "trunk")'
805	@echo ''
806	@echo ' show_version - show version tag'
807	@echo ''
808	@echo $(SEP)
809	@echo ''
810
811	# auto-generate config.makefile:
812
813	CONFIG_MAKEFILE_FOUND=$(wildcard config.makefile)
814
815	config.makefile : config.makefile.template
816	@echo --------------------------------------------------------------------------------
817	ifeq ($(strip $(CONFIG_MAKEFILE_FOUND)),)
818	@cp $< $@
819	@echo '$(ARBHOME)/$@:1: has been generated.'
820	@echo 'Please edit $@ to configure your system!'
821	@echo --------------------------------------------------------------------------------
822	@false
823	else
824	@echo '$(ARBHOME)/$<:1: is more recent than'
825	@echo '$(ARBHOME)/$@:1:'
826	@ls -al config.makefile*
827	@echo --------------------------------------------------------------------------------
828	@echo "Updating $@ (if this fails, check manually)"
829	SOURCE_TOOLS/update_config_makefile.pl
830	@echo "Sucessfully updated $@"
831	@echo --------------------------------------------------------------------------------
832	@ls -al config.makefile*
833	@echo --------------------------------------------------------------------------------
834	@echo "Diff to your old config.makefile:"
835	@echo --------------------------------------------------------------------------------
836	-diff $@.bak $@
837	@echo --------------------------------------------------------------------------------
838	endif
839
840	# check if everything is configured correctly
841
842	check_DEVELOPER:
843	ifndef DEVELOPER
844	@echo 'config.makefile:1: DEVELOPER not defined'
845	@false
846	endif
847
848	check_DEBUG:
849	ifndef dflags
850	@echo 'config.makefile:1: DEBUG has to be defined. Valid values are 0 and 1'
851	@false
852	endif
853
854	check_ARB_64:
855	ifndef ARB_64
856	@echo 'config.makefile:1: ARB_64 has to be defined. Valid values are 0 and 1'
857	@false
858	endif
859
860	# ---------------------------------------- check gcc version
861
862	COMPILER_BROKEN:=0
863
864	# gcc 4.8.0 produces invalid code (see #617)
865	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.8.0')
866	COMPILER_BROKEN:=1
867	endif
868
869	check_same_GCC_VERSION:
870	$(ARBHOME)/SOURCE_TOOLS/check_same_compiler_version.pl $(COMPILER_NAME) $(COMPILER_VERSION_ALLOWED)
871
872	check_GCC_VERSION:
873	@echo 'Compiler version check:'
874	ifeq ('$(COMPILER_VERSION_ALLOWED)', '')
875	@echo " - Your compiler is '$(COMPILER_NAME)' version '$(COMPILER_VERSION)'"
876	@echo ' This version is not in the list of supported $(COMPILER_NAME)-versions:'
877	@$(foreach version,$(ALLOWED_COMPILER_VERSIONS),echo ' * $(version)';)
878	@echo ' - You may either ..'
879	@echo ' - add your version to ALLOWED_$(COMPILER_NAME)_VERSIONS in the Makefile and try it out or'
880	@echo ' - switch to one of the allowed versions (see arb_README_gcc.txt for installing'
881	@echo ' a different version of gcc)'
882	$(error Unsupported compiler '$(COMPILER_NAME)' version '$(COMPILER_VERSION)')
883	else
884	ifeq ($(COMPILER_BROKEN),1)
885	$(error $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)' would build a broken ARB version. Compilation refused)
886	else
887	@echo " - Supported $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)' detected - fine!"
888	@echo ''
889	$(MAKE) check_same_GCC_VERSION
890	endif
891	endif
892
893	#---------------------- check ARBHOME
894
895	# use arb_INSTALL.txt to determine whether ARBHOME points to correct directory
896	ARB_INSTALL_FOUND=$(wildcard $(ARBHOME)/arb_INSTALL.txt)
897
898	check_ARBHOME:
899	ifeq ($(strip $(ARB_INSTALL_FOUND)),)
900	@echo ------------------------------------------------------------
901	@echo "ARBHOME is set to '$(ARBHOME)'"
902	@echo "The environment variable ARBHOME has to point to the top arb source directory."
903	@echo "If you use bash enter:"
904	@echo " export ARBHOME='`pwd`'"
905	@echo ------------------------------------------------------------
906	@false
907	endif
908
909	ARB_PATH_SET=$(findstring $(ARBHOME)/bin,$(PATH))
910
911	check_PATH: check_ARBHOME
912	ifeq ($(strip $(ARB_PATH_SET)),)
913	@echo ------------------------------------------------------------
914	@echo "The environment variable PATH has to contain $(ARBHOME)/bin"
915	@echo "If you use bash enter:"
916	@echo ' export PATH=$$ARBHOME/bin:$$PATH'
917	@echo ------------------------------------------------------------
918	@false
919	endif
920
921	check_TOOLS:
922	@util/arb_check_build_env.pl \
923	"$(A_CC)" \
924	"$(A_CXX)" \
925	"$(MAKEDEPEND_PLAIN)" \
926	"$(LINK_SHARED_LIB)" \
927	"$(LINK_SHARED_LIB)" \
928
929	check_ENVIRONMENT : check_PATH check_TOOLS
930	@echo "-------------------- Environment [start]"
931	@echo "ARBHOME='$(ARBHOME)'"
932	@echo "PATH='$(PATH)'"
933	@echo "LD_LIBRARY_PATH='$(LD_LIBRARY_PATH)'"
934	@echo "-------------------- Environment [end]"
935
936	check_tabs: check_setup
937	ifeq ($(DEBUG),1)
938	@SOURCE_TOOLS/tabBrake.pl
939	endif
940
941	force_tab_check:
942	@touch -t 198001010000 SOURCE_TOOLS/stamp.tabBrake
943	@$(MAKE) check_tabs
944
945
946	# ---------------------
947
948	check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION
949	@echo Your setup seems to be ok.
950
951	checks: check_setup check_tabs
952	@rm -f SOURCE_TOOLS/postcompile.sav
953
954
955	# end test section ------------------------------
956
957	# ---------------------------------------
958	# List of standard top level directories
959	#
960	# sub-makefiles have to define the targets
961	# - 'depends' and
962	# - 'clean'
963	#
964	# when adding new libs here, also add a dependency vs 'links' or 'links_non_perl' in .@DD_links_non_perl
965
966	ARCHS = \
967	$(ARCHS_PT_SERVER) \
968	AISC/AISC.a \
969	AISC_MKPTPS/AISC_MKPTPS.a \
970	ARBDB/libARBDB.a \
971	CORE/libCORE.a \
972	ARB_GDE/ARB_GDE.a \
973	AWT/libAWT.a \
974	AWTC/AWTC.a \
975	AWTI/AWTI.a \
976	CONSENSUS_TREE/CONSENSUS_TREE.a \
977	CONVERTALN/CONVERTALN.a \
978	DBSERVER/DBSERVER.a \
979	DIST/DIST.a \
980	EDIT4/EDIT4.a \
981	EISPACK/EISPACK.a \
982	GDE/GDE.a \
983	GENOM/GENOM.a \
984	GENOM_IMPORT/GENOM_IMPORT.a \
985	GL/GL.a \
986	ISLAND_HOPPING/ISLAND_HOPPING.a \
987	MERGE/MERGE.a \
988	MULTI_PROBE/MULTI_PROBE.a \
989	NALIGNER/NALIGNER.a \
990	NAMES/NAMES.a \
991	NAMES_COM/server.a \
992	NTREE/NTREE.a \
993	PARSIMONY/PARSIMONY.a \
994	PERLTOOLS/PERLTOOLS.a \
995	PHYLO/PHYLO.a \
996	PRIMER_DESIGN/PRIMER_DESIGN.a \
997	PROBE_COM/server.a \
998	PROBE_DESIGN/PROBE_DESIGN.a \
999	PROBE_SET/PROBE_SET.a \
1000	READSEQ/READSEQ.a \
1001	RNA3D/RNA3D.a \
1002	RNACMA/RNACMA.a \
1003	SECEDIT/SECEDIT.a \
1004	SEQ_QUALITY/SEQ_QUALITY.a \
1005	SERVERCNTRL/SERVERCNTRL.a \
1006	SL/SL.a \
1007	STAT/STAT.a \
1008	TOOLS/TOOLS.a \
1009	TREEGEN/TREEGEN.a \
1010	UNIT_TESTER/UNIT_TESTER.a \
1011	WETC/WETC.a \
1012	WINDOW/libWINDOW.a \
1013	XML/XML.a \
1014
1015	# -----------------------
1016	# library packets
1017
1018	ARCHS_CLIENT_PROBE = PROBE_COM/client.a
1019	ARCHS_CLIENT_NAMES = NAMES_COM/client.a
1020
1021	ARCHS_SERVER_PROBE = PROBE_COM/server.a $(ARCHS_CLIENT_PROBE)
1022	ARCHS_SERVER_NAMES = NAMES_COM/server.a $(ARCHS_CLIENT_NAMES)
1023
1024	ARCHS_MAKEBIN = AISC_MKPTPS/AISC_MKPTPS.a AISC/AISC.a
1025
1026	# communication libs need aisc and aisc_mkpts:
1027
1028	AISC/AISC.dummy: proto_tools
1029
1030	comtools: AISC/AISC.dummy
1031
1032	ARCHS_SEQUENCE = \
1033	SL/SEQUENCE/SEQUENCE.a \
1034	SL/ALIVIEW/ALIVIEW.a \
1035	SL/PRONUC/PRONUC.a \
1036
1037	ARCHS_TREE = \
1038	$(ARCHS_SEQUENCE) \
1039	SL/FILTER/FILTER.a \
1040	SL/ARB_TREE/ARB_TREE.a \
1041	SL/ROOTED_TREE/ROOTED_TREE.a \
1042
1043	# parsimony tree (used by NTREE, PARSIMONY, STAT(->EDIT4), DIST(obsolete!))
1044	ARCHS_AP_TREE = \
1045	$(ARCHS_TREE) \
1046	SL/AP_TREE/AP_TREE.a \
1047
1048	# --------------------------------------------------------------------------------
1049	# dependencies for linking shared libs
1050
1051	link_core: core
1052	link_db: db link_core
1053	link_aw: aw link_db
1054	link_awt: awt link_aw
1055
1056	#***************************************************************************************
1057	# Individual_Programs_Section
1058	#***************************************************************************************
1059
1060	arbmainwrapper:
1061	$(MAKE) -C SOURCE_TOOLS -r mainwrapper
1062
1063
1064	#********************************* arb_ntree ************************************
1065	NTREE = bin/arb_ntree
1066	ARCHS_NTREE = \
1067	NTREE/NTREE.a \
1068	$(ARCHS_AP_TREE) \
1069	ARB_GDE/ARB_GDE.a \
1070	AWTC/AWTC.a \
1071	AWTI/AWTI.a \
1072	CONSENSUS_TREE/CONSENSUS_TREE.a \
1073	GENOM/GENOM.a \
1074	GENOM_IMPORT/GENOM_IMPORT.a \
1075	MERGE/MERGE.a \
1076	MULTI_PROBE/MULTI_PROBE.a \
1077	PRIMER_DESIGN/PRIMER_DESIGN.a \
1078	PROBE_DESIGN/PROBE_DESIGN.a \
1079	SEQ_QUALITY/SEQ_QUALITY.a \
1080	SERVERCNTRL/SERVERCNTRL.a \
1081	SL/ALILINK/ALILINK.a \
1082	SL/AW_NAME/AW_NAME.a \
1083	SL/DB_UI/DB_UI.a \
1084	SL/DB_SCANNER/DB_SCANNER.a \
1085	SL/DB_QUERY/DB_QUERY.a \
1086	SL/SEQIO/SEQIO.a \
1087	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1088	SL/HELIX/HELIX.a \
1089	SL/REGEXPR/REGEXPR.a \
1090	SL/REFENTRIES/REFENTRIES.a \
1091	SL/NDS/NDS.a \
1092	SL/ITEMS/ITEMS.a \
1093	SL/INSDEL/INSDEL.a \
1094	SL/LOCATION/LOCATION.a \
1095	SL/MACROS/MACROS.a \
1096	SL/TRANSLATE/TRANSLATE.a \
1097	SL/TREEDISP/TREEDISP.a \
1098	SL/TREE_ADMIN/TREE_ADMIN.a \
1099	SL/TREE_READ/TREE_READ.a \
1100	SL/TREE_WRITE/TREE_WRITE.a \
1101	STAT/STAT.a \
1102	XML/XML.a \
1103
1104	$(NTREE): $(ARCHS_NTREE:.a=.dummy) link_awt
1105	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NTREE) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1106	echo "$(SEP) Link $@"; \
1107	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS)" ; \
1108	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS) && \
1109	echo "$(SEP) Link $@ [done]"; \
1110	)
1111
1112	#********************************* arb_edit4 ************************************
1113	EDIT4 = bin/arb_edit4
1114
1115	ARCHS_EDIT4 := \
1116	EDIT4/EDIT4.a \
1117	$(ARCHS_AP_TREE) \
1118	ARB_GDE/ARB_GDE.a \
1119	AWTC/AWTC.a \
1120	ISLAND_HOPPING/ISLAND_HOPPING.a \
1121	SECEDIT/SECEDIT.a \
1122	SERVERCNTRL/SERVERCNTRL.a \
1123	SL/AW_HELIX/AW_HELIX.a \
1124	SL/AW_NAME/AW_NAME.a \
1125	SL/FAST_ALIGNER/FAST_ALIGNER.a \
1126	SL/ITEMS/ITEMS.a \
1127	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1128	SL/HELIX/HELIX.a \
1129	SL/TRANSLATE/TRANSLATE.a \
1130	SL/MACROS/MACROS.a \
1131	SL/NDS/NDS.a \
1132	STAT/STAT.a \
1133	XML/XML.a \
1134
1135	ifeq ($(OPENGL),1)
1136	ARCHS_EDIT4 += RNA3D/RNA3D.a
1137	endif
1138
1139	LIBS_EDIT4 := $(GL_LIBS)
1140
1141	$(EDIT4): $(ARCHS_EDIT4:.a=.dummy) link_awt
1142	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_EDIT4) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1143	echo "$(SEP) Link $@"; \
1144	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4) $(EXECLIBS)" ; \
1145	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4) $(EXECLIBS) && \
1146	echo "$(SEP) Link $@ [done]"; \
1147	)
1148
1149	#********************************* arb_rnacma ************************************
1150	RNACMA = bin/arb_rnacma
1151	ARCHS_RNACMA = \
1152	RNACMA/RNACMA.a \
1153
1154	$(RNACMA) : $(ARCHS_RNACMA:.a=.dummy) link_db
1155	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_RNACMA) \|\| ( \
1156	echo "$(SEP) Link $@"; \
1157	echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_RNACMA) $(LIBS) $(EXECLIBS)"; \
1158	$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_RNACMA) $(LIBS) $(EXECLIBS) && \
1159	echo "$(SEP) Link $@ [done]"; \
1160	)
1161
1162	#********************************* arb_wetc ************************************
1163	WETC = bin/arb_wetc
1164	ARCHS_WETC = \
1165	WETC/WETC.a \
1166	SL/HELIX/HELIX.a \
1167	SL/FILTER/FILTER.a \
1168	XML/XML.a \
1169
1170	$(WETC): $(ARCHS_WETC:.a=.dummy) link_awt
1171	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_WETC) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1172	echo "$(SEP) Link $@"; \
1173	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC) $(GUI_LIBS) $(EXECLIBS)" ; \
1174	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC) $(GUI_LIBS) $(EXECLIBS) && \
1175	echo "$(SEP) Link $@ [done]"; \
1176	)
1177
1178	#********************************* arb_dist ************************************
1179	DIST = bin/arb_dist
1180	ARCHS_DIST = \
1181	$(ARCHS_AP_TREE) \
1182	CONSENSUS_TREE/CONSENSUS_TREE.a \
1183	DIST/DIST.a \
1184	EISPACK/EISPACK.a \
1185	SERVERCNTRL/SERVERCNTRL.a \
1186	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1187	SL/HELIX/HELIX.a \
1188	SL/MATRIX/MATRIX.a \
1189	SL/MACROS/MACROS.a \
1190	SL/NDS/NDS.a \
1191	SL/ITEMS/ITEMS.a \
1192	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.a \
1193	XML/XML.a \
1194
1195	$(DIST): $(ARCHS_DIST:.a=.dummy) link_awt
1196	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_DIST) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1197	echo "$(SEP) Link $@"; \
1198	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS)" ; \
1199	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS) && \
1200	echo "$(SEP) Link $@ [done]"; \
1201	)
1202
1203	#********************************* arb_pars ************************************
1204	PARSIMONY = bin/arb_pars
1205	ARCHS_PARSIMONY = \
1206	$(ARCHS_AP_TREE) \
1207	PARSIMONY/PARSIMONY.a \
1208	SERVERCNTRL/SERVERCNTRL.a \
1209	SL/AW_NAME/AW_NAME.a \
1210	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1211	SL/HELIX/HELIX.a \
1212	SL/MACROS/MACROS.a \
1213	SL/NDS/NDS.a \
1214	SL/ITEMS/ITEMS.a \
1215	SL/TRANSLATE/TRANSLATE.a \
1216	SL/TREEDISP/TREEDISP.a \
1217	XML/XML.a \
1218
1219	$(PARSIMONY): $(ARCHS_PARSIMONY:.a=.dummy) link_awt
1220	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PARSIMONY) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1221	echo "$(SEP) Link $@"; \
1222	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(EXECLIBS)" ; \
1223	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(EXECLIBS) && \
1224	echo "$(SEP) Link $@ [done]"; \
1225	)
1226
1227	#********************************* arb_convert_aln ************************************
1228	CONVERT_ALN = bin/arb_convert_aln
1229	ARCHS_CONVERT_ALN = \
1230	CONVERTALN/CONVERTALN.a \
1231
1232	$(CONVERT_ALN) : $(ARCHS_CONVERT_ALN:.a=.dummy) link_db
1233	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_CONVERT_ALN) $(use_ARB_main) \|\| ( \
1234	echo "$(SEP) Link $@"; \
1235	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN) $(LIBS) $(EXECLIBS)"; \
1236	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN) $(LIBS) $(EXECLIBS) && \
1237	echo "$(SEP) Link $@ [done]"; \
1238	)
1239
1240	#********************************* arb_treegen ************************************
1241
1242	TREEGEN = bin/arb_treegen
1243	ARCHS_TREEGEN = \
1244	TREEGEN/TREEGEN.a \
1245
1246	$(TREEGEN) : $(ARCHS_TREEGEN:.a=.dummy)
1247	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_TREEGEN) $(use_ARB_main_C) \|\| ( \
1248	echo "$(SEP) Link $@"; \
1249	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN) $(EXECLIBS)" ; \
1250	$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN) $(EXECLIBS) && \
1251	echo "$(SEP) Link $@ [done]"; \
1252	)
1253
1254	#********************************* arb_naligner ************************************
1255	NALIGNER = bin/arb_naligner
1256	ARCHS_NALIGNER = \
1257	NALIGNER/NALIGNER.a \
1258	SERVERCNTRL/SERVERCNTRL.a \
1259	SL/HELIX/HELIX.a \
1260
1261	$(NALIGNER): $(ARCHS_NALIGNER:.a=.dummy) link_db
1262	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NALIGNER) $(use_ARB_main) \|\| ( \
1263	echo "$(SEP) Link $@"; \
1264	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(LIBS) $(EXECLIBS)" ; \
1265	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(LIBS) $(EXECLIBS) && \
1266	echo "$(SEP) Link $@ [done]"; \
1267	)
1268
1269	#********************************* arb_phylo ************************************
1270	PHYLO = bin/arb_phylo
1271	ARCHS_PHYLO = \
1272	PHYLO/PHYLO.a \
1273	SL/HELIX/HELIX.a \
1274	SL/FILTER/FILTER.a \
1275	SL/MATRIX/MATRIX.a \
1276	SL/MACROS/MACROS.a \
1277	XML/XML.a \
1278
1279	$(PHYLO): $(ARCHS_PHYLO:.a=.dummy) link_awt
1280	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PHYLO) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1281	echo "$(SEP) Link $@"; \
1282	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO) $(GUI_LIBS) $(EXECLIBS)" ; \
1283	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO) $(GUI_LIBS) $(EXECLIBS) && \
1284	echo "$(SEP) Link $@ [done]"; \
1285	)
1286
1287	#***************************************************************************************
1288	# SERVER SECTION
1289	#***************************************************************************************
1290
1291	#********************************* arb_db_server ************************************
1292	DBSERVER = bin/arb_db_server
1293	ARCHS_DBSERVER = \
1294	DBSERVER/DBSERVER.a \
1295	SERVERCNTRL/SERVERCNTRL.a \
1296
1297	$(DBSERVER): $(ARCHS_DBSERVER:.a=.dummy) link_db
1298	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_DBSERVER) $(ARBDB_LIB) $(use_ARB_main) \|\| ( \
1299	echo "$(SEP) Link $@"; \
1300	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS) $(EXECLIBS)" ; \
1301	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS) $(EXECLIBS) && \
1302	echo "$(SEP) Link $@ [done]"; \
1303	)
1304
1305	#********************************* arb_pt_server ************************************
1306	PROBE = bin/arb_pt_server
1307	ARCHS_PROBE_COMMON = \
1308	SERVERCNTRL/SERVERCNTRL.a \
1309	SL/HELIX/HELIX.a \
1310	SL/PTCLEAN/PTCLEAN.a \
1311
1312	ARCHS_PROBE_LINK = \
1313	$(ARCHS_PROBE_COMMON) \
1314	$(ARCHS_PT_SERVER_LINK) \
1315
1316	ARCHS_PROBE_DEPEND = \
1317	$(ARCHS_PROBE_COMMON) \
1318	$(ARCHS_PT_SERVER) \
1319
1320	$(PROBE): $(ARCHS_PROBE_DEPEND:.a=.dummy) link_db
1321	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_SERVER_PROBE) config.makefile $(use_ARB_main) \|\| ( \
1322	echo "$(SEP) Link $@"; \
1323	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_SERVER_PROBE) $(SYSLIBS) $(EXECLIBS)" ; \
1324	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_SERVER_PROBE) $(SYSLIBS) $(EXECLIBS) && \
1325	echo "$(SEP) Link $@ [done]"; \
1326	)
1327
1328	#********************************* arb_name_server ************************************
1329	NAMES = bin/arb_name_server
1330	ARCHS_NAMES = \
1331	NAMES/NAMES.a \
1332	SERVERCNTRL/SERVERCNTRL.a \
1333
1334	$(NAMES): $(ARCHS_NAMES:.a=.dummy) link_db
1335	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) $(use_ARB_main) \|\| ( \
1336	echo "$(SEP) Link $@"; \
1337	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS) $(EXECLIBS)" ; \
1338	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS) $(EXECLIBS) && \
1339	echo "$(SEP) Link $@ [done]"; \
1340	)
1341
1342	#********************************* SHARED LIBRARIES SECTION ************************************
1343
1344	prepare_libdir: addlibs
1345
1346	addlibs:
1347	(perl $(ARBHOME)/SOURCE_TOOLS/provide_libs.pl \
1348	"arbhome=$(ARBHOME)" \
1349	"opengl=$(OPENGL)" \
1350	"link_static=$(LINK_STATIC)" \
1351	)
1352
1353	#***************************************************************************************
1354	# Recursive calls to sub-makefiles
1355	#***************************************************************************************
1356
1357	%.depends:
1358	@cp -p $(@D)/Makefile $(@D)/Makefile.old # save old Makefile
1359	@$(MAKE) -C $(@D) -r \
1360	"AUTODEPENDS=1" \
1361	"MAIN=nothing" \
1362	"cflags=noCflagsHere_use_MAKEDEPENDFLAGS" \
1363	"cxxflags=noCxxflagsHere_use_MAKEDEPENDFLAGS" \
1364	depends
1365	@grep "^# DO NOT DELETE" $(@D)/Makefile >/dev/null
1366	@cat $(@D)/Makefile \
1367	\| SOURCE_TOOLS/fix_depends.pl "(from main)" \
1368	>$(@D)/Makefile.2
1369	@mv $(@D)/Makefile.old $(@D)/Makefile # restore old Makefile
1370	@$(ARBHOME)/SOURCE_TOOLS/mv_if_diff $(@D)/Makefile.2 $(@D)/Makefile # update Makefile if changed
1371
1372	%.proto:
1373	@($(MAKE) -C $(@D) \
1374	"AUTODEPENDS=0" \
1375	"MAIN=nothing" \
1376	"cflags=noCflags" \
1377	"cxxflags=noCxxflags" \
1378	proto 2>&1 ) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
1379
1380	%.clean:
1381	@$(MAKE) -C $(@D) \
1382	"AUTODEPENDS=0" \
1383	"MAIN=nothing" \
1384	"cflags=noCflags" \
1385	"cxxflags=noCxxflags" \
1386	clean
1387
1388
1389	# stop wrong targets
1390	target_is_missing_lib_prefix:
1391	@echo "Error: Denied to build shared library target with missing 'lib'-prefix"
1392	false
1393
1394	ARBDB/ARBDB.dummy: target_is_missing_lib_prefix
1395	CORE/CORE.dummy: target_is_missing_lib_prefix
1396	AWT/AWT.dummy: target_is_missing_lib_prefix
1397	WINDOW/WINDOW.dummy: target_is_missing_lib_prefix
1398
1399	# rule to generate main target (normally a library):
1400	# @@@ check effect of setting LANG=C below
1401	%.dummy:
1402	@( export ID=$$$$; LANG=C; \
1403	(( \
1404	echo "$(SEP) Make $(@D)"; \
1405	$(MAKE) -C $(@D) -r \
1406	"AUTODEPENDS=1" \
1407	"MAIN=$(@F:.dummy=.a)" \
1408	"cflags=$(cflags) -DIN_ARB_$(subst /,_,$(@D))" \
1409	&& \
1410	echo "$(SEP) Make $(@D) [done]"; \
1411	) >$(@D).$$ID.log 2>&1 && (cat $(@D).$$ID.log;rm $(@D).$$ID.log)) \|\| (cat $(@D).$$ID.log;rm $(@D).$$ID.log;false))
1412
1413	# Additional dependencies for subtargets:
1414
1415	PROBE_COM/PROBE_COM.dummy : comtools
1416	NAMES_COM/NAMES_COM.dummy : comtools
1417
1418	com: PROBE_COM/PROBE_COM.dummy NAMES_COM/NAMES_COM.dummy
1419
1420	PROBE_COM/server.dummy:
1421	@echo Unwanted request to make target $<
1422	false
1423
1424	PROBE_COM/client.dummy:
1425	@echo Unwanted request to make target $<
1426	false
1427
1428	NAMES_COM/server.dummy:
1429	@echo Unwanted request to make target $<
1430	false
1431
1432	NAMES_COM/client.dummy:
1433	@echo Unwanted request to make target $<
1434	false
1435
1436
1437	ARBDB/libARBDB.dummy: links
1438	CORE/libCORE.dummy: links
1439
1440	PERLTOOLS/PERLTOOLS.dummy: core db
1441
1442	# all subdirs perl not depends on go here (ADD_links_non_perl)
1443	AWT/libAWT.dummy: links_non_perl
1444	AWTI/AWTI.dummy: links_non_perl
1445	CONSENSUS_TREE/CONSENSUS_TREE.dummy: links_non_perl
1446	CONVERTALN/CONVERTALN.dummy: links_non_perl
1447	DBSERVER/DBSERVER.dummy: links_non_perl
1448	DIST/DIST.dummy: links_non_perl
1449	EDIT4/EDIT4.dummy: links_non_perl genheaders com
1450	EISPACK/EISPACK.dummy: links_non_perl
1451	GDE/GDE.dummy: links_non_perl
1452	GENOM/GENOM.dummy: links_non_perl
1453	GENOM_IMPORT/GENOM_IMPORT.dummy: links_non_perl
1454	ISLAND_HOPPING/ISLAND_HOPPING.dummy: links_non_perl
1455	MERGE/MERGE.dummy: links_non_perl
1456	NTREE/NTREE.dummy: links_non_perl genheaders
1457	PARSIMONY/PARSIMONY.dummy: links_non_perl
1458	PHYLO/PHYLO.dummy: links_non_perl
1459	PRIMER_DESIGN/PRIMER_DESIGN.dummy: links_non_perl
1460	PROBE_SET/PROBE_SET.dummy: links_non_perl link_db
1461	READSEQ/READSEQ.dummy: links_non_perl
1462	RNACMA/RNACMA.dummy: links_non_perl header_libs
1463	SECEDIT/SECEDIT.dummy: links_non_perl
1464	SEQ_QUALITY/SEQ_QUALITY.dummy: links_non_perl
1465	SERVERCNTRL/SERVERCNTRL.dummy: links_non_perl com
1466	SL/ALILINK/ALILINK.dummy: links_non_perl
1467	SL/ALIVIEW/ALIVIEW.dummy: links_non_perl
1468	SL/AP_TREE/AP_TREE.dummy: links_non_perl
1469	SL/ARB_TREE/ARB_TREE.dummy: links_non_perl
1470	SL/AW_HELIX/AW_HELIX.dummy: links_non_perl
1471	SL/DB_QUERY/DB_QUERY.dummy: links_non_perl
1472	SL/DB_SCANNER/DB_SCANNER.dummy: links_non_perl
1473	SL/DB_UI/DB_UI.dummy: links_non_perl
1474	SL/FAST_ALIGNER/FAST_ALIGNER.dummy: links_non_perl
1475	SL/FILTER/FILTER.dummy: links_non_perl
1476	SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy: links_non_perl
1477	SL/HELIX/HELIX.dummy: links_non_perl
1478	SL/INSDEL/INSDEL.dummy: links_non_perl
1479	SL/ITEMS/ITEMS.dummy: links_non_perl
1480	SL/LOCATION/LOCATION.dummy: links_non_perl
1481	SL/MACROS/MACROS.dummy: links_non_perl
1482	SL/MATRIX/MATRIX.dummy: links_non_perl
1483	SL/NDS/NDS.dummy: links_non_perl
1484	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.dummy: links_non_perl
1485	SL/PRONUC/PRONUC.dummy: links_non_perl
1486	SL/PTCLEAN/PTCLEAN.dummy: links_non_perl link_db
1487	SL/REFENTRIES/REFENTRIES.dummy: links_non_perl
1488	SL/REGEXPR/REGEXPR.dummy: links_non_perl
1489	SL/ROOTED_TREE/ROOTED_TREE.dummy: links_non_perl
1490	SL/SEQIO/SEQIO.dummy: links_non_perl
1491	SL/SEQUENCE/SEQUENCE.dummy: links_non_perl
1492	SL/TRANSLATE/TRANSLATE.dummy: links_non_perl
1493	SL/TREE_ADMIN/TREE_ADMIN.dummy: links_non_perl
1494	SL/TREE_READ/TREE_READ.dummy: links_non_perl
1495	SL/TREE_WRITE/TREE_WRITE.dummy: links_non_perl
1496	SL/TREEDISP/TREEDISP.dummy: links_non_perl
1497	STAT/STAT.dummy: links_non_perl
1498	TREEGEN/TREEGEN.dummy: links_non_perl
1499	WETC/WETC.dummy: links_non_perl
1500	WINDOW/libWINDOW.dummy: links_non_perl
1501	XML/XML.dummy: links_non_perl
1502
1503	ifeq ($(OPENGL),1)
1504	GL/glAW/glAW.dummy: links_non_perl
1505	GL/glpng/glpng.dummy: links_non_perl
1506	GL/GL.dummy: GL/glAW/glAW.dummy GL/glpng/glpng.dummy
1507	RNA3D/RNA3D.dummy: links_non_perl gl
1508	endif
1509
1510	UNIT_TESTER/UNIT_TESTER.dummy: link_db \
1511	SERVERCNTRL/SERVERCNTRL.dummy \
1512
1513	TOOLS/TOOLS.dummy : links_non_perl link_db \
1514	SERVERCNTRL/SERVERCNTRL.dummy \
1515	SL/ROOTED_TREE/ROOTED_TREE.dummy \
1516	SL/TREE_WRITE/TREE_WRITE.dummy \
1517	SL/TREE_READ/TREE_READ.dummy \
1518	CONSENSUS_TREE/CONSENSUS_TREE.dummy \
1519	XML/XML.dummy \
1520
1521	AWTC/AWTC.dummy : com
1522
1523	NAMES/NAMES.dummy : com
1524	SL/AW_NAME/AW_NAME.dummy : com
1525
1526	PROBE/PROBE.dummy : com
1527	ptpan/PROBE.dummy : com
1528	MULTI_PROBE/MULTI_PROBE.dummy : com
1529	PROBE_DESIGN/PROBE_DESIGN.dummy : com
1530	NALIGNER/NALIGNER.dummy : com
1531
1532	ARB_GDE/ARB_GDE.dummy : proto_tools
1533
1534	compile_compatibility: SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.dummy
1535
1536	#***************************************************************************************
1537	# Short aliases to make targets
1538	#***************************************************************************************
1539
1540	show:
1541	@echo $(SEP)
1542	@echo 'Aliases for often needed targets:'
1543	@echo ''
1544	@echo ' executables:'
1545	@echo ''
1546	@echo ' nt arb_ntree'
1547	@echo ' e4 arb_edit4 (includes secedit)'
1548	@echo ' di arb_dist'
1549	@echo ' ph arb_phylo'
1550	@echo ' pa arb_parsimony'
1551	@echo ' tg arb_treegen'
1552	@echo ' ds arb_dbserver'
1553	@echo ' pt arb_pt_server'
1554	@echo ' na arb_name_server'
1555	@echo ''
1556	@echo ' libraries:'
1557	@echo ''
1558	@echo ' com communication libraries'
1559	@echo ' db ARB database'
1560	@echo ' aw GUI lib'
1561	@echo ' awt GUI toolkit'
1562	@echo ' awtc general purpose library'
1563	@echo ' awti import/export library'
1564	@echo ' mp multi probe library'
1565	@echo ' ge genome library'
1566	@echo ' pd probe design lib'
1567	@echo ' prd primer design lib'
1568	@echo ''
1569	@echo ' other targets:'
1570	@echo ''
1571	@echo ' help recompile help files'
1572	@echo ' tools make small tools used by arb'
1573	@echo ''
1574	@echo ' foreign targets:'
1575	@echo ''
1576	@echo ' gde GDE'
1577	@echo ' agde ARB_GDE'
1578	@echo ''
1579	@echo 'for other targets inspect $(ARBHOME)/Makefile'
1580	@echo ''
1581	@echo $(SEP)
1582
1583	source_doc:
1584	@echo "Remove some links (doxygen crashes otherwise):"
1585	find . \( -name "AISC" -o -name "C" -o -name "GDEHELP" \) -type l -exec rm {} \;
1586	doxygen 2>&1 1>/dev/null
1587	$(MAKE) forcelinks
1588
1589	dep_graph:
1590	@echo "Building some dependency graphs"
1591	SOURCE_TOOLS/dependency_graphs.pl
1592
1593	help: HELP_SOURCE/HELP_SOURCE.dummy
1594
1595	HELP_SOURCE/HELP_SOURCE.dummy: link_core xml menus
1596
1597	db: ARBDB/libARBDB.dummy
1598	core: CORE/libCORE.dummy
1599	aw: WINDOW/libWINDOW.dummy
1600	awt: AWT/libAWT.dummy
1601	awtc: AWTC/AWTC.dummy
1602	awti: AWTI/AWTI.dummy
1603
1604	mp: MULTI_PROBE/MULTI_PROBE.dummy
1605	mg: MERGE/MERGE.dummy
1606	ge: GENOM/GENOM.dummy
1607	prd: PRIMER_DESIGN/PRIMER_DESIGN.dummy
1608
1609	nt: menus $(NTREE)
1610
1611	nal: $(NALIGNER)
1612
1613	di: $(DIST)
1614	ph: $(PHYLO)
1615	pa: $(PARSIMONY)
1616	tg: $(TREEGEN)
1617
1618	ifeq ($(OPENGL),1)
1619	3d: RNA3D/RNA3D.dummy
1620	gl: GL/GL.dummy
1621	else
1622	noopengl:
1623	@echo "invalid target for OPENGL=0"
1624	3d: noopengl
1625	gl: noopengl
1626	endif
1627
1628	SL/SL.dummy: com
1629
1630	ds: $(DBSERVER)
1631	pt: $(PROBE)
1632	pst: PROBE_SET/PROBE_SET.dummy
1633	pd: PROBE_DESIGN/PROBE_DESIGN.dummy
1634	na: $(NAMES)
1635	sq: SEQ_QUALITY/SEQ_QUALITY.dummy
1636	cma: $(RNACMA)
1637
1638	sec: SECEDIT/SECEDIT.dummy
1639
1640	e4: $(EDIT4) readseq menus
1641
1642	gi: GENOM_IMPORT/GENOM_IMPORT.dummy
1643	wetc: $(WETC)
1644
1645	xml: XML/XML.dummy
1646	xmlin: XML_IMPORT/XML_IMPORT.dummy# broken
1647	stat: STAT/STAT.dummy $(NTREE) $(EDIT4)
1648	fa: SL/FAST_ALIGNER/FAST_ALIGNER.dummy
1649
1650	#********************************************************************************
1651
1652	up_by_remake: depends proto
1653
1654	up: up_by_remake tags valgrind_update
1655
1656	#********************************************************************************
1657
1658	touch:
1659	SOURCE_TOOLS/touch_modified.pl
1660
1661	modified: touch
1662	$(MAKE) all
1663
1664	#********************************************************************************
1665
1666	libdepends:
1667	$(MAKE) -C "SOURCE_TOOLS" \
1668	"RNA3D_LIB=$(RNA3D_LIB_4_DEPENDS)" \
1669	libdepends
1670
1671	#********************************************************************************
1672
1673	# create generated headers:
1674	genheaders: TEMPLATES/TEMPLATES.dummy
1675
1676	clrdotdepends:
1677	-rm PROBE_COM/.depends
1678	-rm NAMES_COM/.depends
1679	-rm PERL2ARB/.depends
1680
1681	comdepends: comtools clrdotdepends
1682	@echo "$(SEP) Partially build com interface"
1683	$(MAKE) PROBE_COM/PROBE_COM.depends NAMES_COM/NAMES_COM.depends
1684	$(MAKE) PROBE_COM/server.depends NAMES_COM/server.depends
1685
1686	depends: genheaders comdepends
1687	@echo "$(SEP) Updating other dependencies"
1688	$(MAKE) $(subst NAMES_COM/server.depends,,$(subst PROBE_COM/server.depends,,$(ARCHS:.a=.depends))) \
1689	HELP_SOURCE/HELP_SOURCE.depends \
1690	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.depends \
1691
1692	$(MAKE) libdepends
1693
1694	depend: depends
1695
1696	# ------------------------------------------------------------
1697	# dependency generation tests for AISC code
1698	#(all should work w/o creating wrong dependencies;
1699	# neither in XXX_COM/Makefile nor in code using AISC interface)
1700	dependstest1: silent_clean
1701	$(MAKE) depends
1702	dependstest2: silent_clean
1703	$(MAKE) com
1704	dependstest3: silent_clean
1705	$(MAKE) aw
1706	dependstest4: silent_clean
1707	$(MAKE) pt
1708	dependstest5: silent_clean
1709	$(MAKE) na
1710	dependstest6: silent_clean
1711	$(MAKE) nt
1712	dependstest7: silent_clean
1713	$(MAKE) all
1714	# ------------------------------------------------------------
1715
1716	AISC_MKPTPS/AISC_MKPTPS.dummy: links
1717
1718	proto_tools: AISC_MKPTPS/AISC_MKPTPS.dummy
1719
1720	proto: proto_tools
1721	@echo $(SEP) Updating prototypes
1722	$(MAKE) \
1723	ARBDB/ARBDB.proto \
1724	AISC_COM/AISC_COM.proto \
1725	ARB_GDE/ARB_GDE.proto \
1726	CORE/CORE.proto \
1727	CONVERTALN/CONVERTALN.proto \
1728	NTREE/NTREE.proto \
1729	MERGE/MERGE.proto \
1730	$(ARCHS_PT_SERVER:.a=.proto) \
1731	SERVERCNTRL/SERVERCNTRL.proto \
1732	SL/SL.proto \
1733
1734	#********************************************************************************
1735
1736	valgrind_update: links
1737	@echo $(SEP) Updating for valgrind
1738	$(MAKE) -C SOURCE_TOOLS valgrind_update
1739
1740	#********************************************************************************
1741
1742	TAGFILE=TAGS
1743	TAGFILE_TMP=TAGS.tmp
1744
1745	TAG_SOURCE_HEADERS=TAGS.headers
1746	TAG_SOURCE_CODE=TAGS.codefiles
1747	TAG_SOURCE_LISTS=$(TAG_SOURCE_HEADERS) $(TAG_SOURCE_CODE)
1748
1749	ETAGS=ctags -e -f $(TAGFILE_TMP) --sort=no --if0=no --extra=q
1750	ETAGS_TYPES=--C-kinds=cgnsut --C++-kinds=cgnsut
1751	ETAGS_FUN =--C-kinds=fm --C++-kinds=fm
1752	ETAGS_REST =--C-kinds=dev --C++-kinds=dev
1753
1754	FILTER_TAGS_SOURCES= \
1755	$(SED) -e 's/^.\///g' \| \
1756	grep -P -v -i '^HEADERLIBS\|^GDE/\|/GEN[CH]/'
1757
1758	$(TAG_SOURCE_HEADERS): links
1759	find . \( -name '.hxx' -o -name ".h" \) -type f \| $(FILTER_TAGS_SOURCES) > $@
1760
1761	$(TAG_SOURCE_CODE): links
1762	find . \( -name '.cxx' -o -name ".c" \) -type f \| $(FILTER_TAGS_SOURCES) > $@
1763
1764	tags: $(TAG_SOURCE_LISTS)
1765	$(ETAGS) $(ETAGS_TYPES) -L $(TAG_SOURCE_HEADERS)
1766	$(ETAGS) -a $(ETAGS_FUN) -L $(TAG_SOURCE_HEADERS)
1767	$(ETAGS) -a $(ETAGS_REST) -L $(TAG_SOURCE_HEADERS)
1768	$(ETAGS) -a $(ETAGS_TYPES) -L $(TAG_SOURCE_CODE)
1769	$(ETAGS) -a $(ETAGS_FUN) -L $(TAG_SOURCE_CODE)
1770	$(ETAGS) -a $(ETAGS_REST) -L $(TAG_SOURCE_CODE)
1771	mv_if_diff $(TAGFILE_TMP) $(TAGFILE)
1772	rm $(TAG_SOURCE_LISTS)
1773
1774	#********************************************************************************
1775
1776	LINKSTAMP=SOURCE_TOOLS/stamp.generate_all_links
1777
1778	links: checks $(LINKSTAMP) arbmainwrapper
1779	links_no_checks: $(LINKSTAMP) arbmainwrapper
1780
1781	forcelinks:
1782	-rm $(LINKSTAMP)
1783	$(MAKE) links
1784
1785	$(LINKSTAMP): SOURCE_TOOLS/generate_all_links.sh
1786	+SOURCE_TOOLS/generate_all_links.sh
1787	touch $(LINKSTAMP)
1788
1789	clean_links:
1790	# avoid to delete linked pts, nas or arb_tcp.dat:
1791	find . -path './lib' -prune -o -type l -exec rm {} \;
1792	# removed obsolete file - refuses to disappear due to 'prune' above
1793	@rm -f lib/help/GDEHELP
1794	@rm -f $(LINKSTAMP) lib/inputMasks/format.readme
1795
1796	redo_links: clean_links
1797	$(MAKE) links_no_checks
1798
1799	#********************************************************************************
1800
1801	header_libs:
1802	$(MAKE) -C HEADERLIBS all
1803
1804	#********************************************************************************
1805
1806	gde: GDE/GDE.dummy
1807	GDE: gde
1808	agde: ARB_GDE/ARB_GDE.dummy
1809
1810	tools: TOOLS/TOOLS.dummy
1811
1812	convert: $(CONVERT_ALN)
1813	readseq: READSEQ/READSEQ.dummy
1814
1815	#***************************************************************************************
1816	# Some user commands
1817	#***************************************************************************************
1818
1819	menus: binlink links
1820	@(( \
1821	echo "$(SEP) Make GDEHELP"; \
1822	$(MAKE) -C GDEHELP -r all && \
1823	echo "$(SEP) Make GDEHELP [done]"; \
1824	) > GDEHELP.log 2>&1 && (cat GDEHELP.log;rm GDEHELP.log)) \|\| (cat GDEHELP.log;rm GDEHELP.log;false)
1825
1826	ifeq ($(DEBUG),1)
1827	BIN_TARGET=develall
1828	else
1829	BIN_TARGET=all
1830	endif
1831
1832
1833	binlink:
1834	$(MAKE) -C bin $(BIN_TARGET)
1835
1836	preplib:
1837	(cd lib;$(MAKE) all)
1838
1839	# --------------------------------------------------------------------------------
1840	# This section is quite tricky:
1841	#
1842	# make 'perl' is a BIG target, so when it has to be made, it has to be started
1843	# as early as possible to reduce overall compile time. Since 'make' does not
1844	# provide any priotities, i force it to build all 'perl'-prerequisites early, by
1845	# adding artificial dependencies to these prerequisites
1846	#
1847	# That behavior is likely to be system-dependent.
1848	# My goal was only to make it work on my current development system,
1849	# where this saves about 20% of overall build time.
1850
1851	ifeq ($(WITHPERL),1)
1852	links_non_perl: PERLTOOLS/PERLTOOLS.dummy
1853	perltools: links_non_perl
1854	perl: realperl
1855	else
1856	links_non_perl: links
1857	perl:
1858	$(MAKE) "WITHPERL=1" perl
1859	endif
1860
1861	# ---------------------------------------- perl
1862
1863	ifeq ($(ARB_64),$(BUILDHOST_64))
1864	TEST_PERL_SCRIPTS=$(MAKE) -C PERL_SCRIPTS/test test
1865	else
1866	TEST_PERL_SCRIPTS=echo "skipping perl script compilation (when cross-compiling)"
1867	endif
1868
1869	realperl: perltools
1870	(( \
1871	echo "$(SEP) Make PERL2ARB" ; \
1872	$(TIME) $(MAKE) -C PERL2ARB -r -f Makefile.main \
1873	"AUTODEPENDS=1" \
1874	"dflags=$(dflags)" \
1875	"cross_cflags=$(cross_cflags) $(cxxflags) $(dflags)" \
1876	"cross_lflags=$(cross_lflags)" \
1877	"COMPILER_VERSION=$(COMPILER_VERSION)" \
1878	all && \
1879	$(TEST_PERL_SCRIPTS) && \
1880	echo "$(SEP) Make PERL2ARB [done]" ; \
1881	) > PERL2ARB.log 2>&1 && (cat PERL2ARB.log;rm PERL2ARB.log)) \|\| (cat PERL2ARB.log;rm PERL2ARB.log;false)
1882
1883	perl_clean:
1884	@$(MAKE) -C PERL2ARB -r -f Makefile.main \
1885	"AUTODEPENDS=0" \
1886	clean
1887
1888	PERL2ARB/PERL2ARB.clean:
1889	$(MAKE) perl_clean
1890	$(MAKE) -C PERL_SCRIPTS/test clean
1891
1892	# ---------------------------------------- bindings to script languages
1893
1894	bindings: lib/libCORE.so lib/libARBDB.so
1895	$(MAKE) -C BINDINGS all ARBDEPENDS="$(^:%=../%)" DFLAGS="$(dflags)"
1896
1897	bindings_clean:
1898	$(MAKE) -C BINDINGS clean
1899
1900	# ----------------------------------------
1901
1902	CLOC=cloc-1.08.pl
1903	CLOCFLAGS=--no3 --quiet --progress-rate=0
1904	CLOCARB=--exclude-dir=GDE .
1905	CLOCEXT=GDE
1906	CLOCCODE=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.code.def
1907	CLOCREST=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.rest.def
1908	CLOCFILT=tail --lines=+4
1909
1910	cloc:
1911	@echo 'Arb code:'
1912	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCARB) \| $(CLOCFILT)
1913	@echo 'Arb rest:'
1914	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCARB) \| $(CLOCFILT)
1915	@echo 'External code:'
1916	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCEXT) \| $(CLOCFILT)
1917	@echo 'External rest:'
1918	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCEXT) \| $(CLOCFILT)
1919
1920	# ---------------------------------------- check ressources
1921
1922	check_res:
1923	$(ARBHOME)/SOURCE_TOOLS/check_ressources.pl
1924
1925	# ---------------------------------------- cleaning
1926
1927	rmbak:
1928	@echo "Cleanup:"
1929	@find . \( -name '*%' \
1930	-o -name '*.bak' \
1931	-o -name '*~' \) \
1932	-o \( -name 'core' -a \! -type d \) \
1933	-exec rm -v {} \;
1934
1935	bin_reinit:
1936	$(MAKE) bin/bin.clean
1937	$(MAKE) -C "bin" all
1938
1939	clean_directories:
1940	-rm -rf \
1941	$(ARBHOME)/PROBE_SET/bin \
1942	$(ARBHOME)/INCLUDE \
1943
1944	libclean:
1945	-find $(ARBHOME) -type f \( -name '*.a' ! -type l \) -exec rm -f {} \;
1946
1947	objclean:
1948	-find $(ARBHOME) -type f \( -name '*.o' ! -type l \) -exec rm -f {} \;
1949
1950	# bin.clean and HELP_SOURCE.clean interfere
1951	clean3:
1952	$(MAKE) bin/bin.clean
1953	$(MAKE) HELP_SOURCE/HELP_SOURCE.clean
1954
1955	clean2: $(ARCHS:.a=.clean) \
1956	clean3 \
1957	rmbak \
1958	libclean \
1959	objclean \
1960	lib/lib.clean \
1961	GDEHELP/GDEHELP.clean \
1962	HEADERLIBS/HEADERLIBS.clean \
1963	SOURCE_TOOLS/SOURCE_TOOLS.clean \
1964	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.clean \
1965	UNIT_TESTER/UNIT_TESTER.clean \
1966	TEMPLATES/TEMPLATES.clean \
1967	perl_clean \
1968	clean_directories \
1969
1970	rm -f .last_gcc .last_compiler config.makefile.bak
1971
1972	# links are needed for cleanup
1973	clean: redo_links motif_xpm_hack_clean
1974	$(MAKE) clean2
1975	$(MAKE) clean_cov_all clean_links
1976
1977	silent_clean:
1978	$(MAKE) clean >/dev/null
1979
1980	# 'relocated' is about 50% faster than 'rebuild'
1981	reloc_clean: links
1982	@echo "---------------------------------------- Relocation cleanup"
1983	$(MAKE) \
1984	perl_clean \
1985	GDEHELP/GDEHELP.clean \
1986	HELP_SOURCE/genhelp/genhelp.clean \
1987	bin/bin.clean \
1988	libclean \
1989	objclean
1990
1991	relocated: links
1992	$(MAKE) reloc_clean
1993	@echo "---------------------------------------- and remake"
1994	$(MAKE) build
1995
1996	# -----------------------------------
1997	# some stress tests
1998	# (helpful to reveal race conditions with -j)
1999
2000	rebuild4ever: rebuild
2001	$(MAKE) rebuild4ever
2002
2003	build4ever: build
2004	$(MAKE) build4ever
2005
2006	clean4ever: clean
2007	$(MAKE) clean4ever
2008
2009	test4ever: ut
2010	$(MAKE) test4ever
2011
2012	perl4ever: clean
2013	$(MAKE) links
2014	$(MAKE) perl
2015	$(MAKE) perl4ever
2016
2017	help4ever: clean
2018	$(MAKE) help
2019	$(MAKE) help4ever
2020
2021	# -----------------------------------
2022
2023	rebuild: clean
2024	$(MAKE) all
2025
2026	relink: bin/bin.clean libclean
2027	$(MAKE) build
2028
2029	tarfile: rebuild
2030	$(MAKE) prepare_libdir
2031	util/arb_compress
2032
2033	tarfile_quick: build
2034	$(MAKE) prepare_libdir
2035	util/arb_compress
2036
2037	save: sourcetarfile
2038
2039	patch:
2040	SOURCE_TOOLS/arb_create_patch.sh arbPatch
2041
2042	# test early whether save will work
2043	savetest:
2044	@util/arb_srclst.pl >/dev/null
2045
2046	testsave: savetest
2047
2048	sourcetarfile: rmbak
2049	util/arb_save
2050
2051	save2: rmbak
2052	util/arb_save ignore
2053
2054	save_test: rmbak
2055	@echo "Testing source list.."
2056	@util/arb_srclst.pl > /dev/null
2057
2058	save_test_no_error:
2059	@-$(MAKE) save_test
2060
2061	inc_candi:
2062	touch SOURCE_TOOLS/inc_candi.stamp
2063	$(MAKE) do_version_update
2064
2065	inc_patch:
2066	touch SOURCE_TOOLS/inc_patch.stamp
2067	$(MAKE) do_version_update
2068
2069	inc_minor:
2070	touch SOURCE_TOOLS/inc_minor.stamp
2071	$(MAKE) do_version_update
2072
2073	inc_major:
2074	touch SOURCE_TOOLS/inc_major.stamp
2075	$(MAKE) do_version_update
2076
2077	do_version_update:
2078	@echo Incrementing version information
2079	$(MAKE) testsave
2080	$(MAKE) genheaders # auto upgrades version early
2081
2082	show_version:
2083	$(MAKE) genheaders # updates version info
2084	@echo "$(SEP) ARB version info"
2085	@grep ARB_VERSION TEMPLATES/arb_build.h
2086	@echo "$(SEP)"
2087
2088	release_quick:
2089	-rm arb.tgz arbsrc.tgz
2090	$(MAKE) tarfile_quick
2091	$(MAKE) sourcetarfile
2092
2093	# --------------------------------------------------------------------------------
2094
2095	MAKE_IF_COMMITTED=$(MAKE) -C SOURCE_TOOLS -f Makefile.commitbuild
2096
2097	build_CTARGET:
2098	+$(MAKE_IF_COMMITTED) "CTARGET=$(CTARGET)" build_CTARGET
2099
2100	reset_committed_build:
2101	+$(MAKE_IF_COMMITTED) reset
2102
2103	# --------------------------------------------------------------------------------
2104
2105	arbapplications: nt pa e4 wetc pt na nal di ph ds wetc cma
2106
2107	arb_external: convert tools gde readseq tg pst xmlin
2108
2109	arb_no_perl: arbapplications help arb_external
2110
2111	arb: motif_xpm_hack
2112	$(MAKE) "WITHPERL=1" perl arb_no_perl
2113
2114	motif_xpm_hack:
2115	$(MAKE) -r -C "lib/motifHack" all
2116
2117	motif_xpm_hack_clean:
2118	$(MAKE) -r -C "lib/motifHack" clean
2119
2120	# --------------------------------------------------------------------------------
2121	# special targets for SOURCE_TOOLS/remake_after_change.pl
2122
2123	rac_arb_dist: di
2124	rac_arb_edit4: e4
2125	rac_arb_ntree: nt
2126	rac_arb_pars: pa
2127	rac_arb_phylo: ph
2128	rac_arb_wetc: wetc
2129	rac_arb_naligner: nal
2130	rac_arb_pt_server: pt
2131	rac_arb_db_server: ds
2132	rac_arb_name_server: na
2133	rac_arb_convert_aln: convert
2134	rac_arb_treegen: tg
2135	rac_arb_rnacma: cma
2136	rac_arb_help2xml: help
2137
2138	rac_arb_a2ps: tools
2139	rac_arb_consensus_tree: tools
2140	rac_arb_dnarates: tools
2141	rac_arb_export_rates: tools
2142	rac_arb_export_tree: tools
2143	rac_arb_gene_probe: tools
2144	rac_arb_message: tools
2145	rac_arb_notify: tools
2146	rac_arb_primer: tools
2147	rac_arb_probe: tools
2148	rac_arb_read_tree: tools
2149
2150	# --------------------------------------------------------------------------------
2151	# unit testing
2152	# @@@ work in progress
2153	#
2154	# goal is to automatically test all libraries/executables using TESTED_UNITS_AUTO
2155	#
2156	# currently not all test executables link w/o error
2157	# (see UNITS_WORKING, UNITS_UNTESTABLE_ATM and UNITS_NEED_FIX)
2158
2159	# define RNA3D/RNA3D.test
2160	RNA3D_TEST := $(subst .a,.test,$(RNA3D_LIB))
2161
2162	TESTED_UNITS_AUTO = $(ARCHS:.a=.test)
2163
2164	UNITS_WORKING = \
2165	$(RNA3D_TEST) \
2166	AWTI/AWTI.test \
2167	EISPACK/EISPACK.test \
2168	GENOM/GENOM.test \
2169	GL/glAW/libglAW.test \
2170	GL/glpng/libglpng_arb.test \
2171	ISLAND_HOPPING/ISLAND_HOPPING.test \
2172	NALIGNER/NALIGNER.test \
2173	NAMES/NAMES.test \
2174	PHYLO/PHYLO.test \
2175	PRIMER_DESIGN/PRIMER_DESIGN.test \
2176	PROBE_DESIGN/PROBE_DESIGN.test \
2177	SECEDIT/SECEDIT.test \
2178	SEQ_QUALITY/SEQ_QUALITY.test \
2179	SERVERCNTRL/SERVERCNTRL.test \
2180	SL/ALIVIEW/ALIVIEW.test \
2181	SL/AP_TREE/AP_TREE.test \
2182	SL/ARB_TREE/ARB_TREE.test \
2183	SL/AW_HELIX/AW_HELIX.test \
2184	SL/AW_NAME/AW_NAME.test \
2185	SL/DB_SCANNER/DB_SCANNER.test \
2186	SL/GUI_ALIVIEW/GUI_ALIVIEW.test \
2187	SL/HELIX/HELIX.test \
2188	SL/ITEMS/ITEMS.test \
2189	SL/LOCATION/LOCATION.test \
2190	SL/MATRIX/MATRIX.test \
2191	SL/REFENTRIES/REFENTRIES.test \
2192	SL/SEQUENCE/SEQUENCE.test \
2193	SL/TRANSLATE/TRANSLATE.test \
2194	SL/TREE_ADMIN/TREE_ADMIN.test \
2195	SL/TREE_WRITE/TREE_WRITE.test \
2196	STAT/STAT.test \
2197	TREEGEN/TREEGEN.test \
2198	WETC/WETC.test \
2199	XML/XML.test \
2200	SL/ROOTED_TREE/ROOTED_TREE.test \
2201
2202	# untestable units
2203
2204	UNITS_NEED_FIX = \
2205	ptpan/PROBE.test \
2206
2207	UNITS_UNTESTABLE_ATM = \
2208	PROBE_SET/PROBE_SET.test \
2209	XML_IMPORT/XML_IMPORT.test \
2210
2211	# for the moment, put all units containing tests into UNITS_TESTED or UNITS_TESTED_FIRST
2212
2213	UNITS_TESTED_FIRST = \
2214	DIST/DIST.test \
2215	PARSIMONY/PARSIMONY.test \
2216	EDIT4/EDIT4.test \
2217	NTREE/NTREE.test \
2218	MULTI_PROBE/MULTI_PROBE.test \
2219
2220	# plain test-libaries not linked anywhere
2221	TEST_SANDBOXES = \
2222	SL/CB/CB.test \
2223
2224	UNITS_TESTED = \
2225	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.test \
2226	SL/NDS/NDS.test \
2227	ARB_GDE/ARB_GDE.test \
2228	GENOM_IMPORT/GENOM_IMPORT.test \
2229	SL/MACROS/MACROS.test \
2230	SL/REGEXPR/REGEXPR.test \
2231	SL/FILTER/FILTER.test \
2232	ARBDB/libARBDB.test \
2233	CONSENSUS_TREE/CONSENSUS_TREE.test \
2234	TOOLS/arb_consensus_tree.test \
2235	TOOLS/arb_test.test \
2236	TOOLS/arb_probe.test \
2237	PERLTOOLS/arb_proto_2_xsub.test \
2238	AWTC/AWTC.test \
2239	SL/ALILINK/ALILINK.test \
2240	SL/TREE_READ/TREE_READ.test \
2241	DBSERVER/DBSERVER.test \
2242	AWT/libAWT.test \
2243	CORE/libCORE.test \
2244	SL/INSDEL/INSDEL.test \
2245	SL/TREEDISP/TREEDISP.test \
2246	AISC_MKPTPS/mkptypes.test \
2247	MERGE/MERGE.test \
2248	SERVERCNTRL/SERVERCNTRL.test \
2249	SL/FAST_ALIGNER/FAST_ALIGNER.test \
2250	SL/PRONUC/PRONUC.test \
2251	WINDOW/libWINDOW.test \
2252	HELP_SOURCE/arb_help2xml.test \
2253	CONVERTALN/CONVERTALN.test \
2254	SL/SEQIO/SEQIO.test \
2255	SL/PTCLEAN/PTCLEAN.test \
2256	PROBE/PROBE.test \
2257	SL/DB_QUERY/DB_QUERY.test \
2258
2259	TESTED_UNITS_MANUAL = \
2260	$(TEST_SANDBOXES) \
2261	$(UNITS_TESTED_FIRST) \
2262	$(UNITS_TESTED) \
2263
2264	# $(UNITS_WORKING)
2265
2266	# see UNIT_TESTER/sym2testcode.pl@disableErrorOnUnitsWithoutTests
2267
2268	#TESTED_UNITS = $(TESTED_UNITS_AUTO)
2269	TESTED_UNITS = $(TESTED_UNITS_MANUAL)
2270
2271	# ----------------------------------------
2272
2273	TEST_LOG_DIR = UNIT_TESTER/logs
2274	TEST_RUN_SUITE=$(MAKE) $(NODIR) -C UNIT_TESTER -f Makefile.suite -r
2275	TEST_MAKE_FLAGS=
2276	TEST_POST_CLEAN=
2277	ifeq ($(COVERAGE),1)
2278	TEST_POST_CLEAN=$(MAKE) clean_cov
2279	TEST_MAKE_FLAGS+=-j1
2280	endif
2281
2282
2283	%.test:
2284	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
2285	( \
2286	echo "fake[1]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
2287	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
2288	"UNITDIR=$(@D)" \
2289	"UNITLIBNAME=$(@F:.test=)" \
2290	"COVERAGE=$(COVERAGE)" \
2291	"ARB_PID=$(ARB_PID)_$(@F)" \
2292	runtest; \
2293	echo "fake[1]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"; \
2294	$(TEST_POST_CLEAN) \
2295	) >$(TEST_LOG_DIR)/$(@F).log 2>&1; \
2296	UNIT_TESTER/log_result.pl $(TEST_LOG_DIR)/$(@F).log )
2297
2298
2299	test_base: $(UNIT_TESTER_LIB:.a=.dummy) $(subst .test,.dummy,$(TEST_SANDBOXES))
2300
2301	clean_cov:
2302	find . \( -name ".gcda" -o -name ".gcov" -o -name "*.cov" \) -exec rm {} \;
2303
2304	clean_cov_all: clean_cov
2305	find . \( -name "*.gcno" \) -exec rm {} \;
2306
2307	run_tests: test_base clean_cov
2308	$(MAKE) "ARB_PID=UT_$$$$" run_tests_faked_arbpid
2309
2310	cleanup_faked_arbpids:
2311	@-rm ~/.arb_tmp/tmp/arb_pids_${USER}_${ARB_PID}_*
2312
2313	cleanup_faked_arbpids_and_fail: cleanup_faked_arbpids
2314	@false
2315
2316	run_tests_faked_arbpid:
2317	+@$(TEST_RUN_SUITE) init
2318	@echo "fake[2]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2319	$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(TESTED_UNITS) \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2320	@echo "fake[2]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2321	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2322	@$(MAKE) clean_cov >/dev/null
2323	@$(MAKE) cleanup_faked_arbpids
2324
2325	ut:
2326	ifeq ($(UNIT_TESTS),1)
2327	@echo $(MAKE) run_tests
2328	@$(MAKE) run_tests
2329	else
2330	@echo "Not compiled with unit tests"
2331	endif
2332
2333
2334	aut:
2335	+@$(TEST_RUN_SUITE) unskip
2336	$(MAKE) ut
2337
2338	# --------------------------------------------------------------------------------
2339
2340	TIMELOG=$(ARBHOME)/arb_time.log
2341	TIMEARGS=--append --output=$(TIMELOG) --format=" %E(%S+%U) %P [%C]"
2342	TIMECMD=$(TIME) $(TIMEARGS)
2343
2344	time_one:
2345	ifeq ($(ONE_TIMED_TARGET),)
2346	@echo "Error: You have to pass ONE_TIMED_TARGET to $@"
2347	false
2348	else
2349	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET)"
2350	@$(TIMECMD) $(MAKE) $(ONE_TIMED_TARGET)
2351	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET) [done]"
2352	endif
2353
2354	timed_target:
2355	ifeq ($(TIMED_TARGET),)
2356	@echo "Error: You have to pass TIMED_TARGET to $@"
2357	false
2358	else
2359	@echo "Build time:" > $(TIMELOG)
2360	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2361	@cat $(TIMELOG)
2362	@rm $(TIMELOG)
2363	endif
2364
2365	timed_target_tested:
2366	ifeq ($(TIMED_TARGET),)
2367	@echo "Error: You have to pass TIMED_TARGET to $@"
2368	false
2369	else
2370	@echo "Build time:" > $(TIMELOG)
2371	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2372	$(MAKE) "ONE_TIMED_TARGET=ut" time_one
2373	@cat $(TIMELOG)
2374	@rm $(TIMELOG)
2375	endif
2376
2377	clean_timed_target:
2378	ifeq ($(TIMED_TARGET),)
2379	@echo "Error: You have to pass TIMED_TARGET to $@"
2380	false
2381	else
2382	@echo "Build time:" > $(TIMELOG)
2383	$(MAKE) "ONE_TIMED_TARGET=clean" time_one
2384	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2385	@cat $(TIMELOG)
2386	@rm $(TIMELOG)
2387	endif
2388
2389	# --------------------------------------------------------------------------------
2390
2391	CHECKOUT_MODIFIED=0# set to 1 to temporarily skip test for modifications (do not check in if set to 1)
2392
2393	check_svn_does_not_contain_generated:
2394	ifeq ($(CHECKOUT_MODIFIED),0)
2395	@echo "Testing that build does not modify files in SVN"
2396	@test 0 = `svn status \| wc -l` \|\| ( \
2397	echo "The checkout is not/no longer clean:"; \
2398	svn status; \
2399	echo "- if this fails instantly, your checkout is not clean"; \
2400	echo "- if this fails after other targets, these targets modify checked in data"; \
2401	echo " (a common cause may be that depends are not up to date)"; \
2402	false)
2403	else
2404	grep -Hn 'CHECKOUT_MODIFIED' Makefile
2405	endif
2406
2407	check_svn_ignores_generated:
2408	@test 0 = `svn status \| grep '^\?' \| wc -l` \|\| ( \
2409	echo "There are svn-unignored files:"; \
2410	svn status \| grep '^\?'; \
2411	echo "(all generated files should be svn-ignored)"; \
2412	false)
2413
2414	check_svn_state: check_svn_does_not_contain_generated
2415	$(MAKE) check_svn_ignores_generated
2416	$(MAKE) savetest
2417
2418	things_that_always_should_work: depends proto
2419
2420	post_commit_check:
2421	@echo "---------------------------------------- [Initial]"
2422	$(MAKE) check_svn_state
2423
2424	$(MAKE) clean
2425	@echo "---------------------------------------- [After 'make clean']"
2426	$(MAKE) check_svn_state
2427
2428	$(MAKE) things_that_always_should_work
2429	@echo "---------------------------------------- [After 'make things_that_always_should_work']"
2430	$(MAKE) check_svn_state
2431
2432	$(MAKE) all
2433	@echo "---------------------------------------- [After 'make all']"
2434	$(MAKE) check_svn_state
2435
2436	$(MAKE) things_that_always_should_work
2437	@echo "---------------------------------------- [Final]"
2438	$(MAKE) check_svn_state
2439
2440	# --------------------------------------------------------------------------------
2441
2442	build: arb
2443	$(MAKE) binlink preplib compile_compatibility
2444
2445	all:
2446	@echo "Build time" > $(TIMELOG)
2447	@echo "$(SEP) $(MAKE) build"
2448	@$(TIMECMD) $(MAKE) build
2449	@echo $(SEP)
2450	@echo "made 'all' with success."
2451	@echo "to start arb enter 'arb'"
2452	ifeq ($(UNIT_TESTS),1)
2453	@echo $(MAKE) run_tests
2454	@$(TIMECMD) $(MAKE) run_tests
2455	endif
2456	@echo "$(SEP) $(MAKE) build [done]"
2457	ifeq ($(DEBUG),1)
2458	@$(MAKE) save_test_no_error >/dev/null # just show hints
2459	endif
2460	@cat $(TIMELOG)
2461	@rm $(TIMELOG)
2462

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