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Last change on this file was 15215, checked in by westram, 8 years ago
merge gcc-patches from 'trunk' and 'fix' into 'stable' workaround for gcc 6.1.0 (see #700) tested with gcc 4.9.4 and 5.4.0 adds: [14812/branches/fix] log:trunk@14807:14808,14908,15133
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 65.9 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	# $(MACH) name of the machine (LINUX or DARWIN; see config.makefile)
24	# DEBUG compiles the DEBUG sections
25	# DEBUG_GRAPHICS all X-graphics are flushed immediately (for debugging)
26	# ARB_64=0/1 1=>compile 64 bit version
27	# UNIT_TESTS=0/1 1=>compile in unit tests and call them after build
28	# COVERAGE=0/1/2 compile in gcov support (useful together with UNIT_TESTS=1)
29	# 0=no, 1+2=compile in, 1=show
30	# STABS=0/1 force stabs format? (0 = "use default format")
31	#
32	# -----------------------------------------------------
33	# The ARB source code is aware of the following defines:
34	#
35	# NDEBUG doesn't compile the DEBUG sections
36	# DEVEL_$(DEVELOPER) developer-dependent flag (enables you to have private sections in code)
37	# DEVELOPER='ANY' (default setting) will be ignored
38	# configurable in config.makefile
39	#
40	# -----------------------------------------------------
41	# Read configuration
42	include config.makefile
43
44	# set defaults for variables commented out in config.makefile:
45	ifndef DARWIN
46	DARWIN:=0
47	endif
48	ifndef LINUX
49	LINUX:=0
50	endif
51	ifndef DEBIAN
52	DEBIAN:=0
53	endif
54	ifndef REDHAT
55	REDHAT:=0
56	endif
57	ifndef ARB_64
58	ARB_64=1#default to 64bit
59	endif
60
61	# compiler settings:
62	ifneq ($(CC),use__A_CC__instead_of__CC)
63
64	A_CC:=$(CC)# compile C
65	A_CXX:=$(CXX)# compile C++
66
67	# uncomment to ensure no submakefile uses CC and CXX directly
68	override CC:=use__A_CC__instead_of__CC
69	override CXX:=use__A_CXX__instead_of__CXX
70
71	endif
72
73	export CC CXX A_CC A_CXX
74
75	ifeq ($(LD_LIBRARY_PATH),'')
76	LD_LIBRARY_PATH:=${ARBHOME}/lib
77	endif
78
79	ifeq ($(DARWIN),1)
80	LD_LIBRARY_PATH:=${ARBHOME}/lib
81	endif
82
83	# store LD_LIBRARY_PATH to circumvent SIP restrictions:
84	ARBBUILD_LIBRARY_PATH:=$(LD_LIBRARY_PATH)
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 4.6.4 \
100	4.7.1 4.7.2 4.7.3 \
101	4.8.0 4.8.1 4.8.2 4.8.3 4.8.4 4.8.5 \
102	4.9.0 4.9.1 4.9.2 4.9.3 4.9.4 \
103	5.1.0 5.2.0 5.3.0 5.3.1 5.4.0 \
104	6.1.0 \
105
106
107	# ----------------------
108
109	COMPILER_INFO:=$(shell SOURCE_TOOLS/arb_compiler_version.pl $(A_CXX))
110	COMPILER_NAME:=$(word 1,$(COMPILER_INFO))
111	COMPILER_VERSION:=$(word 2,$(COMPILER_INFO))
112
113	USE_CLANG:=0
114	ifneq ($(COMPILER_NAME),gcc)
115	ifeq ($(COMPILER_NAME),clang)
116	USE_CLANG:=1
117	else
118	$(error failed to detect COMPILER_NAME (got '$(COMPILER_NAME)', expected 'clang' or 'gcc'))
119	endif
120	endif
121
122	ifeq ($(USE_CLANG),1)
123	# accept all clang versions:
124	ALLOWED_COMPILER_VERSIONS=$(COMPILER_VERSION)
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_47_OR_HIGHER:=
141	USE_GCC_48_OR_HIGHER:=
142
143	ifeq ($(USE_CLANG),0)
144	ifeq ($(USE_GCC_MAJOR),4)
145	ifeq ($(USE_GCC_MINOR),5)
146	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),23456789)','')
147	USE_GCC_452_OR_HIGHER:=yes
148	endif
149	else
150	ifneq ('$(findstring $(USE_GCC_MINOR),6789)','')
151	USE_GCC_452_OR_HIGHER:=yes
152	ifneq ($(USE_GCC_MINOR),6)
153	USE_GCC_47_OR_HIGHER:=yes
154	ifneq ($(USE_GCC_MINOR),7)
155	USE_GCC_48_OR_HIGHER:=yes
156	endif
157	endif
158	endif
159	endif
160	else
161	USE_GCC_452_OR_HIGHER:=yes
162	USE_GCC_47_OR_HIGHER:=yes
163	USE_GCC_48_OR_HIGHER:=yes
164	endif
165	endif
166
167	#---------------------- define special directories for non standard builds
168
169	ifeq ($(DARWIN),1)
170	OSX_FW:=/System/Library/Frameworks
171	OSX_FW_OPENGL:=$(OSX_FW)/OpenGL.framework/Versions/A/Libraries
172	OSX_FW_GLUT:=$(OSX_FW)/GLUT.framework/Versions/A/Libraries
173	OSX_FW_IMAGEIO:=$(OSX_FW)/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources
174	endif
175
176	#----------------------
177
178	ifeq ($(DARWIN),1)
179	LINK_STATIC=1# link static
180	else
181	LINK_STATIC=0# link dynamically
182	# LINK_STATIC=1# link static (testing only)
183	endif
184
185	shared_cflags :=# flags for shared lib compilation
186	lflags :=# linker flags
187	clflags :=# linker flags (when passed through gcc)
188	extended_warnings :=# warning flags for C and C++-compiler
189	extended_cpp_warnings :=# warning flags for C++-compiler only
190
191
192	ifeq ($(DEBUG),0)
193	dflags := -DNDEBUG# defines
194	ifeq ($(USE_CLANG),1)
195	cflags := -O3# compiler flags (C and C++)
196	else
197	cflags := -O3# compiler flags (C and C++)
198	lflags += -O2# linker flags
199	clflags += -Wl,-O2# passthrough linker flags
200	endif
201	endif
202
203	ifeq ($(DEBIAN),1)
204	lflags += -rpath=/usr/lib/arb/lib -z relro
205	clflags += -Wl,-rpath=/usr/lib/arb/lib -Wl,-z,relro
206	endif
207
208	ifeq ($(DEBUG),1)
209	dflags := -DDEBUG
210
211	gdb_common := -g -g3 -ggdb -ggdb3
212
213	ifeq ($(STABS),1)
214	cflags := -O0 $(gdb_common) -gstabs+ # using stabs+ (enable this for bigger debug session: debugs inlines, quick var inspect, BUT valgrind stops working :/)
215	else
216	cflags := -O0 $(gdb_common) # (using dwarf - cant debug inlines here, incredible slow on showing variable content)
217	endif
218
219	# cflags := -O0 $(gdb_common) -gdwarf-3 # (specify explicit dwarf format)
220	# cflags := -O0 $(gdb_common) -gstabs # using stabs (same here IIRC)
221	# cflags := -O2 $(gdb_common) # use this for callgrind (force inlining)
222
223	ifeq ($(DARWIN),0)
224	lflags += -g
225	clflags += -Wl,-g
226	endif
227
228	# control how much you get spammed
229	# (please do not change default in SVN, use developer specific setting as below)
230	POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl
231	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --original# dont modify compiler output
232	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --hide-Noncopyable-advices
233	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --show-useless-Weff++
234	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --no-warnings
235	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --only-first-error
236	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --no-warnings --only-first-error
237	ifeq ($(DEVELOPER),ELMAR)
238	POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --only-first-error
239	endif
240
241
242	# Enable extra warnings
243	extended_warnings :=
244	extended_cpp_warnings :=
245
246	# C and C++
247	extended_warnings += -Wwrite-strings -Wunused -Wno-aggregate-return -Wshadow
248
249	# C++ only
250	extended_cpp_warnings += -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute
251	extended_cpp_warnings += -Wctor-dtor-privacy# < gcc 3
252	# extended_cpp_warnings += -Wfloat-equal# gcc 3.0
253
254	# ------- above only warnings available in 3.0
255
256	ifneq ('$(COMPILER_VERSION)','4.7.3') # g++ crashes on GenomeImport.cxx when -Weffc++ is active (bug reported)
257	extended_cpp_warnings += -Weffc++# gcc 3.0.1
258	endif
259	extended_cpp_warnings += -Wmissing-noreturn# gcc 3.0.2
260	# extended_cpp_warnings += -Wold-style-cast# gcc 3.0.4 (warn about 28405 old-style casts)
261	extended_cpp_warnings += -Winit-self# gcc 3.4.0
262	extended_cpp_warnings += -Wstrict-aliasing# gcc 3.4
263	extended_cpp_warnings += -Wextra# gcc 3.4.0
264	ifeq ('$(USE_GCC_452_OR_HIGHER)','yes')
265	extended_cpp_warnings += -Wlogical-op# gcc 4.5.2
266	endif
267
268	ifeq ($(DEBUG_GRAPHICS),1)
269	dflags += -DDEBUG_GRAPHICS
270	endif
271	endif
272
273	#---------------------- turn off clang bogus warnings
274
275	ifeq ($(USE_CLANG),1)
276	# -Wmismatched-tags warns about struct/class mismatch in forward declarations (which is explicitely allowed)
277	# -Wchar-subscripts reports too many bogus warnings for "array['x']" (when 'x' is known to be in range [0..128])
278	# -Wunused-private-field report too many false positives (currently ~ 2 of 3)
279	# -Wstring-plus-int warns about common ARB coding practice
280	# -Wgnu-static-float-init warns about accepted GNU extension
281	extended_cpp_warnings += -Wno-mismatched-tags -Wno-char-subscripts -Wno-unused-private-field -Wno-string-plus-int -Wno-gnu-static-float-init
282	endif
283
284	#---------------------- developer
285
286	ifneq ($(DEVELOPER),ANY) # ANY=default setting (skip all developer specific code)
287	dflags += -DDEVEL_$(DEVELOPER)# activate developer/release specific code
288	endif
289
290	ifndef SHOWTODO
291	ifeq ($(DEVELOPER),RALF)
292	SHOWTODO:=1
293	else
294	SHOWTODO:=0
295	endif
296	endif
297	ifeq ($(SHOWTODO),1)
298	dflags += -DWARN_TODO# activate "TODO" warnings
299	endif
300
301	#---------------------- 32 or 64 bit
302
303	ifndef BUILDHOST_64
304	BUILDHOST_64:=$(ARB_64)# assume build host is same as version (see config.makefile)
305	endif
306
307	cross_cflags:=
308	cross_lflags:=
309	cross_clflags:=
310
311	ifeq ($(ARB_64),1)
312	dflags += -DARB_64 #-fPIC
313	shared_cflags += -fPIC
314
315	ifeq ($(BUILDHOST_64),1)
316	# build 64-bit ARB version on 64-bit host
317	CROSS_LIB:=# empty = autodetect below
318	ifeq ($(DARWIN),1)
319	cross_cflags += -arch x86_64
320	cross_lflags += -arch x86_64
321	cross_clflags += -arch x86_64
322	endif
323	else
324	# build 64-bit ARB version on 32-bit host
325	CROSS_LIB:=/lib64
326	cross_cflags += -m64
327	cross_lflags += -m64 -m elf_x86_64
328	cross_clflags += -m64 -Wl,-m64,-m,elf_x86_64
329	endif
330	else
331	ifeq ($(BUILDHOST_64),1)
332	# build 32-bit ARB version on 64-bit host
333	CROSS_LIB:=# empty = autodetect below
334	cross_cflags += -m32
335	cross_lflags += -m32 -m elf_i386
336	cross_clflags += -m32 -Wl,-m32,-m,elf_i386
337	else
338	# build 32-bit ARB version on 32-bit host
339	CROSS_LIB:=/lib
340	endif
341	endif
342
343	cflags += $(cross_cflags)
344	lflags += $(cross_lflags)
345	clflags += $(cross_clflags)
346
347	ifeq ('$(CROSS_LIB)','')
348	# autodetect libdir
349	ifeq ($(ARB_64),1)
350	CROSS_LIB:=$(shell (test -d /lib64 && echo lib64) \|\| echo lib)
351	else
352	CROSS_LIB:=$(shell (test -d /lib32 && echo lib32) \|\| echo lib)
353	endif
354	endif
355
356	#---------------------- unit tests
357
358	ifndef UNIT_TESTS
359	UNIT_TESTS=0#default is "no tests"
360	endif
361	ifeq ($(UNIT_TESTS),1)
362	dflags += -DUNIT_TESTS
363	UNIT_TESTER_LIB=UNIT_TESTER/UNIT_TESTER.a
364	else
365	UNIT_TESTER_LIB=
366	endif
367
368	#---------------------- use gcov
369
370	ifndef COVERAGE
371	COVERAGE=0#default is "no"
372	endif
373	ifneq ($(COVERAGE),0)
374	GCOVFLAGS=-ftest-coverage -fprofile-arcs
375	cflags += $(GCOVFLAGS)
376	EXECLIBS=-lgcov
377	else
378	GCOVFLAGS=
379	EXECLIBS=
380	endif
381
382	#---------------------- other flags
383
384	dflags += -D$(MACH) # define machine
385
386	ifeq ($(DARWIN),1)
387	shared_cflags += -fno-common
388	else
389	dflags += $(shell getconf LFS_CFLAGS)
390	endif
391
392	cflags += -pipe
393	cflags += -fmessage-length=0# don't wrap compiler output
394	cflags += -fshow-column# show columns
395	cflags += -funit-at-a-time
396	cflags += -fPIC
397	cflags += -fno-common# link all global data into one namespace
398	cflags += -fstrict-aliasing# gcc 3.4
399	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
400	cflags += -fno-diagnostics-show-caret#gcc 4.8 (4.7.?)
401	endif
402	#cflags += -save-temps# uncomment to see preprocessor output
403
404	#---------------------- X11 location
405
406	ifeq ($(DARWIN),1)
407	XHOME:=$(PREFIX)
408	else
409	ifeq ($(DEBIAN),1)
410	XHOME:=$(PREFIX)
411	else
412	XHOME:=/usr/X11R6
413	endif
414	endif
415
416	XINCLUDES:=-I$(XHOME)/include
417	ifeq ($(DARWIN),1)
418	XINCLUDES += -I$(OSX_FW)/GLUT.framework/Headers -I$(OSX_FW)/OpenGL.framework/Headers -I$(OSX_SDK)/usr/include/krb5
419
420	XLIBS := -L$(XHOME)/lib -lXm -lpng -lz -lXt -lX11 -lXext -lXp -lXmu -lXi
421	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGL.dylib:$(OSX_FW_OPENGL)/libGL.dylib
422	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGLU.dylib:$(OSX_FW_OPENGL)/libGLU.dylib
423	else
424	XLIBS:=-L$(XHOME)/$(CROSS_LIB) -lXm -lXpm -lXt -lXext -lX11
425	endif
426
427	#---------------------- open GL
428
429	ifeq ($(OPENGL),1)
430	cflags += -DARB_OPENGL # activate OPENGL code
431	GL := gl # this is the name of the OPENGL base target
432	GL_LIB_SYS := -lGL -lGLU
433	GL_LIB_ARB := -L$(ARBHOME)/GL/glAW -lglAW
434
435	ifeq ($(DARWIN),1)
436	GL_LIB_SYS += -lpthread
437	endif
438
439	GL_PNGLIBS_ARB := -L$(ARBHOME)/GL/glpng -lglpng_arb
440	GL_PNGLIBS_SYS := -lpng
441
442	GLEWLIB := -lGLEW -lGLw
443	ifeq ($(DARWIN),1)
444	GLUTLIB := -glut
445	else
446	GLUTLIB := -lglut
447	endif
448
449	GL_LIBS_SYS := $(GL_LIB_SYS) $(GL_PNGLIBS_SYS) $(GLEWLIB) $(GLUTLIB)
450	GL_LIBS_ARB := $(GL_LIB_ARB) $(GL_PNGLIBS_ARB)
451
452	RNA3D_LIB := RNA3D/RNA3D.a
453
454	else
455
456	GL_LIBS_ARB:=# no opengl -> no libs
457	GL_LIBS_SYS:=# no opengl -> no libs
458	GL:=# don't build ARB openGL libs
459
460	RNA3D_LIB :=
461
462	endif
463
464	RNA3D_LIB_4_DEPENDS := RNA3D/RNA3D.a
465
466	GL_LIBS:=$(GL_LIBS_ARB) $(GL_LIBS_SYS)
467
468	#---------------------- tiff lib:
469
470	TIFFLIBS := -ltiff
471
472	#---------------------- glib:
473
474	ARB_NEEDED_GLIB=glib-2.0
475
476	ARB_GLIB_INCLUDE:=$(strip $(shell pkg-config --cflags $(ARB_NEEDED_GLIB)))
477	ARB_GLIB_LIBS:=$(strip $(shell pkg-config --libs $(ARB_NEEDED_GLIB)))
478
479	#---------------------- basic libs:
480
481	SYSLIBS:=
482
483	ifeq ($(DARWIN),1)
484	SYSLIBS += -lstdc++
485	else
486	SYSLIBS += -lm $(ARB_GLIB_LIBS)
487	endif
488
489	#---------------------- include symbols?
490
491	ifeq ($(TRACESYM),1)
492	ifeq ($(USE_CLANG),0)
493	cflags += -rdynamic
494	lflags += --export-dynamic
495	clflags += -rdynamic -Wl,--export-dynamic
496	endif
497	endif
498
499	#---------------------- system dependent commands
500
501	ifeq ($(DARWIN),1)
502	TIME:=gtime
503	else
504	TIME:=/usr/bin/time
505	endif
506
507	#---------------------- SSE vectorizer
508
509	ifeq ('$(COMPILER_VERSION)','6.1.0')
510	# see http://bugs.arb-home.de/ticket/700
511	cflags += -fno-tree-loop-vectorize
512	DISABLE_VECTORIZE_CHECK:=1
513	endif
514
515	# -------------------------------------------------------------------------
516	# Don't put any machine/version/etc conditionals below!
517	# (instead define variables above)
518	# -------------------------------------------------------------------------
519
520	cflags += -W -Wall $(dflags) $(extended_warnings)
521	cxxflags := $(extended_cpp_warnings)
522
523	# add CFLAGS + CPPFLAGS from environment for DEBIAN build
524	ifeq ($(DEBIAN),1)
525	cflags := $(CFLAGS) $(cflags)
526	cxxflags += $(CPPFLAGS)
527	endif
528
529	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
530	cxxflags += -std=gnu++11# see also TEMPLATES/cxxforward.h@USE_Cxx11
531	else
532	# only use for gcc versions between 4.3 and <4.7 (4.7++ adds -Wc++11-compat above)
533	HAVE_GNUPP0X=`SOURCE_TOOLS/requireVersion.pl 4.3 $(COMPILER_VERSION)`
534	ifeq ($(HAVE_GNUPP0X),1)
535	# ensure compatibility with upcoming C++ standard
536	cxxflags += -std=gnu++0x
537	endif
538	endif
539
540	LINK_STATIC_LIB := ld $(lflags) -r -o# link static lib
541	LINK_EXECUTABLE := $(A_CXX) $(clflags) -o# link executable (c++)
542
543	ifeq ($(LINK_STATIC),1)
544	SHARED_LIB_SUFFIX = a# static lib suffix
545	LINK_SHARED_LIB := $(LINK_STATIC_LIB)
546	else
547	SHARED_LIB_SUFFIX = so# shared lib suffix
548	LINK_SHARED_LIB := $(A_CXX) $(clflags) -shared $(GCOVFLAGS) -o# link shared lib
549	endif
550
551	# delete variables unused below
552	lflags:=
553	clflags:=
554
555	# other used tools
556	MAKEDEPEND_PLAIN = makedepend
557	MAKEDEPEND = $(FORCEMASK);$(MAKEDEPEND_PLAIN)
558
559	#SEP:=--------------------------------------------------------------------------------
560	SEP=[`date +%M:%S.%N`] ------------------------------------------------
561	# to analyse timings run
562	# make -j9 clean; make -j9 all \| grep '^\[' \| sort
563	# make -j9 "TIMED_TARGET=perl" clean_timed_target \| grep '^\[' \| sort
564
565	CORE_LIB=-lCORE
566	ARBDB_LIB=-lARBDB $(CORE_LIB)
567	LIBS = $(ARBDB_LIB) $(SYSLIBS)
568
569	GUI_LIBS_PREFIX:=
570	ifeq ($(DARWIN),1)
571	# this seem to be added at wrong place, since opengl is only needed to link EDIT4
572	GUI_LIBS_PREFIX:=-framework GLUT -framework OpenGL
573	endif
574
575	GUI_LIBS=$(GUI_LIBS_PREFIX) $(LIBS) -lAWT -lWINDOW
576	GUI_LIBS+=$(XLIBS)
577
578	LIBPATH = -L$(ARBHOME)/lib
579
580	DEST_LIB = lib
581	DEST_BIN = bin
582
583	CC_INCLUDES := -I. -I$(ARBHOME)/INCLUDE $(XINCLUDES) $(ARB_GLIB_INCLUDE)
584	CXX_INCLUDES := $(CC_INCLUDES)
585	MAKEDEPENDFLAGS := -- -DARB_OPENGL -DUNIT_TESTS -D__cplusplus -I. -Y$(ARBHOME)/INCLUDE
586
587	# -------------------------------
588	# old PTSERVER or PTPAN?
589
590	ifeq ($(PTPAN),1)
591	# PTPAN only libs
592	ARCHS_PT_SERVER = \
593	ptpan/PROBE.a
594	else
595	ifeq ($(PTPAN),2)
596	# special mode to compile both servers (developers only!)
597	ARCHS_PT_SERVER = \
598	ptpan/PROBE.a \
599	PROBE/PROBE.a
600	ARCHS_PT_SERVER_LINK = PROBE/PROBE.a# default to old ptserver
601	else
602	# PT-server only libs
603	ARCHS_PT_SERVER = \
604	PROBE/PROBE.a
605	endif
606	endif
607
608	ifndef ARCHS_PT_SERVER_LINK
609	ARCHS_PT_SERVER_LINK = $(ARCHS_PT_SERVER)
610	endif
611
612	# ---------------------------------------
613	# wrap main()
614
615	use_ARB_main=$(ARBHOME)/SOURCE_TOOLS/arb_main_cpp.o
616	use_ARB_main_C=$(ARBHOME)/SOURCE_TOOLS/arb_main_c.o
617
618	# -----------------------------------------
619	# export variables to submakefiles
620
621	include SOURCE_TOOLS/export2sub
622
623	# do not define (exported) variables below this point
624
625	# -------------------------
626	# Main arb targets:
627	# -------------------------
628
629	first_target:
630	$(MAKE) checks
631	@echo $(SEP)
632	@echo 'Main targets:'
633	@echo ''
634	@echo ' all - Compile ARB + TOOLs + and copy shared libs + link foreign software'
635	@echo ' (That is most likely the target you want)'
636	@echo ''
637	@echo ' clean - remove generated files ("SUBDIR/SUBDIR.clean" to clean only SUBDIR)'
638	@echo ' rebuild - clean + all'
639	@echo ' relink - remove all binaries and relink them from objects'
640	@echo ''
641	@echo 'Some often used sub targets (make all makes them all):'
642	@echo ''
643	@echo ' arb - Just compile ARB (but none of the integrated tools)'
644	@echo ' menus - create lib/gde/arb.menu from GDEHELP/ARB_GDEmenus.source'
645	@echo ' perl - Compile the PERL XSUBS into lib/ARB.so and create links in lib to perl'
646	@echo ' binlink - Create all links in the bin directory'
647	@echo ''
648	@echo 'Development targets:'
649	@echo ''
650	@echo ' depends - create or update dependencies ("SUBDIR/SUBDIR.depends" to update only SUBDIR)'
651	@echo ' proto - create or update prototypes ("SUBDIR/SUBDIR.proto" to update only SUBDIR)'
652	@echo ' tags - create tags for xemacs'
653	@echo ' show - show available shortcuts (AKA subtargets)'
654	@echo ' up - shortcut for depends+proto+tags'
655	ifeq ($(UNIT_TESTS),1)
656	@echo ' ut - only run tests'
657	endif
658	@echo ' modified - rebuild files modified in svn checkout (does touch)'
659	@echo ' touch - touch files modified in svn checkout'
660	@echo ''
661	@echo 'Internal maintenance:'
662	@echo ''
663	@echo ' relinfo - show help on release targets'
664	@echo ' tarfile - make rebuild and create arb version tarfile ("tarfile_quick" to skip rebuild)'
665	@echo ' save - save all basic ARB sources into arbsrc_DATE ("savetest" to check filelist)'
666	@echo ' patch - save svn diff to patchfile'
667	@echo ' source_doc - create doxygen documentation'
668	@echo ' relocated - rebuild partly (use when you have relocated ARBHOME)'
669	@echo ' check_res - check ressource usage'
670	@echo ' dep_graph - Build dependency graphs'
671	@echo ' clean_cov - Clean coverage results'
672	@echo ''
673	@echo ' post_commit_check - Checks whether'
674	@echo ' * main make targets work,'
675	@echo ' * dependencies and prototypes are up to date,'
676	@echo ' * SVN-controlled files remain unaffected by called targets and'
677	@echo ' * all generated files are ignored.'
678	@echo ' (has to be called in a clean SVN checkout)'
679	@echo $(SEP)
680	@echo ''
681
682	relinfo:
683	@echo ''
684	@echo $(SEP)
685	@echo 'Release targets:'
686	@echo ''
687	@echo ' inc_candi - increase RC candidate-number (only possible in "rc" branch, not needed for RC1)'
688	@echo ' inc_patch - increase release patchlevel (only possible in "stable" branch)'
689	@echo ' inc_minor - increase minor version number (only possible in "trunk")'
690	@echo ' inc_major - increase MAJOR version number (only possible in "trunk")'
691	@echo ''
692	@echo ' show_version - show version tag'
693	@echo ''
694	@echo $(SEP)
695	@echo ''
696
697	# auto-generate config.makefile:
698
699	CONFIG_MAKEFILE_FOUND=$(wildcard config.makefile)
700
701	config.makefile : config.makefile.template
702	@echo --------------------------------------------------------------------------------
703	ifeq ($(strip $(CONFIG_MAKEFILE_FOUND)),)
704	@cp $< $@
705	@echo '$(ARBHOME)/$@:1: has been generated.'
706	@echo 'Please edit $@ to configure your system!'
707	@echo --------------------------------------------------------------------------------
708	@false
709	else
710	@echo '$(ARBHOME)/$<:1: is more recent than'
711	@echo '$(ARBHOME)/$@:1:'
712	@ls -al config.makefile*
713	@echo --------------------------------------------------------------------------------
714	@echo "Updating $@ (if this fails, check manually)"
715	SOURCE_TOOLS/update_config_makefile.pl
716	@echo "Sucessfully updated $@"
717	@echo --------------------------------------------------------------------------------
718	@ls -al config.makefile*
719	@echo --------------------------------------------------------------------------------
720	@echo "Diff to your old config.makefile:"
721	@echo --------------------------------------------------------------------------------
722	-diff $@.bak $@
723	@echo --------------------------------------------------------------------------------
724	endif
725
726	# check if everything is configured correctly
727
728	check_DEVELOPER:
729	ifndef DEVELOPER
730	@echo 'config.makefile:1: DEVELOPER not defined'
731	@false
732	endif
733
734	check_DEBUG:
735	ifndef dflags
736	@echo 'config.makefile:1: DEBUG has to be defined. Valid values are 0 and 1'
737	@false
738	endif
739
740	check_ARB_64:
741	ifndef ARB_64
742	@echo 'config.makefile:1: ARB_64 has to be defined. Valid values are 0 and 1'
743	@false
744	endif
745
746	# ---------------------------------------- check gcc version
747
748	check_same_GCC_VERSION:
749	$(ARBHOME)/SOURCE_TOOLS/check_same_compiler_version.pl $(COMPILER_NAME) $(COMPILER_VERSION_ALLOWED)
750
751	check_GCC_VERSION:
752	@echo 'Compiler version check:'
753	# see .@ALLOWED_gcc_VERSIONS
754	ifeq ('$(COMPILER_VERSION_ALLOWED)', '')
755	@echo " - Your compiler is '$(COMPILER_NAME)' version '$(COMPILER_VERSION)'"
756	@echo ' This version is not in the list of supported $(COMPILER_NAME)-versions:'
757	@$(foreach version,$(ALLOWED_COMPILER_VERSIONS),echo ' * $(version)';)
758	@echo ' - You may either ..'
759	@echo ' - add your version to ALLOWED_$(COMPILER_NAME)_VERSIONS in the Makefile and try it out or'
760	@echo ' - switch to one of the allowed versions (see arb_README_gcc.txt for installing'
761	@echo ' a different version of gcc)'
762	@echo ''
763	@false
764	else
765	@echo " - Supported $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)' detected - fine!"
766	@echo ''
767	$(MAKE) check_same_GCC_VERSION
768
769	endif
770
771	#---------------------- check ARBHOME
772
773	# use arb_INSTALL.txt to determine whether ARBHOME points to correct directory
774	ARB_INSTALL_FOUND=$(wildcard $(ARBHOME)/arb_INSTALL.txt)
775
776	check_ARBHOME:
777	ifeq ($(strip $(ARB_INSTALL_FOUND)),)
778	@echo ------------------------------------------------------------
779	@echo "ARBHOME is set to '$(ARBHOME)'"
780	@echo "The environment variable ARBHOME has to point to the top arb source directory."
781	@echo "If you use bash enter:"
782	@echo " export ARBHOME='`pwd`'"
783	@echo ------------------------------------------------------------
784	@false
785	endif
786
787	ARB_PATH_SET=$(findstring $(ARBHOME)/bin,$(PATH))
788
789	check_PATH: check_ARBHOME
790	ifeq ($(strip $(ARB_PATH_SET)),)
791	@echo ------------------------------------------------------------
792	@echo "The environment variable PATH has to contain $(ARBHOME)/bin"
793	@echo "If you use bash enter:"
794	@echo ' export PATH=$$ARBHOME/bin:$$PATH'
795	@echo ------------------------------------------------------------
796	@false
797	endif
798
799	check_TOOLS:
800	@util/arb_check_build_env.pl \
801	"$(A_CC)" \
802	"$(A_CXX)" \
803	"$(MAKEDEPEND_PLAIN)" \
804	"$(LINK_SHARED_LIB)" \
805	"$(LINK_SHARED_LIB)" \
806
807
808	check_ENVIRONMENT : check_PATH check_TOOLS
809	@echo "-------------------- Environment [start]"
810	@echo "ARBHOME='$(ARBHOME)'"
811	@echo "PATH='$(PATH)'"
812	@echo "LD_LIBRARY_PATH='$(LD_LIBRARY_PATH)'"
813	@echo "-------------------- Environment [end]"
814
815	check_tabs: check_setup
816	ifeq ($(DEBUG),1)
817	@SOURCE_TOOLS/tabBrake.pl
818	endif
819
820	force_tab_check:
821	@touch -t 198001010000 SOURCE_TOOLS/stamp.tabBrake
822	@$(MAKE) check_tabs
823
824
825	# ---------------------
826
827	check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION
828	@echo Your setup seems to be ok.
829
830	checks: check_setup check_tabs
831	@rm -f SOURCE_TOOLS/postcompile.sav
832
833
834	# end test section ------------------------------
835
836	# ---------------------------------------
837	# List of standard top level directories
838	#
839	# sub-makefiles have to define the targets
840	# - 'depends' and
841	# - 'clean'
842	#
843	# when adding new libs here, also add a dependency vs 'links' or 'links_non_perl' in .@DD_links_non_perl
844
845	ARCHS = \
846	$(ARCHS_PT_SERVER) \
847	AISC/AISC.a \
848	AISC_MKPTPS/AISC_MKPTPS.a \
849	ARBDB/libARBDB.a \
850	CORE/libCORE.a \
851	ARB_GDE/ARB_GDE.a \
852	AWT/libAWT.a \
853	AWTC/AWTC.a \
854	AWTI/AWTI.a \
855	CONSENSUS_TREE/CONSENSUS_TREE.a \
856	CONVERTALN/CONVERTALN.a \
857	DBSERVER/DBSERVER.a \
858	DIST/DIST.a \
859	EDIT4/EDIT4.a \
860	EISPACK/EISPACK.a \
861	GDE/GDE.a \
862	GENOM/GENOM.a \
863	GENOM_IMPORT/GENOM_IMPORT.a \
864	GL/GL.a \
865	ISLAND_HOPPING/ISLAND_HOPPING.a \
866	MERGE/MERGE.a \
867	MULTI_PROBE/MULTI_PROBE.a \
868	NALIGNER/NALIGNER.a \
869	NAMES/NAMES.a \
870	NAMES_COM/server.a \
871	NTREE/NTREE.a \
872	PARSIMONY/PARSIMONY.a \
873	PERLTOOLS/PERLTOOLS.a \
874	PHYLO/PHYLO.a \
875	PRIMER_DESIGN/PRIMER_DESIGN.a \
876	PROBE_COM/server.a \
877	PROBE_DESIGN/PROBE_DESIGN.a \
878	PROBE_SET/PROBE_SET.a \
879	READSEQ/READSEQ.a \
880	RNA3D/RNA3D.a \
881	RNACMA/RNACMA.a \
882	SECEDIT/SECEDIT.a \
883	SEQ_QUALITY/SEQ_QUALITY.a \
884	SERVERCNTRL/SERVERCNTRL.a \
885	SL/SL.a \
886	STAT/STAT.a \
887	TOOLS/TOOLS.a \
888	TREEGEN/TREEGEN.a \
889	UNIT_TESTER/UNIT_TESTER.a \
890	WETC/WETC.a \
891	WINDOW/libWINDOW.a \
892	XML/XML.a \
893
894	# -----------------------
895	# library packets
896
897	ARCHS_CLIENT_PROBE = PROBE_COM/client.a PROBE_COM/common.a
898	ARCHS_CLIENT_NAMES = NAMES_COM/client.a NAMES_COM/common.a
899
900	ARCHS_SERVER_PROBE = PROBE_COM/server.a $(ARCHS_CLIENT_PROBE)
901	ARCHS_SERVER_NAMES = NAMES_COM/server.a $(ARCHS_CLIENT_NAMES)
902
903	ARCHS_MAKEBIN = AISC_MKPTPS/AISC_MKPTPS.a AISC/AISC.a
904
905	# communication libs need aisc and aisc_mkpts:
906
907	AISC/AISC.dummy: proto_tools
908
909	comtools: AISC/AISC.dummy
910
911	ARCHS_SEQUENCE = \
912	SL/SEQUENCE/SEQUENCE.a \
913	SL/ALIVIEW/ALIVIEW.a \
914	SL/PRONUC/PRONUC.a \
915
916	ARCHS_TREE = \
917	$(ARCHS_SEQUENCE) \
918	SL/FILTER/FILTER.a \
919	SL/ARB_TREE/ARB_TREE.a \
920	SL/ROOTED_TREE/ROOTED_TREE.a \
921
922	# parsimony tree (used by NTREE, PARSIMONY, STAT(->EDIT4), DIST(obsolete!))
923	ARCHS_AP_TREE = \
924	$(ARCHS_TREE) \
925	SL/AP_TREE/AP_TREE.a \
926
927	# --------------------------------------------------------------------------------
928	# dependencies for linking shared libs
929
930	link_core: core
931	link_db: db link_core
932	link_aw: aw link_db
933	link_awt: awt link_aw
934
935	#***************************************************************************************
936	# Individual_Programs_Section
937	#***************************************************************************************
938
939	arbmainwrapper:
940	$(MAKE) -C SOURCE_TOOLS -r mainwrapper
941
942
943	#********************************* arb_ntree ************************************
944	NTREE = bin/arb_ntree
945	ARCHS_NTREE = \
946	NTREE/NTREE.a \
947	$(ARCHS_AP_TREE) \
948	ARB_GDE/ARB_GDE.a \
949	AWTC/AWTC.a \
950	AWTI/AWTI.a \
951	CONSENSUS_TREE/CONSENSUS_TREE.a \
952	GENOM/GENOM.a \
953	GENOM_IMPORT/GENOM_IMPORT.a \
954	MERGE/MERGE.a \
955	MULTI_PROBE/MULTI_PROBE.a \
956	PRIMER_DESIGN/PRIMER_DESIGN.a \
957	PROBE_DESIGN/PROBE_DESIGN.a \
958	SEQ_QUALITY/SEQ_QUALITY.a \
959	SERVERCNTRL/SERVERCNTRL.a \
960	SL/AW_NAME/AW_NAME.a \
961	SL/DB_UI/DB_UI.a \
962	SL/DB_SCANNER/DB_SCANNER.a \
963	SL/DB_QUERY/DB_QUERY.a \
964	SL/SEQIO/SEQIO.a \
965	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
966	SL/HELIX/HELIX.a \
967	SL/REGEXPR/REGEXPR.a \
968	SL/REFENTRIES/REFENTRIES.a \
969	SL/NDS/NDS.a \
970	SL/ITEMS/ITEMS.a \
971	SL/INSDEL/INSDEL.a \
972	SL/LOCATION/LOCATION.a \
973	SL/MACROS/MACROS.a \
974	SL/TRANSLATE/TRANSLATE.a \
975	SL/TREEDISP/TREEDISP.a \
976	SL/TREE_ADMIN/TREE_ADMIN.a \
977	SL/TREE_READ/TREE_READ.a \
978	SL/TREE_WRITE/TREE_WRITE.a \
979	STAT/STAT.a \
980	XML/XML.a \
981
982	$(NTREE): $(ARCHS_NTREE:.a=.dummy) link_awt
983	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NTREE) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
984	echo "$(SEP) Link $@"; \
985	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS)" ; \
986	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS) && \
987	echo "$(SEP) Link $@ [done]"; \
988	)
989
990	#********************************* arb_edit4 ************************************
991	EDIT4 = bin/arb_edit4
992
993	ARCHS_EDIT4 := \
994	EDIT4/EDIT4.a \
995	$(ARCHS_AP_TREE) \
996	ARB_GDE/ARB_GDE.a \
997	AWTC/AWTC.a \
998	ISLAND_HOPPING/ISLAND_HOPPING.a \
999	SECEDIT/SECEDIT.a \
1000	SERVERCNTRL/SERVERCNTRL.a \
1001	SL/AW_HELIX/AW_HELIX.a \
1002	SL/AW_NAME/AW_NAME.a \
1003	SL/FAST_ALIGNER/FAST_ALIGNER.a \
1004	SL/ITEMS/ITEMS.a \
1005	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1006	SL/HELIX/HELIX.a \
1007	SL/TRANSLATE/TRANSLATE.a \
1008	SL/MACROS/MACROS.a \
1009	SL/NDS/NDS.a \
1010	STAT/STAT.a \
1011	XML/XML.a \
1012
1013	ifeq ($(OPENGL),1)
1014	ARCHS_EDIT4 += RNA3D/RNA3D.a
1015	endif
1016
1017	LIBS_EDIT4 := $(GL_LIBS)
1018
1019	$(EDIT4): $(ARCHS_EDIT4:.a=.dummy) link_awt
1020	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_EDIT4) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1021	echo "$(SEP) Link $@"; \
1022	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4) $(EXECLIBS)" ; \
1023	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4) $(EXECLIBS) && \
1024	echo "$(SEP) Link $@ [done]"; \
1025	)
1026
1027	#********************************* arb_rnacma ************************************
1028	RNACMA = bin/arb_rnacma
1029	ARCHS_RNACMA = \
1030	RNACMA/RNACMA.a \
1031
1032	$(RNACMA) : $(ARCHS_RNACMA:.a=.dummy) link_db
1033	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_RNACMA) \|\| ( \
1034	echo "$(SEP) Link $@"; \
1035	echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_RNACMA) $(LIBS) $(EXECLIBS)"; \
1036	$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_RNACMA) $(LIBS) $(EXECLIBS) && \
1037	echo "$(SEP) Link $@ [done]"; \
1038	)
1039
1040	#********************************* arb_wetc ************************************
1041	WETC = bin/arb_wetc
1042	ARCHS_WETC = \
1043	WETC/WETC.a \
1044	SL/HELIX/HELIX.a \
1045	SL/FILTER/FILTER.a \
1046	XML/XML.a \
1047
1048	$(WETC): $(ARCHS_WETC:.a=.dummy) link_awt
1049	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_WETC) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1050	echo "$(SEP) Link $@"; \
1051	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC) $(GUI_LIBS) $(EXECLIBS)" ; \
1052	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC) $(GUI_LIBS) $(EXECLIBS) && \
1053	echo "$(SEP) Link $@ [done]"; \
1054	)
1055
1056	#********************************* arb_dist ************************************
1057	DIST = bin/arb_dist
1058	ARCHS_DIST = \
1059	$(ARCHS_AP_TREE) \
1060	CONSENSUS_TREE/CONSENSUS_TREE.a \
1061	DIST/DIST.a \
1062	EISPACK/EISPACK.a \
1063	SERVERCNTRL/SERVERCNTRL.a \
1064	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1065	SL/HELIX/HELIX.a \
1066	SL/MATRIX/MATRIX.a \
1067	SL/MACROS/MACROS.a \
1068	SL/NDS/NDS.a \
1069	SL/ITEMS/ITEMS.a \
1070	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.a \
1071	XML/XML.a \
1072
1073	$(DIST): $(ARCHS_DIST:.a=.dummy) link_awt
1074	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_DIST) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1075	echo "$(SEP) Link $@"; \
1076	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS)" ; \
1077	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS) && \
1078	echo "$(SEP) Link $@ [done]"; \
1079	)
1080
1081	#********************************* arb_pars ************************************
1082	PARSIMONY = bin/arb_pars
1083	ARCHS_PARSIMONY = \
1084	$(ARCHS_AP_TREE) \
1085	PARSIMONY/PARSIMONY.a \
1086	SERVERCNTRL/SERVERCNTRL.a \
1087	SL/AW_NAME/AW_NAME.a \
1088	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1089	SL/HELIX/HELIX.a \
1090	SL/MACROS/MACROS.a \
1091	SL/NDS/NDS.a \
1092	SL/ITEMS/ITEMS.a \
1093	SL/TRANSLATE/TRANSLATE.a \
1094	SL/TREEDISP/TREEDISP.a \
1095	XML/XML.a \
1096
1097	$(PARSIMONY): $(ARCHS_PARSIMONY:.a=.dummy) link_awt
1098	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PARSIMONY) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1099	echo "$(SEP) Link $@"; \
1100	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(EXECLIBS)" ; \
1101	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(EXECLIBS) && \
1102	echo "$(SEP) Link $@ [done]"; \
1103	)
1104
1105	#********************************* arb_convert_aln ************************************
1106	CONVERT_ALN = bin/arb_convert_aln
1107	ARCHS_CONVERT_ALN = \
1108	CONVERTALN/CONVERTALN.a \
1109
1110	$(CONVERT_ALN) : $(ARCHS_CONVERT_ALN:.a=.dummy) link_db
1111	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_CONVERT_ALN) $(use_ARB_main) \|\| ( \
1112	echo "$(SEP) Link $@"; \
1113	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN) $(LIBS) $(EXECLIBS)"; \
1114	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN) $(LIBS) $(EXECLIBS) && \
1115	echo "$(SEP) Link $@ [done]"; \
1116	)
1117
1118	#********************************* arb_treegen ************************************
1119
1120	TREEGEN = bin/arb_treegen
1121	ARCHS_TREEGEN = \
1122	TREEGEN/TREEGEN.a \
1123
1124	$(TREEGEN) : $(ARCHS_TREEGEN:.a=.dummy)
1125	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_TREEGEN) $(use_ARB_main_C) \|\| ( \
1126	echo "$(SEP) Link $@"; \
1127	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN) $(EXECLIBS)" ; \
1128	$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN) $(EXECLIBS) && \
1129	echo "$(SEP) Link $@ [done]"; \
1130	)
1131
1132	#********************************* arb_naligner ************************************
1133	NALIGNER = bin/arb_naligner
1134	ARCHS_NALIGNER = \
1135	NALIGNER/NALIGNER.a \
1136	SERVERCNTRL/SERVERCNTRL.a \
1137	SL/HELIX/HELIX.a \
1138
1139	$(NALIGNER): $(ARCHS_NALIGNER:.a=.dummy) link_db
1140	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NALIGNER) $(use_ARB_main) \|\| ( \
1141	echo "$(SEP) Link $@"; \
1142	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(LIBS) $(EXECLIBS)" ; \
1143	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(LIBS) $(EXECLIBS) && \
1144	echo "$(SEP) Link $@ [done]"; \
1145	)
1146
1147	#********************************* arb_phylo ************************************
1148	PHYLO = bin/arb_phylo
1149	ARCHS_PHYLO = \
1150	PHYLO/PHYLO.a \
1151	SL/HELIX/HELIX.a \
1152	SL/FILTER/FILTER.a \
1153	SL/MATRIX/MATRIX.a \
1154	SL/MACROS/MACROS.a \
1155	XML/XML.a \
1156
1157	$(PHYLO): $(ARCHS_PHYLO:.a=.dummy) link_awt
1158	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PHYLO) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1159	echo "$(SEP) Link $@"; \
1160	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO) $(GUI_LIBS) $(EXECLIBS)" ; \
1161	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO) $(GUI_LIBS) $(EXECLIBS) && \
1162	echo "$(SEP) Link $@ [done]"; \
1163	)
1164
1165	#***************************************************************************************
1166	# SERVER SECTION
1167	#***************************************************************************************
1168
1169	#********************************* arb_db_server ************************************
1170	DBSERVER = bin/arb_db_server
1171	ARCHS_DBSERVER = \
1172	DBSERVER/DBSERVER.a \
1173	SERVERCNTRL/SERVERCNTRL.a \
1174
1175	$(DBSERVER): $(ARCHS_DBSERVER:.a=.dummy) link_db
1176	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_DBSERVER) $(ARBDB_LIB) $(use_ARB_main) \|\| ( \
1177	echo "$(SEP) Link $@"; \
1178	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS) $(EXECLIBS)" ; \
1179	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS) $(EXECLIBS) && \
1180	echo "$(SEP) Link $@ [done]"; \
1181	)
1182
1183	#********************************* arb_pt_server ************************************
1184	PROBE = bin/arb_pt_server
1185	ARCHS_PROBE_COMMON = \
1186	SERVERCNTRL/SERVERCNTRL.a \
1187	SL/HELIX/HELIX.a \
1188	SL/PTCLEAN/PTCLEAN.a \
1189
1190	ARCHS_PROBE_LINK = \
1191	$(ARCHS_PROBE_COMMON) \
1192	$(ARCHS_PT_SERVER_LINK) \
1193
1194	ARCHS_PROBE_DEPEND = \
1195	$(ARCHS_PROBE_COMMON) \
1196	$(ARCHS_PT_SERVER) \
1197
1198	$(PROBE): $(ARCHS_PROBE_DEPEND:.a=.dummy) link_db
1199	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) config.makefile $(use_ARB_main) \|\| ( \
1200	echo "$(SEP) Link $@"; \
1201	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_SERVER_PROBE) $(SYSLIBS) $(EXECLIBS)" ; \
1202	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_SERVER_PROBE) $(SYSLIBS) $(EXECLIBS) && \
1203	echo "$(SEP) Link $@ [done]"; \
1204	)
1205
1206	#********************************* arb_name_server ************************************
1207	NAMES = bin/arb_name_server
1208	ARCHS_NAMES = \
1209	NAMES/NAMES.a \
1210	SERVERCNTRL/SERVERCNTRL.a \
1211
1212	$(NAMES): $(ARCHS_NAMES:.a=.dummy) link_db
1213	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) $(use_ARB_main) \|\| ( \
1214	echo "$(SEP) Link $@"; \
1215	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS) $(EXECLIBS)" ; \
1216	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS) $(EXECLIBS) && \
1217	echo "$(SEP) Link $@ [done]"; \
1218	)
1219
1220	#********************************* SHARED LIBRARIES SECTION ************************************
1221
1222	prepare_libdir: addlibs
1223
1224	addlibs:
1225	(perl $(ARBHOME)/SOURCE_TOOLS/provide_libs.pl \
1226	"arbhome=$(ARBHOME)" \
1227	"opengl=$(OPENGL)" \
1228	"link_static=$(LINK_STATIC)" \
1229	)
1230
1231	#***************************************************************************************
1232	# Recursive calls to sub-makefiles
1233	#***************************************************************************************
1234
1235	%.depends:
1236	@cp -p $(@D)/Makefile $(@D)/Makefile.old # save old Makefile
1237	@$(MAKE) -C $(@D) -r \
1238	"AUTODEPENDS=1" \
1239	"MAIN=nothing" \
1240	"cflags=noCflagsHere_use_MAKEDEPENDFLAGS" \
1241	"cxxflags=noCxxflagsHere_use_MAKEDEPENDFLAGS" \
1242	depends
1243	@grep "^# DO NOT DELETE" $(@D)/Makefile >/dev/null
1244	@cat $(@D)/Makefile \
1245	\| SOURCE_TOOLS/fix_depends.pl "(from main)" \
1246	>$(@D)/Makefile.2
1247	@mv $(@D)/Makefile.old $(@D)/Makefile # restore old Makefile
1248	@$(ARBHOME)/SOURCE_TOOLS/mv_if_diff $(@D)/Makefile.2 $(@D)/Makefile # update Makefile if changed
1249
1250	%.proto:
1251	@$(MAKE) -C $(@D) \
1252	"AUTODEPENDS=0" \
1253	"MAIN=nothing" \
1254	"cflags=noCflags" \
1255	"cxxflags=noCxxflags" \
1256	proto
1257
1258	%.clean:
1259	@$(MAKE) -C $(@D) \
1260	"AUTODEPENDS=0" \
1261	"MAIN=nothing" \
1262	"cflags=noCflags" \
1263	"cxxflags=noCxxflags" \
1264	clean
1265
1266
1267	# stop wrong targets
1268	target_is_missing_lib_prefix:
1269	@echo "Error: Denied to build shared library target with missing 'lib'-prefix"
1270	false
1271
1272	ARBDB/ARBDB.dummy: target_is_missing_lib_prefix
1273	CORE/CORE.dummy: target_is_missing_lib_prefix
1274	AWT/AWT.dummy: target_is_missing_lib_prefix
1275	WINDOW/WINDOW.dummy: target_is_missing_lib_prefix
1276
1277	# rule to generate main target (normally a library):
1278	# @@@ check effect of setting LANG=C below
1279	%.dummy:
1280	@( export ID=$$$$; LANG=C; \
1281	(( \
1282	echo "$(SEP) Make $(@D)"; \
1283	$(MAKE) -C $(@D) -r \
1284	"AUTODEPENDS=1" \
1285	"MAIN=$(@F:.dummy=.a)" \
1286	"cflags=$(cflags) -DIN_ARB_$(subst /,_,$(@D))" \
1287	&& \
1288	echo "$(SEP) Make $(@D) [done]"; \
1289	) >$(@D).$$ID.log 2>&1 && (cat $(@D).$$ID.log;rm $(@D).$$ID.log)) \|\| (cat $(@D).$$ID.log;rm $(@D).$$ID.log;false))
1290
1291	# Additional dependencies for subtargets:
1292
1293	PROBE_COM/PROBE_COM.dummy : comtools
1294	NAMES_COM/NAMES_COM.dummy : comtools
1295
1296	com: PROBE_COM/PROBE_COM.dummy NAMES_COM/NAMES_COM.dummy
1297
1298	PROBE_COM/server.dummy:
1299	@echo Unwanted request to make target $<
1300	false
1301
1302	PROBE_COM/client.dummy:
1303	@echo Unwanted request to make target $<
1304	false
1305
1306	NAMES_COM/server.dummy:
1307	@echo Unwanted request to make target $<
1308	false
1309
1310	NAMES_COM/client.dummy:
1311	@echo Unwanted request to make target $<
1312	false
1313
1314
1315	ARBDB/libARBDB.dummy: links
1316	CORE/libCORE.dummy: links
1317
1318	PERLTOOLS/PERLTOOLS.dummy: core db
1319
1320	# all subdirs perl not depends on go here (ADD_links_non_perl)
1321	AWT/libAWT.dummy: links_non_perl
1322	AWTI/AWTI.dummy: links_non_perl
1323	CONSENSUS_TREE/CONSENSUS_TREE.dummy: links_non_perl
1324	CONVERTALN/CONVERTALN.dummy: links_non_perl
1325	DBSERVER/DBSERVER.dummy: links_non_perl
1326	DIST/DIST.dummy: links_non_perl
1327	EDIT4/EDIT4.dummy: links_non_perl genheaders com
1328	EISPACK/EISPACK.dummy: links_non_perl
1329	GDE/GDE.dummy: links_non_perl
1330	GENOM/GENOM.dummy: links_non_perl
1331	GENOM_IMPORT/GENOM_IMPORT.dummy: links_non_perl
1332	ISLAND_HOPPING/ISLAND_HOPPING.dummy: links_non_perl
1333	MERGE/MERGE.dummy: links_non_perl
1334	NTREE/NTREE.dummy: links_non_perl genheaders
1335	PARSIMONY/PARSIMONY.dummy: links_non_perl
1336	PHYLO/PHYLO.dummy: links_non_perl
1337	PRIMER_DESIGN/PRIMER_DESIGN.dummy: links_non_perl
1338	PROBE_SET/PROBE_SET.dummy: links_non_perl link_db
1339	READSEQ/READSEQ.dummy: links_non_perl
1340	RNACMA/RNACMA.dummy: links_non_perl header_libs
1341	SECEDIT/SECEDIT.dummy: links_non_perl
1342	SEQ_QUALITY/SEQ_QUALITY.dummy: links_non_perl
1343	SERVERCNTRL/SERVERCNTRL.dummy: links_non_perl com
1344	SL/ALIVIEW/ALIVIEW.dummy: links_non_perl
1345	SL/AP_TREE/AP_TREE.dummy: links_non_perl
1346	SL/ARB_TREE/ARB_TREE.dummy: links_non_perl
1347	SL/AW_HELIX/AW_HELIX.dummy: links_non_perl
1348	SL/DB_QUERY/DB_QUERY.dummy: links_non_perl
1349	SL/DB_SCANNER/DB_SCANNER.dummy: links_non_perl
1350	SL/DB_UI/DB_UI.dummy: links_non_perl
1351	SL/FAST_ALIGNER/FAST_ALIGNER.dummy: links_non_perl
1352	SL/FILTER/FILTER.dummy: links_non_perl
1353	SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy: links_non_perl
1354	SL/HELIX/HELIX.dummy: links_non_perl
1355	SL/INSDEL/INSDEL.dummy: links_non_perl
1356	SL/ITEMS/ITEMS.dummy: links_non_perl
1357	SL/LOCATION/LOCATION.dummy: links_non_perl
1358	SL/MACROS/MACROS.dummy: links_non_perl
1359	SL/MATRIX/MATRIX.dummy: links_non_perl
1360	SL/NDS/NDS.dummy: links_non_perl
1361	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.dummy: links_non_perl
1362	SL/PRONUC/PRONUC.dummy: links_non_perl
1363	SL/PTCLEAN/PTCLEAN.dummy: links_non_perl link_db
1364	SL/REFENTRIES/REFENTRIES.dummy: links_non_perl
1365	SL/REGEXPR/REGEXPR.dummy: links_non_perl
1366	SL/ROOTED_TREE/ROOTED_TREE.dummy: links_non_perl
1367	SL/SEQIO/SEQIO.dummy: links_non_perl
1368	SL/SEQUENCE/SEQUENCE.dummy: links_non_perl
1369	SL/TRANSLATE/TRANSLATE.dummy: links_non_perl
1370	SL/TREE_ADMIN/TREE_ADMIN.dummy: links_non_perl
1371	SL/TREE_READ/TREE_READ.dummy: links_non_perl
1372	SL/TREE_WRITE/TREE_WRITE.dummy: links_non_perl
1373	SL/TREEDISP/TREEDISP.dummy: links_non_perl
1374	STAT/STAT.dummy: links_non_perl
1375	TREEGEN/TREEGEN.dummy: links_non_perl
1376	WETC/WETC.dummy: links_non_perl
1377	WINDOW/libWINDOW.dummy: links_non_perl
1378	XML/XML.dummy: links_non_perl
1379
1380	ifeq ($(OPENGL),1)
1381	GL/glAW/glAW.dummy: links_non_perl
1382	GL/glpng/glpng.dummy: links_non_perl
1383	GL/GL.dummy: GL/glAW/glAW.dummy GL/glpng/glpng.dummy
1384	RNA3D/RNA3D.dummy: links_non_perl gl
1385	endif
1386
1387	UNIT_TESTER/UNIT_TESTER.dummy: link_db \
1388	SERVERCNTRL/SERVERCNTRL.dummy \
1389
1390	TOOLS/TOOLS.dummy : links_non_perl link_db \
1391	SERVERCNTRL/SERVERCNTRL.dummy \
1392	SL/ROOTED_TREE/ROOTED_TREE.dummy \
1393	SL/TREE_WRITE/TREE_WRITE.dummy \
1394	SL/TREE_READ/TREE_READ.dummy \
1395	CONSENSUS_TREE/CONSENSUS_TREE.dummy \
1396	XML/XML.dummy \
1397
1398	AWTC/AWTC.dummy : com
1399
1400	NAMES/NAMES.dummy : com
1401	SL/AW_NAME/AW_NAME.dummy : com
1402
1403	PROBE/PROBE.dummy : com
1404	ptpan/PROBE.dummy : com
1405	MULTI_PROBE/MULTI_PROBE.dummy : com
1406	PROBE_DESIGN/PROBE_DESIGN.dummy : com
1407	NALIGNER/NALIGNER.dummy : com
1408
1409	ARB_GDE/ARB_GDE.dummy : proto_tools
1410
1411	compile_compatibility: SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.dummy
1412
1413	#***************************************************************************************
1414	# Short aliases to make targets
1415	#***************************************************************************************
1416
1417	show:
1418	@echo $(SEP)
1419	@echo 'Aliases for often needed targets:'
1420	@echo ''
1421	@echo ' executables:'
1422	@echo ''
1423	@echo ' nt arb_ntree'
1424	@echo ' e4 arb_edit4 (includes secedit)'
1425	@echo ' di arb_dist'
1426	@echo ' ph arb_phylo'
1427	@echo ' pa arb_parsimony'
1428	@echo ' tg arb_treegen'
1429	@echo ' ds arb_dbserver'
1430	@echo ' pt arb_pt_server'
1431	@echo ' na arb_name_server'
1432	@echo ''
1433	@echo ' libraries:'
1434	@echo ''
1435	@echo ' com communication libraries'
1436	@echo ' db ARB database'
1437	@echo ' aw GUI lib'
1438	@echo ' awt GUI toolkit'
1439	@echo ' awtc general purpose library'
1440	@echo ' awti import/export library'
1441	@echo ' mp multi probe library'
1442	@echo ' ge genome library'
1443	@echo ' pd probe design lib'
1444	@echo ' prd primer design lib'
1445	@echo ''
1446	@echo ' other targets:'
1447	@echo ''
1448	@echo ' help recompile help files'
1449	@echo ' tools make small tools used by arb'
1450	@echo ''
1451	@echo ' foreign targets:'
1452	@echo ''
1453	@echo ' gde GDE'
1454	@echo ' agde ARB_GDE'
1455	@echo ''
1456	@echo 'for other targets inspect $(ARBHOME)/Makefile'
1457	@echo ''
1458	@echo $(SEP)
1459
1460	source_doc:
1461	@echo "Remove some links (doxygen crashes otherwise):"
1462	find . \( -name "AISC" -o -name "C" -o -name "GDEHELP" \) -type l -exec rm {} \;
1463	doxygen 2>&1 1>/dev/null
1464	$(MAKE) forcelinks
1465
1466	dep_graph:
1467	@echo "Building some dependency graphs"
1468	SOURCE_TOOLS/dependency_graphs.pl
1469
1470	help: HELP_SOURCE/HELP_SOURCE.dummy
1471
1472	HELP_SOURCE/HELP_SOURCE.dummy: link_core xml menus
1473
1474	db: ARBDB/libARBDB.dummy
1475	core: CORE/libCORE.dummy
1476	aw: WINDOW/libWINDOW.dummy
1477	awt: AWT/libAWT.dummy
1478	awtc: AWTC/AWTC.dummy
1479	awti: AWTI/AWTI.dummy
1480
1481	mp: MULTI_PROBE/MULTI_PROBE.dummy
1482	mg: MERGE/MERGE.dummy
1483	ge: GENOM/GENOM.dummy
1484	prd: PRIMER_DESIGN/PRIMER_DESIGN.dummy
1485
1486	nt: menus $(NTREE)
1487
1488	nal: $(NALIGNER)
1489
1490	di: $(DIST)
1491	ph: $(PHYLO)
1492	pa: $(PARSIMONY)
1493	tg: $(TREEGEN)
1494
1495	ifeq ($(OPENGL),1)
1496	3d: RNA3D/RNA3D.dummy
1497	gl: GL/GL.dummy
1498	else
1499	noopengl:
1500	@echo "invalid target for OPENGL=0"
1501	3d: noopengl
1502	gl: noopengl
1503	endif
1504
1505	SL/SL.dummy: com
1506
1507	ds: $(DBSERVER)
1508	pt: $(PROBE)
1509	pst: PROBE_SET/PROBE_SET.dummy
1510	pd: PROBE_DESIGN/PROBE_DESIGN.dummy
1511	na: $(NAMES)
1512	sq: SEQ_QUALITY/SEQ_QUALITY.dummy
1513	cma: $(RNACMA)
1514
1515	sec: SECEDIT/SECEDIT.dummy
1516
1517	e4: $(EDIT4) readseq menus
1518
1519	gi: GENOM_IMPORT/GENOM_IMPORT.dummy
1520	wetc: $(WETC)
1521
1522	xml: XML/XML.dummy
1523	xmlin: XML_IMPORT/XML_IMPORT.dummy# broken
1524	stat: STAT/STAT.dummy $(NTREE) $(EDIT4)
1525	fa: SL/FAST_ALIGNER/FAST_ALIGNER.dummy
1526
1527	#********************************************************************************
1528
1529	up_by_remake: depends proto
1530
1531	up: up_by_remake tags valgrind_update
1532
1533	#********************************************************************************
1534
1535	touch:
1536	SOURCE_TOOLS/touch_modified.pl
1537
1538	modified: touch
1539	$(MAKE) all
1540
1541	#********************************************************************************
1542
1543	libdepends:
1544	$(MAKE) -C "SOURCE_TOOLS" \
1545	"RNA3D_LIB=$(RNA3D_LIB_4_DEPENDS)" \
1546	libdepends
1547
1548	#********************************************************************************
1549
1550	# create generated headers:
1551	genheaders: TEMPLATES/TEMPLATES.dummy
1552
1553	clrdotdepends:
1554	-rm PROBE_COM/.depends
1555	-rm NAMES_COM/.depends
1556	-rm PERL2ARB/.depends
1557
1558	comdepends: comtools clrdotdepends
1559	@echo "$(SEP) Partially build com interface"
1560	$(MAKE) PROBE_COM/PROBE_COM.depends NAMES_COM/NAMES_COM.depends
1561	$(MAKE) PROBE_COM/server.depends NAMES_COM/server.depends
1562
1563	depends: genheaders comdepends
1564	@echo "$(SEP) Updating other dependencies"
1565	$(MAKE) $(subst NAMES_COM/server.depends,,$(subst PROBE_COM/server.depends,,$(ARCHS:.a=.depends))) \
1566	HELP_SOURCE/HELP_SOURCE.depends \
1567	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.depends \
1568
1569	$(MAKE) libdepends
1570
1571	depend: depends
1572
1573	# ------------------------------------------------------------
1574	# dependency generation tests for AISC code
1575	#(all should work w/o creating wrong dependencies;
1576	# neither in XXX_COM/Makefile nor in code using AISC interface)
1577	dependstest1: silent_clean
1578	$(MAKE) depends
1579	dependstest2: silent_clean
1580	$(MAKE) com
1581	dependstest3: silent_clean
1582	$(MAKE) aw
1583	dependstest4: silent_clean
1584	$(MAKE) pt
1585	dependstest5: silent_clean
1586	$(MAKE) na
1587	dependstest6: silent_clean
1588	$(MAKE) nt
1589	dependstest7: silent_clean
1590	$(MAKE) all
1591	# ------------------------------------------------------------
1592
1593	AISC_MKPTPS/AISC_MKPTPS.dummy: links
1594
1595	proto_tools: AISC_MKPTPS/AISC_MKPTPS.dummy
1596
1597	proto: proto_tools
1598	@echo $(SEP) Updating prototypes
1599	$(MAKE) \
1600	ARBDB/ARBDB.proto \
1601	AISC_COM/AISC_COM.proto \
1602	ARB_GDE/ARB_GDE.proto \
1603	CORE/CORE.proto \
1604	CONVERTALN/CONVERTALN.proto \
1605	NTREE/NTREE.proto \
1606	MERGE/MERGE.proto \
1607	$(ARCHS_PT_SERVER:.a=.proto) \
1608	SERVERCNTRL/SERVERCNTRL.proto \
1609	SL/SL.proto \
1610
1611	#********************************************************************************
1612
1613	valgrind_update: links
1614	@echo $(SEP) Updating for valgrind
1615	$(MAKE) -C SOURCE_TOOLS valgrind_update
1616
1617	#********************************************************************************
1618
1619	TAGFILE=TAGS
1620	TAGFILE_TMP=TAGS.tmp
1621
1622	TAG_SOURCE_HEADERS=TAGS.headers
1623	TAG_SOURCE_CODE=TAGS.codefiles
1624	TAG_SOURCE_LISTS=$(TAG_SOURCE_HEADERS) $(TAG_SOURCE_CODE)
1625
1626	ETAGS=ctags -e -f $(TAGFILE_TMP) --sort=no --if0=no --extra=q
1627	ETAGS_TYPES=--C-kinds=cgnsut --C++-kinds=cgnsut
1628	ETAGS_FUN =--C-kinds=fm --C++-kinds=fm
1629	ETAGS_REST =--C-kinds=dev --C++-kinds=dev
1630
1631	FILTER_TAGS_SOURCES= \
1632	$(SED) -e 's/^.\///g' \| \
1633	grep -P -v -i '^HEADERLIBS\|^GDE/\|/GEN[CH]/'
1634
1635	$(TAG_SOURCE_HEADERS): links
1636	find . \( -name '.hxx' -o -name ".h" \) -type f \| $(FILTER_TAGS_SOURCES) > $@
1637
1638	$(TAG_SOURCE_CODE): links
1639	find . \( -name '.cxx' -o -name ".c" \) -type f \| $(FILTER_TAGS_SOURCES) > $@
1640
1641	tags: $(TAG_SOURCE_LISTS)
1642	$(ETAGS) $(ETAGS_TYPES) -L $(TAG_SOURCE_HEADERS)
1643	$(ETAGS) -a $(ETAGS_FUN) -L $(TAG_SOURCE_HEADERS)
1644	$(ETAGS) -a $(ETAGS_REST) -L $(TAG_SOURCE_HEADERS)
1645	$(ETAGS) -a $(ETAGS_TYPES) -L $(TAG_SOURCE_CODE)
1646	$(ETAGS) -a $(ETAGS_FUN) -L $(TAG_SOURCE_CODE)
1647	$(ETAGS) -a $(ETAGS_REST) -L $(TAG_SOURCE_CODE)
1648	mv_if_diff $(TAGFILE_TMP) $(TAGFILE)
1649	rm $(TAG_SOURCE_LISTS)
1650
1651	#********************************************************************************
1652
1653	LINKSTAMP=SOURCE_TOOLS/stamp.generate_all_links
1654
1655	links: checks $(LINKSTAMP) arbmainwrapper
1656	links_no_checks: $(LINKSTAMP) arbmainwrapper
1657
1658	forcelinks:
1659	-rm $(LINKSTAMP)
1660	$(MAKE) links
1661
1662	$(LINKSTAMP): SOURCE_TOOLS/generate_all_links.sh
1663	+SOURCE_TOOLS/generate_all_links.sh
1664	touch $(LINKSTAMP)
1665
1666	clean_links:
1667	# avoid to delete linked pts, nas or arb_tcp.dat:
1668	find . -path './lib' -prune -o -type l -exec rm {} \;
1669	# removed obsolete file - refuses to disappear due to 'prune' above
1670	@rm -f lib/help/GDEHELP
1671	@rm -f $(LINKSTAMP) lib/inputMasks/format.readme
1672
1673	redo_links: clean_links
1674	$(MAKE) links_no_checks
1675
1676	#********************************************************************************
1677
1678	header_libs:
1679	$(MAKE) -C HEADERLIBS all
1680
1681	#********************************************************************************
1682
1683	gde: GDE/GDE.dummy
1684	GDE: gde
1685	agde: ARB_GDE/ARB_GDE.dummy
1686
1687	tools: TOOLS/TOOLS.dummy
1688
1689	convert: $(CONVERT_ALN)
1690	readseq: READSEQ/READSEQ.dummy
1691
1692	#***************************************************************************************
1693	# Some user commands
1694	#***************************************************************************************
1695
1696	menus: binlink links
1697	@(( \
1698	echo "$(SEP) Make GDEHELP"; \
1699	$(MAKE) -C GDEHELP -r all && \
1700	echo "$(SEP) Make GDEHELP [done]"; \
1701	) > GDEHELP.log 2>&1 && (cat GDEHELP.log;rm GDEHELP.log)) \|\| (cat GDEHELP.log;rm GDEHELP.log;false)
1702
1703	ifeq ($(DEBUG),1)
1704	BIN_TARGET=develall
1705	else
1706	BIN_TARGET=all
1707	endif
1708
1709
1710	binlink:
1711	$(MAKE) -C bin $(BIN_TARGET)
1712
1713	preplib:
1714	(cd lib;$(MAKE) all)
1715
1716	# --------------------------------------------------------------------------------
1717	# This section is quite tricky:
1718	#
1719	# make 'perl' is a BIG target, so when it has to be made, it has to be started
1720	# as early as possible to reduce overall compile time. Since 'make' does not
1721	# provide any priotities, i force it to build all 'perl'-prerequisites early, by
1722	# adding artificial dependencies to these prerequisites
1723	#
1724	# That behavior is likely to be system-dependent.
1725	# My goal was only to make it work on my current development system,
1726	# where this saves about 20% of overall build time.
1727
1728	ifeq ($(WITHPERL),1)
1729	links_non_perl: PERLTOOLS/PERLTOOLS.dummy
1730	perltools: links_non_perl
1731	perl: realperl
1732	else
1733	links_non_perl: links
1734	perl:
1735	$(MAKE) "WITHPERL=1" perl
1736	endif
1737
1738	# ---------------------------------------- perl
1739
1740	ifeq ($(ARB_64),$(BUILDHOST_64))
1741	TEST_PERL_SCRIPTS=$(MAKE) -C PERL_SCRIPTS/test test
1742	else
1743	TEST_PERL_SCRIPTS=echo "skipping perl script compilation (when cross-compiling)"
1744	endif
1745
1746	realperl: perltools
1747	(( \
1748	echo "$(SEP) Make PERL2ARB" ; \
1749	$(TIME) $(MAKE) -C PERL2ARB -r -f Makefile.main \
1750	"AUTODEPENDS=1" \
1751	"dflags=$(dflags)" \
1752	"cross_cflags=$(cross_cflags) $(cxxflags) $(dflags)" \
1753	"cross_lflags=$(cross_lflags)" \
1754	"COMPILER_VERSION=$(COMPILER_VERSION)" \
1755	all && \
1756	$(TEST_PERL_SCRIPTS) && \
1757	echo "$(SEP) Make PERL2ARB [done]" ; \
1758	) > PERL2ARB.log 2>&1 && (cat PERL2ARB.log;rm PERL2ARB.log)) \|\| (cat PERL2ARB.log;rm PERL2ARB.log;false)
1759
1760	perl_clean:
1761	@$(MAKE) -C PERL2ARB -r -f Makefile.main \
1762	"AUTODEPENDS=0" \
1763	clean
1764
1765	PERL2ARB/PERL2ARB.clean:
1766	$(MAKE) perl_clean
1767	$(MAKE) -C PERL_SCRIPTS/test clean
1768
1769	# ---------------------------------------- bindings to script languages
1770
1771	bindings: lib/libCORE.so lib/libARBDB.so
1772	$(MAKE) -C BINDINGS all ARBDEPENDS="$(^:%=../%)" DFLAGS="$(dflags)"
1773
1774	bindings_clean:
1775	$(MAKE) -C BINDINGS clean
1776
1777	# ----------------------------------------
1778
1779	CLOC=cloc-1.08.pl
1780	CLOCFLAGS=--no3 --quiet --progress-rate=0
1781	CLOCARB=--exclude-dir=GDE .
1782	CLOCEXT=GDE
1783	CLOCCODE=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.code.def
1784	CLOCREST=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.rest.def
1785	CLOCFILT=tail --lines=+4
1786
1787	cloc:
1788	@echo 'Arb code:'
1789	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCARB) \| $(CLOCFILT)
1790	@echo 'Arb rest:'
1791	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCARB) \| $(CLOCFILT)
1792	@echo 'External code:'
1793	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCEXT) \| $(CLOCFILT)
1794	@echo 'External rest:'
1795	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCEXT) \| $(CLOCFILT)
1796
1797	# ---------------------------------------- check ressources
1798
1799	check_res:
1800	$(ARBHOME)/SOURCE_TOOLS/check_ressources.pl
1801
1802	# ---------------------------------------- cleaning
1803
1804	rmbak:
1805	@echo "Cleanup:"
1806	@find . \( -name '*%' \
1807	-o -name '*.bak' \
1808	-o -name '*~' \) \
1809	-o \( -name 'core' -a \! -type d \) \
1810	-exec rm -v {} \;
1811
1812	bin_reinit:
1813	$(MAKE) bin/bin.clean
1814	$(MAKE) -C "bin" all
1815
1816	clean_directories:
1817	-rm -rf \
1818	$(ARBHOME)/PROBE_SET/bin \
1819	$(ARBHOME)/INCLUDE \
1820
1821	libclean:
1822	-find $(ARBHOME) -type f \( -name '*.a' ! -type l \) -exec rm -f {} \;
1823
1824	objclean:
1825	-find $(ARBHOME) -type f \( -name '*.o' ! -type l \) -exec rm -f {} \;
1826
1827	# bin.clean and HELP_SOURCE.clean interfere
1828	clean3:
1829	$(MAKE) bin/bin.clean
1830	$(MAKE) HELP_SOURCE/HELP_SOURCE.clean
1831
1832	clean2: $(ARCHS:.a=.clean) \
1833	clean3 \
1834	rmbak \
1835	libclean \
1836	objclean \
1837	lib/lib.clean \
1838	GDEHELP/GDEHELP.clean \
1839	HEADERLIBS/HEADERLIBS.clean \
1840	SOURCE_TOOLS/SOURCE_TOOLS.clean \
1841	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.clean \
1842	UNIT_TESTER/UNIT_TESTER.clean \
1843	TEMPLATES/TEMPLATES.clean \
1844	perl_clean \
1845	clean_directories \
1846
1847	rm -f .last_gcc .last_compiler config.makefile.bak
1848
1849	# links are needed for cleanup
1850	clean: redo_links motif_xpm_hack_clean
1851	$(MAKE) clean2
1852	$(MAKE) clean_cov_all clean_links
1853
1854	silent_clean:
1855	$(MAKE) clean >/dev/null
1856
1857	# 'relocated' is about 50% faster than 'rebuild'
1858	reloc_clean: links
1859	@echo "---------------------------------------- Relocation cleanup"
1860	$(MAKE) \
1861	perl_clean \
1862	GDEHELP/GDEHELP.clean \
1863	HELP_SOURCE/genhelp/genhelp.clean \
1864	bin/bin.clean \
1865	libclean \
1866	objclean
1867
1868	relocated: links
1869	$(MAKE) reloc_clean
1870	@echo "---------------------------------------- and remake"
1871	$(MAKE) build
1872
1873	# -----------------------------------
1874	# some stress tests:
1875
1876	rebuild4ever: rebuild
1877	$(MAKE) rebuild4ever
1878
1879	build4ever: build
1880	$(MAKE) build4ever
1881
1882	clean4ever: clean
1883	$(MAKE) clean4ever
1884
1885	test4ever: ut
1886	$(MAKE) test4ever
1887
1888	perl4ever: clean
1889	$(MAKE) links
1890	$(MAKE) perl
1891	$(MAKE) perl4ever
1892
1893
1894	# -----------------------------------
1895
1896	rebuild: clean
1897	$(MAKE) all
1898
1899	relink: bin/bin.clean libclean
1900	$(MAKE) build
1901
1902	tarfile: rebuild
1903	$(MAKE) prepare_libdir
1904	util/arb_compress
1905
1906	tarfile_quick: build
1907	$(MAKE) prepare_libdir
1908	util/arb_compress
1909
1910	save: sourcetarfile
1911
1912	patch:
1913	SOURCE_TOOLS/arb_create_patch.sh arbPatch
1914
1915	# test early whether save will work
1916	savetest:
1917	@util/arb_srclst.pl >/dev/null
1918
1919	testsave: savetest
1920
1921	sourcetarfile: rmbak
1922	util/arb_save
1923
1924	save2: rmbak
1925	util/arb_save ignore
1926
1927	save_test: rmbak
1928	@echo "Testing source list.."
1929	@util/arb_srclst.pl > /dev/null
1930
1931	save_test_no_error:
1932	@-$(MAKE) save_test
1933
1934	inc_candi:
1935	touch SOURCE_TOOLS/inc_candi.stamp
1936	$(MAKE) do_version_update
1937
1938	inc_patch:
1939	touch SOURCE_TOOLS/inc_patch.stamp
1940	$(MAKE) do_version_update
1941
1942	inc_minor:
1943	touch SOURCE_TOOLS/inc_minor.stamp
1944	$(MAKE) do_version_update
1945
1946	inc_major:
1947	touch SOURCE_TOOLS/inc_major.stamp
1948	$(MAKE) do_version_update
1949
1950	do_version_update:
1951	@echo Incrementing version information
1952	$(MAKE) testsave
1953	$(MAKE) genheaders # auto upgrades version early
1954
1955	show_version:
1956	$(MAKE) genheaders # updates version info
1957	@echo "$(SEP) ARB version info"
1958	@grep ARB_VERSION TEMPLATES/arb_build.h
1959	@echo "$(SEP)"
1960
1961	release_quick:
1962	-rm arb.tgz arbsrc.tgz
1963	$(MAKE) tarfile_quick
1964	$(MAKE) sourcetarfile
1965
1966	# --------------------------------------------------------------------------------
1967
1968	MAKE_IF_COMMITTED=$(MAKE) -C SOURCE_TOOLS -f Makefile.commitbuild
1969
1970	build_CTARGET:
1971	+$(MAKE_IF_COMMITTED) "CTARGET=$(CTARGET)" build_CTARGET
1972
1973	reset_committed_build:
1974	+$(MAKE_IF_COMMITTED) reset
1975
1976	# --------------------------------------------------------------------------------
1977
1978	arbapplications: nt pa e4 wetc pt na nal di ph ds wetc cma
1979
1980	arb_external: convert tools gde readseq tg pst xmlin
1981
1982	arb_no_perl: arbapplications help arb_external
1983
1984	arb: motif_xpm_hack
1985	$(MAKE) "WITHPERL=1" perl arb_no_perl
1986
1987	motif_xpm_hack:
1988	$(MAKE) -r -C "lib/motifHack" all
1989
1990	motif_xpm_hack_clean:
1991	$(MAKE) -r -C "lib/motifHack" clean
1992
1993	# --------------------------------------------------------------------------------
1994	# special targets for SOURCE_TOOLS/remake_after_change.pl
1995
1996	rac_arb_dist: di
1997	rac_arb_edit4: e4
1998	rac_arb_ntree: nt
1999	rac_arb_pars: pa
2000	rac_arb_phylo: ph
2001	rac_arb_wetc: wetc
2002	rac_arb_naligner: nal
2003	rac_arb_pt_server: pt
2004	rac_arb_db_server: ds
2005	rac_arb_name_server: na
2006	rac_arb_convert_aln: convert
2007	rac_arb_treegen: tg
2008	rac_arb_rnacma: cma
2009	rac_arb_help2xml: help
2010
2011	rac_arb_a2ps: tools
2012	rac_arb_consensus_tree: tools
2013	rac_arb_dnarates: tools
2014	rac_arb_export_rates: tools
2015	rac_arb_export_tree: tools
2016	rac_arb_gene_probe: tools
2017	rac_arb_message: tools
2018	rac_arb_notify: tools
2019	rac_arb_primer: tools
2020	rac_arb_probe: tools
2021	rac_arb_read_tree: tools
2022
2023	# --------------------------------------------------------------------------------
2024	# unit testing
2025	# @@@ work in progress
2026	#
2027	# goal is to automatically test all libraries/executables using TESTED_UNITS_AUTO
2028	#
2029	# currently not all test executables link w/o error
2030	# (see UNITS_WORKING, UNITS_UNTESTABLE_ATM and UNITS_NEED_FIX)
2031
2032	# define RNA3D/RNA3D.test
2033	RNA3D_TEST := $(subst .a,.test,$(RNA3D_LIB))
2034
2035	TESTED_UNITS_AUTO = $(ARCHS:.a=.test)
2036
2037	UNITS_WORKING = \
2038	$(RNA3D_TEST) \
2039	AWTI/AWTI.test \
2040	DIST/DIST.test \
2041	EISPACK/EISPACK.test \
2042	GENOM/GENOM.test \
2043	GL/glAW/libglAW.test \
2044	GL/glpng/libglpng_arb.test \
2045	ISLAND_HOPPING/ISLAND_HOPPING.test \
2046	NALIGNER/NALIGNER.test \
2047	NAMES/NAMES.test \
2048	PHYLO/PHYLO.test \
2049	PRIMER_DESIGN/PRIMER_DESIGN.test \
2050	PROBE_DESIGN/PROBE_DESIGN.test \
2051	SECEDIT/SECEDIT.test \
2052	SEQ_QUALITY/SEQ_QUALITY.test \
2053	SERVERCNTRL/SERVERCNTRL.test \
2054	SL/ALIVIEW/ALIVIEW.test \
2055	SL/AP_TREE/AP_TREE.test \
2056	SL/ARB_TREE/ARB_TREE.test \
2057	SL/AW_HELIX/AW_HELIX.test \
2058	SL/AW_NAME/AW_NAME.test \
2059	SL/DB_SCANNER/DB_SCANNER.test \
2060	SL/GUI_ALIVIEW/GUI_ALIVIEW.test \
2061	SL/HELIX/HELIX.test \
2062	SL/ITEMS/ITEMS.test \
2063	SL/LOCATION/LOCATION.test \
2064	SL/MATRIX/MATRIX.test \
2065	SL/REFENTRIES/REFENTRIES.test \
2066	SL/SEQUENCE/SEQUENCE.test \
2067	SL/TRANSLATE/TRANSLATE.test \
2068	SL/TREE_ADMIN/TREE_ADMIN.test \
2069	SL/TREE_WRITE/TREE_WRITE.test \
2070	STAT/STAT.test \
2071	TREEGEN/TREEGEN.test \
2072	WETC/WETC.test \
2073	XML/XML.test \
2074	SL/ROOTED_TREE/ROOTED_TREE.test \
2075
2076	# untestable units
2077
2078	UNITS_NEED_FIX = \
2079	ptpan/PROBE.test \
2080
2081	UNITS_UNTESTABLE_ATM = \
2082	PROBE_SET/PROBE_SET.test \
2083	XML_IMPORT/XML_IMPORT.test \
2084
2085	# for the moment, put all units containing tests into UNITS_TESTED or UNITS_TESTED_FIRST
2086
2087	UNITS_TESTED_FIRST = \
2088	PARSIMONY/PARSIMONY.test \
2089	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.test \
2090	SL/NDS/NDS.test \
2091	ARB_GDE/ARB_GDE.test \
2092	GENOM_IMPORT/GENOM_IMPORT.test \
2093	SL/MACROS/MACROS.test \
2094	SL/REGEXPR/REGEXPR.test \
2095	SL/FILTER/FILTER.test \
2096	ARBDB/libARBDB.test \
2097	CONSENSUS_TREE/CONSENSUS_TREE.test \
2098	TOOLS/arb_consensus_tree.test \
2099	TOOLS/arb_test.test \
2100	TOOLS/arb_probe.test \
2101	PERLTOOLS/arb_proto_2_xsub.test \
2102	AWTC/AWTC.test \
2103
2104	# plain test-libaries not linked anywhere
2105	TEST_SANDBOXES = \
2106	SL/CB/CB.test \
2107
2108	UNITS_TESTED = \
2109	SL/TREE_READ/TREE_READ.test \
2110	DBSERVER/DBSERVER.test \
2111	AWT/libAWT.test \
2112	CORE/libCORE.test \
2113	SL/INSDEL/INSDEL.test \
2114	SL/TREEDISP/TREEDISP.test \
2115	NTREE/NTREE.test \
2116	AISC_MKPTPS/mkptypes.test \
2117	EDIT4/EDIT4.test \
2118	MERGE/MERGE.test \
2119	MULTI_PROBE/MULTI_PROBE.test \
2120	SERVERCNTRL/SERVERCNTRL.test \
2121	SL/FAST_ALIGNER/FAST_ALIGNER.test \
2122	SL/PRONUC/PRONUC.test \
2123	WINDOW/libWINDOW.test \
2124	HELP_SOURCE/arb_help2xml.test \
2125	CONVERTALN/CONVERTALN.test \
2126	SL/SEQIO/SEQIO.test \
2127	SL/PTCLEAN/PTCLEAN.test \
2128	PROBE/PROBE.test \
2129	SL/DB_QUERY/DB_QUERY.test \
2130
2131	TESTED_UNITS_MANUAL = \
2132	$(TEST_SANDBOXES) \
2133	$(UNITS_TESTED_FIRST) \
2134	$(UNITS_TESTED) \
2135
2136	# $(UNITS_WORKING)
2137
2138	# see UNIT_TESTER/sym2testcode.pl@disableErrorOnUnitsWithoutTests
2139
2140	#TESTED_UNITS = $(TESTED_UNITS_AUTO)
2141	TESTED_UNITS = $(TESTED_UNITS_MANUAL)
2142
2143	# ----------------------------------------
2144
2145	TEST_LOG_DIR = UNIT_TESTER/logs
2146	TEST_RUN_SUITE=$(MAKE) $(NODIR) -C UNIT_TESTER -f Makefile.suite -r
2147	TEST_MAKE_FLAGS=
2148	TEST_POST_CLEAN=
2149	ifeq ($(COVERAGE),1)
2150	TEST_POST_CLEAN=$(MAKE) clean_cov
2151	TEST_MAKE_FLAGS+=-j1
2152	endif
2153
2154
2155	%.test:
2156	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
2157	( \
2158	echo "fake[1]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
2159	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
2160	"UNITDIR=$(@D)" \
2161	"UNITLIBNAME=$(@F:.test=)" \
2162	"COVERAGE=$(COVERAGE)" \
2163	"ARB_PID=$(ARB_PID)_$(@F)" \
2164	runtest; \
2165	echo "fake[1]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"; \
2166	$(TEST_POST_CLEAN) \
2167	) >$(TEST_LOG_DIR)/$(@F).log 2>&1; \
2168	UNIT_TESTER/log_result.pl $(TEST_LOG_DIR)/$(@F).log )
2169
2170
2171	test_base: $(UNIT_TESTER_LIB:.a=.dummy) $(subst .test,.dummy,$(TEST_SANDBOXES))
2172
2173	clean_cov:
2174	find . \( -name ".gcda" -o -name ".gcov" -o -name "*.cov" \) -exec rm {} \;
2175
2176	clean_cov_all: clean_cov
2177	find . \( -name "*.gcno" \) -exec rm {} \;
2178
2179	run_tests: test_base clean_cov
2180	$(MAKE) "ARB_PID=UT_$$$$" run_tests_faked_arbpid
2181
2182	cleanup_faked_arbpids:
2183	@-rm ~/.arb_tmp/tmp/arb_pids_${USER}_${ARB_PID}_*
2184
2185	cleanup_faked_arbpids_and_fail: cleanup_faked_arbpids
2186	@false
2187
2188	run_tests_faked_arbpid:
2189	+@$(TEST_RUN_SUITE) init
2190	@echo "fake[2]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2191	$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(TESTED_UNITS) \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2192	@echo "fake[2]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2193	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2194	@$(MAKE) clean_cov >/dev/null
2195	@$(MAKE) cleanup_faked_arbpids
2196
2197	ut:
2198	ifeq ($(UNIT_TESTS),1)
2199	@echo $(MAKE) run_tests
2200	@$(MAKE) run_tests
2201	else
2202	@echo "Not compiled with unit tests"
2203	endif
2204
2205
2206	aut:
2207	+@$(TEST_RUN_SUITE) unskip
2208	$(MAKE) ut
2209
2210	# --------------------------------------------------------------------------------
2211
2212	TIMELOG=$(ARBHOME)/arb_time.log
2213	TIMEARGS=--append --output=$(TIMELOG) --format=" %E(%S+%U) %P [%C]"
2214	TIMECMD=$(TIME) $(TIMEARGS)
2215
2216	time_one:
2217	ifeq ($(ONE_TIMED_TARGET),)
2218	@echo "Error: You have to pass ONE_TIMED_TARGET to $@"
2219	false
2220	else
2221	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET)"
2222	@$(TIMECMD) $(MAKE) $(ONE_TIMED_TARGET)
2223	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET) [done]"
2224	endif
2225
2226	timed_target:
2227	ifeq ($(TIMED_TARGET),)
2228	@echo "Error: You have to pass TIMED_TARGET to $@"
2229	false
2230	else
2231	@echo "Build time:" > $(TIMELOG)
2232	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2233	@cat $(TIMELOG)
2234	@rm $(TIMELOG)
2235	endif
2236
2237	timed_target_tested:
2238	ifeq ($(TIMED_TARGET),)
2239	@echo "Error: You have to pass TIMED_TARGET to $@"
2240	false
2241	else
2242	@echo "Build time:" > $(TIMELOG)
2243	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2244	$(MAKE) "ONE_TIMED_TARGET=ut" time_one
2245	@cat $(TIMELOG)
2246	@rm $(TIMELOG)
2247	endif
2248
2249	clean_timed_target:
2250	ifeq ($(TIMED_TARGET),)
2251	@echo "Error: You have to pass TIMED_TARGET to $@"
2252	false
2253	else
2254	@echo "Build time:" > $(TIMELOG)
2255	$(MAKE) "ONE_TIMED_TARGET=clean" time_one
2256	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2257	@cat $(TIMELOG)
2258	@rm $(TIMELOG)
2259	endif
2260
2261	# --------------------------------------------------------------------------------
2262
2263	CHECKOUT_MODIFIED=0# set to 1 to temporarily skip test for modifications (do not check in if set to 1)
2264
2265	check_svn_does_not_contain_generated:
2266	ifeq ($(CHECKOUT_MODIFIED),0)
2267	@echo "Testing that build does not modify files in SVN"
2268	@test 0 = `svn status \| wc -l` \|\| ( \
2269	echo "The checkout is not/no longer clean:"; \
2270	svn status; \
2271	echo "- if this fails instantly, your checkout is not clean"; \
2272	echo "- if this fails after other targets, these targets modify checked in data"; \
2273	echo " (a common cause may be that depends are not up to date)"; \
2274	false)
2275	else
2276	grep -Hn 'CHECKOUT_MODIFIED' Makefile
2277	endif
2278
2279	check_svn_ignores_generated:
2280	@test 0 = `svn status \| grep '^\?' \| wc -l` \|\| ( \
2281	echo "There are svn-unignored files:"; \
2282	svn status \| grep '^\?'; \
2283	echo "(all generated files should be svn-ignored)"; \
2284	false)
2285
2286	check_svn_state: check_svn_does_not_contain_generated
2287	$(MAKE) check_svn_ignores_generated
2288	$(MAKE) savetest
2289
2290	things_that_always_should_work: depends proto
2291
2292	post_commit_check:
2293	@echo "---------------------------------------- [Initial]"
2294	$(MAKE) check_svn_state
2295
2296	$(MAKE) clean
2297	@echo "---------------------------------------- [After 'make clean']"
2298	$(MAKE) check_svn_state
2299
2300	$(MAKE) things_that_always_should_work
2301	@echo "---------------------------------------- [After 'make things_that_always_should_work']"
2302	$(MAKE) check_svn_state
2303
2304	$(MAKE) all
2305	@echo "---------------------------------------- [After 'make all']"
2306	$(MAKE) check_svn_state
2307
2308	$(MAKE) things_that_always_should_work
2309	@echo "---------------------------------------- [Final]"
2310	$(MAKE) check_svn_state
2311
2312	# --------------------------------------------------------------------------------
2313
2314	build: arb
2315	$(MAKE) binlink preplib compile_compatibility
2316
2317	all:
2318	@echo "Build time" > $(TIMELOG)
2319	@echo "$(SEP) $(MAKE) build"
2320	@$(TIMECMD) $(MAKE) build
2321	@echo $(SEP)
2322	@echo "made 'all' with success."
2323	@echo "to start arb enter 'arb'"
2324	ifeq ($(UNIT_TESTS),1)
2325	@echo $(MAKE) run_tests
2326	@$(TIMECMD) $(MAKE) run_tests
2327	endif
2328	@echo "$(SEP) $(MAKE) build [done]"
2329	@$(MAKE) save_test_no_error >/dev/null # just show hints
2330	@cat $(TIMELOG)
2331	@rm $(TIMELOG)
2332

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