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Last change on this file was 12754, checked in by westram, 11 years ago
reintegrates 'alilink' into 'trunk' DRYed ali admin(s) adds: log:branches/alilink@12708:12753
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 66.3 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:=${ARBHOME}/lib
81	endif
82
83	FORCEMASK = umask 002
84	NODIR=--no-print-directory
85
86	SED:=$(ARBHOME)/SH/arb_sed
87	READLINK:=$(ARBHOME)/SH/arb_readlink
88
89	# ---------------------- compiler version detection
90
91	# supported gcc versions:
92	ALLOWED_gcc_VERSIONS=\
93	4.3.1 4.3.2 4.3.3 4.3.4 \
94	4.4.1 4.4.3 4.4.5 4.4.6 4.4.7 \
95	4.5.2 \
96	4.6.1 4.6.2 4.6.3 \
97	4.7.1 4.7.2 4.7.3 \
98	4.8.0 4.8.1 4.8.2 4.8.3 \
99	4.9.0 4.9.1 \
100
101	# supported clang versions:
102	ALLOWED_clang_VERSIONS=\
103	4.2.1 \
104
105	# ----------------------
106
107	COMPILER_INFO:=$(shell SOURCE_TOOLS/arb_compiler_version.pl $(A_CXX))
108	COMPILER_NAME:=$(word 1,$(COMPILER_INFO))
109	COMPILER_VERSION:=$(word 2,$(COMPILER_INFO))
110
111	USE_CLANG:=0
112	ifneq ($(COMPILER_NAME),gcc)
113	ifeq ($(COMPILER_NAME),clang)
114	USE_CLANG:=1
115	else
116	$(error failed to detect COMPILER_NAME (got '$(COMPILER_NAME)', expected 'clang' or 'gcc'))
117	endif
118	endif
119
120	ifeq ($(USE_CLANG),1)
121	ALLOWED_COMPILER_VERSIONS=$(ALLOWED_clang_VERSIONS)
122	else
123	ALLOWED_COMPILER_VERSIONS=$(ALLOWED_gcc_VERSIONS)
124	endif
125
126	COMPILER_VERSION_ALLOWED=$(strip $(subst ___,,$(foreach version,$(ALLOWED_COMPILER_VERSIONS),$(findstring ___$(version)___,___$(COMPILER_VERSION)___))))
127
128	#---------------------- split gcc version
129
130	SPLITTED_VERSION:=$(subst ., ,$(COMPILER_VERSION))
131
132	USE_GCC_MAJOR:=$(word 1,$(SPLITTED_VERSION))
133	USE_GCC_MINOR:=$(word 2,$(SPLITTED_VERSION))
134	USE_GCC_PATCHLEVEL:=$(word 3,$(SPLITTED_VERSION))
135
136	USE_GCC_452_OR_HIGHER:=
137	USE_GCC_46_OR_HIGHER:=
138	USE_GCC_47_OR_HIGHER:=
139	USE_GCC_48_OR_HIGHER:=
140
141
142	ifeq ($(USE_GCC_MAJOR),4)
143	ifeq ($(USE_GCC_MINOR),5)
144	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),23456789)','')
145	USE_GCC_452_OR_HIGHER:=yes
146	endif
147	else
148	ifneq ('$(findstring $(USE_GCC_MINOR),6789)','')
149	USE_GCC_452_OR_HIGHER:=yes
150	USE_GCC_46_OR_HIGHER:=yes
151	ifneq ($(USE_GCC_MINOR),6)
152	USE_GCC_47_OR_HIGHER:=yes
153	ifneq ($(USE_GCC_MINOR),7)
154	USE_GCC_48_OR_HIGHER:=yes
155	endif
156	endif
157	endif
158	endif
159	else
160	USE_GCC_452_OR_HIGHER:=yes
161	USE_GCC_46_OR_HIGHER:=yes
162	USE_GCC_47_OR_HIGHER:=yes
163	USE_GCC_48_OR_HIGHER:=yes
164	endif
165
166	#---------------------- define special directories for non standard builds
167
168	ifeq ($(DARWIN),1)
169	OSX_FW:=/System/Library/Frameworks
170	OSX_FW_OPENGL:=$(OSX_FW)/OpenGL.framework/Versions/A/Libraries
171	OSX_FW_GLUT:=$(OSX_FW)/GLUT.framework/Versions/A/Libraries
172	OSX_FW_IMAGEIO:=$(OSX_FW)/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources
173	endif
174
175	#----------------------
176
177	ifeq ($(DARWIN),1)
178	LINK_STATIC=1# link static
179	else
180	LINK_STATIC=0# link dynamically
181	# LINK_STATIC=1# link static (testing only)
182	endif
183
184	shared_cflags :=# flags for shared lib compilation
185	lflags :=# linker flags
186	clflags :=# linker flags (when passed through gcc)
187	extended_warnings :=# warning flags for C and C++-compiler
188	extended_cpp_warnings :=# warning flags for C++-compiler only
189
190
191	ifeq ($(DEBUG),0)
192	dflags := -DNDEBUG# defines
193	ifeq ($(USE_CLANG),1)
194	cflags := -O3# compiler flags (C and C++)
195	else
196	cflags := -O4# compiler flags (C and C++)
197	lflags += -O2# linker flags
198	clflags += -Wl,-O2# passthrough linker flags
199	endif
200	endif
201
202	ifeq ($(DEBIAN),1)
203	lflags += -rpath=/usr/lib/arb/lib -z relro
204	clflags += -Wl,-rpath=/usr/lib/arb/lib -Wl,-z,relro
205	endif
206
207	ifeq ($(DEBUG),1)
208	dflags := -DDEBUG
209
210	gdb_common := -g -g3 -ggdb -ggdb3
211
212	ifeq ($(DEVELOPER),RALF)
213	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
214	STABS:=1
215	endif
216	endif
217
218	DBGOPTI:=-O0
219	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
220	DBGOPTI:=-Og
221	endif
222
223	ifeq ($(STABS),1)
224	cflags := $(DBGOPTI) $(gdb_common) -gstabs+ # using stabs+ (enable this for bigger debug session: debugs inlines, quick var inspect, BUT valgrind stops working :/)
225	else
226	cflags := $(DBGOPTI) $(gdb_common) # (using dwarf - cant debug inlines here, incredible slow on showing variable content)
227	endif
228
229	# cflags := $(DBGOPTI) $(gdb_common) -gdwarf-3 # (specify explicit dwarf format)
230	# cflags := $(DBGOPTI) $(gdb_common) -gstabs # using stabs (same here IIRC)
231	# cflags := -O2 $(gdb_common) # use this for callgrind (force inlining)
232
233	ifeq ($(DARWIN),0)
234	lflags += -g
235	clflags += -Wl,-g
236	endif
237
238	# control how much you get spammed
239	# (please do not change default in SVN, use developer specific setting as below)
240	POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl
241	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --original# dont modify compiler output
242	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --hide-Noncopyable-advices
243	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --show-useless-Weff++
244	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --no-warnings
245	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --only-first-error
246	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --no-warnings --only-first-error
247	ifeq ($(DEVELOPER),ELMAR)
248	POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --only-first-error
249	endif
250
251
252	# Enable extra warnings
253	extended_warnings :=
254	extended_cpp_warnings :=
255
256	# C and C++
257	extended_warnings += -Wwrite-strings -Wunused -Wno-aggregate-return -Wshadow
258
259	# C++ only
260	extended_cpp_warnings += -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute
261	extended_cpp_warnings += -Wctor-dtor-privacy# < gcc 3
262	# extended_cpp_warnings += -Wfloat-equal# gcc 3.0
263
264	# ------- above only warnings available in 3.0
265
266	ifneq ('$(COMPILER_VERSION)','4.7.3') # g++ crashes on GenomeImport.cxx when -Weffc++ is active (bug reported)
267	extended_cpp_warnings += -Weffc++# gcc 3.0.1
268	endif
269	extended_cpp_warnings += -Wmissing-noreturn# gcc 3.0.2
270	# extended_cpp_warnings += -Wold-style-cast# gcc 3.0.4 (warn about 28405 old-style casts)
271	extended_cpp_warnings += -Winit-self# gcc 3.4.0
272	extended_cpp_warnings += -Wstrict-aliasing# gcc 3.4
273	extended_cpp_warnings += -Wextra# gcc 3.4.0
274	ifeq ('$(USE_GCC_452_OR_HIGHER)','yes')
275	extended_cpp_warnings += -Wlogical-op# gcc 4.5.2
276	endif
277	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
278	# extended_cpp_warnings += -Wunused-local-typedefs# gcc 4.7 (fails for each STATIC_ASSERT, enable only for Cxx11)
279	# extended_cpp_warnings += -Wzero-as-null-pointer-constant# gcc 4.7 #@@@ activate
280	endif
281	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
282	extended_cpp_warnings += -Wunused-local-typedefs# available since gcc 4.7 (but fails for each STATIC_ASSERT, so enable only for Cxx11)
283	endif
284
285	ifeq ($(DEBUG_GRAPHICS),1)
286	dflags += -DDEBUG_GRAPHICS
287	endif
288	endif
289
290	#---------------------- turn off clang bogus warnings
291
292	ifeq ($(USE_CLANG),1)
293	# -Wmismatched-tags warns about struct/class mismatch in forward declarations (which is explicitely allowed)
294	# -Wchar-subscripts reports too many bogus warnings for "array['x']" (when 'x' is known to be in range [0..128])
295	# -Wunused-private-field report too many false positives (currently ~ 2 of 3)
296	# -Wstring-plus-int warns about common ARB coding practice
297	# -Wgnu-static-float-init warns about accepted GNU extension
298	extended_cpp_warnings += -Wno-mismatched-tags -Wno-char-subscripts -Wno-unused-private-field -Wno-string-plus-int -Wno-gnu-static-float-init
299	endif
300
301	#---------------------- developer
302
303	ifneq ($(DEVELOPER),ANY) # ANY=default setting (skip all developer specific code)
304	dflags += -DDEVEL_$(DEVELOPER)# activate developer/release specific code
305	endif
306
307	ifndef SHOWTODO
308	ifeq ($(DEVELOPER),RALF)
309	SHOWTODO:=1
310	else
311	SHOWTODO:=0
312	endif
313	endif
314	ifeq ($(SHOWTODO),1)
315	dflags += -DWARN_TODO# activate "TODO" warnings
316	endif
317
318	#---------------------- 32 or 64 bit
319
320	ifndef BUILDHOST_64
321	BUILDHOST_64:=$(ARB_64)# assume build host is same as version (see config.makefile)
322	endif
323
324	cross_cflags:=
325	cross_lflags:=
326	cross_clflags:=
327
328	ifeq ($(ARB_64),1)
329	dflags += -DARB_64 #-fPIC
330	shared_cflags += -fPIC
331
332	ifeq ($(BUILDHOST_64),1)
333	# build 64-bit ARB version on 64-bit host
334	CROSS_LIB:=# empty = autodetect below
335	ifeq ($(DARWIN),1)
336	cross_cflags += -arch x86_64
337	cross_lflags += -arch x86_64
338	cross_clflags += -arch x86_64
339	endif
340	else
341	# build 64-bit ARB version on 32-bit host
342	CROSS_LIB:=/lib64
343	cross_cflags += -m64
344	cross_lflags += -m64 -m elf_x86_64
345	cross_clflags += -m64 -Wl,-m64,-m,elf_x86_64
346	endif
347	else
348	ifeq ($(BUILDHOST_64),1)
349	# build 32-bit ARB version on 64-bit host
350	CROSS_LIB:=# empty = autodetect below
351	cross_cflags += -m32
352	cross_lflags += -m32 -m elf_i386
353	cross_clflags += -m32 -Wl,-m32,-m,elf_i386
354	else
355	# build 32-bit ARB version on 32-bit host
356	CROSS_LIB:=/lib
357	endif
358	endif
359
360	cflags += $(cross_cflags)
361	lflags += $(cross_lflags)
362	clflags += $(cross_clflags)
363
364	ifeq ('$(CROSS_LIB)','')
365	# autodetect libdir
366	ifeq ($(ARB_64),1)
367	CROSS_LIB:=$(shell (test -d /lib64 && echo lib64) \|\| echo lib)
368	else
369	CROSS_LIB:=$(shell (test -d /lib32 && echo lib32) \|\| echo lib)
370	endif
371	endif
372
373	#---------------------- unit tests
374
375	ifndef UNIT_TESTS
376	UNIT_TESTS=0#default is "no tests"
377	endif
378	ifeq ($(UNIT_TESTS),1)
379	dflags += -DUNIT_TESTS
380	UNIT_TESTER_LIB=UNIT_TESTER/UNIT_TESTER.a
381	else
382	UNIT_TESTER_LIB=
383	endif
384
385	#---------------------- use gcov
386
387	ifndef COVERAGE
388	COVERAGE=0#default is "no"
389	endif
390	ifneq ($(COVERAGE),0)
391	GCOVFLAGS=-ftest-coverage -fprofile-arcs
392	cflags += $(GCOVFLAGS)
393	EXECLIBS=-lgcov
394	else
395	GCOVFLAGS=
396	EXECLIBS=
397	endif
398
399	#---------------------- other flags
400
401	dflags += -D$(MACH) # define machine
402
403	ifeq ($(DARWIN),1)
404	shared_cflags += -fno-common
405	else
406	dflags += $(shell getconf LFS_CFLAGS)
407	endif
408
409	cflags += -pipe
410	cflags += -fmessage-length=0# don't wrap compiler output
411	cflags += -fshow-column# show columns
412	cflags += -funit-at-a-time
413	cflags += -fPIC
414	cflags += -fno-common# link all global data into one namespace
415	cflags += -fstrict-aliasing# gcc 3.4
416	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
417	cflags += -fno-diagnostics-show-caret#gcc 4.8 (4.7.?)
418	endif
419	#cflags += -save-temps# uncomment to see preprocessor output
420
421	#---------------------- X11 location
422
423	ifeq ($(DARWIN),1)
424	XHOME:=$(PREFIX)
425	else
426	ifeq ($(DEBIAN),1)
427	XHOME:=$(PREFIX)
428	else
429	XHOME:=/usr/X11R6
430	endif
431	endif
432
433	XINCLUDES:=-I$(XHOME)/include
434	ifeq ($(DARWIN),1)
435	XINCLUDES += -I$(OSX_FW)/GLUT.framework/Headers -I$(OSX_FW)/OpenGL.framework/Headers -I$(OSX_SDK)/usr/include/krb5
436
437	XLIBS := -L$(XHOME)/lib -lXm -lpng -lz -lXt -lX11 -lXext -lXp -lXmu -lXi
438	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGL.dylib:$(OSX_FW_OPENGL)/libGL.dylib
439	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGLU.dylib:$(OSX_FW_OPENGL)/libGLU.dylib
440	else
441	XLIBS:=-L$(XHOME)/$(CROSS_LIB) -lXm -lXpm -lXt -lXext -lX11
442	endif
443
444	dflags += -DARB_MOTIF
445
446	#---------------------- open GL
447
448	ifeq ($(OPENGL),1)
449	cflags += -DARB_OPENGL # activate OPENGL code
450	GL := gl # this is the name of the OPENGL base target
451	GL_LIB_SYS := -lGL -lGLU
452	GL_LIB_ARB := -L$(ARBHOME)/GL/glAW -lglAW
453
454	ifeq ($(DARWIN),1)
455	GL_LIB_SYS += -lpthread
456	endif
457
458	GL_PNGLIBS_ARB := -L$(ARBHOME)/GL/glpng -lglpng_arb
459	GL_PNGLIBS_SYS := -lpng
460
461	GLEWLIB := -lGLEW -lGLw
462	ifeq ($(DARWIN),1)
463	GLUTLIB := -glut
464	else
465	GLUTLIB := -lglut
466	endif
467
468	GL_LIBS_SYS := $(GL_LIB_SYS) $(GL_PNGLIBS_SYS) $(GLEWLIB) $(GLUTLIB)
469	GL_LIBS_ARB := $(GL_LIB_ARB) $(GL_PNGLIBS_ARB)
470
471	RNA3D_LIB := RNA3D/RNA3D.a
472
473	else
474
475	GL_LIBS_ARB:=# no opengl -> no libs
476	GL_LIBS_SYS:=# no opengl -> no libs
477	GL:=# don't build ARB openGL libs
478
479	RNA3D_LIB :=
480
481	endif
482
483	RNA3D_LIB_4_DEPENDS := RNA3D/RNA3D.a
484
485	GL_LIBS:=$(GL_LIBS_ARB) $(GL_LIBS_SYS)
486
487	#---------------------- tiff lib:
488
489	TIFFLIBS := -ltiff
490
491	#---------------------- glib:
492
493	ARB_NEEDED_GLIB=glib-2.0
494
495	ARB_GLIB_INCLUDE:=$(strip $(shell pkg-config --cflags $(ARB_NEEDED_GLIB)))
496	ARB_GLIB_LIBS:=$(strip $(shell pkg-config --libs $(ARB_NEEDED_GLIB)))
497
498	#---------------------- basic libs:
499
500	SYSLIBS:=
501
502	ifeq ($(DARWIN),1)
503	SYSLIBS += -lstdc++
504	else
505	SYSLIBS += -lm $(ARB_GLIB_LIBS)
506	endif
507
508	#---------------------- include symbols?
509
510	ifeq ($(TRACESYM),1)
511	ifeq ($(USE_CLANG),0)
512	cflags += -rdynamic
513	lflags += --export-dynamic
514	clflags += -rdynamic -Wl,--export-dynamic
515	endif
516	endif
517
518	#---------------------- system dependent commands
519
520	ifeq ($(DARWIN),1)
521	TIME:=gtime
522	else
523	TIME:=/usr/bin/time
524	endif
525
526	# -------------------------------------------------------------------------
527	# Don't put any machine/version/etc conditionals below!
528	# (instead define variables above)
529	# -------------------------------------------------------------------------
530
531	cflags += -W -Wall $(dflags) $(extended_warnings)
532	cxxflags := $(extended_cpp_warnings)
533
534	# add CFLAGS + CPPFLAGS from environment for DEBIAN build
535	ifeq ($(DEBIAN),1)
536	cflags := $(CFLAGS) $(cflags)
537	cxxflags += $(CPPFLAGS)
538	endif
539
540	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
541	cxxflags += -std=gnu++11# see also TEMPLATES/cxxforward.h@USE_Cxx11
542	else
543	# only use for gcc versions between 4.3 and <4.7 (4.7++ adds -Wc++11-compat above)
544	HAVE_GNUPP0X=`SOURCE_TOOLS/requireVersion.pl 4.3 $(COMPILER_VERSION)`
545	ifeq ($(HAVE_GNUPP0X),1)
546	# ensure compatibility with upcoming C++ standard
547	cxxflags += -std=gnu++0x
548	endif
549	endif
550
551	LINK_STATIC_LIB := ld $(lflags) -r -o# link static lib
552	LINK_EXECUTABLE := $(A_CXX) $(clflags) -o# link executable (c++)
553
554	ifeq ($(LINK_STATIC),1)
555	SHARED_LIB_SUFFIX = a# static lib suffix
556	LINK_SHARED_LIB := $(LINK_STATIC_LIB)
557	else
558	SHARED_LIB_SUFFIX = so# shared lib suffix
559	LINK_SHARED_LIB := $(A_CXX) $(clflags) -shared $(GCOVFLAGS) -o# link shared lib
560	endif
561
562	# delete variables unused below
563	lflags:=
564	clflags:=
565
566	# other used tools
567	MAKEDEPEND_PLAIN = makedepend
568	MAKEDEPEND = $(FORCEMASK);$(MAKEDEPEND_PLAIN)
569
570	#SEP:=--------------------------------------------------------------------------------
571	SEP=[`date +%M:%S.%N`] ------------------------------------------------
572	# to analyse timings run
573	# make -j9 clean; make -j9 all \| grep '^\[' \| sort
574	# make -j9 "TIMED_TARGET=perl" clean_timed_target \| grep '^\[' \| sort
575
576	CORE_LIB=-lCORE
577	ARBDB_LIB=-lARBDB $(CORE_LIB)
578	LIBS = $(ARBDB_LIB) $(SYSLIBS)
579
580	GUI_LIBS_PREFIX:=
581	ifeq ($(DARWIN),1)
582	# this seem to be added at wrong place, since opengl is only needed to link EDIT4
583	GUI_LIBS_PREFIX:=-framework GLUT -framework OpenGL
584	endif
585
586	GUI_LIBS=$(GUI_LIBS_PREFIX) $(LIBS) -lAWT -lWINDOW
587	GUI_LIBS+=$(XLIBS)
588
589	LIBPATH = -L$(ARBHOME)/lib
590
591	DEST_LIB = lib
592	DEST_BIN = bin
593
594	CC_INCLUDES := -I. -I$(ARBHOME)/INCLUDE $(XINCLUDES) $(ARB_GLIB_INCLUDE)
595	CXX_INCLUDES := $(CC_INCLUDES)
596	MAKEDEPENDFLAGS := -- -DARB_OPENGL -DUNIT_TESTS -D__cplusplus -I. -Y$(ARBHOME)/INCLUDE
597
598	# -------------------------------
599	# old PTSERVER or PTPAN?
600
601	ifeq ($(PTPAN),1)
602	# PTPAN only libs
603	ARCHS_PT_SERVER = \
604	ptpan/PROBE.a
605	else
606	ifeq ($(PTPAN),2)
607	# special mode to compile both servers (developers only!)
608	ARCHS_PT_SERVER = \
609	ptpan/PROBE.a \
610	PROBE/PROBE.a
611	ARCHS_PT_SERVER_LINK = PROBE/PROBE.a# default to old ptserver
612	else
613	# PT-server only libs
614	ARCHS_PT_SERVER = \
615	PROBE/PROBE.a
616	endif
617	endif
618
619	ifndef ARCHS_PT_SERVER_LINK
620	ARCHS_PT_SERVER_LINK = $(ARCHS_PT_SERVER)
621	endif
622
623	# ---------------------------------------
624	# wrap main()
625
626	use_ARB_main=$(ARBHOME)/SOURCE_TOOLS/arb_main_cpp.o
627	use_ARB_main_C=$(ARBHOME)/SOURCE_TOOLS/arb_main_c.o
628
629	# -----------------------------------------
630	# export variables to submakefiles
631
632	include SOURCE_TOOLS/export2sub
633
634	# do not define (exported) variables below this point
635
636	# -------------------------
637	# Main arb targets:
638	# -------------------------
639
640	first_target:
641	$(MAKE) checks
642	@echo $(SEP)
643	@echo 'Main targets:'
644	@echo ''
645	@echo ' all - Compile ARB + TOOLs + and copy shared libs + link foreign software'
646	@echo ' (That is most likely the target you want)'
647	@echo ''
648	@echo ' clean - remove generated files ("SUBDIR/SUBDIR.clean" to clean only SUBDIR)'
649	@echo ' rebuild - clean + all'
650	@echo ' relink - remove all binaries and relink them from objects'
651	@echo ''
652	@echo 'Some often used sub targets (make all makes them all):'
653	@echo ''
654	@echo ' arb - Just compile ARB (but none of the integrated tools)'
655	@echo ' menus - create lib/gde/arb.menu from GDEHELP/ARB_GDEmenus.source'
656	@echo ' perl - Compile the PERL XSUBS into lib/ARB.so and create links in lib to perl'
657	@echo ' binlink - Create all links in the bin directory'
658	@echo ''
659	@echo 'Development targets:'
660	@echo ''
661	@echo ' depends - create or update dependencies ("SUBDIR/SUBDIR.depends" to update only SUBDIR)'
662	@echo ' proto - create or update prototypes ("SUBDIR/SUBDIR.proto" to update only SUBDIR)'
663	@echo ' tags - create tags for xemacs'
664	@echo ' show - show available shortcuts (AKA subtargets)'
665	@echo ' up - shortcut for depends+proto+tags'
666	ifeq ($(UNIT_TESTS),1)
667	@echo ' ut - only run tests'
668	endif
669	@echo ' modified - rebuild files modified in svn checkout (does touch)'
670	@echo ' touch - touch files modified in svn checkout'
671	@echo ''
672	@echo 'Internal maintenance:'
673	@echo ''
674	@echo ' relinfo - show help on release targets'
675	@echo ' tarfile - make rebuild and create arb version tarfile ("tarfile_quick" to skip rebuild)'
676	@echo ' save - save all basic ARB sources into arbsrc_DATE ("savetest" to check filelist)'
677	@echo ' patch - save svn diff to patchfile'
678	@echo ' source_doc - create doxygen documentation'
679	@echo ' relocated - rebuild partly (use when you have relocated ARBHOME)'
680	@echo ' check_res - check ressource usage'
681	@echo ' dep_graph - Build dependency graphs'
682	@echo ' clean_cov - Clean coverage results'
683	@echo ''
684	@echo ' post_commit_check - Checks whether'
685	@echo ' * main make targets work,'
686	@echo ' * dependencies and prototypes are up to date,'
687	@echo ' * SVN-controlled files remain unaffected by called targets and'
688	@echo ' * all generated files are ignored.'
689	@echo ' (has to be called in a clean SVN checkout)'
690	@echo $(SEP)
691	@echo ''
692
693	relinfo:
694	@echo ''
695	@echo $(SEP)
696	@echo 'Release targets:'
697	@echo ''
698	@echo ' inc_candi - increase RC candidate-number (only possible in "rc" branch, not needed for RC1)'
699	@echo ' inc_patch - increase release patchlevel (only possible in "stable" branch)'
700	@echo ' inc_minor - increase minor version number (only possible in "trunk")'
701	@echo ' inc_major - increase MAJOR version number (only possible in "trunk")'
702	@echo ''
703	@echo ' show_version - show version tag'
704	@echo ''
705	@echo $(SEP)
706	@echo ''
707
708	# auto-generate config.makefile:
709
710	CONFIG_MAKEFILE_FOUND=$(wildcard config.makefile)
711
712	config.makefile : config.makefile.template
713	@echo --------------------------------------------------------------------------------
714	ifeq ($(strip $(CONFIG_MAKEFILE_FOUND)),)
715	@cp $< $@
716	@echo '$(ARBHOME)/$@:1: has been generated.'
717	@echo 'Please edit $@ to configure your system!'
718	@echo --------------------------------------------------------------------------------
719	@false
720	else
721	@echo '$(ARBHOME)/$<:1: is more recent than'
722	@echo '$(ARBHOME)/$@:1:'
723	@ls -al config.makefile*
724	@echo --------------------------------------------------------------------------------
725	@echo "Updating $@ (if this fails, check manually)"
726	SOURCE_TOOLS/update_config_makefile.pl
727	@echo "Sucessfully updated $@"
728	@echo --------------------------------------------------------------------------------
729	@ls -al config.makefile*
730	@echo --------------------------------------------------------------------------------
731	@echo "Diff to your old config.makefile:"
732	@echo --------------------------------------------------------------------------------
733	-diff $@.bak $@
734	@echo --------------------------------------------------------------------------------
735	endif
736
737	# check if everything is configured correctly
738
739	check_DEVELOPER:
740	ifndef DEVELOPER
741	@echo 'config.makefile:1: DEVELOPER not defined'
742	@false
743	endif
744
745	check_DEBUG:
746	ifndef dflags
747	@echo 'config.makefile:1: DEBUG has to be defined. Valid values are 0 and 1'
748	@false
749	endif
750
751	check_ARB_64:
752	ifndef ARB_64
753	@echo 'config.makefile:1: ARB_64 has to be defined. Valid values are 0 and 1'
754	@false
755	endif
756
757	# ---------------------------------------- check gcc version
758
759	check_same_GCC_VERSION:
760	$(ARBHOME)/SOURCE_TOOLS/check_same_compiler_version.pl $(COMPILER_NAME) $(COMPILER_VERSION_ALLOWED)
761
762	check_GCC_VERSION:
763	@echo 'Compiler version check:'
764	ifeq ('$(COMPILER_VERSION_ALLOWED)', '')
765	@echo " - Your compiler is '$(COMPILER_NAME)' version '$(COMPILER_VERSION)'"
766	@echo ' This version is not in the list of supported $(COMPILER_NAME)-versions:'
767	@$(foreach version,$(ALLOWED_COMPILER_VERSIONS),echo ' * $(version)';)
768	@echo ' - You may either ..'
769	@echo ' - add your version to ALLOWED_$(COMPILER_NAME)_VERSIONS in the Makefile and try it out or'
770	@echo ' - switch to one of the allowed versions (see arb_README_gcc.txt for installing'
771	@echo ' a different version of gcc)'
772	@echo ''
773	@false
774	else
775	@echo " - Supported $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)' detected - fine!"
776	@echo ''
777	$(MAKE) check_same_GCC_VERSION
778
779	endif
780
781	#---------------------- check ARBHOME
782
783	# use arb_INSTALL.txt to determine whether ARBHOME points to correct directory
784	ARB_INSTALL_FOUND=$(wildcard $(ARBHOME)/arb_INSTALL.txt)
785
786	check_ARBHOME:
787	ifeq ($(strip $(ARB_INSTALL_FOUND)),)
788	@echo ------------------------------------------------------------
789	@echo "ARBHOME is set to '$(ARBHOME)'"
790	@echo "The environment variable ARBHOME has to point to the top arb source directory."
791	@echo "If you use bash enter:"
792	@echo " export ARBHOME='`pwd`'"
793	@echo ------------------------------------------------------------
794	@false
795	endif
796
797	ARB_PATH_SET=$(findstring $(ARBHOME)/bin,$(PATH))
798
799	check_PATH: check_ARBHOME
800	ifeq ($(strip $(ARB_PATH_SET)),)
801	@echo ------------------------------------------------------------
802	@echo "The environment variable PATH has to contain $(ARBHOME)/bin"
803	@echo "If you use bash enter:"
804	@echo ' export PATH=$$ARBHOME/bin:$$PATH'
805	@echo ------------------------------------------------------------
806	@false
807	endif
808
809	check_TOOLS:
810	@util/arb_check_build_env.pl \
811	"$(A_CC)" \
812	"$(A_CXX)" \
813	"$(MAKEDEPEND_PLAIN)" \
814	"$(LINK_SHARED_LIB)" \
815	"$(LINK_SHARED_LIB)" \
816
817
818	check_ENVIRONMENT : check_PATH check_TOOLS
819	@echo "-------------------- Environment [start]"
820	@echo "ARBHOME='$(ARBHOME)'"
821	@echo "PATH='$(PATH)'"
822	@echo "LD_LIBRARY_PATH='$(LD_LIBRARY_PATH)'"
823	@echo "-------------------- Environment [end]"
824
825	check_tabs: check_setup
826	ifeq ($(DEBUG),1)
827	@SOURCE_TOOLS/tabBrake.pl
828	endif
829
830	force_tab_check:
831	@touch -t 198001010000 SOURCE_TOOLS/stamp.tabBrake
832	@$(MAKE) check_tabs
833
834
835	# ---------------------
836
837	check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION
838	@echo Your setup seems to be ok.
839
840	checks: check_setup check_tabs
841	@rm -f SOURCE_TOOLS/postcompile.sav
842
843
844	# end test section ------------------------------
845
846	# ---------------------------------------
847	# List of standard top level directories
848	#
849	# sub-makefiles have to define the targets
850	# - 'depends' and
851	# - 'clean'
852	#
853	# when adding new libs here, also add a dependency vs 'links' or 'links_non_perl' in .@DD_links_non_perl
854
855	ARCHS = \
856	$(ARCHS_PT_SERVER) \
857	AISC/AISC.a \
858	AISC_MKPTPS/AISC_MKPTPS.a \
859	ARBDB/libARBDB.a \
860	CORE/libCORE.a \
861	ARB_GDE/ARB_GDE.a \
862	AWT/libAWT.a \
863	AWTC/AWTC.a \
864	AWTI/AWTI.a \
865	CONSENSUS_TREE/CONSENSUS_TREE.a \
866	CONVERTALN/CONVERTALN.a \
867	DBSERVER/DBSERVER.a \
868	DIST/DIST.a \
869	EDIT4/EDIT4.a \
870	EISPACK/EISPACK.a \
871	GDE/GDE.a \
872	GENOM/GENOM.a \
873	GENOM_IMPORT/GENOM_IMPORT.a \
874	GL/GL.a \
875	ISLAND_HOPPING/ISLAND_HOPPING.a \
876	MERGE/MERGE.a \
877	MULTI_PROBE/MULTI_PROBE.a \
878	NALIGNER/NALIGNER.a \
879	NAMES/NAMES.a \
880	NAMES_COM/server.a \
881	NTREE/NTREE.a \
882	PARSIMONY/PARSIMONY.a \
883	PERLTOOLS/PERLTOOLS.a \
884	PHYLO/PHYLO.a \
885	PRIMER_DESIGN/PRIMER_DESIGN.a \
886	PROBE_COM/server.a \
887	PROBE_DESIGN/PROBE_DESIGN.a \
888	PROBE_SET/PROBE_SET.a \
889	READSEQ/READSEQ.a \
890	RNA3D/RNA3D.a \
891	RNACMA/RNACMA.a \
892	SECEDIT/SECEDIT.a \
893	SEQ_QUALITY/SEQ_QUALITY.a \
894	SERVERCNTRL/SERVERCNTRL.a \
895	SL/SL.a \
896	STAT/STAT.a \
897	TOOLS/TOOLS.a \
898	TREEGEN/TREEGEN.a \
899	UNIT_TESTER/UNIT_TESTER.a \
900	WETC/WETC.a \
901	WINDOW/libWINDOW.a \
902	XML/XML.a \
903
904	# -----------------------
905	# library packets
906
907	ARCHS_CLIENT_PROBE = PROBE_COM/client.a
908	ARCHS_CLIENT_NAMES = NAMES_COM/client.a
909
910	ARCHS_SERVER_PROBE = PROBE_COM/server.a $(ARCHS_CLIENT_PROBE)
911	ARCHS_SERVER_NAMES = NAMES_COM/server.a $(ARCHS_CLIENT_NAMES)
912
913	ARCHS_MAKEBIN = AISC_MKPTPS/AISC_MKPTPS.a AISC/AISC.a
914
915	# communication libs need aisc and aisc_mkpts:
916
917	AISC/AISC.dummy: proto_tools
918
919	comtools: AISC/AISC.dummy
920
921	ARCHS_SEQUENCE = \
922	SL/SEQUENCE/SEQUENCE.a \
923	SL/ALIVIEW/ALIVIEW.a \
924	SL/PRONUC/PRONUC.a \
925
926	ARCHS_TREE = \
927	$(ARCHS_SEQUENCE) \
928	SL/FILTER/FILTER.a \
929	SL/ARB_TREE/ARB_TREE.a \
930	SL/ROOTED_TREE/ROOTED_TREE.a \
931
932	# parsimony tree (used by NTREE, PARSIMONY, STAT(->EDIT4), DIST(obsolete!))
933	ARCHS_AP_TREE = \
934	$(ARCHS_TREE) \
935	SL/AP_TREE/AP_TREE.a \
936
937	# --------------------------------------------------------------------------------
938	# dependencies for linking shared libs
939
940	link_core: core
941	link_db: db link_core
942	link_aw: aw link_db
943	link_awt: awt link_aw
944
945	#***************************************************************************************
946	# Individual_Programs_Section
947	#***************************************************************************************
948
949	arbmainwrapper:
950	$(MAKE) -C SOURCE_TOOLS -r mainwrapper
951
952
953	#********************************* arb_ntree ************************************
954	NTREE = bin/arb_ntree
955	ARCHS_NTREE = \
956	NTREE/NTREE.a \
957	$(ARCHS_AP_TREE) \
958	ARB_GDE/ARB_GDE.a \
959	AWTC/AWTC.a \
960	AWTI/AWTI.a \
961	CONSENSUS_TREE/CONSENSUS_TREE.a \
962	GENOM/GENOM.a \
963	GENOM_IMPORT/GENOM_IMPORT.a \
964	MERGE/MERGE.a \
965	MULTI_PROBE/MULTI_PROBE.a \
966	PRIMER_DESIGN/PRIMER_DESIGN.a \
967	PROBE_DESIGN/PROBE_DESIGN.a \
968	SEQ_QUALITY/SEQ_QUALITY.a \
969	SERVERCNTRL/SERVERCNTRL.a \
970	SL/ALILINK/ALILINK.a \
971	SL/AW_NAME/AW_NAME.a \
972	SL/DB_UI/DB_UI.a \
973	SL/DB_SCANNER/DB_SCANNER.a \
974	SL/DB_QUERY/DB_QUERY.a \
975	SL/SEQIO/SEQIO.a \
976	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
977	SL/HELIX/HELIX.a \
978	SL/REGEXPR/REGEXPR.a \
979	SL/REFENTRIES/REFENTRIES.a \
980	SL/NDS/NDS.a \
981	SL/ITEMS/ITEMS.a \
982	SL/INSDEL/INSDEL.a \
983	SL/LOCATION/LOCATION.a \
984	SL/MACROS/MACROS.a \
985	SL/TRANSLATE/TRANSLATE.a \
986	SL/TREEDISP/TREEDISP.a \
987	SL/TREE_ADMIN/TREE_ADMIN.a \
988	SL/TREE_READ/TREE_READ.a \
989	SL/TREE_WRITE/TREE_WRITE.a \
990	STAT/STAT.a \
991	XML/XML.a \
992
993	$(NTREE): $(ARCHS_NTREE:.a=.dummy) link_awt
994	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NTREE) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
995	echo "$(SEP) Link $@"; \
996	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS)" ; \
997	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS) && \
998	echo "$(SEP) Link $@ [done]"; \
999	)
1000
1001	#********************************* arb_edit4 ************************************
1002	EDIT4 = bin/arb_edit4
1003
1004	ARCHS_EDIT4 := \
1005	EDIT4/EDIT4.a \
1006	$(ARCHS_AP_TREE) \
1007	ARB_GDE/ARB_GDE.a \
1008	AWTC/AWTC.a \
1009	ISLAND_HOPPING/ISLAND_HOPPING.a \
1010	SECEDIT/SECEDIT.a \
1011	SERVERCNTRL/SERVERCNTRL.a \
1012	SL/AW_HELIX/AW_HELIX.a \
1013	SL/AW_NAME/AW_NAME.a \
1014	SL/FAST_ALIGNER/FAST_ALIGNER.a \
1015	SL/ITEMS/ITEMS.a \
1016	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1017	SL/HELIX/HELIX.a \
1018	SL/TRANSLATE/TRANSLATE.a \
1019	SL/MACROS/MACROS.a \
1020	SL/NDS/NDS.a \
1021	STAT/STAT.a \
1022	XML/XML.a \
1023
1024	ifeq ($(OPENGL),1)
1025	ARCHS_EDIT4 += RNA3D/RNA3D.a
1026	endif
1027
1028	LIBS_EDIT4 := $(GL_LIBS)
1029
1030	$(EDIT4): $(ARCHS_EDIT4:.a=.dummy) link_awt
1031	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_EDIT4) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1032	echo "$(SEP) Link $@"; \
1033	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4) $(EXECLIBS)" ; \
1034	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4) $(EXECLIBS) && \
1035	echo "$(SEP) Link $@ [done]"; \
1036	)
1037
1038	#********************************* arb_rnacma ************************************
1039	RNACMA = bin/arb_rnacma
1040	ARCHS_RNACMA = \
1041	RNACMA/RNACMA.a \
1042
1043	$(RNACMA) : $(ARCHS_RNACMA:.a=.dummy) link_db
1044	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_RNACMA) \|\| ( \
1045	echo "$(SEP) Link $@"; \
1046	echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_RNACMA) $(LIBS) $(EXECLIBS)"; \
1047	$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_RNACMA) $(LIBS) $(EXECLIBS) && \
1048	echo "$(SEP) Link $@ [done]"; \
1049	)
1050
1051	#********************************* arb_wetc ************************************
1052	WETC = bin/arb_wetc
1053	ARCHS_WETC = \
1054	WETC/WETC.a \
1055	SL/HELIX/HELIX.a \
1056	SL/FILTER/FILTER.a \
1057	XML/XML.a \
1058
1059	$(WETC): $(ARCHS_WETC:.a=.dummy) link_awt
1060	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_WETC) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1061	echo "$(SEP) Link $@"; \
1062	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC) $(GUI_LIBS) $(EXECLIBS)" ; \
1063	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC) $(GUI_LIBS) $(EXECLIBS) && \
1064	echo "$(SEP) Link $@ [done]"; \
1065	)
1066
1067	#********************************* arb_dist ************************************
1068	DIST = bin/arb_dist
1069	ARCHS_DIST = \
1070	$(ARCHS_AP_TREE) \
1071	CONSENSUS_TREE/CONSENSUS_TREE.a \
1072	DIST/DIST.a \
1073	EISPACK/EISPACK.a \
1074	SERVERCNTRL/SERVERCNTRL.a \
1075	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1076	SL/HELIX/HELIX.a \
1077	SL/MATRIX/MATRIX.a \
1078	SL/MACROS/MACROS.a \
1079	SL/NDS/NDS.a \
1080	SL/ITEMS/ITEMS.a \
1081	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.a \
1082	XML/XML.a \
1083
1084	$(DIST): $(ARCHS_DIST:.a=.dummy) link_awt
1085	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_DIST) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1086	echo "$(SEP) Link $@"; \
1087	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS)" ; \
1088	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS) && \
1089	echo "$(SEP) Link $@ [done]"; \
1090	)
1091
1092	#********************************* arb_pars ************************************
1093	PARSIMONY = bin/arb_pars
1094	ARCHS_PARSIMONY = \
1095	$(ARCHS_AP_TREE) \
1096	PARSIMONY/PARSIMONY.a \
1097	SERVERCNTRL/SERVERCNTRL.a \
1098	SL/AW_NAME/AW_NAME.a \
1099	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1100	SL/HELIX/HELIX.a \
1101	SL/MACROS/MACROS.a \
1102	SL/NDS/NDS.a \
1103	SL/ITEMS/ITEMS.a \
1104	SL/TRANSLATE/TRANSLATE.a \
1105	SL/TREEDISP/TREEDISP.a \
1106	XML/XML.a \
1107
1108	$(PARSIMONY): $(ARCHS_PARSIMONY:.a=.dummy) link_awt
1109	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PARSIMONY) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1110	echo "$(SEP) Link $@"; \
1111	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(EXECLIBS)" ; \
1112	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(EXECLIBS) && \
1113	echo "$(SEP) Link $@ [done]"; \
1114	)
1115
1116	#********************************* arb_convert_aln ************************************
1117	CONVERT_ALN = bin/arb_convert_aln
1118	ARCHS_CONVERT_ALN = \
1119	CONVERTALN/CONVERTALN.a \
1120
1121	$(CONVERT_ALN) : $(ARCHS_CONVERT_ALN:.a=.dummy) link_db
1122	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_CONVERT_ALN) $(use_ARB_main) \|\| ( \
1123	echo "$(SEP) Link $@"; \
1124	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN) $(LIBS) $(EXECLIBS)"; \
1125	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN) $(LIBS) $(EXECLIBS) && \
1126	echo "$(SEP) Link $@ [done]"; \
1127	)
1128
1129	#********************************* arb_treegen ************************************
1130
1131	TREEGEN = bin/arb_treegen
1132	ARCHS_TREEGEN = \
1133	TREEGEN/TREEGEN.a \
1134
1135	$(TREEGEN) : $(ARCHS_TREEGEN:.a=.dummy)
1136	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_TREEGEN) $(use_ARB_main_C) \|\| ( \
1137	echo "$(SEP) Link $@"; \
1138	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN) $(EXECLIBS)" ; \
1139	$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN) $(EXECLIBS) && \
1140	echo "$(SEP) Link $@ [done]"; \
1141	)
1142
1143	#********************************* arb_naligner ************************************
1144	NALIGNER = bin/arb_naligner
1145	ARCHS_NALIGNER = \
1146	NALIGNER/NALIGNER.a \
1147	SERVERCNTRL/SERVERCNTRL.a \
1148	SL/HELIX/HELIX.a \
1149
1150	$(NALIGNER): $(ARCHS_NALIGNER:.a=.dummy) link_db
1151	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NALIGNER) $(use_ARB_main) \|\| ( \
1152	echo "$(SEP) Link $@"; \
1153	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(LIBS) $(EXECLIBS)" ; \
1154	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(LIBS) $(EXECLIBS) && \
1155	echo "$(SEP) Link $@ [done]"; \
1156	)
1157
1158	#********************************* arb_phylo ************************************
1159	PHYLO = bin/arb_phylo
1160	ARCHS_PHYLO = \
1161	PHYLO/PHYLO.a \
1162	SL/HELIX/HELIX.a \
1163	SL/FILTER/FILTER.a \
1164	SL/MATRIX/MATRIX.a \
1165	SL/MACROS/MACROS.a \
1166	XML/XML.a \
1167
1168	$(PHYLO): $(ARCHS_PHYLO:.a=.dummy) link_awt
1169	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PHYLO) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1170	echo "$(SEP) Link $@"; \
1171	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO) $(GUI_LIBS) $(EXECLIBS)" ; \
1172	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO) $(GUI_LIBS) $(EXECLIBS) && \
1173	echo "$(SEP) Link $@ [done]"; \
1174	)
1175
1176	#***************************************************************************************
1177	# SERVER SECTION
1178	#***************************************************************************************
1179
1180	#********************************* arb_db_server ************************************
1181	DBSERVER = bin/arb_db_server
1182	ARCHS_DBSERVER = \
1183	DBSERVER/DBSERVER.a \
1184	SERVERCNTRL/SERVERCNTRL.a \
1185
1186	$(DBSERVER): $(ARCHS_DBSERVER:.a=.dummy) link_db
1187	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_DBSERVER) $(ARBDB_LIB) $(use_ARB_main) \|\| ( \
1188	echo "$(SEP) Link $@"; \
1189	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS) $(EXECLIBS)" ; \
1190	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS) $(EXECLIBS) && \
1191	echo "$(SEP) Link $@ [done]"; \
1192	)
1193
1194	#********************************* arb_pt_server ************************************
1195	PROBE = bin/arb_pt_server
1196	ARCHS_PROBE_COMMON = \
1197	SERVERCNTRL/SERVERCNTRL.a \
1198	SL/HELIX/HELIX.a \
1199	SL/PTCLEAN/PTCLEAN.a \
1200
1201	ARCHS_PROBE_LINK = \
1202	$(ARCHS_PROBE_COMMON) \
1203	$(ARCHS_PT_SERVER_LINK) \
1204
1205	ARCHS_PROBE_DEPEND = \
1206	$(ARCHS_PROBE_COMMON) \
1207	$(ARCHS_PT_SERVER) \
1208
1209	$(PROBE): $(ARCHS_PROBE_DEPEND:.a=.dummy) link_db
1210	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) config.makefile $(use_ARB_main) \|\| ( \
1211	echo "$(SEP) Link $@"; \
1212	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_SERVER_PROBE) $(SYSLIBS) $(EXECLIBS)" ; \
1213	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_SERVER_PROBE) $(SYSLIBS) $(EXECLIBS) && \
1214	echo "$(SEP) Link $@ [done]"; \
1215	)
1216
1217	#********************************* arb_name_server ************************************
1218	NAMES = bin/arb_name_server
1219	ARCHS_NAMES = \
1220	NAMES/NAMES.a \
1221	SERVERCNTRL/SERVERCNTRL.a \
1222
1223	$(NAMES): $(ARCHS_NAMES:.a=.dummy) link_db
1224	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) $(use_ARB_main) \|\| ( \
1225	echo "$(SEP) Link $@"; \
1226	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS) $(EXECLIBS)" ; \
1227	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS) $(EXECLIBS) && \
1228	echo "$(SEP) Link $@ [done]"; \
1229	)
1230
1231	#********************************* SHARED LIBRARIES SECTION ************************************
1232
1233	prepare_libdir: addlibs
1234
1235	addlibs:
1236	(perl $(ARBHOME)/SOURCE_TOOLS/provide_libs.pl \
1237	"arbhome=$(ARBHOME)" \
1238	"opengl=$(OPENGL)" \
1239	"link_static=$(LINK_STATIC)" \
1240	)
1241
1242	#***************************************************************************************
1243	# Recursive calls to sub-makefiles
1244	#***************************************************************************************
1245
1246	%.depends:
1247	@cp -p $(@D)/Makefile $(@D)/Makefile.old # save old Makefile
1248	@$(MAKE) -C $(@D) -r \
1249	"AUTODEPENDS=1" \
1250	"MAIN=nothing" \
1251	"cflags=noCflagsHere_use_MAKEDEPENDFLAGS" \
1252	"cxxflags=noCxxflagsHere_use_MAKEDEPENDFLAGS" \
1253	depends
1254	@grep "^# DO NOT DELETE" $(@D)/Makefile >/dev/null
1255	@cat $(@D)/Makefile \
1256	\| SOURCE_TOOLS/fix_depends.pl "(from main)" \
1257	>$(@D)/Makefile.2
1258	@mv $(@D)/Makefile.old $(@D)/Makefile # restore old Makefile
1259	@$(ARBHOME)/SOURCE_TOOLS/mv_if_diff $(@D)/Makefile.2 $(@D)/Makefile # update Makefile if changed
1260
1261	%.proto:
1262	@$(MAKE) -C $(@D) \
1263	"AUTODEPENDS=0" \
1264	"MAIN=nothing" \
1265	"cflags=noCflags" \
1266	"cxxflags=noCxxflags" \
1267	proto
1268
1269	%.clean:
1270	@$(MAKE) -C $(@D) \
1271	"AUTODEPENDS=0" \
1272	"MAIN=nothing" \
1273	"cflags=noCflags" \
1274	"cxxflags=noCxxflags" \
1275	clean
1276
1277
1278	# stop wrong targets
1279	target_is_missing_lib_prefix:
1280	@echo "Error: Denied to build shared library target with missing 'lib'-prefix"
1281	false
1282
1283	ARBDB/ARBDB.dummy: target_is_missing_lib_prefix
1284	CORE/CORE.dummy: target_is_missing_lib_prefix
1285	AWT/AWT.dummy: target_is_missing_lib_prefix
1286	WINDOW/WINDOW.dummy: target_is_missing_lib_prefix
1287
1288	# rule to generate main target (normally a library):
1289	# @@@ check effect of setting LANG=C below
1290	%.dummy:
1291	@( export ID=$$$$; LANG=C; \
1292	(( \
1293	echo "$(SEP) Make $(@D)"; \
1294	$(MAKE) -C $(@D) -r \
1295	"AUTODEPENDS=1" \
1296	"MAIN=$(@F:.dummy=.a)" \
1297	"cflags=$(cflags) -DIN_ARB_$(subst /,_,$(@D))" \
1298	&& \
1299	echo "$(SEP) Make $(@D) [done]"; \
1300	) >$(@D).$$ID.log 2>&1 && (cat $(@D).$$ID.log;rm $(@D).$$ID.log)) \|\| (cat $(@D).$$ID.log;rm $(@D).$$ID.log;false))
1301
1302	# Additional dependencies for subtargets:
1303
1304	PROBE_COM/PROBE_COM.dummy : comtools
1305	NAMES_COM/NAMES_COM.dummy : comtools
1306
1307	com: PROBE_COM/PROBE_COM.dummy NAMES_COM/NAMES_COM.dummy
1308
1309	PROBE_COM/server.dummy:
1310	@echo Unwanted request to make target $<
1311	false
1312
1313	PROBE_COM/client.dummy:
1314	@echo Unwanted request to make target $<
1315	false
1316
1317	NAMES_COM/server.dummy:
1318	@echo Unwanted request to make target $<
1319	false
1320
1321	NAMES_COM/client.dummy:
1322	@echo Unwanted request to make target $<
1323	false
1324
1325
1326	ARBDB/libARBDB.dummy: links
1327	CORE/libCORE.dummy: links
1328
1329	PERLTOOLS/PERLTOOLS.dummy: core db
1330
1331	# all subdirs perl not depends on go here (ADD_links_non_perl)
1332	AWT/libAWT.dummy: links_non_perl
1333	AWTI/AWTI.dummy: links_non_perl
1334	CONSENSUS_TREE/CONSENSUS_TREE.dummy: links_non_perl
1335	CONVERTALN/CONVERTALN.dummy: links_non_perl
1336	DBSERVER/DBSERVER.dummy: links_non_perl
1337	DIST/DIST.dummy: links_non_perl
1338	EDIT4/EDIT4.dummy: links_non_perl genheaders com
1339	EISPACK/EISPACK.dummy: links_non_perl
1340	GDE/GDE.dummy: links_non_perl
1341	GENOM/GENOM.dummy: links_non_perl
1342	GENOM_IMPORT/GENOM_IMPORT.dummy: links_non_perl
1343	ISLAND_HOPPING/ISLAND_HOPPING.dummy: links_non_perl
1344	MERGE/MERGE.dummy: links_non_perl
1345	NTREE/NTREE.dummy: links_non_perl genheaders
1346	PARSIMONY/PARSIMONY.dummy: links_non_perl
1347	PHYLO/PHYLO.dummy: links_non_perl
1348	PRIMER_DESIGN/PRIMER_DESIGN.dummy: links_non_perl
1349	PROBE_SET/PROBE_SET.dummy: links_non_perl link_db
1350	READSEQ/READSEQ.dummy: links_non_perl
1351	RNACMA/RNACMA.dummy: links_non_perl header_libs
1352	SECEDIT/SECEDIT.dummy: links_non_perl
1353	SEQ_QUALITY/SEQ_QUALITY.dummy: links_non_perl
1354	SERVERCNTRL/SERVERCNTRL.dummy: links_non_perl com
1355	SL/ALILINK/ALILINK.dummy: links_non_perl
1356	SL/ALIVIEW/ALIVIEW.dummy: links_non_perl
1357	SL/AP_TREE/AP_TREE.dummy: links_non_perl
1358	SL/ARB_TREE/ARB_TREE.dummy: links_non_perl
1359	SL/AW_HELIX/AW_HELIX.dummy: links_non_perl
1360	SL/DB_QUERY/DB_QUERY.dummy: links_non_perl
1361	SL/DB_SCANNER/DB_SCANNER.dummy: links_non_perl
1362	SL/DB_UI/DB_UI.dummy: links_non_perl
1363	SL/FAST_ALIGNER/FAST_ALIGNER.dummy: links_non_perl
1364	SL/FILTER/FILTER.dummy: links_non_perl
1365	SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy: links_non_perl
1366	SL/HELIX/HELIX.dummy: links_non_perl
1367	SL/INSDEL/INSDEL.dummy: links_non_perl
1368	SL/ITEMS/ITEMS.dummy: links_non_perl
1369	SL/LOCATION/LOCATION.dummy: links_non_perl
1370	SL/MACROS/MACROS.dummy: links_non_perl
1371	SL/MATRIX/MATRIX.dummy: links_non_perl
1372	SL/NDS/NDS.dummy: links_non_perl
1373	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.dummy: links_non_perl
1374	SL/PRONUC/PRONUC.dummy: links_non_perl
1375	SL/PTCLEAN/PTCLEAN.dummy: links_non_perl link_db
1376	SL/REFENTRIES/REFENTRIES.dummy: links_non_perl
1377	SL/REGEXPR/REGEXPR.dummy: links_non_perl
1378	SL/ROOTED_TREE/ROOTED_TREE.dummy: links_non_perl
1379	SL/SEQIO/SEQIO.dummy: links_non_perl
1380	SL/SEQUENCE/SEQUENCE.dummy: links_non_perl
1381	SL/TRANSLATE/TRANSLATE.dummy: links_non_perl
1382	SL/TREE_ADMIN/TREE_ADMIN.dummy: links_non_perl
1383	SL/TREE_READ/TREE_READ.dummy: links_non_perl
1384	SL/TREE_WRITE/TREE_WRITE.dummy: links_non_perl
1385	SL/TREEDISP/TREEDISP.dummy: links_non_perl
1386	STAT/STAT.dummy: links_non_perl
1387	TREEGEN/TREEGEN.dummy: links_non_perl
1388	WETC/WETC.dummy: links_non_perl
1389	WINDOW/libWINDOW.dummy: links_non_perl
1390	XML/XML.dummy: links_non_perl
1391
1392	ifeq ($(OPENGL),1)
1393	GL/glAW/glAW.dummy: links_non_perl
1394	GL/glpng/glpng.dummy: links_non_perl
1395	GL/GL.dummy: GL/glAW/glAW.dummy GL/glpng/glpng.dummy
1396	RNA3D/RNA3D.dummy: links_non_perl gl
1397	endif
1398
1399	UNIT_TESTER/UNIT_TESTER.dummy: link_db \
1400	SERVERCNTRL/SERVERCNTRL.dummy \
1401
1402	TOOLS/TOOLS.dummy : links_non_perl link_db \
1403	SERVERCNTRL/SERVERCNTRL.dummy \
1404	SL/ROOTED_TREE/ROOTED_TREE.dummy \
1405	SL/TREE_WRITE/TREE_WRITE.dummy \
1406	SL/TREE_READ/TREE_READ.dummy \
1407	CONSENSUS_TREE/CONSENSUS_TREE.dummy \
1408	XML/XML.dummy \
1409
1410	AWTC/AWTC.dummy : com
1411
1412	NAMES/NAMES.dummy : com
1413	SL/AW_NAME/AW_NAME.dummy : com
1414
1415	PROBE/PROBE.dummy : com
1416	ptpan/PROBE.dummy : com
1417	MULTI_PROBE/MULTI_PROBE.dummy : com
1418	PROBE_DESIGN/PROBE_DESIGN.dummy : com
1419	NALIGNER/NALIGNER.dummy : com
1420
1421	ARB_GDE/ARB_GDE.dummy : proto_tools
1422
1423	compile_compatibility: SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.dummy
1424
1425	#***************************************************************************************
1426	# Short aliases to make targets
1427	#***************************************************************************************
1428
1429	show:
1430	@echo $(SEP)
1431	@echo 'Aliases for often needed targets:'
1432	@echo ''
1433	@echo ' executables:'
1434	@echo ''
1435	@echo ' nt arb_ntree'
1436	@echo ' e4 arb_edit4 (includes secedit)'
1437	@echo ' di arb_dist'
1438	@echo ' ph arb_phylo'
1439	@echo ' pa arb_parsimony'
1440	@echo ' tg arb_treegen'
1441	@echo ' ds arb_dbserver'
1442	@echo ' pt arb_pt_server'
1443	@echo ' na arb_name_server'
1444	@echo ''
1445	@echo ' libraries:'
1446	@echo ''
1447	@echo ' com communication libraries'
1448	@echo ' db ARB database'
1449	@echo ' aw GUI lib'
1450	@echo ' awt GUI toolkit'
1451	@echo ' awtc general purpose library'
1452	@echo ' awti import/export library'
1453	@echo ' mp multi probe library'
1454	@echo ' ge genome library'
1455	@echo ' pd probe design lib'
1456	@echo ' prd primer design lib'
1457	@echo ''
1458	@echo ' other targets:'
1459	@echo ''
1460	@echo ' help recompile help files'
1461	@echo ' tools make small tools used by arb'
1462	@echo ''
1463	@echo ' foreign targets:'
1464	@echo ''
1465	@echo ' gde GDE'
1466	@echo ' agde ARB_GDE'
1467	@echo ''
1468	@echo 'for other targets inspect $(ARBHOME)/Makefile'
1469	@echo ''
1470	@echo $(SEP)
1471
1472	source_doc:
1473	@echo "Remove some links (doxygen crashes otherwise):"
1474	find . \( -name "AISC" -o -name "C" -o -name "GDEHELP" \) -type l -exec rm {} \;
1475	doxygen 2>&1 1>/dev/null
1476	$(MAKE) forcelinks
1477
1478	dep_graph:
1479	@echo "Building some dependency graphs"
1480	SOURCE_TOOLS/dependency_graphs.pl
1481
1482	help: HELP_SOURCE/HELP_SOURCE.dummy
1483
1484	HELP_SOURCE/HELP_SOURCE.dummy: link_core xml menus
1485
1486	db: ARBDB/libARBDB.dummy
1487	core: CORE/libCORE.dummy
1488	aw: WINDOW/libWINDOW.dummy
1489	awt: AWT/libAWT.dummy
1490	awtc: AWTC/AWTC.dummy
1491	awti: AWTI/AWTI.dummy
1492
1493	mp: MULTI_PROBE/MULTI_PROBE.dummy
1494	mg: MERGE/MERGE.dummy
1495	ge: GENOM/GENOM.dummy
1496	prd: PRIMER_DESIGN/PRIMER_DESIGN.dummy
1497
1498	nt: menus $(NTREE)
1499
1500	nal: $(NALIGNER)
1501
1502	di: $(DIST)
1503	ph: $(PHYLO)
1504	pa: $(PARSIMONY)
1505	tg: $(TREEGEN)
1506
1507	ifeq ($(OPENGL),1)
1508	3d: RNA3D/RNA3D.dummy
1509	gl: GL/GL.dummy
1510	else
1511	noopengl:
1512	@echo "invalid target for OPENGL=0"
1513	3d: noopengl
1514	gl: noopengl
1515	endif
1516
1517	SL/SL.dummy: com
1518
1519	ds: $(DBSERVER)
1520	pt: $(PROBE)
1521	pst: PROBE_SET/PROBE_SET.dummy
1522	pd: PROBE_DESIGN/PROBE_DESIGN.dummy
1523	na: $(NAMES)
1524	sq: SEQ_QUALITY/SEQ_QUALITY.dummy
1525	cma: $(RNACMA)
1526
1527	sec: SECEDIT/SECEDIT.dummy
1528
1529	e4: $(EDIT4) readseq menus
1530
1531	gi: GENOM_IMPORT/GENOM_IMPORT.dummy
1532	wetc: $(WETC)
1533
1534	xml: XML/XML.dummy
1535	xmlin: XML_IMPORT/XML_IMPORT.dummy# broken
1536	stat: STAT/STAT.dummy $(NTREE) $(EDIT4)
1537	fa: SL/FAST_ALIGNER/FAST_ALIGNER.dummy
1538
1539	#********************************************************************************
1540
1541	up_by_remake: depends proto
1542
1543	up: up_by_remake tags valgrind_update
1544
1545	#********************************************************************************
1546
1547	touch:
1548	SOURCE_TOOLS/touch_modified.pl
1549
1550	modified: touch
1551	$(MAKE) all
1552
1553	#********************************************************************************
1554
1555	libdepends:
1556	$(MAKE) -C "SOURCE_TOOLS" \
1557	"RNA3D_LIB=$(RNA3D_LIB_4_DEPENDS)" \
1558	libdepends
1559
1560	#********************************************************************************
1561
1562	# create generated headers:
1563	genheaders: TEMPLATES/TEMPLATES.dummy
1564
1565	clrdotdepends:
1566	-rm PROBE_COM/.depends
1567	-rm NAMES_COM/.depends
1568	-rm PERL2ARB/.depends
1569
1570	comdepends: comtools clrdotdepends
1571	@echo "$(SEP) Partially build com interface"
1572	$(MAKE) PROBE_COM/PROBE_COM.depends NAMES_COM/NAMES_COM.depends
1573	$(MAKE) PROBE_COM/server.depends NAMES_COM/server.depends
1574
1575	depends: genheaders comdepends
1576	@echo "$(SEP) Updating other dependencies"
1577	$(MAKE) $(subst NAMES_COM/server.depends,,$(subst PROBE_COM/server.depends,,$(ARCHS:.a=.depends))) \
1578	HELP_SOURCE/HELP_SOURCE.depends \
1579	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.depends \
1580
1581	$(MAKE) libdepends
1582
1583	depend: depends
1584
1585	# ------------------------------------------------------------
1586	# dependency generation tests for AISC code
1587	#(all should work w/o creating wrong dependencies;
1588	# neither in XXX_COM/Makefile nor in code using AISC interface)
1589	dependstest1: silent_clean
1590	$(MAKE) depends
1591	dependstest2: silent_clean
1592	$(MAKE) com
1593	dependstest3: silent_clean
1594	$(MAKE) aw
1595	dependstest4: silent_clean
1596	$(MAKE) pt
1597	dependstest5: silent_clean
1598	$(MAKE) na
1599	dependstest6: silent_clean
1600	$(MAKE) nt
1601	dependstest7: silent_clean
1602	$(MAKE) all
1603	# ------------------------------------------------------------
1604
1605	AISC_MKPTPS/AISC_MKPTPS.dummy: links
1606
1607	proto_tools: AISC_MKPTPS/AISC_MKPTPS.dummy
1608
1609	proto: proto_tools
1610	@echo $(SEP) Updating prototypes
1611	$(MAKE) \
1612	ARBDB/ARBDB.proto \
1613	AISC_COM/AISC_COM.proto \
1614	ARB_GDE/ARB_GDE.proto \
1615	CORE/CORE.proto \
1616	CONVERTALN/CONVERTALN.proto \
1617	NTREE/NTREE.proto \
1618	MERGE/MERGE.proto \
1619	$(ARCHS_PT_SERVER:.a=.proto) \
1620	SERVERCNTRL/SERVERCNTRL.proto \
1621	SL/SL.proto \
1622
1623	#********************************************************************************
1624
1625	valgrind_update: links
1626	@echo $(SEP) Updating for valgrind
1627	$(MAKE) -C SOURCE_TOOLS valgrind_update
1628
1629	#********************************************************************************
1630
1631	TAGFILE=TAGS
1632	TAGFILE_TMP=TAGS.tmp
1633
1634	TAG_SOURCE_HEADERS=TAGS.headers
1635	TAG_SOURCE_CODE=TAGS.codefiles
1636	TAG_SOURCE_LISTS=$(TAG_SOURCE_HEADERS) $(TAG_SOURCE_CODE)
1637
1638	ETAGS=ctags -e -f $(TAGFILE_TMP) --sort=no --if0=no --extra=q
1639	ETAGS_TYPES=--C-kinds=cgnsut --C++-kinds=cgnsut
1640	ETAGS_FUN =--C-kinds=fm --C++-kinds=fm
1641	ETAGS_REST =--C-kinds=dev --C++-kinds=dev
1642
1643	FILTER_TAGS_SOURCES= \
1644	$(SED) -e 's/^.\///g' \| \
1645	grep -P -v -i '^HEADERLIBS\|^GDE/\|/GEN[CH]/'
1646
1647	$(TAG_SOURCE_HEADERS): links
1648	find . \( -name '.hxx' -o -name ".h" \) -type f \| $(FILTER_TAGS_SOURCES) > $@
1649
1650	$(TAG_SOURCE_CODE): links
1651	find . \( -name '.cxx' -o -name ".c" \) -type f \| $(FILTER_TAGS_SOURCES) > $@
1652
1653	tags: $(TAG_SOURCE_LISTS)
1654	$(ETAGS) $(ETAGS_TYPES) -L $(TAG_SOURCE_HEADERS)
1655	$(ETAGS) -a $(ETAGS_FUN) -L $(TAG_SOURCE_HEADERS)
1656	$(ETAGS) -a $(ETAGS_REST) -L $(TAG_SOURCE_HEADERS)
1657	$(ETAGS) -a $(ETAGS_TYPES) -L $(TAG_SOURCE_CODE)
1658	$(ETAGS) -a $(ETAGS_FUN) -L $(TAG_SOURCE_CODE)
1659	$(ETAGS) -a $(ETAGS_REST) -L $(TAG_SOURCE_CODE)
1660	mv_if_diff $(TAGFILE_TMP) $(TAGFILE)
1661	rm $(TAG_SOURCE_LISTS)
1662
1663	#********************************************************************************
1664
1665	LINKSTAMP=SOURCE_TOOLS/stamp.generate_all_links
1666
1667	links: checks $(LINKSTAMP) arbmainwrapper
1668	links_no_checks: $(LINKSTAMP) arbmainwrapper
1669
1670	forcelinks:
1671	-rm $(LINKSTAMP)
1672	$(MAKE) links
1673
1674	$(LINKSTAMP): SOURCE_TOOLS/generate_all_links.sh
1675	+SOURCE_TOOLS/generate_all_links.sh
1676	touch $(LINKSTAMP)
1677
1678	clean_links:
1679	# avoid to delete linked pts, nas or arb_tcp.dat:
1680	find . -path './lib' -prune -o -type l -exec rm {} \;
1681	# removed obsolete file - refuses to disappear due to 'prune' above
1682	@rm -f lib/help/GDEHELP
1683	@rm -f $(LINKSTAMP) lib/inputMasks/format.readme
1684
1685	redo_links: clean_links
1686	$(MAKE) links_no_checks
1687
1688	#********************************************************************************
1689
1690	header_libs:
1691	$(MAKE) -C HEADERLIBS all
1692
1693	#********************************************************************************
1694
1695	gde: GDE/GDE.dummy
1696	GDE: gde
1697	agde: ARB_GDE/ARB_GDE.dummy
1698
1699	tools: TOOLS/TOOLS.dummy
1700
1701	convert: $(CONVERT_ALN)
1702	readseq: READSEQ/READSEQ.dummy
1703
1704	#***************************************************************************************
1705	# Some user commands
1706	#***************************************************************************************
1707
1708	menus: binlink links
1709	@(( \
1710	echo "$(SEP) Make GDEHELP"; \
1711	$(MAKE) -C GDEHELP -r all && \
1712	echo "$(SEP) Make GDEHELP [done]"; \
1713	) > GDEHELP.log 2>&1 && (cat GDEHELP.log;rm GDEHELP.log)) \|\| (cat GDEHELP.log;rm GDEHELP.log;false)
1714
1715	ifeq ($(DEBUG),1)
1716	BIN_TARGET=develall
1717	else
1718	BIN_TARGET=all
1719	endif
1720
1721
1722	binlink:
1723	$(MAKE) -C bin $(BIN_TARGET)
1724
1725	preplib:
1726	(cd lib;$(MAKE) all)
1727
1728	# --------------------------------------------------------------------------------
1729	# This section is quite tricky:
1730	#
1731	# make 'perl' is a BIG target, so when it has to be made, it has to be started
1732	# as early as possible to reduce overall compile time. Since 'make' does not
1733	# provide any priotities, i force it to build all 'perl'-prerequisites early, by
1734	# adding artificial dependencies to these prerequisites
1735	#
1736	# That behavior is likely to be system-dependent.
1737	# My goal was only to make it work on my current development system,
1738	# where this saves about 20% of overall build time.
1739
1740	ifeq ($(WITHPERL),1)
1741	links_non_perl: PERLTOOLS/PERLTOOLS.dummy
1742	perltools: links_non_perl
1743	perl: realperl
1744	else
1745	links_non_perl: links
1746	perl:
1747	$(MAKE) "WITHPERL=1" perl
1748	endif
1749
1750	# ---------------------------------------- perl
1751
1752	ifeq ($(ARB_64),$(BUILDHOST_64))
1753	TEST_PERL_SCRIPTS=$(MAKE) -C PERL_SCRIPTS/test test
1754	else
1755	TEST_PERL_SCRIPTS=echo "skipping perl script compilation (when cross-compiling)"
1756	endif
1757
1758	realperl: perltools
1759	(( \
1760	echo "$(SEP) Make PERL2ARB" ; \
1761	$(TIME) $(MAKE) -C PERL2ARB -r -f Makefile.main \
1762	"AUTODEPENDS=1" \
1763	"dflags=$(dflags)" \
1764	"cross_cflags=$(cross_cflags) $(cxxflags) $(dflags)" \
1765	"cross_lflags=$(cross_lflags)" \
1766	"COMPILER_VERSION=$(COMPILER_VERSION)" \
1767	all && \
1768	$(TEST_PERL_SCRIPTS) && \
1769	echo "$(SEP) Make PERL2ARB [done]" ; \
1770	) > PERL2ARB.log 2>&1 && (cat PERL2ARB.log;rm PERL2ARB.log)) \|\| (cat PERL2ARB.log;rm PERL2ARB.log;false)
1771
1772	perl_clean:
1773	@$(MAKE) -C PERL2ARB -r -f Makefile.main \
1774	"AUTODEPENDS=0" \
1775	clean
1776
1777	PERL2ARB/PERL2ARB.clean:
1778	$(MAKE) perl_clean
1779	$(MAKE) -C PERL_SCRIPTS/test clean
1780
1781	# ---------------------------------------- bindings to script languages
1782
1783	bindings: lib/libCORE.so lib/libARBDB.so
1784	$(MAKE) -C BINDINGS all ARBDEPENDS="$(^:%=../%)" DFLAGS="$(dflags)"
1785
1786	bindings_clean:
1787	$(MAKE) -C BINDINGS clean
1788
1789	# ----------------------------------------
1790
1791	CLOC=cloc-1.08.pl
1792	CLOCFLAGS=--no3 --quiet --progress-rate=0
1793	CLOCARB=--exclude-dir=GDE .
1794	CLOCEXT=GDE
1795	CLOCCODE=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.code.def
1796	CLOCREST=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.rest.def
1797	CLOCFILT=tail --lines=+4
1798
1799	cloc:
1800	@echo 'Arb code:'
1801	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCARB) \| $(CLOCFILT)
1802	@echo 'Arb rest:'
1803	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCARB) \| $(CLOCFILT)
1804	@echo 'External code:'
1805	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCEXT) \| $(CLOCFILT)
1806	@echo 'External rest:'
1807	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCEXT) \| $(CLOCFILT)
1808
1809	# ---------------------------------------- check ressources
1810
1811	check_res:
1812	$(ARBHOME)/SOURCE_TOOLS/check_ressources.pl
1813
1814	# ---------------------------------------- cleaning
1815
1816	rmbak:
1817	@echo "Cleanup:"
1818	@find . \( -name '*%' \
1819	-o -name '*.bak' \
1820	-o -name '*~' \) \
1821	-o \( -name 'core' -a \! -type d \) \
1822	-exec rm -v {} \;
1823
1824	bin_reinit:
1825	$(MAKE) bin/bin.clean
1826	$(MAKE) -C "bin" all
1827
1828	clean_directories:
1829	-rm -rf \
1830	$(ARBHOME)/PROBE_SET/bin \
1831	$(ARBHOME)/INCLUDE \
1832
1833	libclean:
1834	-find $(ARBHOME) -type f \( -name '*.a' ! -type l \) -exec rm -f {} \;
1835
1836	objclean:
1837	-find $(ARBHOME) -type f \( -name '*.o' ! -type l \) -exec rm -f {} \;
1838
1839	# bin.clean and HELP_SOURCE.clean interfere
1840	clean3:
1841	$(MAKE) bin/bin.clean
1842	$(MAKE) HELP_SOURCE/HELP_SOURCE.clean
1843
1844	clean2: $(ARCHS:.a=.clean) \
1845	clean3 \
1846	rmbak \
1847	libclean \
1848	objclean \
1849	lib/lib.clean \
1850	GDEHELP/GDEHELP.clean \
1851	HEADERLIBS/HEADERLIBS.clean \
1852	SOURCE_TOOLS/SOURCE_TOOLS.clean \
1853	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.clean \
1854	UNIT_TESTER/UNIT_TESTER.clean \
1855	TEMPLATES/TEMPLATES.clean \
1856	perl_clean \
1857	clean_directories \
1858
1859	rm -f .last_gcc .last_compiler config.makefile.bak
1860
1861	# links are needed for cleanup
1862	clean: redo_links motif_xpm_hack_clean
1863	$(MAKE) clean2
1864	$(MAKE) clean_cov_all clean_links
1865
1866	silent_clean:
1867	$(MAKE) clean >/dev/null
1868
1869	# 'relocated' is about 50% faster than 'rebuild'
1870	reloc_clean: links
1871	@echo "---------------------------------------- Relocation cleanup"
1872	$(MAKE) \
1873	perl_clean \
1874	GDEHELP/GDEHELP.clean \
1875	HELP_SOURCE/genhelp/genhelp.clean \
1876	bin/bin.clean \
1877	libclean \
1878	objclean
1879
1880	relocated: links
1881	$(MAKE) reloc_clean
1882	@echo "---------------------------------------- and remake"
1883	$(MAKE) build
1884
1885	# -----------------------------------
1886	# some stress tests
1887	# (helpful to reveal race conditions with -j)
1888
1889	rebuild4ever: rebuild
1890	$(MAKE) rebuild4ever
1891
1892	build4ever: build
1893	$(MAKE) build4ever
1894
1895	clean4ever: clean
1896	$(MAKE) clean4ever
1897
1898	test4ever: ut
1899	$(MAKE) test4ever
1900
1901	perl4ever: clean
1902	$(MAKE) links
1903	$(MAKE) perl
1904	$(MAKE) perl4ever
1905
1906	help4ever: clean
1907	$(MAKE) help
1908	$(MAKE) help4ever
1909
1910	# -----------------------------------
1911
1912	rebuild: clean
1913	$(MAKE) all
1914
1915	relink: bin/bin.clean libclean
1916	$(MAKE) build
1917
1918	tarfile: rebuild
1919	$(MAKE) prepare_libdir
1920	util/arb_compress
1921
1922	tarfile_quick: build
1923	$(MAKE) prepare_libdir
1924	util/arb_compress
1925
1926	save: sourcetarfile
1927
1928	patch:
1929	SOURCE_TOOLS/arb_create_patch.sh arbPatch
1930
1931	# test early whether save will work
1932	savetest:
1933	@util/arb_srclst.pl >/dev/null
1934
1935	testsave: savetest
1936
1937	sourcetarfile: rmbak
1938	util/arb_save
1939
1940	save2: rmbak
1941	util/arb_save ignore
1942
1943	save_test: rmbak
1944	@echo "Testing source list.."
1945	@util/arb_srclst.pl > /dev/null
1946
1947	save_test_no_error:
1948	@-$(MAKE) save_test
1949
1950	inc_candi:
1951	touch SOURCE_TOOLS/inc_candi.stamp
1952	$(MAKE) do_version_update
1953
1954	inc_patch:
1955	touch SOURCE_TOOLS/inc_patch.stamp
1956	$(MAKE) do_version_update
1957
1958	inc_minor:
1959	touch SOURCE_TOOLS/inc_minor.stamp
1960	$(MAKE) do_version_update
1961
1962	inc_major:
1963	touch SOURCE_TOOLS/inc_major.stamp
1964	$(MAKE) do_version_update
1965
1966	do_version_update:
1967	@echo Incrementing version information
1968	$(MAKE) testsave
1969	$(MAKE) genheaders # auto upgrades version early
1970
1971	show_version:
1972	$(MAKE) genheaders # updates version info
1973	@echo "$(SEP) ARB version info"
1974	@grep ARB_VERSION TEMPLATES/arb_build.h
1975	@echo "$(SEP)"
1976
1977	release_quick:
1978	-rm arb.tgz arbsrc.tgz
1979	$(MAKE) tarfile_quick
1980	$(MAKE) sourcetarfile
1981
1982	# --------------------------------------------------------------------------------
1983
1984	MAKE_IF_COMMITTED=$(MAKE) -C SOURCE_TOOLS -f Makefile.commitbuild
1985
1986	build_CTARGET:
1987	+$(MAKE_IF_COMMITTED) "CTARGET=$(CTARGET)" build_CTARGET
1988
1989	reset_committed_build:
1990	+$(MAKE_IF_COMMITTED) reset
1991
1992	# --------------------------------------------------------------------------------
1993
1994	arbapplications: nt pa e4 wetc pt na nal di ph ds wetc cma
1995
1996	arb_external: convert tools gde readseq tg pst xmlin
1997
1998	arb_no_perl: arbapplications help arb_external
1999
2000	arb: motif_xpm_hack
2001	$(MAKE) "WITHPERL=1" perl arb_no_perl
2002
2003	motif_xpm_hack:
2004	$(MAKE) -r -C "lib/motifHack" all
2005
2006	motif_xpm_hack_clean:
2007	$(MAKE) -r -C "lib/motifHack" clean
2008
2009	# --------------------------------------------------------------------------------
2010	# special targets for SOURCE_TOOLS/remake_after_change.pl
2011
2012	rac_arb_dist: di
2013	rac_arb_edit4: e4
2014	rac_arb_ntree: nt
2015	rac_arb_pars: pa
2016	rac_arb_phylo: ph
2017	rac_arb_wetc: wetc
2018	rac_arb_naligner: nal
2019	rac_arb_pt_server: pt
2020	rac_arb_db_server: ds
2021	rac_arb_name_server: na
2022	rac_arb_convert_aln: convert
2023	rac_arb_treegen: tg
2024	rac_arb_rnacma: cma
2025	rac_arb_help2xml: help
2026
2027	rac_arb_a2ps: tools
2028	rac_arb_consensus_tree: tools
2029	rac_arb_dnarates: tools
2030	rac_arb_export_rates: tools
2031	rac_arb_export_tree: tools
2032	rac_arb_gene_probe: tools
2033	rac_arb_message: tools
2034	rac_arb_notify: tools
2035	rac_arb_primer: tools
2036	rac_arb_probe: tools
2037	rac_arb_read_tree: tools
2038
2039	# --------------------------------------------------------------------------------
2040	# unit testing
2041	# @@@ work in progress
2042	#
2043	# goal is to automatically test all libraries/executables using TESTED_UNITS_AUTO
2044	#
2045	# currently not all test executables link w/o error
2046	# (see UNITS_WORKING, UNITS_UNTESTABLE_ATM and UNITS_NEED_FIX)
2047
2048	# define RNA3D/RNA3D.test
2049	RNA3D_TEST := $(subst .a,.test,$(RNA3D_LIB))
2050
2051	TESTED_UNITS_AUTO = $(ARCHS:.a=.test)
2052
2053	UNITS_WORKING = \
2054	$(RNA3D_TEST) \
2055	AWTI/AWTI.test \
2056	DIST/DIST.test \
2057	EISPACK/EISPACK.test \
2058	GENOM/GENOM.test \
2059	GL/glAW/libglAW.test \
2060	GL/glpng/libglpng_arb.test \
2061	ISLAND_HOPPING/ISLAND_HOPPING.test \
2062	NALIGNER/NALIGNER.test \
2063	NAMES/NAMES.test \
2064	PHYLO/PHYLO.test \
2065	PRIMER_DESIGN/PRIMER_DESIGN.test \
2066	PROBE_DESIGN/PROBE_DESIGN.test \
2067	SECEDIT/SECEDIT.test \
2068	SEQ_QUALITY/SEQ_QUALITY.test \
2069	SERVERCNTRL/SERVERCNTRL.test \
2070	SL/ALIVIEW/ALIVIEW.test \
2071	SL/AP_TREE/AP_TREE.test \
2072	SL/ARB_TREE/ARB_TREE.test \
2073	SL/AW_HELIX/AW_HELIX.test \
2074	SL/AW_NAME/AW_NAME.test \
2075	SL/DB_SCANNER/DB_SCANNER.test \
2076	SL/GUI_ALIVIEW/GUI_ALIVIEW.test \
2077	SL/HELIX/HELIX.test \
2078	SL/ITEMS/ITEMS.test \
2079	SL/LOCATION/LOCATION.test \
2080	SL/MATRIX/MATRIX.test \
2081	SL/REFENTRIES/REFENTRIES.test \
2082	SL/SEQUENCE/SEQUENCE.test \
2083	SL/TRANSLATE/TRANSLATE.test \
2084	SL/TREE_ADMIN/TREE_ADMIN.test \
2085	SL/TREE_WRITE/TREE_WRITE.test \
2086	STAT/STAT.test \
2087	TREEGEN/TREEGEN.test \
2088	WETC/WETC.test \
2089	XML/XML.test \
2090	SL/ROOTED_TREE/ROOTED_TREE.test \
2091
2092	# untestable units
2093
2094	UNITS_NEED_FIX = \
2095	ptpan/PROBE.test \
2096
2097	UNITS_UNTESTABLE_ATM = \
2098	PROBE_SET/PROBE_SET.test \
2099	XML_IMPORT/XML_IMPORT.test \
2100
2101	# for the moment, put all units containing tests into UNITS_TESTED or UNITS_TESTED_FIRST
2102
2103	UNITS_TESTED_FIRST = \
2104	PARSIMONY/PARSIMONY.test \
2105	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.test \
2106	SL/NDS/NDS.test \
2107	ARB_GDE/ARB_GDE.test \
2108	GENOM_IMPORT/GENOM_IMPORT.test \
2109	SL/MACROS/MACROS.test \
2110	SL/REGEXPR/REGEXPR.test \
2111	SL/FILTER/FILTER.test \
2112	ARBDB/libARBDB.test \
2113	CONSENSUS_TREE/CONSENSUS_TREE.test \
2114	TOOLS/arb_consensus_tree.test \
2115	TOOLS/arb_test.test \
2116	TOOLS/arb_probe.test \
2117	PERLTOOLS/arb_proto_2_xsub.test \
2118	AWTC/AWTC.test \
2119
2120	# plain test-libaries not linked anywhere
2121	TEST_SANDBOXES = \
2122	SL/CB/CB.test \
2123
2124	UNITS_TESTED = \
2125	SL/ALILINK/ALILINK.test \
2126	SL/TREE_READ/TREE_READ.test \
2127	DBSERVER/DBSERVER.test \
2128	AWT/libAWT.test \
2129	CORE/libCORE.test \
2130	SL/INSDEL/INSDEL.test \
2131	SL/TREEDISP/TREEDISP.test \
2132	NTREE/NTREE.test \
2133	AISC_MKPTPS/mkptypes.test \
2134	EDIT4/EDIT4.test \
2135	MERGE/MERGE.test \
2136	MULTI_PROBE/MULTI_PROBE.test \
2137	SERVERCNTRL/SERVERCNTRL.test \
2138	SL/FAST_ALIGNER/FAST_ALIGNER.test \
2139	SL/PRONUC/PRONUC.test \
2140	WINDOW/libWINDOW.test \
2141	HELP_SOURCE/arb_help2xml.test \
2142	CONVERTALN/CONVERTALN.test \
2143	SL/SEQIO/SEQIO.test \
2144	SL/PTCLEAN/PTCLEAN.test \
2145	PROBE/PROBE.test \
2146	SL/DB_QUERY/DB_QUERY.test \
2147
2148	TESTED_UNITS_MANUAL = \
2149	$(TEST_SANDBOXES) \
2150	$(UNITS_TESTED_FIRST) \
2151	$(UNITS_TESTED) \
2152
2153	# $(UNITS_WORKING)
2154
2155	# see UNIT_TESTER/sym2testcode.pl@disableErrorOnUnitsWithoutTests
2156
2157	#TESTED_UNITS = $(TESTED_UNITS_AUTO)
2158	TESTED_UNITS = $(TESTED_UNITS_MANUAL)
2159
2160	# ----------------------------------------
2161
2162	TEST_LOG_DIR = UNIT_TESTER/logs
2163	TEST_RUN_SUITE=$(MAKE) $(NODIR) -C UNIT_TESTER -f Makefile.suite -r
2164	TEST_MAKE_FLAGS=
2165	TEST_POST_CLEAN=
2166	ifeq ($(COVERAGE),1)
2167	TEST_POST_CLEAN=$(MAKE) clean_cov
2168	TEST_MAKE_FLAGS+=-j1
2169	endif
2170
2171
2172	%.test:
2173	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
2174	( \
2175	echo "fake[1]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
2176	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
2177	"UNITDIR=$(@D)" \
2178	"UNITLIBNAME=$(@F:.test=)" \
2179	"COVERAGE=$(COVERAGE)" \
2180	"ARB_PID=$(ARB_PID)_$(@F)" \
2181	runtest; \
2182	echo "fake[1]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"; \
2183	$(TEST_POST_CLEAN) \
2184	) >$(TEST_LOG_DIR)/$(@F).log 2>&1; \
2185	UNIT_TESTER/log_result.pl $(TEST_LOG_DIR)/$(@F).log )
2186
2187
2188	test_base: $(UNIT_TESTER_LIB:.a=.dummy) $(subst .test,.dummy,$(TEST_SANDBOXES))
2189
2190	clean_cov:
2191	find . \( -name ".gcda" -o -name ".gcov" -o -name "*.cov" \) -exec rm {} \;
2192
2193	clean_cov_all: clean_cov
2194	find . \( -name "*.gcno" \) -exec rm {} \;
2195
2196	run_tests: test_base clean_cov
2197	$(MAKE) "ARB_PID=UT_$$$$" run_tests_faked_arbpid
2198
2199	cleanup_faked_arbpids:
2200	@-rm ~/.arb_tmp/tmp/arb_pids_${USER}_${ARB_PID}_*
2201
2202	cleanup_faked_arbpids_and_fail: cleanup_faked_arbpids
2203	@false
2204
2205	run_tests_faked_arbpid:
2206	+@$(TEST_RUN_SUITE) init
2207	@echo "fake[2]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2208	$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(TESTED_UNITS) \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2209	@echo "fake[2]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2210	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2211	@$(MAKE) clean_cov >/dev/null
2212	@$(MAKE) cleanup_faked_arbpids
2213
2214	ut:
2215	ifeq ($(UNIT_TESTS),1)
2216	@echo $(MAKE) run_tests
2217	@$(MAKE) run_tests
2218	else
2219	@echo "Not compiled with unit tests"
2220	endif
2221
2222
2223	aut:
2224	+@$(TEST_RUN_SUITE) unskip
2225	$(MAKE) ut
2226
2227	# --------------------------------------------------------------------------------
2228
2229	TIMELOG=$(ARBHOME)/arb_time.log
2230	TIMEARGS=--append --output=$(TIMELOG) --format=" %E(%S+%U) %P [%C]"
2231	TIMECMD=$(TIME) $(TIMEARGS)
2232
2233	time_one:
2234	ifeq ($(ONE_TIMED_TARGET),)
2235	@echo "Error: You have to pass ONE_TIMED_TARGET to $@"
2236	false
2237	else
2238	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET)"
2239	@$(TIMECMD) $(MAKE) $(ONE_TIMED_TARGET)
2240	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET) [done]"
2241	endif
2242
2243	timed_target:
2244	ifeq ($(TIMED_TARGET),)
2245	@echo "Error: You have to pass TIMED_TARGET to $@"
2246	false
2247	else
2248	@echo "Build time:" > $(TIMELOG)
2249	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2250	@cat $(TIMELOG)
2251	@rm $(TIMELOG)
2252	endif
2253
2254	timed_target_tested:
2255	ifeq ($(TIMED_TARGET),)
2256	@echo "Error: You have to pass TIMED_TARGET to $@"
2257	false
2258	else
2259	@echo "Build time:" > $(TIMELOG)
2260	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2261	$(MAKE) "ONE_TIMED_TARGET=ut" time_one
2262	@cat $(TIMELOG)
2263	@rm $(TIMELOG)
2264	endif
2265
2266	clean_timed_target:
2267	ifeq ($(TIMED_TARGET),)
2268	@echo "Error: You have to pass TIMED_TARGET to $@"
2269	false
2270	else
2271	@echo "Build time:" > $(TIMELOG)
2272	$(MAKE) "ONE_TIMED_TARGET=clean" time_one
2273	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2274	@cat $(TIMELOG)
2275	@rm $(TIMELOG)
2276	endif
2277
2278	# --------------------------------------------------------------------------------
2279
2280	CHECKOUT_MODIFIED=0# set to 1 to temporarily skip test for modifications (do not check in if set to 1)
2281
2282	check_svn_does_not_contain_generated:
2283	ifeq ($(CHECKOUT_MODIFIED),0)
2284	@echo "Testing that build does not modify files in SVN"
2285	@test 0 = `svn status \| wc -l` \|\| ( \
2286	echo "The checkout is not/no longer clean:"; \
2287	svn status; \
2288	echo "- if this fails instantly, your checkout is not clean"; \
2289	echo "- if this fails after other targets, these targets modify checked in data"; \
2290	echo " (a common cause may be that depends are not up to date)"; \
2291	false)
2292	else
2293	grep -Hn 'CHECKOUT_MODIFIED' Makefile
2294	endif
2295
2296	check_svn_ignores_generated:
2297	@test 0 = `svn status \| grep '^\?' \| wc -l` \|\| ( \
2298	echo "There are svn-unignored files:"; \
2299	svn status \| grep '^\?'; \
2300	echo "(all generated files should be svn-ignored)"; \
2301	false)
2302
2303	check_svn_state: check_svn_does_not_contain_generated
2304	$(MAKE) check_svn_ignores_generated
2305	$(MAKE) savetest
2306
2307	things_that_always_should_work: depends proto
2308
2309	post_commit_check:
2310	@echo "---------------------------------------- [Initial]"
2311	$(MAKE) check_svn_state
2312
2313	$(MAKE) clean
2314	@echo "---------------------------------------- [After 'make clean']"
2315	$(MAKE) check_svn_state
2316
2317	$(MAKE) things_that_always_should_work
2318	@echo "---------------------------------------- [After 'make things_that_always_should_work']"
2319	$(MAKE) check_svn_state
2320
2321	$(MAKE) all
2322	@echo "---------------------------------------- [After 'make all']"
2323	$(MAKE) check_svn_state
2324
2325	$(MAKE) things_that_always_should_work
2326	@echo "---------------------------------------- [Final]"
2327	$(MAKE) check_svn_state
2328
2329	# --------------------------------------------------------------------------------
2330
2331	build: arb
2332	$(MAKE) binlink preplib compile_compatibility
2333
2334	all:
2335	@echo "Build time" > $(TIMELOG)
2336	@echo "$(SEP) $(MAKE) build"
2337	@$(TIMECMD) $(MAKE) build
2338	@echo $(SEP)
2339	@echo "made 'all' with success."
2340	@echo "to start arb enter 'arb'"
2341	ifeq ($(UNIT_TESTS),1)
2342	@echo $(MAKE) run_tests
2343	@$(TIMECMD) $(MAKE) run_tests
2344	endif
2345	@echo "$(SEP) $(MAKE) build [done]"
2346	ifeq ($(DEBUG),1)
2347	@$(MAKE) save_test_no_error >/dev/null # just show hints
2348	endif
2349	@cat $(TIMELOG)
2350	@rm $(TIMELOG)
2351

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