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Last change on this file was 12313, checked in by westram, 11 years ago
merge bugfixes from 'trunk' into 'rc' fixes build process when CC and CXX are passed via make-CLI adds: log:trunk@12299,12307:12312
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 65.4 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:=$(ARBHOME)/SH/arb_readlink
88
89	# ---------------------- compiler version detection
90
91	# supported gcc versions:
92	ALLOWED_gcc_VERSIONS=\
93	4.3.1 4.3.2 4.3.3 4.3.4 \
94	4.4.1 4.4.3 4.4.5 4.4.6 4.4.7 \
95	4.5.2 \
96	4.6.1 4.6.2 4.6.3 \
97	4.7.1 4.7.2 4.7.3 \
98	4.8.0 4.8.1 4.8.2 4.8.3 \
99	4.9.0 \
100
101	# supported clang versions:
102	ALLOWED_clang_VERSIONS=\
103	4.2.1 \
104
105	# ----------------------
106
107	COMPILER_INFO:=$(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_47_OR_HIGHER:=
138	USE_GCC_48_OR_HIGHER:=
139
140	ifeq ($(USE_GCC_MAJOR),4)
141	ifeq ($(USE_GCC_MINOR),5)
142	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),23456789)','')
143	USE_GCC_452_OR_HIGHER:=yes
144	endif
145	else
146	ifneq ('$(findstring $(USE_GCC_MINOR),6789)','')
147	USE_GCC_452_OR_HIGHER:=yes
148	ifneq ($(USE_GCC_MINOR),6)
149	USE_GCC_47_OR_HIGHER:=yes
150	ifneq ($(USE_GCC_MINOR),7)
151	USE_GCC_48_OR_HIGHER:=yes
152	endif
153	endif
154	endif
155	endif
156	else
157	USE_GCC_452_OR_HIGHER:=yes
158	USE_GCC_47_OR_HIGHER:=yes
159	USE_GCC_48_OR_HIGHER:=yes
160	endif
161
162	#---------------------- define special directories for non standard builds
163
164	ifeq ($(DARWIN),1)
165	OSX_FW:=/System/Library/Frameworks
166	OSX_FW_OPENGL:=$(OSX_FW)/OpenGL.framework/Versions/A/Libraries
167	OSX_FW_GLUT:=$(OSX_FW)/GLUT.framework/Versions/A/Libraries
168	OSX_FW_IMAGEIO:=$(OSX_FW)/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources
169	endif
170
171	#----------------------
172
173	ifeq ($(DARWIN),1)
174	LINK_STATIC=1# link static
175	else
176	LINK_STATIC=0# link dynamically
177	# LINK_STATIC=1# link static (testing only)
178	endif
179
180	shared_cflags :=# flags for shared lib compilation
181	lflags :=# linker flags
182	clflags :=# linker flags (when passed through gcc)
183	extended_warnings :=# warning flags for C and C++-compiler
184	extended_cpp_warnings :=# warning flags for C++-compiler only
185
186
187	ifeq ($(DEBUG),0)
188	dflags := -DNDEBUG# defines
189	ifeq ($(USE_CLANG),1)
190	cflags := -O3# compiler flags (C and C++)
191	else
192	cflags := -O4# compiler flags (C and C++)
193	lflags += -O2# linker flags
194	clflags += -Wl,-O2# passthrough linker flags
195	endif
196	endif
197
198	ifeq ($(DEBIAN),1)
199	lflags += -rpath=/usr/lib/arb/lib -z relro
200	clflags += -Wl,-rpath=/usr/lib/arb/lib -Wl,-z,relro
201	endif
202
203	ifeq ($(DEBUG),1)
204	dflags := -DDEBUG
205
206	gdb_common := -g -g3 -ggdb -ggdb3
207
208	ifeq ($(STABS),1)
209	cflags := -O0 $(gdb_common) -gstabs+ # using stabs+ (enable this for bigger debug session: debugs inlines, quick var inspect, BUT valgrind stops working :/)
210	else
211	cflags := -O0 $(gdb_common) # (using dwarf - cant debug inlines here, incredible slow on showing variable content)
212	endif
213
214	# cflags := -O0 $(gdb_common) -gdwarf-3 # (specify explicit dwarf format)
215	# cflags := -O0 $(gdb_common) -gstabs # using stabs (same here IIRC)
216	# cflags := -O2 $(gdb_common) # use this for callgrind (force inlining)
217
218	ifeq ($(DARWIN),0)
219	lflags += -g
220	clflags += -Wl,-g
221	endif
222
223	# control how much you get spammed
224	# (please do not change default in SVN, use developer specific setting as below)
225	POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl
226	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --original# dont modify compiler output
227	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --hide-Noncopyable-advices
228	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --show-useless-Weff++
229	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --no-warnings
230	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --only-first-error
231	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --no-warnings --only-first-error
232	ifeq ($(DEVELOPER),ELMAR)
233	POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --only-first-error
234	endif
235
236
237	# Enable extra warnings
238	extended_warnings :=
239	extended_cpp_warnings :=
240
241	# C and C++
242	extended_warnings += -Wwrite-strings -Wunused -Wno-aggregate-return -Wshadow
243
244	# C++ only
245	extended_cpp_warnings += -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute
246	extended_cpp_warnings += -Wctor-dtor-privacy# < gcc 3
247	# extended_cpp_warnings += -Wfloat-equal# gcc 3.0
248
249	# ------- above only warnings available in 3.0
250
251	ifneq ('$(COMPILER_VERSION)','4.7.3') # g++ crashes on GenomeImport.cxx when -Weffc++ is active (bug reported)
252	extended_cpp_warnings += -Weffc++# gcc 3.0.1
253	endif
254	extended_cpp_warnings += -Wmissing-noreturn# gcc 3.0.2
255	# extended_cpp_warnings += -Wold-style-cast# gcc 3.0.4 (warn about 28405 old-style casts)
256	extended_cpp_warnings += -Winit-self# gcc 3.4.0
257	extended_cpp_warnings += -Wstrict-aliasing# gcc 3.4
258	extended_cpp_warnings += -Wextra# gcc 3.4.0
259	ifeq ('$(USE_GCC_452_OR_HIGHER)','yes')
260	extended_cpp_warnings += -Wlogical-op# gcc 4.5.2
261	endif
262
263	ifeq ($(DEBUG_GRAPHICS),1)
264	dflags += -DDEBUG_GRAPHICS
265	endif
266	endif
267
268	#---------------------- turn off clang bogus warnings
269
270	ifeq ($(USE_CLANG),1)
271	# -Wmismatched-tags warns about struct/class mismatch in forward declarations (which is explicitely allowed)
272	# -Wchar-subscripts reports too many bogus warnings for "array['x']" (when 'x' is known to be in range [0..128])
273	# -Wunused-private-field report too many false positives (currently ~ 2 of 3)
274	# -Wstring-plus-int warns about common ARB coding practice
275	# -Wgnu-static-float-init warns about accepted GNU extension
276	extended_cpp_warnings += -Wno-mismatched-tags -Wno-char-subscripts -Wno-unused-private-field -Wno-string-plus-int -Wno-gnu-static-float-init
277	endif
278
279	#---------------------- developer
280
281	ifneq ($(DEVELOPER),ANY) # ANY=default setting (skip all developer specific code)
282	dflags += -DDEVEL_$(DEVELOPER)# activate developer/release specific code
283	endif
284
285	ifndef SHOWTODO
286	ifeq ($(DEVELOPER),RALF)
287	SHOWTODO:=1
288	else
289	SHOWTODO:=0
290	endif
291	endif
292	ifeq ($(SHOWTODO),1)
293	dflags += -DWARN_TODO# activate "TODO" warnings
294	endif
295
296	#---------------------- 32 or 64 bit
297
298	ifndef BUILDHOST_64
299	BUILDHOST_64:=$(ARB_64)# assume build host is same as version (see config.makefile)
300	endif
301
302	cross_cflags:=
303	cross_lflags:=
304	cross_clflags:=
305
306	ifeq ($(ARB_64),1)
307	dflags += -DARB_64 #-fPIC
308	shared_cflags += -fPIC
309
310	ifeq ($(BUILDHOST_64),1)
311	# build 64-bit ARB version on 64-bit host
312	CROSS_LIB:=# empty = autodetect below
313	ifeq ($(DARWIN),1)
314	cross_cflags += -arch x86_64
315	cross_lflags += -arch x86_64
316	cross_clflags += -arch x86_64
317	endif
318	else
319	# build 64-bit ARB version on 32-bit host
320	CROSS_LIB:=/lib64
321	cross_cflags += -m64
322	cross_lflags += -m64 -m elf_x86_64
323	cross_clflags += -m64 -Wl,-m64,-m,elf_x86_64
324	endif
325	else
326	ifeq ($(BUILDHOST_64),1)
327	# build 32-bit ARB version on 64-bit host
328	CROSS_LIB:=# empty = autodetect below
329	cross_cflags += -m32
330	cross_lflags += -m32 -m elf_i386
331	cross_clflags += -m32 -Wl,-m32,-m,elf_i386
332	else
333	# build 32-bit ARB version on 32-bit host
334	CROSS_LIB:=/lib
335	endif
336	endif
337
338	cflags += $(cross_cflags)
339	lflags += $(cross_lflags)
340	clflags += $(cross_clflags)
341
342	ifeq ('$(CROSS_LIB)','')
343	# autodetect libdir
344	ifeq ($(ARB_64),1)
345	CROSS_LIB:=$(shell (test -d /lib64 && echo lib64) \|\| echo lib)
346	else
347	CROSS_LIB:=$(shell (test -d /lib32 && echo lib32) \|\| echo lib)
348	endif
349	endif
350
351	#---------------------- unit tests
352
353	ifndef UNIT_TESTS
354	UNIT_TESTS=0#default is "no tests"
355	endif
356	ifeq ($(UNIT_TESTS),1)
357	dflags += -DUNIT_TESTS
358	UNIT_TESTER_LIB=UNIT_TESTER/UNIT_TESTER.a
359	else
360	UNIT_TESTER_LIB=
361	endif
362
363	#---------------------- use gcov
364
365	ifndef COVERAGE
366	COVERAGE=0#default is "no"
367	endif
368	ifneq ($(COVERAGE),0)
369	GCOVFLAGS=-ftest-coverage -fprofile-arcs
370	cflags += $(GCOVFLAGS)
371	EXECLIBS=-lgcov
372	else
373	GCOVFLAGS=
374	EXECLIBS=
375	endif
376
377	#---------------------- other flags
378
379	dflags += -D$(MACH) # define machine
380
381	ifeq ($(DARWIN),1)
382	shared_cflags += -fno-common
383	else
384	dflags += $(shell getconf LFS_CFLAGS)
385	endif
386
387	cflags += -pipe
388	cflags += -fmessage-length=0# don't wrap compiler output
389	cflags += -fshow-column# show columns
390	cflags += -funit-at-a-time
391	cflags += -fPIC
392	cflags += -fno-common# link all global data into one namespace
393	cflags += -fstrict-aliasing# gcc 3.4
394	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
395	cflags += -fno-diagnostics-show-caret#gcc 4.8 (4.7.?)
396	endif
397	#cflags += -save-temps# uncomment to see preprocessor output
398
399	#---------------------- X11 location
400
401	ifeq ($(DARWIN),1)
402	XHOME:=$(PREFIX)
403	else
404	ifeq ($(DEBIAN),1)
405	XHOME:=$(PREFIX)
406	else
407	XHOME:=/usr/X11R6
408	endif
409	endif
410
411	XINCLUDES:=-I$(XHOME)/include
412	ifeq ($(DARWIN),1)
413	XINCLUDES += -I$(OSX_FW)/GLUT.framework/Headers -I$(OSX_FW)/OpenGL.framework/Headers -I$(OSX_SDK)/usr/include/krb5
414
415	XLIBS := -L$(XHOME)/lib -lXm -lpng -lz -lXt -lX11 -lXext -lXp -lXmu -lXi
416	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGL.dylib:$(OSX_FW_OPENGL)/libGL.dylib
417	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGLU.dylib:$(OSX_FW_OPENGL)/libGLU.dylib
418	else
419	XLIBS:=-L$(XHOME)/$(CROSS_LIB) -lXm -lXpm -lXt -lXext -lX11
420	endif
421
422	#---------------------- open GL
423
424	ifeq ($(OPENGL),1)
425	cflags += -DARB_OPENGL # activate OPENGL code
426	GL := gl # this is the name of the OPENGL base target
427	GL_LIB_SYS := -lGL -lGLU
428	GL_LIB_ARB := -L$(ARBHOME)/GL/glAW -lglAW
429
430	ifeq ($(DARWIN),1)
431	GL_LIB_SYS += -lpthread
432	endif
433
434	GL_PNGLIBS_ARB := -L$(ARBHOME)/GL/glpng -lglpng_arb
435	GL_PNGLIBS_SYS := -lpng
436
437	GLEWLIB := -lGLEW -lGLw
438	ifeq ($(DARWIN),1)
439	GLUTLIB := -glut
440	else
441	GLUTLIB := -lglut
442	endif
443
444	GL_LIBS_SYS := $(GL_LIB_SYS) $(GL_PNGLIBS_SYS) $(GLEWLIB) $(GLUTLIB)
445	GL_LIBS_ARB := $(GL_LIB_ARB) $(GL_PNGLIBS_ARB)
446
447	RNA3D_LIB := RNA3D/RNA3D.a
448
449	else
450
451	GL_LIBS_ARB:=# no opengl -> no libs
452	GL_LIBS_SYS:=# no opengl -> no libs
453	GL:=# don't build ARB openGL libs
454
455	RNA3D_LIB :=
456
457	endif
458
459	RNA3D_LIB_4_DEPENDS := RNA3D/RNA3D.a
460
461	GL_LIBS:=$(GL_LIBS_ARB) $(GL_LIBS_SYS)
462
463	#---------------------- tiff lib:
464
465	TIFFLIBS := -ltiff
466
467	#---------------------- glib:
468
469	ARB_NEEDED_GLIB=glib-2.0
470
471	ARB_GLIB_INCLUDE:=$(strip $(shell pkg-config --cflags $(ARB_NEEDED_GLIB)))
472	ARB_GLIB_LIBS:=$(strip $(shell pkg-config --libs $(ARB_NEEDED_GLIB)))
473
474	#---------------------- basic libs:
475
476	SYSLIBS:=
477
478	ifeq ($(DARWIN),1)
479	SYSLIBS += -lstdc++
480	else
481	SYSLIBS += -lm $(ARB_GLIB_LIBS)
482	endif
483
484	#---------------------- include symbols?
485
486	ifeq ($(TRACESYM),1)
487	ifeq ($(USE_CLANG),0)
488	cflags += -rdynamic
489	lflags += --export-dynamic
490	clflags += -rdynamic -Wl,--export-dynamic
491	endif
492	endif
493
494	#---------------------- system dependent commands
495
496	ifeq ($(DARWIN),1)
497	TIME:=gtime
498	else
499	TIME:=/usr/bin/time
500	endif
501
502	# -------------------------------------------------------------------------
503	# Don't put any machine/version/etc conditionals below!
504	# (instead define variables above)
505	# -------------------------------------------------------------------------
506
507	cflags += -W -Wall $(dflags) $(extended_warnings)
508	cxxflags := $(extended_cpp_warnings)
509
510	# add CFLAGS + CPPFLAGS from environment for DEBIAN build
511	ifeq ($(DEBIAN),1)
512	cflags := $(CFLAGS) $(cflags)
513	cxxflags += $(CPPFLAGS)
514	endif
515
516	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
517	cxxflags += -std=gnu++11# see also TEMPLATES/cxxforward.h@USE_Cxx11
518	else
519	# only use for gcc versions between 4.3 and <4.7 (4.7++ adds -Wc++11-compat above)
520	HAVE_GNUPP0X=`SOURCE_TOOLS/requireVersion.pl 4.3 $(COMPILER_VERSION)`
521	ifeq ($(HAVE_GNUPP0X),1)
522	# ensure compatibility with upcoming C++ standard
523	cxxflags += -std=gnu++0x
524	endif
525	endif
526
527	LINK_STATIC_LIB := ld $(lflags) -r -o# link static lib
528	LINK_EXECUTABLE := $(A_CXX) $(clflags) -o# link executable (c++)
529
530	ifeq ($(LINK_STATIC),1)
531	SHARED_LIB_SUFFIX = a# static lib suffix
532	LINK_SHARED_LIB := $(LINK_STATIC_LIB)
533	else
534	SHARED_LIB_SUFFIX = so# shared lib suffix
535	LINK_SHARED_LIB := $(A_CXX) $(clflags) -shared $(GCOVFLAGS) -o# link shared lib
536	endif
537
538	# delete variables unused below
539	lflags:=
540	clflags:=
541
542	# other used tools
543	MAKEDEPEND_PLAIN = makedepend
544	MAKEDEPEND = $(FORCEMASK);$(MAKEDEPEND_PLAIN)
545
546	#SEP:=--------------------------------------------------------------------------------
547	SEP=[`date +%M:%S.%N`] ------------------------------------------------
548	# to analyse timings run
549	# make -j9 clean; make -j9 all \| grep '^\[' \| sort
550	# make -j9 "TIMED_TARGET=perl" clean_timed_target \| grep '^\[' \| sort
551
552	CORE_LIB=-lCORE
553	ARBDB_LIB=-lARBDB $(CORE_LIB)
554	LIBS = $(ARBDB_LIB) $(SYSLIBS)
555
556	GUI_LIBS_PREFIX:=
557	ifeq ($(DARWIN),1)
558	# this seem to be added at wrong place, since opengl is only needed to link EDIT4
559	GUI_LIBS_PREFIX:=-framework GLUT -framework OpenGL
560	endif
561
562	GUI_LIBS=$(GUI_LIBS_PREFIX) $(LIBS) -lAWT -lWINDOW
563	GUI_LIBS+=$(XLIBS)
564
565	LIBPATH = -L$(ARBHOME)/lib
566
567	DEST_LIB = lib
568	DEST_BIN = bin
569
570	CC_INCLUDES := -I. -I$(ARBHOME)/INCLUDE $(XINCLUDES) $(ARB_GLIB_INCLUDE)
571	CXX_INCLUDES := $(CC_INCLUDES)
572	MAKEDEPENDFLAGS := -- -DARB_OPENGL -DUNIT_TESTS -D__cplusplus -I. -Y$(ARBHOME)/INCLUDE
573
574	# -------------------------------
575	# old PTSERVER or PTPAN?
576
577	ifeq ($(PTPAN),1)
578	# PTPAN only libs
579	ARCHS_PT_SERVER = \
580	ptpan/PROBE.a
581	else
582	ifeq ($(PTPAN),2)
583	# special mode to compile both servers (developers only!)
584	ARCHS_PT_SERVER = \
585	ptpan/PROBE.a \
586	PROBE/PROBE.a
587	ARCHS_PT_SERVER_LINK = PROBE/PROBE.a# default to old ptserver
588	else
589	# PT-server only libs
590	ARCHS_PT_SERVER = \
591	PROBE/PROBE.a
592	endif
593	endif
594
595	ifndef ARCHS_PT_SERVER_LINK
596	ARCHS_PT_SERVER_LINK = $(ARCHS_PT_SERVER)
597	endif
598
599	# ---------------------------------------
600	# wrap main()
601
602	use_ARB_main=$(ARBHOME)/SOURCE_TOOLS/arb_main_cpp.o
603	use_ARB_main_C=$(ARBHOME)/SOURCE_TOOLS/arb_main_c.o
604
605	# -----------------------------------------
606	# export variables to submakefiles
607
608	include SOURCE_TOOLS/export2sub
609
610	# do not define (exported) variables below this point
611
612	# -------------------------
613	# Main arb targets:
614	# -------------------------
615
616	first_target:
617	$(MAKE) checks
618	@echo $(SEP)
619	@echo 'Main targets:'
620	@echo ''
621	@echo ' all - Compile ARB + TOOLs + and copy shared libs + link foreign software'
622	@echo ' (That is most likely the target you want)'
623	@echo ''
624	@echo ' clean - remove generated files ("SUBDIR/SUBDIR.clean" to clean only SUBDIR)'
625	@echo ' rebuild - clean + all'
626	@echo ' relink - remove all binaries and relink them from objects'
627	@echo ''
628	@echo 'Some often used sub targets (make all makes them all):'
629	@echo ''
630	@echo ' arb - Just compile ARB (but none of the integrated tools)'
631	@echo ' menus - create lib/gde/arb.menu from GDEHELP/ARB_GDEmenus.source'
632	@echo ' perl - Compile the PERL XSUBS into lib/ARB.so and create links in lib to perl'
633	@echo ' binlink - Create all links in the bin directory'
634	@echo ''
635	@echo 'Development targets:'
636	@echo ''
637	@echo ' depends - create or update dependencies ("SUBDIR/SUBDIR.depends" to update only SUBDIR)'
638	@echo ' proto - create or update prototypes ("SUBDIR/SUBDIR.proto" to update only SUBDIR)'
639	@echo ' tags - create tags for xemacs'
640	@echo ' show - show available shortcuts (AKA subtargets)'
641	@echo ' up - shortcut for depends+proto+tags'
642	ifeq ($(UNIT_TESTS),1)
643	@echo ' ut - only run tests'
644	endif
645	@echo ' modified - rebuild files modified in svn checkout (does touch)'
646	@echo ' touch - touch files modified in svn checkout'
647	@echo ''
648	@echo 'Internal maintenance:'
649	@echo ''
650	@echo ' relinfo - show help on release targets'
651	@echo ' tarfile - make rebuild and create arb version tarfile ("tarfile_quick" to skip rebuild)'
652	@echo ' save - save all basic ARB sources into arbsrc_DATE ("savetest" to check filelist)'
653	@echo ' patch - save svn diff to patchfile'
654	@echo ' source_doc - create doxygen documentation'
655	@echo ' relocated - rebuild partly (use when you have relocated ARBHOME)'
656	@echo ' check_res - check ressource usage'
657	@echo ' dep_graph - Build dependency graphs'
658	@echo ' clean_cov - Clean coverage results'
659	@echo ''
660	@echo ' post_commit_check - Checks whether'
661	@echo ' * main make targets work,'
662	@echo ' * dependencies and prototypes are up to date,'
663	@echo ' * SVN-controlled files remain unaffected by called targets and'
664	@echo ' * all generated files are ignored.'
665	@echo ' (has to be called in a clean SVN checkout)'
666	@echo $(SEP)
667	@echo ''
668
669	relinfo:
670	@echo ''
671	@echo $(SEP)
672	@echo 'Release targets:'
673	@echo ''
674	@echo ' inc_candi - increase RC candidate-number (only possible in "rc" branch, not needed for RC1)'
675	@echo ' inc_patch - increase release patchlevel (only possible in "stable" branch)'
676	@echo ' inc_minor - increase minor version number (only possible in "trunk")'
677	@echo ' inc_major - increase MAJOR version number (only possible in "trunk")'
678	@echo ''
679	@echo ' show_version - show version tag'
680	@echo ''
681	@echo $(SEP)
682	@echo ''
683
684	# auto-generate config.makefile:
685
686	CONFIG_MAKEFILE_FOUND=$(wildcard config.makefile)
687
688	config.makefile : config.makefile.template
689	@echo --------------------------------------------------------------------------------
690	ifeq ($(strip $(CONFIG_MAKEFILE_FOUND)),)
691	@cp $< $@
692	@echo '$(ARBHOME)/$@:1: has been generated.'
693	@echo 'Please edit $@ to configure your system!'
694	@echo --------------------------------------------------------------------------------
695	@false
696	else
697	@echo '$(ARBHOME)/$<:1: is more recent than'
698	@echo '$(ARBHOME)/$@:1:'
699	@ls -al config.makefile*
700	@echo --------------------------------------------------------------------------------
701	@echo "Updating $@ (if this fails, check manually)"
702	SOURCE_TOOLS/update_config_makefile.pl
703	@echo "Sucessfully updated $@"
704	@echo --------------------------------------------------------------------------------
705	@ls -al config.makefile*
706	@echo --------------------------------------------------------------------------------
707	@echo "Diff to your old config.makefile:"
708	@echo --------------------------------------------------------------------------------
709	-diff $@.bak $@
710	@echo --------------------------------------------------------------------------------
711	endif
712
713	# check if everything is configured correctly
714
715	check_DEVELOPER:
716	ifndef DEVELOPER
717	@echo 'config.makefile:1: DEVELOPER not defined'
718	@false
719	endif
720
721	check_DEBUG:
722	ifndef dflags
723	@echo 'config.makefile:1: DEBUG has to be defined. Valid values are 0 and 1'
724	@false
725	endif
726
727	check_ARB_64:
728	ifndef ARB_64
729	@echo 'config.makefile:1: ARB_64 has to be defined. Valid values are 0 and 1'
730	@false
731	endif
732
733	# ---------------------------------------- check gcc version
734
735	check_same_GCC_VERSION:
736	$(ARBHOME)/SOURCE_TOOLS/check_same_compiler_version.pl $(COMPILER_NAME) $(COMPILER_VERSION_ALLOWED)
737
738	check_GCC_VERSION:
739	@echo 'Compiler version check:'
740	ifeq ('$(COMPILER_VERSION_ALLOWED)', '')
741	@echo " - Your compiler is '$(COMPILER_NAME)' version '$(COMPILER_VERSION)'"
742	@echo ' This version is not in the list of supported $(COMPILER_NAME)-versions:'
743	@$(foreach version,$(ALLOWED_COMPILER_VERSIONS),echo ' * $(version)';)
744	@echo ' - You may either ..'
745	@echo ' - add your version to ALLOWED_$(COMPILER_NAME)_VERSIONS in the Makefile and try it out or'
746	@echo ' - switch to one of the allowed versions (see arb_README_gcc.txt for installing'
747	@echo ' a different version of gcc)'
748	@echo ''
749	@false
750	else
751	@echo " - Supported $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)' detected - fine!"
752	@echo ''
753	$(MAKE) check_same_GCC_VERSION
754
755	endif
756
757	#---------------------- check ARBHOME
758
759	# use arb_INSTALL.txt to determine whether ARBHOME points to correct directory
760	ARB_INSTALL_FOUND=$(wildcard $(ARBHOME)/arb_INSTALL.txt)
761
762	check_ARBHOME:
763	ifeq ($(strip $(ARB_INSTALL_FOUND)),)
764	@echo ------------------------------------------------------------
765	@echo "ARBHOME is set to '$(ARBHOME)'"
766	@echo "The environment variable ARBHOME has to point to the top arb source directory."
767	@echo "If you use bash enter:"
768	@echo " export ARBHOME='`pwd`'"
769	@echo ------------------------------------------------------------
770	@false
771	endif
772
773	ARB_PATH_SET=$(findstring $(ARBHOME)/bin,$(PATH))
774
775	check_PATH: check_ARBHOME
776	ifeq ($(strip $(ARB_PATH_SET)),)
777	@echo ------------------------------------------------------------
778	@echo "The environment variable PATH has to contain $(ARBHOME)/bin"
779	@echo "If you use bash enter:"
780	@echo ' export PATH=$$ARBHOME/bin:$$PATH'
781	@echo ------------------------------------------------------------
782	@false
783	endif
784
785	check_TOOLS:
786	@util/arb_check_build_env.pl \
787	"$(A_CC)" \
788	"$(A_CXX)" \
789	"$(MAKEDEPEND_PLAIN)" \
790	"$(LINK_SHARED_LIB)" \
791	"$(LINK_SHARED_LIB)" \
792
793
794	check_ENVIRONMENT : check_PATH check_TOOLS
795	@echo "-------------------- Environment [start]"
796	@echo "ARBHOME='$(ARBHOME)'"
797	@echo "PATH='$(PATH)'"
798	@echo "LD_LIBRARY_PATH='$(LD_LIBRARY_PATH)'"
799	@echo "-------------------- Environment [end]"
800
801	check_tabs: check_setup
802	ifeq ($(DEBUG),1)
803	@SOURCE_TOOLS/tabBrake.pl
804	endif
805
806	force_tab_check:
807	@touch -t 198001010000 SOURCE_TOOLS/stamp.tabBrake
808	@$(MAKE) check_tabs
809
810
811	# ---------------------
812
813	check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION
814	@echo Your setup seems to be ok.
815
816	checks: check_setup check_tabs
817	@rm -f SOURCE_TOOLS/postcompile.sav
818
819
820	# end test section ------------------------------
821
822	# ---------------------------------------
823	# List of standard top level directories
824	#
825	# sub-makefiles have to define the targets
826	# - 'depends' and
827	# - 'clean'
828	#
829	# when adding new libs here, also add a dependency vs 'links' or 'links_non_perl' in .@DD_links_non_perl
830
831	ARCHS = \
832	$(ARCHS_PT_SERVER) \
833	AISC/AISC.a \
834	AISC_MKPTPS/AISC_MKPTPS.a \
835	ARBDB/libARBDB.a \
836	CORE/libCORE.a \
837	ARB_GDE/ARB_GDE.a \
838	AWT/libAWT.a \
839	AWTC/AWTC.a \
840	AWTI/AWTI.a \
841	CONSENSUS_TREE/CONSENSUS_TREE.a \
842	CONVERTALN/CONVERTALN.a \
843	DBSERVER/DBSERVER.a \
844	DIST/DIST.a \
845	EDIT4/EDIT4.a \
846	EISPACK/EISPACK.a \
847	GDE/GDE.a \
848	GENOM/GENOM.a \
849	GENOM_IMPORT/GENOM_IMPORT.a \
850	GL/GL.a \
851	ISLAND_HOPPING/ISLAND_HOPPING.a \
852	MERGE/MERGE.a \
853	MULTI_PROBE/MULTI_PROBE.a \
854	NALIGNER/NALIGNER.a \
855	NAMES/NAMES.a \
856	NAMES_COM/server.a \
857	NTREE/NTREE.a \
858	PARSIMONY/PARSIMONY.a \
859	PERLTOOLS/PERLTOOLS.a \
860	PHYLO/PHYLO.a \
861	PRIMER_DESIGN/PRIMER_DESIGN.a \
862	PROBE_COM/server.a \
863	PROBE_DESIGN/PROBE_DESIGN.a \
864	PROBE_SET/PROBE_SET.a \
865	READSEQ/READSEQ.a \
866	RNA3D/RNA3D.a \
867	RNACMA/RNACMA.a \
868	SECEDIT/SECEDIT.a \
869	SEQ_QUALITY/SEQ_QUALITY.a \
870	SERVERCNTRL/SERVERCNTRL.a \
871	SL/SL.a \
872	STAT/STAT.a \
873	TOOLS/TOOLS.a \
874	TREEGEN/TREEGEN.a \
875	UNIT_TESTER/UNIT_TESTER.a \
876	WETC/WETC.a \
877	WINDOW/libWINDOW.a \
878	XML/XML.a \
879
880	# -----------------------
881	# library packets
882
883	ARCHS_CLIENT_PROBE = PROBE_COM/client.a PROBE_COM/common.a
884	ARCHS_CLIENT_NAMES = NAMES_COM/client.a NAMES_COM/common.a
885
886	ARCHS_SERVER_PROBE = PROBE_COM/server.a $(ARCHS_CLIENT_PROBE)
887	ARCHS_SERVER_NAMES = NAMES_COM/server.a $(ARCHS_CLIENT_NAMES)
888
889	ARCHS_MAKEBIN = AISC_MKPTPS/AISC_MKPTPS.a AISC/AISC.a
890
891	# communication libs need aisc and aisc_mkpts:
892
893	AISC/AISC.dummy: proto_tools
894
895	comtools: AISC/AISC.dummy
896
897	ARCHS_SEQUENCE = \
898	SL/SEQUENCE/SEQUENCE.a \
899	SL/ALIVIEW/ALIVIEW.a \
900	SL/PRONUC/PRONUC.a \
901
902	ARCHS_TREE = \
903	$(ARCHS_SEQUENCE) \
904	SL/FILTER/FILTER.a \
905	SL/ARB_TREE/ARB_TREE.a \
906	SL/ROOTED_TREE/ROOTED_TREE.a \
907
908	# parsimony tree (used by NTREE, PARSIMONY, STAT(->EDIT4), DIST(obsolete!))
909	ARCHS_AP_TREE = \
910	$(ARCHS_TREE) \
911	SL/AP_TREE/AP_TREE.a \
912
913	# --------------------------------------------------------------------------------
914	# dependencies for linking shared libs
915
916	link_core: core
917	link_db: db link_core
918	link_aw: aw link_db
919	link_awt: awt link_aw
920
921	#***************************************************************************************
922	# Individual_Programs_Section
923	#***************************************************************************************
924
925	arbmainwrapper:
926	$(MAKE) -C SOURCE_TOOLS -r mainwrapper
927
928
929	#********************************* arb_ntree ************************************
930	NTREE = bin/arb_ntree
931	ARCHS_NTREE = \
932	NTREE/NTREE.a \
933	$(ARCHS_AP_TREE) \
934	ARB_GDE/ARB_GDE.a \
935	AWTC/AWTC.a \
936	AWTI/AWTI.a \
937	CONSENSUS_TREE/CONSENSUS_TREE.a \
938	GENOM/GENOM.a \
939	GENOM_IMPORT/GENOM_IMPORT.a \
940	MERGE/MERGE.a \
941	MULTI_PROBE/MULTI_PROBE.a \
942	PRIMER_DESIGN/PRIMER_DESIGN.a \
943	PROBE_DESIGN/PROBE_DESIGN.a \
944	SEQ_QUALITY/SEQ_QUALITY.a \
945	SERVERCNTRL/SERVERCNTRL.a \
946	SL/AW_NAME/AW_NAME.a \
947	SL/DB_UI/DB_UI.a \
948	SL/DB_SCANNER/DB_SCANNER.a \
949	SL/DB_QUERY/DB_QUERY.a \
950	SL/SEQIO/SEQIO.a \
951	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
952	SL/HELIX/HELIX.a \
953	SL/REGEXPR/REGEXPR.a \
954	SL/REFENTRIES/REFENTRIES.a \
955	SL/NDS/NDS.a \
956	SL/ITEMS/ITEMS.a \
957	SL/INSDEL/INSDEL.a \
958	SL/LOCATION/LOCATION.a \
959	SL/MACROS/MACROS.a \
960	SL/TRANSLATE/TRANSLATE.a \
961	SL/TREEDISP/TREEDISP.a \
962	SL/TREE_ADMIN/TREE_ADMIN.a \
963	SL/TREE_READ/TREE_READ.a \
964	SL/TREE_WRITE/TREE_WRITE.a \
965	STAT/STAT.a \
966	XML/XML.a \
967
968	$(NTREE): $(ARCHS_NTREE:.a=.dummy) link_awt
969	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NTREE) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
970	echo "$(SEP) Link $@"; \
971	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS)" ; \
972	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS) && \
973	echo "$(SEP) Link $@ [done]"; \
974	)
975
976	#********************************* arb_edit4 ************************************
977	EDIT4 = bin/arb_edit4
978
979	ARCHS_EDIT4 := \
980	EDIT4/EDIT4.a \
981	$(ARCHS_AP_TREE) \
982	ARB_GDE/ARB_GDE.a \
983	AWTC/AWTC.a \
984	ISLAND_HOPPING/ISLAND_HOPPING.a \
985	SECEDIT/SECEDIT.a \
986	SERVERCNTRL/SERVERCNTRL.a \
987	SL/AW_HELIX/AW_HELIX.a \
988	SL/AW_NAME/AW_NAME.a \
989	SL/FAST_ALIGNER/FAST_ALIGNER.a \
990	SL/ITEMS/ITEMS.a \
991	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
992	SL/HELIX/HELIX.a \
993	SL/TRANSLATE/TRANSLATE.a \
994	SL/MACROS/MACROS.a \
995	SL/NDS/NDS.a \
996	STAT/STAT.a \
997	XML/XML.a \
998
999	ifeq ($(OPENGL),1)
1000	ARCHS_EDIT4 += RNA3D/RNA3D.a
1001	endif
1002
1003	LIBS_EDIT4 := $(GL_LIBS)
1004
1005	$(EDIT4): $(ARCHS_EDIT4:.a=.dummy) link_awt
1006	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_EDIT4) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1007	echo "$(SEP) Link $@"; \
1008	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4) $(EXECLIBS)" ; \
1009	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4) $(EXECLIBS) && \
1010	echo "$(SEP) Link $@ [done]"; \
1011	)
1012
1013	#********************************* arb_rnacma ************************************
1014	RNACMA = bin/arb_rnacma
1015	ARCHS_RNACMA = \
1016	RNACMA/RNACMA.a \
1017
1018	$(RNACMA) : $(ARCHS_RNACMA:.a=.dummy) link_db
1019	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_RNACMA) \|\| ( \
1020	echo "$(SEP) Link $@"; \
1021	echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_RNACMA) $(LIBS) $(EXECLIBS)"; \
1022	$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_RNACMA) $(LIBS) $(EXECLIBS) && \
1023	echo "$(SEP) Link $@ [done]"; \
1024	)
1025
1026	#********************************* arb_wetc ************************************
1027	WETC = bin/arb_wetc
1028	ARCHS_WETC = \
1029	WETC/WETC.a \
1030	SL/HELIX/HELIX.a \
1031	SL/FILTER/FILTER.a \
1032	XML/XML.a \
1033
1034	$(WETC): $(ARCHS_WETC:.a=.dummy) link_awt
1035	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_WETC) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1036	echo "$(SEP) Link $@"; \
1037	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC) $(GUI_LIBS) $(EXECLIBS)" ; \
1038	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC) $(GUI_LIBS) $(EXECLIBS) && \
1039	echo "$(SEP) Link $@ [done]"; \
1040	)
1041
1042	#********************************* arb_dist ************************************
1043	DIST = bin/arb_dist
1044	ARCHS_DIST = \
1045	$(ARCHS_AP_TREE) \
1046	CONSENSUS_TREE/CONSENSUS_TREE.a \
1047	DIST/DIST.a \
1048	EISPACK/EISPACK.a \
1049	SERVERCNTRL/SERVERCNTRL.a \
1050	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1051	SL/HELIX/HELIX.a \
1052	SL/MATRIX/MATRIX.a \
1053	SL/MACROS/MACROS.a \
1054	SL/NDS/NDS.a \
1055	SL/ITEMS/ITEMS.a \
1056	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.a \
1057	XML/XML.a \
1058
1059	$(DIST): $(ARCHS_DIST:.a=.dummy) link_awt
1060	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_DIST) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1061	echo "$(SEP) Link $@"; \
1062	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS)" ; \
1063	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS) && \
1064	echo "$(SEP) Link $@ [done]"; \
1065	)
1066
1067	#********************************* arb_pars ************************************
1068	PARSIMONY = bin/arb_pars
1069	ARCHS_PARSIMONY = \
1070	$(ARCHS_AP_TREE) \
1071	PARSIMONY/PARSIMONY.a \
1072	SERVERCNTRL/SERVERCNTRL.a \
1073	SL/AW_NAME/AW_NAME.a \
1074	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1075	SL/HELIX/HELIX.a \
1076	SL/MACROS/MACROS.a \
1077	SL/NDS/NDS.a \
1078	SL/ITEMS/ITEMS.a \
1079	SL/TRANSLATE/TRANSLATE.a \
1080	SL/TREEDISP/TREEDISP.a \
1081	XML/XML.a \
1082
1083	$(PARSIMONY): $(ARCHS_PARSIMONY:.a=.dummy) link_awt
1084	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PARSIMONY) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1085	echo "$(SEP) Link $@"; \
1086	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(EXECLIBS)" ; \
1087	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(EXECLIBS) && \
1088	echo "$(SEP) Link $@ [done]"; \
1089	)
1090
1091	#********************************* arb_convert_aln ************************************
1092	CONVERT_ALN = bin/arb_convert_aln
1093	ARCHS_CONVERT_ALN = \
1094	CONVERTALN/CONVERTALN.a \
1095
1096	$(CONVERT_ALN) : $(ARCHS_CONVERT_ALN:.a=.dummy) link_db
1097	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_CONVERT_ALN) $(use_ARB_main) \|\| ( \
1098	echo "$(SEP) Link $@"; \
1099	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN) $(LIBS) $(EXECLIBS)"; \
1100	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN) $(LIBS) $(EXECLIBS) && \
1101	echo "$(SEP) Link $@ [done]"; \
1102	)
1103
1104	#********************************* arb_treegen ************************************
1105
1106	TREEGEN = bin/arb_treegen
1107	ARCHS_TREEGEN = \
1108	TREEGEN/TREEGEN.a \
1109
1110	$(TREEGEN) : $(ARCHS_TREEGEN:.a=.dummy)
1111	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_TREEGEN) $(use_ARB_main_C) \|\| ( \
1112	echo "$(SEP) Link $@"; \
1113	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN) $(EXECLIBS)" ; \
1114	$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN) $(EXECLIBS) && \
1115	echo "$(SEP) Link $@ [done]"; \
1116	)
1117
1118	#********************************* arb_naligner ************************************
1119	NALIGNER = bin/arb_naligner
1120	ARCHS_NALIGNER = \
1121	NALIGNER/NALIGNER.a \
1122	SERVERCNTRL/SERVERCNTRL.a \
1123	SL/HELIX/HELIX.a \
1124
1125	$(NALIGNER): $(ARCHS_NALIGNER:.a=.dummy) link_db
1126	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NALIGNER) $(use_ARB_main) \|\| ( \
1127	echo "$(SEP) Link $@"; \
1128	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(LIBS) $(EXECLIBS)" ; \
1129	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(LIBS) $(EXECLIBS) && \
1130	echo "$(SEP) Link $@ [done]"; \
1131	)
1132
1133	#********************************* arb_phylo ************************************
1134	PHYLO = bin/arb_phylo
1135	ARCHS_PHYLO = \
1136	PHYLO/PHYLO.a \
1137	SL/HELIX/HELIX.a \
1138	SL/FILTER/FILTER.a \
1139	SL/MATRIX/MATRIX.a \
1140	SL/MACROS/MACROS.a \
1141	XML/XML.a \
1142
1143	$(PHYLO): $(ARCHS_PHYLO:.a=.dummy) link_awt
1144	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PHYLO) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1145	echo "$(SEP) Link $@"; \
1146	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO) $(GUI_LIBS) $(EXECLIBS)" ; \
1147	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO) $(GUI_LIBS) $(EXECLIBS) && \
1148	echo "$(SEP) Link $@ [done]"; \
1149	)
1150
1151	#***************************************************************************************
1152	# SERVER SECTION
1153	#***************************************************************************************
1154
1155	#********************************* arb_db_server ************************************
1156	DBSERVER = bin/arb_db_server
1157	ARCHS_DBSERVER = \
1158	DBSERVER/DBSERVER.a \
1159	SERVERCNTRL/SERVERCNTRL.a \
1160
1161	$(DBSERVER): $(ARCHS_DBSERVER:.a=.dummy) link_db
1162	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_DBSERVER) $(ARBDB_LIB) $(use_ARB_main) \|\| ( \
1163	echo "$(SEP) Link $@"; \
1164	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS) $(EXECLIBS)" ; \
1165	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS) $(EXECLIBS) && \
1166	echo "$(SEP) Link $@ [done]"; \
1167	)
1168
1169	#********************************* arb_pt_server ************************************
1170	PROBE = bin/arb_pt_server
1171	ARCHS_PROBE_COMMON = \
1172	SERVERCNTRL/SERVERCNTRL.a \
1173	SL/HELIX/HELIX.a \
1174	SL/PTCLEAN/PTCLEAN.a \
1175
1176	ARCHS_PROBE_LINK = \
1177	$(ARCHS_PROBE_COMMON) \
1178	$(ARCHS_PT_SERVER_LINK) \
1179
1180	ARCHS_PROBE_DEPEND = \
1181	$(ARCHS_PROBE_COMMON) \
1182	$(ARCHS_PT_SERVER) \
1183
1184	$(PROBE): $(ARCHS_PROBE_DEPEND:.a=.dummy) link_db
1185	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) config.makefile $(use_ARB_main) \|\| ( \
1186	echo "$(SEP) Link $@"; \
1187	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_SERVER_PROBE) $(SYSLIBS) $(EXECLIBS)" ; \
1188	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_SERVER_PROBE) $(SYSLIBS) $(EXECLIBS) && \
1189	echo "$(SEP) Link $@ [done]"; \
1190	)
1191
1192	#********************************* arb_name_server ************************************
1193	NAMES = bin/arb_name_server
1194	ARCHS_NAMES = \
1195	NAMES/NAMES.a \
1196	SERVERCNTRL/SERVERCNTRL.a \
1197
1198	$(NAMES): $(ARCHS_NAMES:.a=.dummy) link_db
1199	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) $(use_ARB_main) \|\| ( \
1200	echo "$(SEP) Link $@"; \
1201	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS) $(EXECLIBS)" ; \
1202	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS) $(EXECLIBS) && \
1203	echo "$(SEP) Link $@ [done]"; \
1204	)
1205
1206	#********************************* SHARED LIBRARIES SECTION ************************************
1207
1208	prepare_libdir: addlibs
1209
1210	addlibs:
1211	(perl $(ARBHOME)/SOURCE_TOOLS/provide_libs.pl \
1212	"arbhome=$(ARBHOME)" \
1213	"opengl=$(OPENGL)" \
1214	"link_static=$(LINK_STATIC)" \
1215	)
1216
1217	#***************************************************************************************
1218	# Recursive calls to sub-makefiles
1219	#***************************************************************************************
1220
1221	%.depends:
1222	@cp -p $(@D)/Makefile $(@D)/Makefile.old # save old Makefile
1223	@$(MAKE) -C $(@D) -r \
1224	"AUTODEPENDS=1" \
1225	"MAIN=nothing" \
1226	"cflags=noCflagsHere_use_MAKEDEPENDFLAGS" \
1227	"cxxflags=noCxxflagsHere_use_MAKEDEPENDFLAGS" \
1228	depends
1229	@grep "^# DO NOT DELETE" $(@D)/Makefile >/dev/null
1230	@cat $(@D)/Makefile \
1231	\| SOURCE_TOOLS/fix_depends.pl "(from main)" \
1232	>$(@D)/Makefile.2
1233	@mv $(@D)/Makefile.old $(@D)/Makefile # restore old Makefile
1234	@$(ARBHOME)/SOURCE_TOOLS/mv_if_diff $(@D)/Makefile.2 $(@D)/Makefile # update Makefile if changed
1235
1236	%.proto:
1237	@$(MAKE) -C $(@D) \
1238	"AUTODEPENDS=0" \
1239	"MAIN=nothing" \
1240	"cflags=noCflags" \
1241	"cxxflags=noCxxflags" \
1242	proto
1243
1244	%.clean:
1245	@$(MAKE) -C $(@D) \
1246	"AUTODEPENDS=0" \
1247	"MAIN=nothing" \
1248	"cflags=noCflags" \
1249	"cxxflags=noCxxflags" \
1250	clean
1251
1252
1253	# stop wrong targets
1254	target_is_missing_lib_prefix:
1255	@echo "Error: Denied to build shared library target with missing 'lib'-prefix"
1256	false
1257
1258	ARBDB/ARBDB.dummy: target_is_missing_lib_prefix
1259	CORE/CORE.dummy: target_is_missing_lib_prefix
1260	AWT/AWT.dummy: target_is_missing_lib_prefix
1261	WINDOW/WINDOW.dummy: target_is_missing_lib_prefix
1262
1263	# rule to generate main target (normally a library):
1264	# @@@ check effect of setting LANG=C below
1265	%.dummy:
1266	@( export ID=$$$$; LANG=C; \
1267	(( \
1268	echo "$(SEP) Make $(@D)"; \
1269	$(MAKE) -C $(@D) -r \
1270	"AUTODEPENDS=1" \
1271	"MAIN=$(@F:.dummy=.a)" \
1272	"cflags=$(cflags) -DIN_ARB_$(subst /,_,$(@D))" \
1273	&& \
1274	echo "$(SEP) Make $(@D) [done]"; \
1275	) >$(@D).$$ID.log 2>&1 && (cat $(@D).$$ID.log;rm $(@D).$$ID.log)) \|\| (cat $(@D).$$ID.log;rm $(@D).$$ID.log;false))
1276
1277	# Additional dependencies for subtargets:
1278
1279	PROBE_COM/PROBE_COM.dummy : comtools
1280	NAMES_COM/NAMES_COM.dummy : comtools
1281
1282	com: PROBE_COM/PROBE_COM.dummy NAMES_COM/NAMES_COM.dummy
1283
1284	PROBE_COM/server.dummy:
1285	@echo Unwanted request to make target $<
1286	false
1287
1288	PROBE_COM/client.dummy:
1289	@echo Unwanted request to make target $<
1290	false
1291
1292	NAMES_COM/server.dummy:
1293	@echo Unwanted request to make target $<
1294	false
1295
1296	NAMES_COM/client.dummy:
1297	@echo Unwanted request to make target $<
1298	false
1299
1300
1301	ARBDB/libARBDB.dummy: links
1302	CORE/libCORE.dummy: links
1303
1304	PERLTOOLS/PERLTOOLS.dummy: core db
1305
1306	# all subdirs perl not depends on go here (ADD_links_non_perl)
1307	AWT/libAWT.dummy: links_non_perl
1308	AWTI/AWTI.dummy: links_non_perl
1309	CONSENSUS_TREE/CONSENSUS_TREE.dummy: links_non_perl
1310	CONVERTALN/CONVERTALN.dummy: links_non_perl
1311	DBSERVER/DBSERVER.dummy: links_non_perl
1312	DIST/DIST.dummy: links_non_perl
1313	EDIT4/EDIT4.dummy: links_non_perl genheaders com
1314	EISPACK/EISPACK.dummy: links_non_perl
1315	GDE/GDE.dummy: links_non_perl
1316	GENOM/GENOM.dummy: links_non_perl
1317	GENOM_IMPORT/GENOM_IMPORT.dummy: links_non_perl
1318	ISLAND_HOPPING/ISLAND_HOPPING.dummy: links_non_perl
1319	MERGE/MERGE.dummy: links_non_perl
1320	NTREE/NTREE.dummy: links_non_perl genheaders
1321	PARSIMONY/PARSIMONY.dummy: links_non_perl
1322	PHYLO/PHYLO.dummy: links_non_perl
1323	PRIMER_DESIGN/PRIMER_DESIGN.dummy: links_non_perl
1324	PROBE_SET/PROBE_SET.dummy: links_non_perl link_db
1325	READSEQ/READSEQ.dummy: links_non_perl
1326	RNACMA/RNACMA.dummy: links_non_perl header_libs
1327	SECEDIT/SECEDIT.dummy: links_non_perl
1328	SEQ_QUALITY/SEQ_QUALITY.dummy: links_non_perl
1329	SERVERCNTRL/SERVERCNTRL.dummy: links_non_perl com
1330	SL/ALIVIEW/ALIVIEW.dummy: links_non_perl
1331	SL/AP_TREE/AP_TREE.dummy: links_non_perl
1332	SL/ARB_TREE/ARB_TREE.dummy: links_non_perl
1333	SL/AW_HELIX/AW_HELIX.dummy: links_non_perl
1334	SL/DB_QUERY/DB_QUERY.dummy: links_non_perl
1335	SL/DB_SCANNER/DB_SCANNER.dummy: links_non_perl
1336	SL/DB_UI/DB_UI.dummy: links_non_perl
1337	SL/FAST_ALIGNER/FAST_ALIGNER.dummy: links_non_perl
1338	SL/FILTER/FILTER.dummy: links_non_perl
1339	SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy: links_non_perl
1340	SL/HELIX/HELIX.dummy: links_non_perl
1341	SL/INSDEL/INSDEL.dummy: links_non_perl
1342	SL/ITEMS/ITEMS.dummy: links_non_perl
1343	SL/LOCATION/LOCATION.dummy: links_non_perl
1344	SL/MACROS/MACROS.dummy: links_non_perl
1345	SL/MATRIX/MATRIX.dummy: links_non_perl
1346	SL/NDS/NDS.dummy: links_non_perl
1347	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.dummy: links_non_perl
1348	SL/PRONUC/PRONUC.dummy: links_non_perl
1349	SL/PTCLEAN/PTCLEAN.dummy: links_non_perl link_db
1350	SL/REFENTRIES/REFENTRIES.dummy: links_non_perl
1351	SL/REGEXPR/REGEXPR.dummy: links_non_perl
1352	SL/ROOTED_TREE/ROOTED_TREE.dummy: links_non_perl
1353	SL/SEQIO/SEQIO.dummy: links_non_perl
1354	SL/SEQUENCE/SEQUENCE.dummy: links_non_perl
1355	SL/TRANSLATE/TRANSLATE.dummy: links_non_perl
1356	SL/TREE_ADMIN/TREE_ADMIN.dummy: links_non_perl
1357	SL/TREE_READ/TREE_READ.dummy: links_non_perl
1358	SL/TREE_WRITE/TREE_WRITE.dummy: links_non_perl
1359	SL/TREEDISP/TREEDISP.dummy: links_non_perl
1360	STAT/STAT.dummy: links_non_perl
1361	TREEGEN/TREEGEN.dummy: links_non_perl
1362	WETC/WETC.dummy: links_non_perl
1363	WINDOW/libWINDOW.dummy: links_non_perl
1364	XML/XML.dummy: links_non_perl
1365
1366	ifeq ($(OPENGL),1)
1367	GL/glAW/glAW.dummy: links_non_perl
1368	GL/glpng/glpng.dummy: links_non_perl
1369	GL/GL.dummy: GL/glAW/glAW.dummy GL/glpng/glpng.dummy
1370	RNA3D/RNA3D.dummy: links_non_perl gl
1371	endif
1372
1373	UNIT_TESTER/UNIT_TESTER.dummy: link_db \
1374	SERVERCNTRL/SERVERCNTRL.dummy \
1375
1376	TOOLS/TOOLS.dummy : links_non_perl link_db \
1377	SERVERCNTRL/SERVERCNTRL.dummy \
1378	SL/ROOTED_TREE/ROOTED_TREE.dummy \
1379	SL/TREE_WRITE/TREE_WRITE.dummy \
1380	SL/TREE_READ/TREE_READ.dummy \
1381	CONSENSUS_TREE/CONSENSUS_TREE.dummy \
1382	XML/XML.dummy \
1383
1384	AWTC/AWTC.dummy : com
1385
1386	NAMES/NAMES.dummy : com
1387	SL/AW_NAME/AW_NAME.dummy : com
1388
1389	PROBE/PROBE.dummy : com
1390	ptpan/PROBE.dummy : com
1391	MULTI_PROBE/MULTI_PROBE.dummy : com
1392	PROBE_DESIGN/PROBE_DESIGN.dummy : com
1393	NALIGNER/NALIGNER.dummy : com
1394
1395	ARB_GDE/ARB_GDE.dummy : proto_tools
1396
1397	compile_compatibility: SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.dummy
1398
1399	#***************************************************************************************
1400	# Short aliases to make targets
1401	#***************************************************************************************
1402
1403	show:
1404	@echo $(SEP)
1405	@echo 'Aliases for often needed targets:'
1406	@echo ''
1407	@echo ' executables:'
1408	@echo ''
1409	@echo ' nt arb_ntree'
1410	@echo ' e4 arb_edit4 (includes secedit)'
1411	@echo ' di arb_dist'
1412	@echo ' ph arb_phylo'
1413	@echo ' pa arb_parsimony'
1414	@echo ' tg arb_treegen'
1415	@echo ' ds arb_dbserver'
1416	@echo ' pt arb_pt_server'
1417	@echo ' na arb_name_server'
1418	@echo ''
1419	@echo ' libraries:'
1420	@echo ''
1421	@echo ' com communication libraries'
1422	@echo ' db ARB database'
1423	@echo ' aw GUI lib'
1424	@echo ' awt GUI toolkit'
1425	@echo ' awtc general purpose library'
1426	@echo ' awti import/export library'
1427	@echo ' mp multi probe library'
1428	@echo ' ge genome library'
1429	@echo ' pd probe design lib'
1430	@echo ' prd primer design lib'
1431	@echo ''
1432	@echo ' other targets:'
1433	@echo ''
1434	@echo ' help recompile help files'
1435	@echo ' tools make small tools used by arb'
1436	@echo ''
1437	@echo ' foreign targets:'
1438	@echo ''
1439	@echo ' gde GDE'
1440	@echo ' agde ARB_GDE'
1441	@echo ''
1442	@echo 'for other targets inspect $(ARBHOME)/Makefile'
1443	@echo ''
1444	@echo $(SEP)
1445
1446	source_doc:
1447	@echo "Remove some links (doxygen crashes otherwise):"
1448	find . \( -name "AISC" -o -name "C" -o -name "GDEHELP" \) -type l -exec rm {} \;
1449	doxygen 2>&1 1>/dev/null
1450	$(MAKE) forcelinks
1451
1452	dep_graph:
1453	@echo "Building some dependency graphs"
1454	SOURCE_TOOLS/dependency_graphs.pl
1455
1456	help: HELP_SOURCE/HELP_SOURCE.dummy
1457
1458	HELP_SOURCE/HELP_SOURCE.dummy: link_core xml menus
1459
1460	db: ARBDB/libARBDB.dummy
1461	core: CORE/libCORE.dummy
1462	aw: WINDOW/libWINDOW.dummy
1463	awt: AWT/libAWT.dummy
1464	awtc: AWTC/AWTC.dummy
1465	awti: AWTI/AWTI.dummy
1466
1467	mp: MULTI_PROBE/MULTI_PROBE.dummy
1468	mg: MERGE/MERGE.dummy
1469	ge: GENOM/GENOM.dummy
1470	prd: PRIMER_DESIGN/PRIMER_DESIGN.dummy
1471
1472	nt: menus $(NTREE)
1473
1474	nal: $(NALIGNER)
1475
1476	di: $(DIST)
1477	ph: $(PHYLO)
1478	pa: $(PARSIMONY)
1479	tg: $(TREEGEN)
1480
1481	ifeq ($(OPENGL),1)
1482	3d: RNA3D/RNA3D.dummy
1483	gl: GL/GL.dummy
1484	else
1485	noopengl:
1486	@echo "invalid target for OPENGL=0"
1487	3d: noopengl
1488	gl: noopengl
1489	endif
1490
1491	SL/SL.dummy: com
1492
1493	ds: $(DBSERVER)
1494	pt: $(PROBE)
1495	pst: PROBE_SET/PROBE_SET.dummy
1496	pd: PROBE_DESIGN/PROBE_DESIGN.dummy
1497	na: $(NAMES)
1498	sq: SEQ_QUALITY/SEQ_QUALITY.dummy
1499	cma: $(RNACMA)
1500
1501	sec: SECEDIT/SECEDIT.dummy
1502
1503	e4: $(EDIT4) readseq menus
1504
1505	gi: GENOM_IMPORT/GENOM_IMPORT.dummy
1506	wetc: $(WETC)
1507
1508	xml: XML/XML.dummy
1509	xmlin: XML_IMPORT/XML_IMPORT.dummy# broken
1510	stat: STAT/STAT.dummy $(NTREE) $(EDIT4)
1511	fa: SL/FAST_ALIGNER/FAST_ALIGNER.dummy
1512
1513	#********************************************************************************
1514
1515	up_by_remake: depends proto
1516
1517	up: up_by_remake tags valgrind_update
1518
1519	#********************************************************************************
1520
1521	touch:
1522	SOURCE_TOOLS/touch_modified.pl
1523
1524	modified: touch
1525	$(MAKE) all
1526
1527	#********************************************************************************
1528
1529	libdepends:
1530	$(MAKE) -C "SOURCE_TOOLS" \
1531	"RNA3D_LIB=$(RNA3D_LIB_4_DEPENDS)" \
1532	libdepends
1533
1534	#********************************************************************************
1535
1536	# create generated headers:
1537	genheaders: TEMPLATES/TEMPLATES.dummy
1538
1539	clrdotdepends:
1540	-rm PROBE_COM/.depends
1541	-rm NAMES_COM/.depends
1542	-rm PERL2ARB/.depends
1543
1544	comdepends: comtools clrdotdepends
1545	@echo "$(SEP) Partially build com interface"
1546	$(MAKE) PROBE_COM/PROBE_COM.depends NAMES_COM/NAMES_COM.depends
1547	$(MAKE) PROBE_COM/server.depends NAMES_COM/server.depends
1548
1549	depends: genheaders comdepends
1550	@echo "$(SEP) Updating other dependencies"
1551	$(MAKE) $(subst NAMES_COM/server.depends,,$(subst PROBE_COM/server.depends,,$(ARCHS:.a=.depends))) \
1552	HELP_SOURCE/HELP_SOURCE.depends \
1553	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.depends \
1554
1555	$(MAKE) libdepends
1556
1557	depend: depends
1558
1559	# ------------------------------------------------------------
1560	# dependency generation tests for AISC code
1561	#(all should work w/o creating wrong dependencies;
1562	# neither in XXX_COM/Makefile nor in code using AISC interface)
1563	dependstest1: silent_clean
1564	$(MAKE) depends
1565	dependstest2: silent_clean
1566	$(MAKE) com
1567	dependstest3: silent_clean
1568	$(MAKE) aw
1569	dependstest4: silent_clean
1570	$(MAKE) pt
1571	dependstest5: silent_clean
1572	$(MAKE) na
1573	dependstest6: silent_clean
1574	$(MAKE) nt
1575	dependstest7: silent_clean
1576	$(MAKE) all
1577	# ------------------------------------------------------------
1578
1579	AISC_MKPTPS/AISC_MKPTPS.dummy: links
1580
1581	proto_tools: AISC_MKPTPS/AISC_MKPTPS.dummy
1582
1583	proto: proto_tools
1584	@echo $(SEP) Updating prototypes
1585	$(MAKE) \
1586	ARBDB/ARBDB.proto \
1587	AISC_COM/AISC_COM.proto \
1588	ARB_GDE/ARB_GDE.proto \
1589	CORE/CORE.proto \
1590	CONVERTALN/CONVERTALN.proto \
1591	NTREE/NTREE.proto \
1592	MERGE/MERGE.proto \
1593	$(ARCHS_PT_SERVER:.a=.proto) \
1594	SERVERCNTRL/SERVERCNTRL.proto \
1595	SL/SL.proto \
1596
1597	#********************************************************************************
1598
1599	valgrind_update: links
1600	@echo $(SEP) Updating for valgrind
1601	$(MAKE) -C SOURCE_TOOLS valgrind_update
1602
1603	#********************************************************************************
1604
1605	TAGFILE=TAGS
1606	TAGFILE_TMP=TAGS.tmp
1607
1608	TAG_SOURCE_HEADERS=TAGS.headers
1609	TAG_SOURCE_CODE=TAGS.codefiles
1610	TAG_SOURCE_LISTS=$(TAG_SOURCE_HEADERS) $(TAG_SOURCE_CODE)
1611
1612	ETAGS=ctags -e -f $(TAGFILE_TMP) --sort=no --if0=no --extra=q
1613	ETAGS_TYPES=--C-kinds=cgnsut --C++-kinds=cgnsut
1614	ETAGS_FUN =--C-kinds=fm --C++-kinds=fm
1615	ETAGS_REST =--C-kinds=dev --C++-kinds=dev
1616
1617	FILTER_TAGS_SOURCES= \
1618	$(SED) -e 's/^.\///g' \| \
1619	grep -P -v -i '^HEADERLIBS\|^GDE/\|/GEN[CH]/'
1620
1621	$(TAG_SOURCE_HEADERS): links
1622	find . \( -name '.hxx' -o -name ".h" \) -type f \| $(FILTER_TAGS_SOURCES) > $@
1623
1624	$(TAG_SOURCE_CODE): links
1625	find . \( -name '.cxx' -o -name ".c" \) -type f \| $(FILTER_TAGS_SOURCES) > $@
1626
1627	tags: $(TAG_SOURCE_LISTS)
1628	$(ETAGS) $(ETAGS_TYPES) -L $(TAG_SOURCE_HEADERS)
1629	$(ETAGS) -a $(ETAGS_FUN) -L $(TAG_SOURCE_HEADERS)
1630	$(ETAGS) -a $(ETAGS_REST) -L $(TAG_SOURCE_HEADERS)
1631	$(ETAGS) -a $(ETAGS_TYPES) -L $(TAG_SOURCE_CODE)
1632	$(ETAGS) -a $(ETAGS_FUN) -L $(TAG_SOURCE_CODE)
1633	$(ETAGS) -a $(ETAGS_REST) -L $(TAG_SOURCE_CODE)
1634	mv_if_diff $(TAGFILE_TMP) $(TAGFILE)
1635	rm $(TAG_SOURCE_LISTS)
1636
1637	#********************************************************************************
1638
1639	LINKSTAMP=SOURCE_TOOLS/stamp.generate_all_links
1640
1641	links: checks $(LINKSTAMP) arbmainwrapper
1642	links_no_checks: $(LINKSTAMP) arbmainwrapper
1643
1644	forcelinks:
1645	-rm $(LINKSTAMP)
1646	$(MAKE) links
1647
1648	$(LINKSTAMP): SOURCE_TOOLS/generate_all_links.sh
1649	+SOURCE_TOOLS/generate_all_links.sh
1650	touch $(LINKSTAMP)
1651
1652	clean_links:
1653	# avoid to delete linked pts, nas or arb_tcp.dat:
1654	find . -path './lib' -prune -o -type l -exec rm {} \;
1655	# removed obsolete file - refuses to disappear due to 'prune' above
1656	@rm -f lib/help/GDEHELP
1657	@rm -f $(LINKSTAMP) lib/inputMasks/format.readme
1658
1659	redo_links: clean_links
1660	$(MAKE) links_no_checks
1661
1662	#********************************************************************************
1663
1664	header_libs:
1665	$(MAKE) -C HEADERLIBS all
1666
1667	#********************************************************************************
1668
1669	gde: GDE/GDE.dummy
1670	GDE: gde
1671	agde: ARB_GDE/ARB_GDE.dummy
1672
1673	tools: TOOLS/TOOLS.dummy
1674
1675	convert: $(CONVERT_ALN)
1676	readseq: READSEQ/READSEQ.dummy
1677
1678	#***************************************************************************************
1679	# Some user commands
1680	#***************************************************************************************
1681
1682	menus: binlink links
1683	@(( \
1684	echo "$(SEP) Make GDEHELP"; \
1685	$(MAKE) -C GDEHELP -r all && \
1686	echo "$(SEP) Make GDEHELP [done]"; \
1687	) > GDEHELP.log 2>&1 && (cat GDEHELP.log;rm GDEHELP.log)) \|\| (cat GDEHELP.log;rm GDEHELP.log;false)
1688
1689	ifeq ($(DEBUG),1)
1690	BIN_TARGET=develall
1691	else
1692	BIN_TARGET=all
1693	endif
1694
1695
1696	binlink:
1697	$(MAKE) -C bin $(BIN_TARGET)
1698
1699	preplib:
1700	(cd lib;$(MAKE) all)
1701
1702	# --------------------------------------------------------------------------------
1703	# This section is quite tricky:
1704	#
1705	# make 'perl' is a BIG target, so when it has to be made, it has to be started
1706	# as early as possible to reduce overall compile time. Since 'make' does not
1707	# provide any priotities, i force it to build all 'perl'-prerequisites early, by
1708	# adding artificial dependencies to these prerequisites
1709	#
1710	# That behavior is likely to be system-dependent.
1711	# My goal was only to make it work on my current development system,
1712	# where this saves about 20% of overall build time.
1713
1714	ifeq ($(WITHPERL),1)
1715	links_non_perl: PERLTOOLS/PERLTOOLS.dummy
1716	perltools: links_non_perl
1717	perl: realperl
1718	else
1719	links_non_perl: links
1720	perl:
1721	$(MAKE) "WITHPERL=1" perl
1722	endif
1723
1724	# ---------------------------------------- perl
1725
1726	ifeq ($(ARB_64),$(BUILDHOST_64))
1727	TEST_PERL_SCRIPTS=$(MAKE) -C PERL_SCRIPTS/test test
1728	else
1729	TEST_PERL_SCRIPTS=echo "skipping perl script compilation (when cross-compiling)"
1730	endif
1731
1732	realperl: perltools
1733	(( \
1734	echo "$(SEP) Make PERL2ARB" ; \
1735	$(TIME) $(MAKE) -C PERL2ARB -r -f Makefile.main \
1736	"AUTODEPENDS=1" \
1737	"dflags=$(dflags)" \
1738	"cross_cflags=$(cross_cflags) $(cxxflags) $(dflags)" \
1739	"cross_lflags=$(cross_lflags)" \
1740	"COMPILER_VERSION=$(COMPILER_VERSION)" \
1741	all && \
1742	$(TEST_PERL_SCRIPTS) && \
1743	echo "$(SEP) Make PERL2ARB [done]" ; \
1744	) > PERL2ARB.log 2>&1 && (cat PERL2ARB.log;rm PERL2ARB.log)) \|\| (cat PERL2ARB.log;rm PERL2ARB.log;false)
1745
1746	perl_clean:
1747	@$(MAKE) -C PERL2ARB -r -f Makefile.main \
1748	"AUTODEPENDS=0" \
1749	clean
1750
1751	PERL2ARB/PERL2ARB.clean:
1752	$(MAKE) perl_clean
1753
1754	# ---------------------------------------- bindings to script languages
1755
1756	bindings: lib/libCORE.so lib/libARBDB.so
1757	$(MAKE) -C BINDINGS all ARBDEPENDS="$(^:%=../%)" DFLAGS="$(dflags)"
1758
1759	bindings_clean:
1760	$(MAKE) -C BINDINGS clean
1761
1762	# ----------------------------------------
1763
1764	CLOC=cloc-1.08.pl
1765	CLOCFLAGS=--no3 --quiet --progress-rate=0
1766	CLOCARB=--exclude-dir=GDE .
1767	CLOCEXT=GDE
1768	CLOCCODE=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.code.def
1769	CLOCREST=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.rest.def
1770	CLOCFILT=tail --lines=+4
1771
1772	cloc:
1773	@echo 'Arb code:'
1774	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCARB) \| $(CLOCFILT)
1775	@echo 'Arb rest:'
1776	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCARB) \| $(CLOCFILT)
1777	@echo 'External code:'
1778	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCEXT) \| $(CLOCFILT)
1779	@echo 'External rest:'
1780	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCEXT) \| $(CLOCFILT)
1781
1782	# ---------------------------------------- check ressources
1783
1784	check_res:
1785	$(ARBHOME)/SOURCE_TOOLS/check_ressources.pl
1786
1787	# ---------------------------------------- cleaning
1788
1789	rmbak:
1790	@echo "Cleanup:"
1791	@find . \( -name '*%' \
1792	-o -name '*.bak' \
1793	-o -name '*~' \) \
1794	-o \( -name 'core' -a \! -type d \) \
1795	-exec rm -v {} \;
1796
1797	bin_reinit:
1798	$(MAKE) bin/bin.clean
1799	$(MAKE) -C "bin" all
1800
1801	clean_directories:
1802	-rm -rf \
1803	$(ARBHOME)/PROBE_SET/bin \
1804	$(ARBHOME)/INCLUDE \
1805
1806	libclean:
1807	-find $(ARBHOME) -type f \( -name '*.a' ! -type l \) -exec rm -f {} \;
1808
1809	objclean:
1810	-find $(ARBHOME) -type f \( -name '*.o' ! -type l \) -exec rm -f {} \;
1811
1812	# bin.clean and HELP_SOURCE.clean interfere
1813	clean3:
1814	$(MAKE) bin/bin.clean
1815	$(MAKE) HELP_SOURCE/HELP_SOURCE.clean
1816
1817	clean2: $(ARCHS:.a=.clean) \
1818	clean3 \
1819	rmbak \
1820	libclean \
1821	objclean \
1822	lib/lib.clean \
1823	GDEHELP/GDEHELP.clean \
1824	HEADERLIBS/HEADERLIBS.clean \
1825	SOURCE_TOOLS/SOURCE_TOOLS.clean \
1826	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.clean \
1827	UNIT_TESTER/UNIT_TESTER.clean \
1828	TEMPLATES/TEMPLATES.clean \
1829	perl_clean \
1830	clean_directories \
1831
1832	rm -f .last_gcc .last_compiler config.makefile.bak
1833
1834	# links are needed for cleanup
1835	clean: redo_links motif_xpm_hack_clean
1836	$(MAKE) clean2
1837	$(MAKE) clean_cov_all clean_links
1838
1839	silent_clean:
1840	$(MAKE) clean >/dev/null
1841
1842	# 'relocated' is about 50% faster than 'rebuild'
1843	reloc_clean: links
1844	@echo "---------------------------------------- Relocation cleanup"
1845	$(MAKE) \
1846	perl_clean \
1847	GDEHELP/GDEHELP.clean \
1848	HELP_SOURCE/genhelp/genhelp.clean \
1849	bin/bin.clean \
1850	libclean \
1851	objclean
1852
1853	relocated: links
1854	$(MAKE) reloc_clean
1855	@echo "---------------------------------------- and remake"
1856	$(MAKE) build
1857
1858	# -----------------------------------
1859	# some stress tests:
1860
1861	rebuild4ever: rebuild
1862	$(MAKE) rebuild4ever
1863
1864	build4ever: build
1865	$(MAKE) build4ever
1866
1867	clean4ever: clean
1868	$(MAKE) clean4ever
1869
1870	test4ever: ut
1871	$(MAKE) test4ever
1872
1873	perl4ever: clean
1874	$(MAKE) links
1875	$(MAKE) perl
1876	$(MAKE) perl4ever
1877
1878
1879	# -----------------------------------
1880
1881	rebuild: clean
1882	$(MAKE) all
1883
1884	relink: bin/bin.clean libclean
1885	$(MAKE) build
1886
1887	tarfile: rebuild
1888	$(MAKE) prepare_libdir
1889	util/arb_compress
1890
1891	tarfile_quick: build
1892	$(MAKE) prepare_libdir
1893	util/arb_compress
1894
1895	save: sourcetarfile
1896
1897	patch:
1898	SOURCE_TOOLS/arb_create_patch.sh arbPatch
1899
1900	# test early whether save will work
1901	savetest:
1902	@util/arb_srclst.pl >/dev/null
1903
1904	testsave: savetest
1905
1906	sourcetarfile: rmbak
1907	util/arb_save
1908
1909	save2: rmbak
1910	util/arb_save ignore
1911
1912	save_test: rmbak
1913	@echo "Testing source list.."
1914	@util/arb_srclst.pl > /dev/null
1915
1916	save_test_no_error:
1917	@-$(MAKE) save_test
1918
1919	inc_candi:
1920	touch SOURCE_TOOLS/inc_candi.stamp
1921	$(MAKE) do_version_update
1922
1923	inc_patch:
1924	touch SOURCE_TOOLS/inc_patch.stamp
1925	$(MAKE) do_version_update
1926
1927	inc_minor:
1928	touch SOURCE_TOOLS/inc_minor.stamp
1929	$(MAKE) do_version_update
1930
1931	inc_major:
1932	touch SOURCE_TOOLS/inc_major.stamp
1933	$(MAKE) do_version_update
1934
1935	do_version_update:
1936	@echo Incrementing version information
1937	$(MAKE) testsave
1938	$(MAKE) genheaders # auto upgrades version early
1939
1940	show_version:
1941	$(MAKE) genheaders # updates version info
1942	@echo "$(SEP) ARB version info"
1943	@grep ARB_VERSION TEMPLATES/arb_build.h
1944	@echo "$(SEP)"
1945
1946	release_quick:
1947	-rm arb.tgz arbsrc.tgz
1948	$(MAKE) tarfile_quick
1949	$(MAKE) sourcetarfile
1950
1951	# --------------------------------------------------------------------------------
1952
1953	MAKE_IF_COMMITTED=$(MAKE) -C SOURCE_TOOLS -f Makefile.commitbuild
1954
1955	build_CTARGET:
1956	+$(MAKE_IF_COMMITTED) "CTARGET=$(CTARGET)" build_CTARGET
1957
1958	reset_committed_build:
1959	+$(MAKE_IF_COMMITTED) reset
1960
1961	# --------------------------------------------------------------------------------
1962
1963	arbapplications: nt pa e4 wetc pt na nal di ph ds wetc cma
1964
1965	arb_external: convert tools gde readseq tg pst xmlin
1966
1967	arb_no_perl: arbapplications help arb_external
1968
1969	arb: motif_xpm_hack
1970	$(MAKE) "WITHPERL=1" perl arb_no_perl
1971
1972	motif_xpm_hack:
1973	$(MAKE) -r -C "lib/motifHack" all
1974
1975	motif_xpm_hack_clean:
1976	$(MAKE) -r -C "lib/motifHack" clean
1977
1978	# --------------------------------------------------------------------------------
1979	# special targets for SOURCE_TOOLS/remake_after_change.pl
1980
1981	rac_arb_dist: di
1982	rac_arb_edit4: e4
1983	rac_arb_ntree: nt
1984	rac_arb_pars: pa
1985	rac_arb_phylo: ph
1986	rac_arb_wetc: wetc
1987	rac_arb_naligner: nal
1988	rac_arb_pt_server: pt
1989	rac_arb_db_server: ds
1990	rac_arb_name_server: na
1991	rac_arb_convert_aln: convert
1992	rac_arb_treegen: tg
1993	rac_arb_rnacma: cma
1994	rac_arb_help2xml: help
1995
1996	rac_arb_a2ps: tools
1997	rac_arb_consensus_tree: tools
1998	rac_arb_dnarates: tools
1999	rac_arb_export_rates: tools
2000	rac_arb_export_tree: tools
2001	rac_arb_gene_probe: tools
2002	rac_arb_message: tools
2003	rac_arb_notify: tools
2004	rac_arb_primer: tools
2005	rac_arb_probe: tools
2006	rac_arb_read_tree: tools
2007
2008	# --------------------------------------------------------------------------------
2009	# unit testing
2010	# @@@ work in progress
2011	#
2012	# goal is to automatically test all libraries/executables using TESTED_UNITS_AUTO
2013	#
2014	# currently not all test executables link w/o error
2015	# (see UNITS_WORKING, UNITS_UNTESTABLE_ATM and UNITS_NEED_FIX)
2016
2017	# define RNA3D/RNA3D.test
2018	RNA3D_TEST := $(subst .a,.test,$(RNA3D_LIB))
2019
2020	TESTED_UNITS_AUTO = $(ARCHS:.a=.test)
2021
2022	UNITS_WORKING = \
2023	$(RNA3D_TEST) \
2024	AWTI/AWTI.test \
2025	DIST/DIST.test \
2026	EISPACK/EISPACK.test \
2027	GENOM/GENOM.test \
2028	GL/glAW/libglAW.test \
2029	GL/glpng/libglpng_arb.test \
2030	ISLAND_HOPPING/ISLAND_HOPPING.test \
2031	NALIGNER/NALIGNER.test \
2032	NAMES/NAMES.test \
2033	PHYLO/PHYLO.test \
2034	PRIMER_DESIGN/PRIMER_DESIGN.test \
2035	PROBE_DESIGN/PROBE_DESIGN.test \
2036	SECEDIT/SECEDIT.test \
2037	SEQ_QUALITY/SEQ_QUALITY.test \
2038	SERVERCNTRL/SERVERCNTRL.test \
2039	SL/ALIVIEW/ALIVIEW.test \
2040	SL/AP_TREE/AP_TREE.test \
2041	SL/ARB_TREE/ARB_TREE.test \
2042	SL/AW_HELIX/AW_HELIX.test \
2043	SL/AW_NAME/AW_NAME.test \
2044	SL/DB_SCANNER/DB_SCANNER.test \
2045	SL/GUI_ALIVIEW/GUI_ALIVIEW.test \
2046	SL/HELIX/HELIX.test \
2047	SL/ITEMS/ITEMS.test \
2048	SL/LOCATION/LOCATION.test \
2049	SL/MATRIX/MATRIX.test \
2050	SL/REFENTRIES/REFENTRIES.test \
2051	SL/SEQUENCE/SEQUENCE.test \
2052	SL/TRANSLATE/TRANSLATE.test \
2053	SL/TREE_ADMIN/TREE_ADMIN.test \
2054	SL/TREE_WRITE/TREE_WRITE.test \
2055	STAT/STAT.test \
2056	TREEGEN/TREEGEN.test \
2057	WETC/WETC.test \
2058	XML/XML.test \
2059	SL/ROOTED_TREE/ROOTED_TREE.test \
2060
2061	# untestable units
2062
2063	UNITS_NEED_FIX = \
2064	ptpan/PROBE.test \
2065
2066	UNITS_UNTESTABLE_ATM = \
2067	PROBE_SET/PROBE_SET.test \
2068	XML_IMPORT/XML_IMPORT.test \
2069
2070	# for the moment, put all units containing tests into UNITS_TESTED or UNITS_TESTED_FIRST
2071
2072	UNITS_TESTED_FIRST = \
2073	PARSIMONY/PARSIMONY.test \
2074	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.test \
2075	SL/NDS/NDS.test \
2076	ARB_GDE/ARB_GDE.test \
2077	GENOM_IMPORT/GENOM_IMPORT.test \
2078	SL/MACROS/MACROS.test \
2079	SL/REGEXPR/REGEXPR.test \
2080	SL/FILTER/FILTER.test \
2081	ARBDB/libARBDB.test \
2082	CONSENSUS_TREE/CONSENSUS_TREE.test \
2083	TOOLS/arb_consensus_tree.test \
2084	TOOLS/arb_test.test \
2085	TOOLS/arb_probe.test \
2086	PERLTOOLS/arb_proto_2_xsub.test \
2087	AWTC/AWTC.test \
2088
2089	# plain test-libaries not linked anywhere
2090	TEST_SANDBOXES = \
2091	SL/CB/CB.test \
2092
2093	UNITS_TESTED = \
2094	SL/TREE_READ/TREE_READ.test \
2095	DBSERVER/DBSERVER.test \
2096	AWT/libAWT.test \
2097	CORE/libCORE.test \
2098	SL/INSDEL/INSDEL.test \
2099	SL/TREEDISP/TREEDISP.test \
2100	NTREE/NTREE.test \
2101	AISC_MKPTPS/mkptypes.test \
2102	EDIT4/EDIT4.test \
2103	MERGE/MERGE.test \
2104	MULTI_PROBE/MULTI_PROBE.test \
2105	SERVERCNTRL/SERVERCNTRL.test \
2106	SL/FAST_ALIGNER/FAST_ALIGNER.test \
2107	SL/PRONUC/PRONUC.test \
2108	WINDOW/libWINDOW.test \
2109	HELP_SOURCE/arb_help2xml.test \
2110	CONVERTALN/CONVERTALN.test \
2111	SL/SEQIO/SEQIO.test \
2112	SL/PTCLEAN/PTCLEAN.test \
2113	PROBE/PROBE.test \
2114	SL/DB_QUERY/DB_QUERY.test \
2115
2116	TESTED_UNITS_MANUAL = \
2117	$(TEST_SANDBOXES) \
2118	$(UNITS_TESTED_FIRST) \
2119	$(UNITS_TESTED) \
2120
2121	# $(UNITS_WORKING)
2122
2123	# see UNIT_TESTER/sym2testcode.pl@disableErrorOnUnitsWithoutTests
2124
2125	#TESTED_UNITS = $(TESTED_UNITS_AUTO)
2126	TESTED_UNITS = $(TESTED_UNITS_MANUAL)
2127
2128	# ----------------------------------------
2129
2130	TEST_LOG_DIR = UNIT_TESTER/logs
2131	TEST_RUN_SUITE=$(MAKE) $(NODIR) -C UNIT_TESTER -f Makefile.suite -r
2132	TEST_MAKE_FLAGS=
2133	TEST_POST_CLEAN=
2134	ifeq ($(COVERAGE),1)
2135	TEST_POST_CLEAN=$(MAKE) clean_cov
2136	TEST_MAKE_FLAGS+=-j1
2137	endif
2138
2139
2140	%.test:
2141	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
2142	( \
2143	echo "fake[1]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
2144	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
2145	"UNITDIR=$(@D)" \
2146	"UNITLIBNAME=$(@F:.test=)" \
2147	"COVERAGE=$(COVERAGE)" \
2148	"ARB_PID=$(ARB_PID)_$(@F)" \
2149	runtest; \
2150	echo "fake[1]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"; \
2151	$(TEST_POST_CLEAN) \
2152	) >$(TEST_LOG_DIR)/$(@F).log 2>&1; \
2153	UNIT_TESTER/log_result.pl $(TEST_LOG_DIR)/$(@F).log )
2154
2155
2156	test_base: $(UNIT_TESTER_LIB:.a=.dummy) $(subst .test,.dummy,$(TEST_SANDBOXES))
2157
2158	clean_cov:
2159	find . \( -name ".gcda" -o -name ".gcov" -o -name "*.cov" \) -exec rm {} \;
2160
2161	clean_cov_all: clean_cov
2162	find . \( -name "*.gcno" \) -exec rm {} \;
2163
2164	run_tests: test_base clean_cov
2165	$(MAKE) "ARB_PID=UT_$$$$" run_tests_faked_arbpid
2166
2167	cleanup_faked_arbpids:
2168	@-rm ~/.arb_tmp/tmp/arb_pids_${USER}_${ARB_PID}_*
2169
2170	cleanup_faked_arbpids_and_fail: cleanup_faked_arbpids
2171	@false
2172
2173	run_tests_faked_arbpid:
2174	+@$(TEST_RUN_SUITE) init
2175	@echo "fake[2]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2176	$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(TESTED_UNITS) \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2177	@echo "fake[2]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2178	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2179	@$(MAKE) clean_cov >/dev/null
2180	@$(MAKE) cleanup_faked_arbpids
2181
2182	ut:
2183	ifeq ($(UNIT_TESTS),1)
2184	@echo $(MAKE) run_tests
2185	@$(MAKE) run_tests
2186	else
2187	@echo "Not compiled with unit tests"
2188	endif
2189
2190
2191	aut:
2192	+@$(TEST_RUN_SUITE) unskip
2193	$(MAKE) ut
2194
2195	# --------------------------------------------------------------------------------
2196
2197	TIMELOG=$(ARBHOME)/arb_time.log
2198	TIMEARGS=--append --output=$(TIMELOG) --format=" %E(%S+%U) %P [%C]"
2199	TIMECMD=$(TIME) $(TIMEARGS)
2200
2201	time_one:
2202	ifeq ($(ONE_TIMED_TARGET),)
2203	@echo "Error: You have to pass ONE_TIMED_TARGET to $@"
2204	false
2205	else
2206	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET)"
2207	@$(TIMECMD) $(MAKE) $(ONE_TIMED_TARGET)
2208	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET) [done]"
2209	endif
2210
2211	timed_target:
2212	ifeq ($(TIMED_TARGET),)
2213	@echo "Error: You have to pass TIMED_TARGET to $@"
2214	false
2215	else
2216	@echo "Build time:" > $(TIMELOG)
2217	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2218	@cat $(TIMELOG)
2219	@rm $(TIMELOG)
2220	endif
2221
2222	timed_target_tested:
2223	ifeq ($(TIMED_TARGET),)
2224	@echo "Error: You have to pass TIMED_TARGET to $@"
2225	false
2226	else
2227	@echo "Build time:" > $(TIMELOG)
2228	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2229	$(MAKE) "ONE_TIMED_TARGET=ut" time_one
2230	@cat $(TIMELOG)
2231	@rm $(TIMELOG)
2232	endif
2233
2234	clean_timed_target:
2235	ifeq ($(TIMED_TARGET),)
2236	@echo "Error: You have to pass TIMED_TARGET to $@"
2237	false
2238	else
2239	@echo "Build time:" > $(TIMELOG)
2240	$(MAKE) "ONE_TIMED_TARGET=clean" time_one
2241	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2242	@cat $(TIMELOG)
2243	@rm $(TIMELOG)
2244	endif
2245
2246	# --------------------------------------------------------------------------------
2247
2248	CHECKOUT_MODIFIED=0# set to 1 to temporarily skip test for modifications (do not check in if set to 1)
2249
2250	check_svn_does_not_contain_generated:
2251	ifeq ($(CHECKOUT_MODIFIED),0)
2252	@echo "Testing that build does not modify files in SVN"
2253	@test 0 = `svn status \| wc -l` \|\| ( \
2254	echo "The checkout is not/no longer clean:"; \
2255	svn status; \
2256	echo "- if this fails instantly, your checkout is not clean"; \
2257	echo "- if this fails after other targets, these targets modify checked in data"; \
2258	echo " (a common cause may be that depends are not up to date)"; \
2259	false)
2260	else
2261	grep -Hn 'CHECKOUT_MODIFIED' Makefile
2262	endif
2263
2264	check_svn_ignores_generated:
2265	@test 0 = `svn status \| grep '^\?' \| wc -l` \|\| ( \
2266	echo "There are svn-unignored files:"; \
2267	svn status \| grep '^\?'; \
2268	echo "(all generated files should be svn-ignored)"; \
2269	false)
2270
2271	check_svn_state: check_svn_does_not_contain_generated
2272	$(MAKE) check_svn_ignores_generated
2273	$(MAKE) savetest
2274
2275	things_that_always_should_work: depends proto
2276
2277	post_commit_check:
2278	@echo "---------------------------------------- [Initial]"
2279	$(MAKE) check_svn_state
2280
2281	$(MAKE) clean
2282	@echo "---------------------------------------- [After 'make clean']"
2283	$(MAKE) check_svn_state
2284
2285	$(MAKE) things_that_always_should_work
2286	@echo "---------------------------------------- [After 'make things_that_always_should_work']"
2287	$(MAKE) check_svn_state
2288
2289	$(MAKE) all
2290	@echo "---------------------------------------- [After 'make all']"
2291	$(MAKE) check_svn_state
2292
2293	$(MAKE) things_that_always_should_work
2294	@echo "---------------------------------------- [Final]"
2295	$(MAKE) check_svn_state
2296
2297	# --------------------------------------------------------------------------------
2298
2299	build: arb
2300	$(MAKE) binlink preplib compile_compatibility
2301
2302	all:
2303	@echo "Build time" > $(TIMELOG)
2304	@echo "$(SEP) $(MAKE) build"
2305	@$(TIMECMD) $(MAKE) build
2306	@echo $(SEP)
2307	@echo "made 'all' with success."
2308	@echo "to start arb enter 'arb'"
2309	ifeq ($(UNIT_TESTS),1)
2310	@echo $(MAKE) run_tests
2311	@$(TIMECMD) $(MAKE) run_tests
2312	endif
2313	@echo "$(SEP) $(MAKE) build [done]"
2314	@$(MAKE) save_test_no_error >/dev/null # just show hints
2315	@cat $(TIMELOG)
2316	@rm $(TIMELOG)
2317

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