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Last change on this file was 13145, checked in by westram, 10 years ago
partial update from 'trunk' into 'pars' skip same as in [13079] adds: log:trunk@13131:13144
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 70.1 KB

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1	# =============================================================== #
2	# #
3	# File : Makefile #
4	# #
5	# Institute of Microbiology (Technical University Munich) #
6	# http://www.arb-home.de/ #
7	# #
8	# =============================================================== #
9
10	# -----------------------------------------------------
11	# The ARB Makefile is aware of the following defines:
12	#
13	# CC C compiler (should be defined by OS)
14	# CXX C++ compiler (should be defined by OS)
15	#
16	# BUILDHOST_64=0/1 1=>compile on 64 bit platform (defaults to ARB_64)
17	# DEVELOPER=name special compilation (values: ANY,RELEASE,your name)
18	# OPENGL=0/1 whether OPENGL is available
19	#
20	# -----------------------------------------------------
21	# ARB Makefile and ARB source code are aware of the following defines:
22	#
23	# $(MACH) name of the machine (LINUX or DARWIN; see config.makefile)
24	# DEBUG compiles the DEBUG sections
25	# DEBUG_GRAPHICS all X-graphics are flushed immediately (for debugging)
26	# ARB_64=0/1 1=>compile 64 bit version
27	# UNIT_TESTS=0/1 1=>compile in unit tests and call them after build
28	# COVERAGE=0/1/2 compile in gcov support (useful together with UNIT_TESTS=1)
29	# 0=no, 1+2=compile in, 1=show
30	# STABS=0/1 force stabs format? (0 = "use default format")
31	# SANITIZE=0/#/all use Sanitizer? (defaults to 0,
32	# 1=AddressSanitizer+LeakSanitizer,
33	# 2=UndefinedBehaviorSanitizer,
34	# combine bit-values to activate multiple Sanitizers,
35	# specify 'all' to activate all)
36	# SHOWTODO=0/1 activate TODO-warnings? (defaults to 0, except for ralf)
37	#
38	# -----------------------------------------------------
39	# The ARB source code is aware of the following defines:
40	#
41	# NDEBUG doesn't compile the DEBUG sections
42	# DEVEL_$(DEVELOPER) developer-dependent flag (enables you to have private sections in code)
43	# DEVELOPER='ANY' (default setting) will be ignored
44	# configurable in config.makefile
45	#
46	# -----------------------------------------------------
47	# Read configuration
48	include config.makefile
49
50	# set defaults for variables commented out in config.makefile:
51	ifndef DARWIN
52	DARWIN:=0
53	endif
54	ifndef LINUX
55	LINUX:=0
56	endif
57	ifndef DEBIAN
58	DEBIAN:=0
59	endif
60	ifndef REDHAT
61	REDHAT:=0
62	endif
63	ifndef ARB_64
64	ARB_64=1#default to 64bit
65	endif
66
67	# compiler settings:
68	ifneq ($(CC),use__A_CC__instead_of__CC)
69
70	A_CC:=$(CC)# compile C
71	A_CXX:=$(CXX)# compile C++
72
73	# uncomment to ensure no submakefile uses CC and CXX directly
74	override CC:=use__A_CC__instead_of__CC
75	override CXX:=use__A_CXX__instead_of__CXX
76
77	endif
78
79	export CC CXX A_CC A_CXX
80
81	# unconditionally prepend $(ARBHOME)/lib to LD_LIBRARY_PATH if not found
82	ifeq ($(findstring $(ARBHOME)/lib,$(LD_LIBRARY_PATH)),)
83	LD_LIBRARY_PATH:=${ARBHOME}/lib:$(LD_LIBRARY_PATH)
84	endif
85
86	FORCEMASK = umask 002
87	NODIR=--no-print-directory
88
89	SED:=$(ARBHOME)/SH/arb_sed
90	READLINK:=$(ARBHOME)/SH/arb_readlink
91
92	# ---------------------- compiler version detection
93
94	# supported gcc versions:
95	ALLOWED_gcc_VERSIONS=\
96	4.3.1 4.3.2 4.3.3 4.3.4 \
97	4.4.1 4.4.3 4.4.5 4.4.6 4.4.7 \
98	4.5.2 \
99	4.6.1 4.6.2 4.6.3 \
100	4.7.1 4.7.2 4.7.3 4.7.4 \
101	4.8.0 4.8.1 4.8.2 4.8.3 \
102	4.9.0 4.9.1 4.9.2 \
103
104	# supported clang versions:
105	ALLOWED_clang_VERSIONS=\
106	4.2.1 \
107
108	# ----------------------
109
110	COMPILER_INFO:=$(shell SOURCE_TOOLS/arb_compiler_version.pl $(A_CXX))
111	COMPILER_NAME:=$(word 1,$(COMPILER_INFO))
112	COMPILER_VERSION:=$(word 2,$(COMPILER_INFO))
113
114	USE_CLANG:=0
115	ifneq ($(COMPILER_NAME),gcc)
116	ifeq ($(COMPILER_NAME),clang)
117	USE_CLANG:=1
118	else
119	$(error failed to detect COMPILER_NAME (got '$(COMPILER_NAME)', expected 'clang' or 'gcc'))
120	endif
121	endif
122
123	ifeq ($(USE_CLANG),1)
124	ALLOWED_COMPILER_VERSIONS=$(ALLOWED_clang_VERSIONS)
125	else
126	ALLOWED_COMPILER_VERSIONS=$(ALLOWED_gcc_VERSIONS)
127	endif
128
129	COMPILER_VERSION_ALLOWED=$(strip $(subst ___,,$(foreach version,$(ALLOWED_COMPILER_VERSIONS),$(findstring ___$(version)___,___$(COMPILER_VERSION)___))))
130
131	#---------------------- split gcc version
132
133	SPLITTED_VERSION:=$(subst ., ,$(COMPILER_VERSION))
134
135	USE_GCC_MAJOR:=$(word 1,$(SPLITTED_VERSION))
136	USE_GCC_MINOR:=$(word 2,$(SPLITTED_VERSION))
137	USE_GCC_PATCHLEVEL:=$(word 3,$(SPLITTED_VERSION))
138
139	USE_GCC_452_OR_HIGHER:=
140	USE_GCC_46_OR_HIGHER:=
141	USE_GCC_47_OR_HIGHER:=
142	USE_GCC_48_OR_HIGHER:=
143	USE_GCC_49_OR_HIGHER:=
144
145	ifeq ($(USE_GCC_MAJOR),4)
146	ifeq ($(USE_GCC_MINOR),5)
147	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),23456789)','')
148	USE_GCC_452_OR_HIGHER:=yes
149	endif
150	else
151	ifneq ('$(findstring $(USE_GCC_MINOR),6789)','')
152	USE_GCC_452_OR_HIGHER:=yes
153	USE_GCC_46_OR_HIGHER:=yes
154	ifneq ($(USE_GCC_MINOR),6)
155	USE_GCC_47_OR_HIGHER:=yes
156	ifneq ($(USE_GCC_MINOR),7)
157	USE_GCC_48_OR_HIGHER:=yes
158	ifneq ($(USE_GCC_MINOR),8)
159	USE_GCC_49_OR_HIGHER:=yes
160	endif
161	endif
162	endif
163	endif
164	endif
165	else
166	USE_GCC_452_OR_HIGHER:=yes
167	USE_GCC_46_OR_HIGHER:=yes
168	USE_GCC_47_OR_HIGHER:=yes
169	USE_GCC_48_OR_HIGHER:=yes
170	USE_GCC_49_OR_HIGHER:=yes
171	endif
172
173	#---------------------- define special directories for non standard builds
174
175	ifeq ($(DARWIN),1)
176	OSX_FW:=/System/Library/Frameworks
177	OSX_FW_OPENGL:=$(OSX_FW)/OpenGL.framework/Versions/A/Libraries
178	OSX_FW_GLUT:=$(OSX_FW)/GLUT.framework/Versions/A/Libraries
179	OSX_FW_IMAGEIO:=$(OSX_FW)/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources
180	endif
181
182	#----------------------
183
184	ifeq ($(DARWIN),1)
185	LINK_STATIC=1# link static
186	else
187	LINK_STATIC=0# link dynamically
188	# LINK_STATIC=1# link static (testing only)
189	endif
190
191	shared_cflags :=# flags for shared lib compilation
192	lflags :=# linker flags
193	clflags :=# linker flags (when passed through gcc)
194	extended_warnings :=# warning flags for C and C++-compiler
195	extended_cpp_warnings :=# warning flags for C++-compiler only
196
197	# TEMPORARY WORKAROUND for linker issues with launchpad binutils
198	# code was added to ld to check for overlapping FDEs. Since ARB
199	# worked before, we want this not to fail for the moment.
200	# FIXME: remove this!
201	clflags += -Wl,-noinhibit-exec
202
203
204	ifeq ($(DEBUG),0)
205	dflags := -DNDEBUG# defines
206	ifeq ($(USE_CLANG),1)
207	cflags := -O3# compiler flags (C and C++)
208	else
209	cflags := -O4# compiler flags (C and C++)
210	lflags += -O2# linker flags
211	clflags += -Wl,-O2# passthrough linker flags
212	endif
213	endif
214
215	ifeq ($(DEBIAN),1)
216	lflags += -rpath=/usr/lib/arb/lib -z relro
217	clflags += -Wl,-rpath=/usr/lib/arb/lib -Wl,-z,relro
218	endif
219
220	ifeq ($(DEBUG),1)
221	dflags := -DDEBUG
222
223	gdb_common := -g -g3 -ggdb -ggdb3
224
225	DBGOPTI:=-O0
226	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
227	DBGOPTI:=-Og
228	endif
229
230	ifeq ($(STABS),1)
231	cflags := $(DBGOPTI) $(gdb_common) -gstabs+ # using stabs+ (enable this for bigger debug session: debugs inlines, quick var inspect, BUT valgrind stops working :/)
232	else
233	cflags := $(DBGOPTI) $(gdb_common) # (using dwarf - cant debug inlines here, incredible slow on showing variable content)
234	endif
235
236	# cflags := $(DBGOPTI) $(gdb_common) -gdwarf-3 # (specify explicit dwarf format)
237	# cflags := $(DBGOPTI) $(gdb_common) -gstabs # using stabs (same here IIRC)
238	# cflags := -O2 $(gdb_common) # use this for callgrind (force inlining)
239
240	ifeq ($(DARWIN),0)
241	lflags += -g
242	clflags += -Wl,-g
243	endif
244
245	ifeq ($(DEBUG_GRAPHICS),1)
246	dflags += -DDEBUG_GRAPHICS
247	endif
248
249	endif # DEBUG only
250
251	# control how much you get spammed
252	# (please do not change default in SVN, use developer specific setting as below)
253	POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl
254	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --original# dont modify compiler output
255	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --hide-Noncopyable-advices
256	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --show-useless-Weff++
257	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --no-warnings
258	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --only-first-error
259	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --no-warnings --only-first-error
260	ifeq ($(DEVELOPER),ELMAR)
261	POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --only-first-error
262	endif
263
264	# Enable extra warnings
265	extended_warnings :=
266	extended_cpp_warnings :=
267
268	# C and C++
269	extended_warnings += -Wwrite-strings -Wunused -Wno-aggregate-return -Wshadow
270
271	# C++ only
272	extended_cpp_warnings += -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute
273	extended_cpp_warnings += -Wctor-dtor-privacy# < gcc 3
274	# extended_cpp_warnings += -Wfloat-equal# gcc 3.0
275
276	# ------- above only warnings available in 3.0
277
278	WEFFC_BROKEN:=0
279	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
280	ifneq ('$(USE_GCC_48_OR_HIGHER)','yes')
281	# -Weffc++ broken in 4.7.x series
282	# gcc 4.7.3 crashes on GenomeImport.cxx when -Weffc++ is active
283	# (bug reported https://gcc.gnu.org/bugzilla/show_bug.cgi?id=56923; apparently wont be fixed for 4.7-series)
284	# gcc 4.7.4 crashes on DBwriter.cxx when -Weffc++ is active
285	WEFFC_BROKEN:=1
286	endif
287	endif
288	ifeq ('$(WEFFC_BROKEN)','0')
289	extended_cpp_warnings += -Weffc++# gcc 3.0.1
290	endif
291	extended_cpp_warnings += -Wmissing-noreturn# gcc 3.0.2
292	# extended_cpp_warnings += -Wold-style-cast# gcc 3.0.4 (warn about 28405 old-style casts)
293	extended_cpp_warnings += -Winit-self# gcc 3.4.0
294	extended_cpp_warnings += -Wstrict-aliasing# gcc 3.4
295	extended_cpp_warnings += -Wextra# gcc 3.4.0
296	ifeq ($(DEBUG),1)
297	# turn off -Wmaybe-uninitialized in debug mode (gets activated with -Wextra). too many bogus warnings
298	extended_cpp_warnings += -Wno-maybe-uninitialized
299	endif
300	ifeq ('$(USE_GCC_452_OR_HIGHER)','yes')
301	extended_cpp_warnings += -Wlogical-op# gcc 4.5.2
302	endif
303	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
304	# extended_cpp_warnings += -Wunused-local-typedefs# gcc 4.7 (fails for each STATIC_ASSERT, enable only for Cxx11)
305	# extended_cpp_warnings += -Wzero-as-null-pointer-constant# gcc 4.7 #@@@ activate
306	endif
307	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
308	extended_cpp_warnings += -Wunused-local-typedefs# available since gcc 4.7 (but fails for each STATIC_ASSERT, so enable only for Cxx11)
309	endif
310
311	#---------------------- turn off clang bogus warnings
312
313	ifeq ($(USE_CLANG),1)
314	# -Wmismatched-tags warns about struct/class mismatch in forward declarations (which is explicitely allowed)
315	# -Wchar-subscripts reports too many bogus warnings for "array['x']" (when 'x' is known to be in range [0..128])
316	# -Wunused-private-field report too many false positives (currently ~ 2 of 3)
317	# -Wstring-plus-int warns about common ARB coding practice
318	# -Wgnu-static-float-init warns about accepted GNU extension
319	extended_cpp_warnings += -Wno-mismatched-tags -Wno-char-subscripts -Wno-unused-private-field -Wno-string-plus-int -Wno-gnu-static-float-init
320	endif
321
322	#---------------------- developer
323
324	ifneq ($(DEVELOPER),ANY) # ANY=default setting (skip all developer specific code)
325	dflags += -DDEVEL_$(DEVELOPER)# activate developer/release specific code
326	endif
327
328	#---------------------- activate TODO warnings?
329
330	ifndef SHOWTODO
331	ifeq ($(DEVELOPER),RALF)
332	SHOWTODO:=1
333	else
334	SHOWTODO:=0
335	endif
336	endif
337	ifeq ($(SHOWTODO),1)
338	dflags += -DWARN_TODO# activate "TODO" warnings
339	endif
340
341	#---------------------- activate Sanitizers?
342
343	ASAN_OPTIONS:=handle_segv=0:color=0
344	ASAN_OPTIONS+=:detect_leaks=1 # comment-out to disable leak-detection
345	ASAN_OPTIONS+=:check_initialization_order=1
346
347	# suppressions: SOURCE_TOOLS/arb.leaksan.supp
348	LSAN_OPTIONS:=max_leaks=3:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp
349
350
351	ifndef SANITIZE
352	SANITIZE:=0
353	endif
354
355	SANITIZE_ADDRESS:=0
356	SANITIZE_UNDEFINED:=0
357
358	ifneq ($(SANITIZE),0)
359	ifeq ($(SANITIZE),all)
360	SANITIZE:=3
361	endif
362
363	ifeq ($(SANITIZE),1)
364	SANITIZE_ADDRESS:=1
365	else
366	ifeq ($(SANITIZE),2)
367	SANITIZE_UNDEFINED:=1
368	else
369	ifeq ($(SANITIZE),3)
370	SANITIZE_ADDRESS:=1
371	SANITIZE_UNDEFINED:=1
372	else
373	$(error Unknown value '$(SANITIZE)' specified for SANITIZE in config.makefile)
374	endif
375	endif
376	endif
377	endif
378
379	ifeq ($(SANITIZE_ADDRESS),1)
380	ifneq ('$(USE_GCC_48_OR_HIGHER)','yes')
381	$(info AddressSanitizer not usable with gcc $(COMPILER_VERSION) - disabled)
382	SANITIZE_ADDRESS:=0
383	else
384	ifneq ('$(USE_GCC_49_OR_HIGHER)','yes')
385	$(warning note that LeakSanitizer does not work with gcc $(COMPILER_VERSION))
386	endif
387	endif
388	endif
389
390	ifeq ($(SANITIZE_UNDEFINED),1)
391	ifneq ('$(USE_GCC_49_OR_HIGHER)','yes')
392	$(info UndefinedBehaviorSanitizer not usable with gcc $(COMPILER_VERSION) - disabled)
393	SANITIZE_UNDEFINED:=0
394	endif
395	endif
396
397	#---------------------- 32 or 64 bit
398
399	ifndef BUILDHOST_64
400	BUILDHOST_64:=$(ARB_64)# assume build host is same as version (see config.makefile)
401	endif
402
403	cross_cflags:=
404	cross_lflags:=
405	cross_clflags:=
406
407	ifeq ($(ARB_64),1)
408	dflags += -DARB_64 #-fPIC
409	shared_cflags += -fPIC
410
411	ifeq ($(BUILDHOST_64),1)
412	# build 64-bit ARB version on 64-bit host
413	CROSS_LIB:=# empty = autodetect below
414	ifeq ($(DARWIN),1)
415	cross_cflags += -arch x86_64
416	cross_lflags += -arch x86_64
417	cross_clflags += -arch x86_64
418	endif
419	else
420	# build 64-bit ARB version on 32-bit host
421	CROSS_LIB:=/lib64
422	cross_cflags += -m64
423	cross_lflags += -m64 -m elf_x86_64
424	cross_clflags += -m64 -Wl,-m64,-m,elf_x86_64
425	endif
426	else
427	ifeq ($(BUILDHOST_64),1)
428	# build 32-bit ARB version on 64-bit host
429	CROSS_LIB:=# empty = autodetect below
430	cross_cflags += -m32
431	cross_lflags += -m32 -m elf_i386
432	cross_clflags += -m32 -Wl,-m32,-m,elf_i386
433	else
434	# build 32-bit ARB version on 32-bit host
435	CROSS_LIB:=/lib
436	endif
437	endif
438
439	cflags += $(cross_cflags)
440	lflags += $(cross_lflags)
441	clflags += $(cross_clflags)
442
443	ifeq ('$(CROSS_LIB)','')
444	# autodetect libdir
445	ifeq ($(ARB_64),1)
446	CROSS_LIB:=$(shell (test -d /lib64 && echo lib64) \|\| echo lib)
447	else
448	CROSS_LIB:=$(shell (test -d /lib32 && echo lib32) \|\| echo lib)
449	endif
450	endif
451
452	#---------------------- unit tests
453
454	ifndef UNIT_TESTS
455	UNIT_TESTS=0#default is "no tests"
456	endif
457	ifeq ($(UNIT_TESTS),1)
458	dflags += -DUNIT_TESTS
459	UNIT_TESTER_LIB=UNIT_TESTER/UNIT_TESTER.a
460	else
461	UNIT_TESTER_LIB=
462	endif
463
464	#---------------------- use gcov
465
466	ifndef COVERAGE
467	COVERAGE=0#default is "no"
468	endif
469	ifneq ($(COVERAGE),0)
470	GCOVFLAGS=-ftest-coverage -fprofile-arcs
471	cflags += $(GCOVFLAGS)
472	EXECLIBS=-lgcov
473	else
474	GCOVFLAGS=
475	EXECLIBS=
476	endif
477
478	#---------------------- other flags
479
480	dflags += -D$(MACH) # define machine
481
482	ifeq ($(DARWIN),1)
483	shared_cflags += -fno-common
484	else
485	dflags += $(shell getconf LFS_CFLAGS)
486	endif
487
488	cflags += -pipe
489	cflags += -fmessage-length=0# don't wrap compiler output
490	cflags += -fshow-column# show columns
491	cflags += -funit-at-a-time
492	cflags += -fPIC
493	cflags += -fno-common# link all global data into one namespace
494	cflags += -fstrict-aliasing# gcc 3.4
495	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
496	cflags += -fno-diagnostics-show-caret#gcc 4.8 (4.7.?)
497	endif
498	#cflags += -save-temps# uncomment to see preprocessor output
499
500	#---------------------- various sanitizers
501
502	COMMON_SANITIZE_FLAGS:=-ggdb3 -fno-omit-frame-pointer
503
504	# activate AddressSanitizer+LeakSanitizer?
505	ifeq ($(SANITIZE_ADDRESS),1)
506	cflags += $(COMMON_SANITIZE_FLAGS) -fsanitize=address
507	EXECLIBS += -lasan
508	# EXECLIBS += -static-libasan
509	endif
510
511	# activate UndefinedBehaviorSanitizer?
512	ifeq ($(SANITIZE_UNDEFINED),1)
513	cflags += $(COMMON_SANITIZE_FLAGS) -fsanitize=undefined
514	ifeq ('$(DEBUG)','1')
515	ifeq ($(USE_GCC_MAJOR),4)
516	ifeq ($(USE_GCC_MINOR),9)
517	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),01)','')
518	# workaround https://gcc.gnu.org/bugzilla/show_bug.cgi?id=63531 for 4.9.0 + 4.9.1
519	# (problem is fixed in 4.9.2 release)
520	extended_cpp_warnings:=$(subst -Weffc++,,$(extended_cpp_warnings))
521	endif
522	endif
523	endif
524	endif
525	EXECLIBS += -lubsan
526	endif
527
528	#---------------------- X11 location
529
530	ifeq ($(DARWIN),1)
531	XHOME:=$(PREFIX)
532	else
533	ifeq ($(DEBIAN),1)
534	XHOME:=$(PREFIX)
535	else
536	XHOME:=/usr/X11R6
537	endif
538	endif
539
540	XINCLUDES:=-I$(XHOME)/include
541	ifeq ($(DARWIN),1)
542	XINCLUDES += -I$(OSX_FW)/GLUT.framework/Headers -I$(OSX_FW)/OpenGL.framework/Headers -I$(OSX_SDK)/usr/include/krb5
543
544	XLIBS := -L$(XHOME)/lib -lXm -lpng -lz -lXt -lX11 -lXext -lXp -lXmu -lXi
545	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGL.dylib:$(OSX_FW_OPENGL)/libGL.dylib
546	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGLU.dylib:$(OSX_FW_OPENGL)/libGLU.dylib
547	else
548	XLIBS:=-L$(XHOME)/$(CROSS_LIB) -lXm -lXpm -lXt -lXext -lX11
549	endif
550
551	dflags += -DARB_MOTIF
552
553	#---------------------- open GL
554
555	ifeq ($(OPENGL),1)
556	cflags += -DARB_OPENGL # activate OPENGL code
557	GL := gl # this is the name of the OPENGL base target
558	GL_LIB_SYS := -lGL -lGLU
559	GL_LIB_ARB := -L$(ARBHOME)/GL/glAW -lglAW
560
561	ifeq ($(DARWIN),1)
562	GL_LIB_SYS += -lpthread
563	endif
564
565	GL_PNGLIBS_ARB := -L$(ARBHOME)/GL/glpng -lglpng_arb
566	GL_PNGLIBS_SYS := -lpng
567
568	GLEWLIB := -lGLEW -lGLw
569	ifeq ($(DARWIN),1)
570	GLUTLIB := -glut
571	else
572	GLUTLIB := -lglut
573	endif
574
575	GL_LIBS_SYS := $(GL_LIB_SYS) $(GL_PNGLIBS_SYS) $(GLEWLIB) $(GLUTLIB)
576	GL_LIBS_ARB := $(GL_LIB_ARB) $(GL_PNGLIBS_ARB)
577
578	RNA3D_LIB := RNA3D/RNA3D.a
579
580	else
581
582	GL_LIBS_ARB:=# no opengl -> no libs
583	GL_LIBS_SYS:=# no opengl -> no libs
584	GL:=# don't build ARB openGL libs
585
586	RNA3D_LIB :=
587
588	endif
589
590	RNA3D_LIB_4_DEPENDS := RNA3D/RNA3D.a
591
592	GL_LIBS:=$(GL_LIBS_ARB) $(GL_LIBS_SYS)
593
594	#---------------------- tiff lib:
595
596	TIFFLIBS := -ltiff
597
598	#---------------------- glib:
599
600	ARB_NEEDED_GLIB=glib-2.0
601
602	ARB_GLIB_INCLUDE:=$(strip $(shell pkg-config --cflags $(ARB_NEEDED_GLIB)))
603	ARB_GLIB_LIBS:=$(strip $(shell pkg-config --libs $(ARB_NEEDED_GLIB)))
604
605	#---------------------- basic libs:
606
607	SYSLIBS:=
608
609	ifeq ($(DARWIN),1)
610	SYSLIBS += -lstdc++
611	else
612	SYSLIBS += -lm $(ARB_GLIB_LIBS)
613	endif
614
615	#---------------------- include symbols?
616
617	ifeq ($(TRACESYM),1)
618	ifeq ($(USE_CLANG),0)
619	cflags += -rdynamic
620	lflags += --export-dynamic
621	clflags += -rdynamic -Wl,--export-dynamic
622	endif
623	endif
624
625	#---------------------- system dependent commands
626
627	ifeq ($(DARWIN),1)
628	TIME:=gtime
629	else
630	TIME:=/usr/bin/time
631	endif
632
633	# -------------------------------------------------------------------------
634	# Don't put any machine/version/etc conditionals below!
635	# (instead define variables above)
636	# -------------------------------------------------------------------------
637
638	cflags += -W -Wall $(dflags) $(extended_warnings)
639	cxxflags := $(extended_cpp_warnings)
640
641	# add CFLAGS + CPPFLAGS from environment for DEBIAN build
642	ifeq ($(DEBIAN),1)
643	cflags := $(CFLAGS) $(cflags)
644	cxxflags += $(CPPFLAGS)
645	endif
646
647	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
648	cxxflags += -std=gnu++11# see also TEMPLATES/cxxforward.h@USE_Cxx11
649	else
650	# only use for gcc versions between 4.3 and <4.7 (4.7++ adds -Wc++11-compat above)
651	HAVE_GNUPP0X=`SOURCE_TOOLS/requireVersion.pl 4.3 $(COMPILER_VERSION)`
652	ifeq ($(HAVE_GNUPP0X),1)
653	# ensure compatibility with upcoming C++ standard
654	cxxflags += -std=gnu++0x
655	endif
656	endif
657
658	LINK_STATIC_LIB := ld $(lflags) -r -o# link static lib
659	LINK_EXECUTABLE := $(A_CXX) $(clflags) -o# link executable (c++)
660
661	ifeq ($(LINK_STATIC),1)
662	SHARED_LIB_SUFFIX = a# static lib suffix
663	LINK_SHARED_LIB := $(LINK_STATIC_LIB)
664	else
665	SHARED_LIB_SUFFIX = so# shared lib suffix
666	LINK_SHARED_LIB := $(A_CXX) $(clflags) -shared $(GCOVFLAGS) -o# link shared lib
667	endif
668
669	# delete variables unused below
670	lflags:=
671	clflags:=
672
673	# other used tools
674	MAKEDEPEND_PLAIN = makedepend
675	MAKEDEPEND = $(FORCEMASK);$(MAKEDEPEND_PLAIN)
676
677	#SEP:=--------------------------------------------------------------------------------
678	SEP=[`date +%M:%S.%N`] ------------------------------------------------
679	# to analyse timings run
680	# make -j9 clean; make -j9 all \| grep '^\[' \| sort
681	# make -j9 "TIMED_TARGET=perl" clean_timed_target \| grep '^\[' \| sort
682
683	CORE_LIB=-lCORE
684	ARBDB_LIB=-lARBDB $(CORE_LIB)
685	LIBS = $(ARBDB_LIB) $(SYSLIBS)
686
687	GUI_LIBS_PREFIX:=
688	ifeq ($(DARWIN),1)
689	# this seem to be added at wrong place, since opengl is only needed to link EDIT4
690	GUI_LIBS_PREFIX:=-framework GLUT -framework OpenGL
691	endif
692
693	GUI_LIBS=$(GUI_LIBS_PREFIX) $(LIBS) -lAWT -lWINDOW
694	GUI_LIBS+=$(XLIBS)
695
696	LIBPATH = -L$(ARBHOME)/lib
697
698	DEST_LIB = lib
699	DEST_BIN = bin
700
701	CC_INCLUDES := -I. -I$(ARBHOME)/INCLUDE $(XINCLUDES) $(ARB_GLIB_INCLUDE)
702	CXX_INCLUDES := $(CC_INCLUDES)
703	MAKEDEPENDFLAGS := -- -DARB_OPENGL -DUNIT_TESTS -D__cplusplus -I. -Y$(ARBHOME)/INCLUDE
704
705	# -------------------------------
706	# old PTSERVER or PTPAN?
707
708	ifeq ($(PTPAN),1)
709	# PTPAN only libs
710	ARCHS_PT_SERVER = \
711	ptpan/PROBE.a
712	else
713	ifeq ($(PTPAN),2)
714	# special mode to compile both servers (developers only!)
715	ARCHS_PT_SERVER = \
716	ptpan/PROBE.a \
717	PROBE/PROBE.a
718	ARCHS_PT_SERVER_LINK = PROBE/PROBE.a# default to old ptserver
719	else
720	# PT-server only libs
721	ARCHS_PT_SERVER = \
722	PROBE/PROBE.a
723	endif
724	endif
725
726	ifndef ARCHS_PT_SERVER_LINK
727	ARCHS_PT_SERVER_LINK = $(ARCHS_PT_SERVER)
728	endif
729
730	# ---------------------------------------
731	# wrap main()
732
733	use_ARB_main=$(ARBHOME)/SOURCE_TOOLS/arb_main_cpp.o
734	use_ARB_main_C=$(ARBHOME)/SOURCE_TOOLS/arb_main_c.o
735
736	# -----------------------------------------
737	# export variables to submakefiles
738
739	include SOURCE_TOOLS/export2sub
740
741	# do not define (exported) variables below this point
742
743	# -------------------------
744	# Main arb targets:
745	# -------------------------
746
747	first_target:
748	$(MAKE) checks
749	@echo $(SEP)
750	@echo 'Main targets:'
751	@echo ''
752	@echo ' all - Compile ARB + TOOLs + and copy shared libs + link foreign software'
753	@echo ' (That is most likely the target you want)'
754	@echo ''
755	@echo ' clean - remove generated files ("SUBDIR/SUBDIR.clean" to clean only SUBDIR)'
756	@echo ' rebuild - clean + all'
757	@echo ' relink - remove all binaries and relink them from objects'
758	@echo ''
759	@echo 'Some often used sub targets (make all makes them all):'
760	@echo ''
761	@echo ' arb - Just compile ARB (but none of the integrated tools)'
762	@echo ' menus - create lib/gde/arb.menu from GDEHELP/ARB_GDEmenus.source'
763	@echo ' perl - Compile the PERL XSUBS into lib/ARB.so and create links in lib to perl'
764	@echo ' binlink - Create all links in the bin directory'
765	@echo ''
766	@echo 'Development targets:'
767	@echo ''
768	@echo ' depends - create or update dependencies ("SUBDIR/SUBDIR.depends" to update only SUBDIR)'
769	@echo ' proto - create or update prototypes ("SUBDIR/SUBDIR.proto" to update only SUBDIR)'
770	@echo ' tags - create tags for xemacs'
771	@echo ' show - show available shortcuts (AKA subtargets)'
772	@echo ' up - shortcut for depends+proto+tags'
773	ifeq ($(UNIT_TESTS),1)
774	@echo ' ut - only run tests'
775	endif
776	@echo ' modified - rebuild files modified in svn checkout (does touch)'
777	@echo ' touch - touch files modified in svn checkout'
778	@echo ''
779	@echo 'Internal maintenance:'
780	@echo ''
781	@echo ' relinfo - show help on release targets'
782	@echo ' tarfile - make rebuild and create arb version tarfile ("tarfile_quick" to skip rebuild)'
783	@echo ' save - save all basic ARB sources into arbsrc_DATE ("savetest" to check filelist)'
784	@echo ' patch - save svn diff to patchfile'
785	@echo ' source_doc - create doxygen documentation'
786	@echo ' relocated - rebuild partly (use when you have relocated ARBHOME)'
787	@echo ' check_res - check ressource usage'
788	@echo ' dep_graph - Build dependency graphs'
789	@echo ' clean_cov - Clean coverage results'
790	@echo ''
791	@echo ' post_commit_check - Checks whether'
792	@echo ' * main make targets work,'
793	@echo ' * dependencies and prototypes are up to date,'
794	@echo ' * SVN-controlled files remain unaffected by called targets and'
795	@echo ' * all generated files are ignored.'
796	@echo ' (has to be called in a clean SVN checkout)'
797	@echo $(SEP)
798	@echo ''
799
800	relinfo:
801	@echo ''
802	@echo $(SEP)
803	@echo 'Release targets:'
804	@echo ''
805	@echo ' inc_candi - increase RC candidate-number (only possible in "rc" branch, not needed for RC1)'
806	@echo ' inc_patch - increase release patchlevel (only possible in "stable" branch)'
807	@echo ' inc_minor - increase minor version number (only possible in "trunk")'
808	@echo ' inc_major - increase MAJOR version number (only possible in "trunk")'
809	@echo ''
810	@echo ' show_version - show version tag'
811	@echo ''
812	@echo $(SEP)
813	@echo ''
814
815	# auto-generate config.makefile:
816
817	CONFIG_MAKEFILE_FOUND=$(wildcard config.makefile)
818
819	config.makefile : config.makefile.template
820	@echo --------------------------------------------------------------------------------
821	ifeq ($(strip $(CONFIG_MAKEFILE_FOUND)),)
822	@cp $< $@
823	@echo '$(ARBHOME)/$@:1: has been generated.'
824	@echo 'Please edit $@ to configure your system!'
825	@echo --------------------------------------------------------------------------------
826	@false
827	else
828	@echo '$(ARBHOME)/$<:1: is more recent than'
829	@echo '$(ARBHOME)/$@:1:'
830	@ls -al config.makefile*
831	@echo --------------------------------------------------------------------------------
832	@echo "Updating $@ (if this fails, check manually)"
833	SOURCE_TOOLS/update_config_makefile.pl
834	@echo "Sucessfully updated $@"
835	@echo --------------------------------------------------------------------------------
836	@ls -al config.makefile*
837	@echo --------------------------------------------------------------------------------
838	@echo "Diff to your old config.makefile:"
839	@echo --------------------------------------------------------------------------------
840	-diff $@.bak $@
841	@echo --------------------------------------------------------------------------------
842	endif
843
844	# check if everything is configured correctly
845
846	check_DEVELOPER:
847	ifndef DEVELOPER
848	@echo 'config.makefile:1: DEVELOPER not defined'
849	@false
850	endif
851
852	check_DEBUG:
853	ifndef dflags
854	@echo 'config.makefile:1: DEBUG has to be defined. Valid values are 0 and 1'
855	@false
856	endif
857
858	check_ARB_64:
859	ifndef ARB_64
860	@echo 'config.makefile:1: ARB_64 has to be defined. Valid values are 0 and 1'
861	@false
862	endif
863
864	# ---------------------------------------- check gcc version
865
866	COMPILER_BROKEN:=0
867
868	# gcc 4.8.0 produces invalid code (see #617)
869	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.8.0')
870	COMPILER_BROKEN:=1
871	endif
872
873	check_same_GCC_VERSION:
874	$(ARBHOME)/SOURCE_TOOLS/check_same_compiler_version.pl $(COMPILER_NAME) $(COMPILER_VERSION_ALLOWED)
875
876	check_GCC_VERSION:
877	@echo 'Compiler version check:'
878	ifeq ('$(COMPILER_VERSION_ALLOWED)', '')
879	@echo " - Your compiler is '$(COMPILER_NAME)' version '$(COMPILER_VERSION)'"
880	@echo ' This version is not in the list of supported $(COMPILER_NAME)-versions:'
881	@$(foreach version,$(ALLOWED_COMPILER_VERSIONS),echo ' * $(version)';)
882	@echo ' - You may either ..'
883	@echo ' - add your version to ALLOWED_$(COMPILER_NAME)_VERSIONS in the Makefile and try it out or'
884	@echo ' - switch to one of the allowed versions (see arb_README_gcc.txt for installing'
885	@echo ' a different version of gcc)'
886	$(error Unsupported compiler '$(COMPILER_NAME)' version '$(COMPILER_VERSION)')
887	else
888	ifeq ($(COMPILER_BROKEN),1)
889	$(error $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)' would build a broken ARB version. Compilation refused)
890	else
891	@echo " - Supported $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)' detected - fine!"
892	@echo ''
893	$(MAKE) check_same_GCC_VERSION
894	endif
895	endif
896
897	#---------------------- check ARBHOME
898
899	# use arb_INSTALL.txt to determine whether ARBHOME points to correct directory
900	ARB_INSTALL_FOUND=$(wildcard $(ARBHOME)/arb_INSTALL.txt)
901
902	check_ARBHOME:
903	ifeq ($(strip $(ARB_INSTALL_FOUND)),)
904	@echo ------------------------------------------------------------
905	@echo "ARBHOME is set to '$(ARBHOME)'"
906	@echo "The environment variable ARBHOME has to point to the top arb source directory."
907	@echo "If you use bash enter:"
908	@echo " export ARBHOME='`pwd`'"
909	@echo ------------------------------------------------------------
910	@false
911	endif
912
913	ARB_PATH_SET=$(findstring $(ARBHOME)/bin,$(PATH))
914
915	check_PATH: check_ARBHOME
916	ifeq ($(strip $(ARB_PATH_SET)),)
917	@echo ------------------------------------------------------------
918	@echo "The environment variable PATH has to contain $(ARBHOME)/bin"
919	@echo "If you use bash enter:"
920	@echo ' export PATH=$$ARBHOME/bin:$$PATH'
921	@echo ------------------------------------------------------------
922	@false
923	endif
924
925	check_TOOLS:
926	@util/arb_check_build_env.pl \
927	"$(A_CC)" \
928	"$(A_CXX)" \
929	"$(MAKEDEPEND_PLAIN)" \
930	"$(LINK_SHARED_LIB)" \
931	"$(LINK_SHARED_LIB)" \
932
933	check_ENVIRONMENT : check_PATH check_TOOLS
934	@echo "-------------------- Environment [start]"
935	@echo "ARBHOME='$(ARBHOME)'"
936	@echo "PATH='$(PATH)'"
937	@echo "LD_LIBRARY_PATH='$(LD_LIBRARY_PATH)'"
938	@echo "-------------------- Environment [end]"
939
940	check_tabs: check_setup
941	ifeq ($(DEBUG),1)
942	@SOURCE_TOOLS/tabBrake.pl
943	endif
944
945	force_tab_check:
946	@touch -t 198001010000 SOURCE_TOOLS/stamp.tabBrake
947	@$(MAKE) check_tabs
948
949
950	# ---------------------
951
952	check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION
953	@echo Your setup seems to be ok.
954
955	checks: check_setup check_tabs
956	@rm -f SOURCE_TOOLS/postcompile.sav
957
958
959	# end test section ------------------------------
960
961	# ---------------------------------------
962	# List of standard top level directories
963	#
964	# sub-makefiles have to define the targets
965	# - 'depends' and
966	# - 'clean'
967	#
968	# when adding new libs here, also add a dependency vs 'links' or 'links_non_perl' in .@DD_links_non_perl
969
970	ARCHS = \
971	$(ARCHS_PT_SERVER) \
972	AISC/AISC.a \
973	AISC_MKPTPS/AISC_MKPTPS.a \
974	ARBDB/libARBDB.a \
975	CORE/libCORE.a \
976	ARB_GDE/ARB_GDE.a \
977	AWT/libAWT.a \
978	AWTC/AWTC.a \
979	AWTI/AWTI.a \
980	CONSENSUS_TREE/CONSENSUS_TREE.a \
981	CONVERTALN/CONVERTALN.a \
982	DBSERVER/DBSERVER.a \
983	DIST/DIST.a \
984	EDIT4/EDIT4.a \
985	EISPACK/EISPACK.a \
986	GDE/GDE.a \
987	GENOM/GENOM.a \
988	GENOM_IMPORT/GENOM_IMPORT.a \
989	GL/GL.a \
990	ISLAND_HOPPING/ISLAND_HOPPING.a \
991	MERGE/MERGE.a \
992	MULTI_PROBE/MULTI_PROBE.a \
993	NALIGNER/NALIGNER.a \
994	NAMES/NAMES.a \
995	NAMES_COM/server.a \
996	NTREE/NTREE.a \
997	PARSIMONY/PARSIMONY.a \
998	PERLTOOLS/PERLTOOLS.a \
999	PHYLO/PHYLO.a \
1000	PRIMER_DESIGN/PRIMER_DESIGN.a \
1001	PROBE_COM/server.a \
1002	PROBE_DESIGN/PROBE_DESIGN.a \
1003	PROBE_SET/PROBE_SET.a \
1004	READSEQ/READSEQ.a \
1005	RNA3D/RNA3D.a \
1006	RNACMA/RNACMA.a \
1007	SECEDIT/SECEDIT.a \
1008	SEQ_QUALITY/SEQ_QUALITY.a \
1009	SERVERCNTRL/SERVERCNTRL.a \
1010	SL/SL.a \
1011	STAT/STAT.a \
1012	TOOLS/TOOLS.a \
1013	TREEGEN/TREEGEN.a \
1014	UNIT_TESTER/UNIT_TESTER.a \
1015	WETC/WETC.a \
1016	WINDOW/libWINDOW.a \
1017	XML/XML.a \
1018
1019	# -----------------------
1020	# library packets
1021
1022	ARCHS_CLIENT_PROBE = PROBE_COM/client.a
1023	ARCHS_CLIENT_NAMES = NAMES_COM/client.a
1024
1025	ARCHS_SERVER_PROBE = PROBE_COM/server.a $(ARCHS_CLIENT_PROBE)
1026	ARCHS_SERVER_NAMES = NAMES_COM/server.a $(ARCHS_CLIENT_NAMES)
1027
1028	ARCHS_MAKEBIN = AISC_MKPTPS/AISC_MKPTPS.a AISC/AISC.a
1029
1030	# communication libs need aisc and aisc_mkpts:
1031
1032	AISC/AISC.dummy: proto_tools
1033
1034	comtools: AISC/AISC.dummy
1035
1036	ARCHS_SEQUENCE = \
1037	SL/SEQUENCE/SEQUENCE.a \
1038	SL/ALIVIEW/ALIVIEW.a \
1039	SL/PRONUC/PRONUC.a \
1040
1041	ARCHS_TREE = \
1042	$(ARCHS_SEQUENCE) \
1043	SL/FILTER/FILTER.a \
1044	SL/ARB_TREE/ARB_TREE.a \
1045	SL/ROOTED_TREE/ROOTED_TREE.a \
1046
1047	# parsimony tree (used by NTREE, PARSIMONY, STAT(->EDIT4), DIST(obsolete!))
1048	ARCHS_AP_TREE = \
1049	$(ARCHS_TREE) \
1050	SL/AP_TREE/AP_TREE.a \
1051
1052	# --------------------------------------------------------------------------------
1053	# dependencies for linking shared libs
1054
1055	link_core: core
1056	link_db: db link_core
1057	link_aw: aw link_db
1058	link_awt: awt link_aw
1059
1060	#***************************************************************************************
1061	# Individual_Programs_Section
1062	#***************************************************************************************
1063
1064	arbmainwrapper:
1065	$(MAKE) -C SOURCE_TOOLS -r mainwrapper
1066
1067
1068	#********************************* arb_ntree ************************************
1069	NTREE = bin/arb_ntree
1070	ARCHS_NTREE = \
1071	NTREE/NTREE.a \
1072	$(ARCHS_AP_TREE) \
1073	ARB_GDE/ARB_GDE.a \
1074	AWTC/AWTC.a \
1075	AWTI/AWTI.a \
1076	CONSENSUS_TREE/CONSENSUS_TREE.a \
1077	GENOM/GENOM.a \
1078	GENOM_IMPORT/GENOM_IMPORT.a \
1079	MERGE/MERGE.a \
1080	MULTI_PROBE/MULTI_PROBE.a \
1081	PRIMER_DESIGN/PRIMER_DESIGN.a \
1082	PROBE_DESIGN/PROBE_DESIGN.a \
1083	SEQ_QUALITY/SEQ_QUALITY.a \
1084	SERVERCNTRL/SERVERCNTRL.a \
1085	SL/ALILINK/ALILINK.a \
1086	SL/AW_NAME/AW_NAME.a \
1087	SL/DB_UI/DB_UI.a \
1088	SL/DB_SCANNER/DB_SCANNER.a \
1089	SL/DB_QUERY/DB_QUERY.a \
1090	SL/SEQIO/SEQIO.a \
1091	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1092	SL/HELIX/HELIX.a \
1093	SL/REGEXPR/REGEXPR.a \
1094	SL/REFENTRIES/REFENTRIES.a \
1095	SL/NDS/NDS.a \
1096	SL/ITEMS/ITEMS.a \
1097	SL/INSDEL/INSDEL.a \
1098	SL/LOCATION/LOCATION.a \
1099	SL/MACROS/MACROS.a \
1100	SL/TRANSLATE/TRANSLATE.a \
1101	SL/TREEDISP/TREEDISP.a \
1102	SL/TREE_ADMIN/TREE_ADMIN.a \
1103	SL/TREE_READ/TREE_READ.a \
1104	SL/TREE_WRITE/TREE_WRITE.a \
1105	STAT/STAT.a \
1106	XML/XML.a \
1107
1108	$(NTREE): $(ARCHS_NTREE:.a=.dummy) link_awt
1109	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NTREE) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1110	echo "$(SEP) Link $@"; \
1111	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS)" ; \
1112	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS) && \
1113	echo "$(SEP) Link $@ [done]"; \
1114	)
1115
1116	#********************************* arb_edit4 ************************************
1117	EDIT4 = bin/arb_edit4
1118
1119	ARCHS_EDIT4 := \
1120	EDIT4/EDIT4.a \
1121	$(ARCHS_AP_TREE) \
1122	ARB_GDE/ARB_GDE.a \
1123	AWTC/AWTC.a \
1124	ISLAND_HOPPING/ISLAND_HOPPING.a \
1125	SECEDIT/SECEDIT.a \
1126	SERVERCNTRL/SERVERCNTRL.a \
1127	SL/AW_HELIX/AW_HELIX.a \
1128	SL/AW_NAME/AW_NAME.a \
1129	SL/FAST_ALIGNER/FAST_ALIGNER.a \
1130	SL/ITEMS/ITEMS.a \
1131	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1132	SL/HELIX/HELIX.a \
1133	SL/TRANSLATE/TRANSLATE.a \
1134	SL/MACROS/MACROS.a \
1135	SL/NDS/NDS.a \
1136	STAT/STAT.a \
1137	XML/XML.a \
1138
1139	ifeq ($(OPENGL),1)
1140	ARCHS_EDIT4 += RNA3D/RNA3D.a
1141	endif
1142
1143	LIBS_EDIT4 := $(GL_LIBS)
1144
1145	$(EDIT4): $(ARCHS_EDIT4:.a=.dummy) link_awt
1146	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_EDIT4) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1147	echo "$(SEP) Link $@"; \
1148	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4) $(EXECLIBS)" ; \
1149	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4) $(EXECLIBS) && \
1150	echo "$(SEP) Link $@ [done]"; \
1151	)
1152
1153	#********************************* arb_rnacma ************************************
1154	RNACMA = bin/arb_rnacma
1155	ARCHS_RNACMA = \
1156	RNACMA/RNACMA.a \
1157
1158	$(RNACMA) : $(ARCHS_RNACMA:.a=.dummy) link_db
1159	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_RNACMA) \|\| ( \
1160	echo "$(SEP) Link $@"; \
1161	echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_RNACMA) $(LIBS) $(EXECLIBS)"; \
1162	$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_RNACMA) $(LIBS) $(EXECLIBS) && \
1163	echo "$(SEP) Link $@ [done]"; \
1164	)
1165
1166	#********************************* arb_wetc ************************************
1167	WETC = bin/arb_wetc
1168	ARCHS_WETC = \
1169	WETC/WETC.a \
1170	SL/HELIX/HELIX.a \
1171	SL/FILTER/FILTER.a \
1172	XML/XML.a \
1173
1174	$(WETC): $(ARCHS_WETC:.a=.dummy) link_awt
1175	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_WETC) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1176	echo "$(SEP) Link $@"; \
1177	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC) $(GUI_LIBS) $(EXECLIBS)" ; \
1178	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC) $(GUI_LIBS) $(EXECLIBS) && \
1179	echo "$(SEP) Link $@ [done]"; \
1180	)
1181
1182	#********************************* arb_dist ************************************
1183	DIST = bin/arb_dist
1184	ARCHS_DIST = \
1185	$(ARCHS_AP_TREE) \
1186	CONSENSUS_TREE/CONSENSUS_TREE.a \
1187	DIST/DIST.a \
1188	EISPACK/EISPACK.a \
1189	SERVERCNTRL/SERVERCNTRL.a \
1190	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1191	SL/HELIX/HELIX.a \
1192	SL/MATRIX/MATRIX.a \
1193	SL/MACROS/MACROS.a \
1194	SL/NDS/NDS.a \
1195	SL/ITEMS/ITEMS.a \
1196	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.a \
1197	XML/XML.a \
1198
1199	$(DIST): $(ARCHS_DIST:.a=.dummy) link_awt
1200	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_DIST) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1201	echo "$(SEP) Link $@"; \
1202	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS)" ; \
1203	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS) && \
1204	echo "$(SEP) Link $@ [done]"; \
1205	)
1206
1207	#********************************* arb_pars ************************************
1208	PARSIMONY = bin/arb_pars
1209	ARCHS_PARSIMONY = \
1210	$(ARCHS_AP_TREE) \
1211	PARSIMONY/PARSIMONY.a \
1212	SERVERCNTRL/SERVERCNTRL.a \
1213	SL/AW_NAME/AW_NAME.a \
1214	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1215	SL/HELIX/HELIX.a \
1216	SL/MACROS/MACROS.a \
1217	SL/NDS/NDS.a \
1218	SL/ITEMS/ITEMS.a \
1219	SL/TRANSLATE/TRANSLATE.a \
1220	SL/TREEDISP/TREEDISP.a \
1221	XML/XML.a \
1222
1223	$(PARSIMONY): $(ARCHS_PARSIMONY:.a=.dummy) link_awt
1224	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PARSIMONY) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1225	echo "$(SEP) Link $@"; \
1226	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(EXECLIBS)" ; \
1227	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(EXECLIBS) && \
1228	echo "$(SEP) Link $@ [done]"; \
1229	)
1230
1231	#********************************* arb_convert_aln ************************************
1232	CONVERT_ALN = bin/arb_convert_aln
1233	ARCHS_CONVERT_ALN = \
1234	CONVERTALN/CONVERTALN.a \
1235
1236	$(CONVERT_ALN) : $(ARCHS_CONVERT_ALN:.a=.dummy) link_db
1237	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_CONVERT_ALN) $(use_ARB_main) \|\| ( \
1238	echo "$(SEP) Link $@"; \
1239	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN) $(LIBS) $(EXECLIBS)"; \
1240	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN) $(LIBS) $(EXECLIBS) && \
1241	echo "$(SEP) Link $@ [done]"; \
1242	)
1243
1244	#********************************* arb_treegen ************************************
1245
1246	TREEGEN = bin/arb_treegen
1247	ARCHS_TREEGEN = \
1248	TREEGEN/TREEGEN.a \
1249
1250	$(TREEGEN) : $(ARCHS_TREEGEN:.a=.dummy)
1251	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_TREEGEN) $(use_ARB_main_C) \|\| ( \
1252	echo "$(SEP) Link $@"; \
1253	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN) $(EXECLIBS)" ; \
1254	$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN) $(EXECLIBS) && \
1255	echo "$(SEP) Link $@ [done]"; \
1256	)
1257
1258	#********************************* arb_naligner ************************************
1259	NALIGNER = bin/arb_naligner
1260	ARCHS_NALIGNER = \
1261	NALIGNER/NALIGNER.a \
1262	SERVERCNTRL/SERVERCNTRL.a \
1263	SL/HELIX/HELIX.a \
1264
1265	$(NALIGNER): $(ARCHS_NALIGNER:.a=.dummy) link_db
1266	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NALIGNER) $(use_ARB_main) \|\| ( \
1267	echo "$(SEP) Link $@"; \
1268	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(LIBS) $(EXECLIBS)" ; \
1269	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(LIBS) $(EXECLIBS) && \
1270	echo "$(SEP) Link $@ [done]"; \
1271	)
1272
1273	#********************************* arb_phylo ************************************
1274	PHYLO = bin/arb_phylo
1275	ARCHS_PHYLO = \
1276	PHYLO/PHYLO.a \
1277	SL/HELIX/HELIX.a \
1278	SL/FILTER/FILTER.a \
1279	SL/MATRIX/MATRIX.a \
1280	SL/MACROS/MACROS.a \
1281	XML/XML.a \
1282
1283	$(PHYLO): $(ARCHS_PHYLO:.a=.dummy) link_awt
1284	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PHYLO) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1285	echo "$(SEP) Link $@"; \
1286	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO) $(GUI_LIBS) $(EXECLIBS)" ; \
1287	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO) $(GUI_LIBS) $(EXECLIBS) && \
1288	echo "$(SEP) Link $@ [done]"; \
1289	)
1290
1291	#***************************************************************************************
1292	# SERVER SECTION
1293	#***************************************************************************************
1294
1295	#********************************* arb_db_server ************************************
1296	DBSERVER = bin/arb_db_server
1297	ARCHS_DBSERVER = \
1298	DBSERVER/DBSERVER.a \
1299	SERVERCNTRL/SERVERCNTRL.a \
1300
1301	$(DBSERVER): $(ARCHS_DBSERVER:.a=.dummy) link_db
1302	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_DBSERVER) $(ARBDB_LIB) $(use_ARB_main) \|\| ( \
1303	echo "$(SEP) Link $@"; \
1304	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS) $(EXECLIBS)" ; \
1305	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS) $(EXECLIBS) && \
1306	echo "$(SEP) Link $@ [done]"; \
1307	)
1308
1309	#********************************* arb_pt_server ************************************
1310	PROBE = bin/arb_pt_server
1311	ARCHS_PROBE_COMMON = \
1312	SERVERCNTRL/SERVERCNTRL.a \
1313	SL/HELIX/HELIX.a \
1314	SL/PTCLEAN/PTCLEAN.a \
1315
1316	ARCHS_PROBE_LINK = \
1317	$(ARCHS_PROBE_COMMON) \
1318	$(ARCHS_PT_SERVER_LINK) \
1319
1320	ARCHS_PROBE_DEPEND = \
1321	$(ARCHS_PROBE_COMMON) \
1322	$(ARCHS_PT_SERVER) \
1323
1324	$(PROBE): $(ARCHS_PROBE_DEPEND:.a=.dummy) link_db
1325	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_SERVER_PROBE) config.makefile $(use_ARB_main) \|\| ( \
1326	echo "$(SEP) Link $@"; \
1327	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_SERVER_PROBE) $(SYSLIBS) $(EXECLIBS)" ; \
1328	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_SERVER_PROBE) $(SYSLIBS) $(EXECLIBS) && \
1329	echo "$(SEP) Link $@ [done]"; \
1330	)
1331
1332	#********************************* arb_name_server ************************************
1333	NAMES = bin/arb_name_server
1334	ARCHS_NAMES = \
1335	NAMES/NAMES.a \
1336	SERVERCNTRL/SERVERCNTRL.a \
1337
1338	$(NAMES): $(ARCHS_NAMES:.a=.dummy) link_db
1339	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) $(use_ARB_main) \|\| ( \
1340	echo "$(SEP) Link $@"; \
1341	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS) $(EXECLIBS)" ; \
1342	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS) $(EXECLIBS) && \
1343	echo "$(SEP) Link $@ [done]"; \
1344	)
1345
1346	#********************************* SHARED LIBRARIES SECTION ************************************
1347
1348	prepare_libdir: addlibs
1349
1350	addlibs:
1351	(perl $(ARBHOME)/SOURCE_TOOLS/provide_libs.pl \
1352	"arbhome=$(ARBHOME)" \
1353	"opengl=$(OPENGL)" \
1354	"link_static=$(LINK_STATIC)" \
1355	)
1356
1357	#***************************************************************************************
1358	# Recursive calls to sub-makefiles
1359	#***************************************************************************************
1360
1361	%.depends:
1362	@cp -p $(@D)/Makefile $(@D)/Makefile.old # save old Makefile
1363	@$(MAKE) -C $(@D) -r \
1364	"AUTODEPENDS=1" \
1365	"MAIN=nothing" \
1366	"cflags=noCflagsHere_use_MAKEDEPENDFLAGS" \
1367	"cxxflags=noCxxflagsHere_use_MAKEDEPENDFLAGS" \
1368	depends
1369	@grep "^# DO NOT DELETE" $(@D)/Makefile >/dev/null
1370	@cat $(@D)/Makefile \
1371	\| SOURCE_TOOLS/fix_depends.pl "(from main)" \
1372	>$(@D)/Makefile.2
1373	@mv $(@D)/Makefile.old $(@D)/Makefile # restore old Makefile
1374	@$(ARBHOME)/SOURCE_TOOLS/mv_if_diff $(@D)/Makefile.2 $(@D)/Makefile # update Makefile if changed
1375
1376	%.proto:
1377	@($(MAKE) -C $(@D) \
1378	"AUTODEPENDS=0" \
1379	"MAIN=nothing" \
1380	"cflags=noCflags" \
1381	"cxxflags=noCxxflags" \
1382	proto 2>&1 ) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
1383
1384	%.clean:
1385	@$(MAKE) -C $(@D) \
1386	"AUTODEPENDS=0" \
1387	"MAIN=nothing" \
1388	"cflags=noCflags" \
1389	"cxxflags=noCxxflags" \
1390	clean
1391
1392
1393	# stop wrong targets
1394	target_is_missing_lib_prefix:
1395	@echo "Error: Denied to build shared library target with missing 'lib'-prefix"
1396	false
1397
1398	ARBDB/ARBDB.dummy: target_is_missing_lib_prefix
1399	CORE/CORE.dummy: target_is_missing_lib_prefix
1400	AWT/AWT.dummy: target_is_missing_lib_prefix
1401	WINDOW/WINDOW.dummy: target_is_missing_lib_prefix
1402
1403	# rule to generate main target (normally a library):
1404	# @@@ check effect of setting LANG=C below
1405	%.dummy:
1406	@( export ID=$$$$; LANG=C; \
1407	(( \
1408	echo "$(SEP) Make $(@D)"; \
1409	$(MAKE) -C $(@D) -r \
1410	"AUTODEPENDS=1" \
1411	"MAIN=$(@F:.dummy=.a)" \
1412	"cflags=$(cflags) -DIN_ARB_$(subst /,_,$(@D))" \
1413	&& \
1414	echo "$(SEP) Make $(@D) [done]"; \
1415	) >$(@D).$$ID.log 2>&1 && (cat $(@D).$$ID.log;rm $(@D).$$ID.log)) \|\| (cat $(@D).$$ID.log;rm $(@D).$$ID.log;false))
1416
1417	# Additional dependencies for subtargets:
1418
1419	PROBE_COM/PROBE_COM.dummy : comtools
1420	NAMES_COM/NAMES_COM.dummy : comtools
1421
1422	com: PROBE_COM/PROBE_COM.dummy NAMES_COM/NAMES_COM.dummy
1423
1424	PROBE_COM/server.dummy:
1425	@echo Unwanted request to make target $<
1426	false
1427
1428	PROBE_COM/client.dummy:
1429	@echo Unwanted request to make target $<
1430	false
1431
1432	NAMES_COM/server.dummy:
1433	@echo Unwanted request to make target $<
1434	false
1435
1436	NAMES_COM/client.dummy:
1437	@echo Unwanted request to make target $<
1438	false
1439
1440
1441	ARBDB/libARBDB.dummy: links
1442	CORE/libCORE.dummy: links
1443
1444	PERLTOOLS/PERLTOOLS.dummy: core db
1445
1446	# all subdirs perl not depends on go here (ADD_links_non_perl)
1447	AWT/libAWT.dummy: links_non_perl
1448	AWTI/AWTI.dummy: links_non_perl
1449	CONSENSUS_TREE/CONSENSUS_TREE.dummy: links_non_perl
1450	CONVERTALN/CONVERTALN.dummy: links_non_perl
1451	DBSERVER/DBSERVER.dummy: links_non_perl
1452	DIST/DIST.dummy: links_non_perl
1453	EDIT4/EDIT4.dummy: links_non_perl genheaders com
1454	EISPACK/EISPACK.dummy: links_non_perl
1455	GDE/GDE.dummy: links_non_perl
1456	GENOM/GENOM.dummy: links_non_perl
1457	GENOM_IMPORT/GENOM_IMPORT.dummy: links_non_perl
1458	ISLAND_HOPPING/ISLAND_HOPPING.dummy: links_non_perl
1459	MERGE/MERGE.dummy: links_non_perl
1460	NTREE/NTREE.dummy: links_non_perl genheaders
1461	PARSIMONY/PARSIMONY.dummy: links_non_perl
1462	PHYLO/PHYLO.dummy: links_non_perl
1463	PRIMER_DESIGN/PRIMER_DESIGN.dummy: links_non_perl
1464	PROBE_SET/PROBE_SET.dummy: links_non_perl link_db
1465	READSEQ/READSEQ.dummy: links_non_perl
1466	RNACMA/RNACMA.dummy: links_non_perl header_libs
1467	SECEDIT/SECEDIT.dummy: links_non_perl
1468	SEQ_QUALITY/SEQ_QUALITY.dummy: links_non_perl
1469	SERVERCNTRL/SERVERCNTRL.dummy: links_non_perl com
1470	SL/ALILINK/ALILINK.dummy: links_non_perl
1471	SL/ALIVIEW/ALIVIEW.dummy: links_non_perl
1472	SL/AP_TREE/AP_TREE.dummy: links_non_perl
1473	SL/ARB_TREE/ARB_TREE.dummy: links_non_perl
1474	SL/AW_HELIX/AW_HELIX.dummy: links_non_perl
1475	SL/DB_QUERY/DB_QUERY.dummy: links_non_perl
1476	SL/DB_SCANNER/DB_SCANNER.dummy: links_non_perl
1477	SL/DB_UI/DB_UI.dummy: links_non_perl
1478	SL/FAST_ALIGNER/FAST_ALIGNER.dummy: links_non_perl
1479	SL/FILTER/FILTER.dummy: links_non_perl
1480	SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy: links_non_perl
1481	SL/HELIX/HELIX.dummy: links_non_perl
1482	SL/INSDEL/INSDEL.dummy: links_non_perl
1483	SL/ITEMS/ITEMS.dummy: links_non_perl
1484	SL/LOCATION/LOCATION.dummy: links_non_perl
1485	SL/MACROS/MACROS.dummy: links_non_perl
1486	SL/MATRIX/MATRIX.dummy: links_non_perl
1487	SL/NDS/NDS.dummy: links_non_perl
1488	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.dummy: links_non_perl
1489	SL/PRONUC/PRONUC.dummy: links_non_perl
1490	SL/PTCLEAN/PTCLEAN.dummy: links_non_perl link_db
1491	SL/REFENTRIES/REFENTRIES.dummy: links_non_perl
1492	SL/REGEXPR/REGEXPR.dummy: links_non_perl
1493	SL/ROOTED_TREE/ROOTED_TREE.dummy: links_non_perl
1494	SL/SEQIO/SEQIO.dummy: links_non_perl
1495	SL/SEQUENCE/SEQUENCE.dummy: links_non_perl
1496	SL/TRANSLATE/TRANSLATE.dummy: links_non_perl
1497	SL/TREE_ADMIN/TREE_ADMIN.dummy: links_non_perl
1498	SL/TREE_READ/TREE_READ.dummy: links_non_perl
1499	SL/TREE_WRITE/TREE_WRITE.dummy: links_non_perl
1500	SL/TREEDISP/TREEDISP.dummy: links_non_perl
1501	STAT/STAT.dummy: links_non_perl
1502	TREEGEN/TREEGEN.dummy: links_non_perl
1503	WETC/WETC.dummy: links_non_perl
1504	WINDOW/libWINDOW.dummy: links_non_perl
1505	XML/XML.dummy: links_non_perl
1506
1507	ifeq ($(OPENGL),1)
1508	GL/glAW/glAW.dummy: links_non_perl
1509	GL/glpng/glpng.dummy: links_non_perl
1510	GL/GL.dummy: GL/glAW/glAW.dummy GL/glpng/glpng.dummy
1511	RNA3D/RNA3D.dummy: links_non_perl gl
1512	endif
1513
1514	UNIT_TESTER/UNIT_TESTER.dummy: link_db \
1515	SERVERCNTRL/SERVERCNTRL.dummy \
1516
1517	TOOLS/TOOLS.dummy : links_non_perl link_db \
1518	SERVERCNTRL/SERVERCNTRL.dummy \
1519	SL/ROOTED_TREE/ROOTED_TREE.dummy \
1520	SL/TREE_WRITE/TREE_WRITE.dummy \
1521	SL/TREE_READ/TREE_READ.dummy \
1522	CONSENSUS_TREE/CONSENSUS_TREE.dummy \
1523	XML/XML.dummy \
1524
1525	AWTC/AWTC.dummy : com
1526
1527	NAMES/NAMES.dummy : com
1528	SL/AW_NAME/AW_NAME.dummy : com
1529
1530	PROBE/PROBE.dummy : com
1531	ptpan/PROBE.dummy : com
1532	MULTI_PROBE/MULTI_PROBE.dummy : com
1533	PROBE_DESIGN/PROBE_DESIGN.dummy : com
1534	NALIGNER/NALIGNER.dummy : com
1535
1536	ARB_GDE/ARB_GDE.dummy : proto_tools
1537
1538	compile_compatibility: SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.dummy
1539
1540	#***************************************************************************************
1541	# Short aliases to make targets
1542	#***************************************************************************************
1543
1544	show:
1545	@echo $(SEP)
1546	@echo 'Aliases for often needed targets:'
1547	@echo ''
1548	@echo ' executables:'
1549	@echo ''
1550	@echo ' nt arb_ntree'
1551	@echo ' e4 arb_edit4 (includes secedit)'
1552	@echo ' di arb_dist'
1553	@echo ' ph arb_phylo'
1554	@echo ' pa arb_parsimony'
1555	@echo ' tg arb_treegen'
1556	@echo ' ds arb_dbserver'
1557	@echo ' pt arb_pt_server'
1558	@echo ' na arb_name_server'
1559	@echo ''
1560	@echo ' libraries:'
1561	@echo ''
1562	@echo ' com communication libraries'
1563	@echo ' db ARB database'
1564	@echo ' aw GUI lib'
1565	@echo ' awt GUI toolkit'
1566	@echo ' awtc general purpose library'
1567	@echo ' awti import/export library'
1568	@echo ' mp multi probe library'
1569	@echo ' ge genome library'
1570	@echo ' pd probe design lib'
1571	@echo ' prd primer design lib'
1572	@echo ''
1573	@echo ' other targets:'
1574	@echo ''
1575	@echo ' help recompile help files'
1576	@echo ' tools make small tools used by arb'
1577	@echo ''
1578	@echo ' foreign targets:'
1579	@echo ''
1580	@echo ' gde GDE'
1581	@echo ' agde ARB_GDE'
1582	@echo ''
1583	@echo 'for other targets inspect $(ARBHOME)/Makefile'
1584	@echo ''
1585	@echo $(SEP)
1586
1587	source_doc:
1588	@echo "Remove some links (doxygen crashes otherwise):"
1589	find . \( -name "AISC" -o -name "C" -o -name "GDEHELP" \) -type l -exec rm {} \;
1590	doxygen 2>&1 1>/dev/null
1591	$(MAKE) forcelinks
1592
1593	dep_graph:
1594	@echo "Building some dependency graphs"
1595	SOURCE_TOOLS/dependency_graphs.pl
1596
1597	help: HELP_SOURCE/HELP_SOURCE.dummy
1598
1599	HELP_SOURCE/HELP_SOURCE.dummy: link_core xml menus
1600
1601	db: ARBDB/libARBDB.dummy
1602	core: CORE/libCORE.dummy
1603	aw: WINDOW/libWINDOW.dummy
1604	awt: AWT/libAWT.dummy
1605	awtc: AWTC/AWTC.dummy
1606	awti: AWTI/AWTI.dummy
1607
1608	mp: MULTI_PROBE/MULTI_PROBE.dummy
1609	mg: MERGE/MERGE.dummy
1610	ge: GENOM/GENOM.dummy
1611	prd: PRIMER_DESIGN/PRIMER_DESIGN.dummy
1612
1613	nt: menus $(NTREE)
1614
1615	nal: $(NALIGNER)
1616
1617	di: $(DIST)
1618	ph: $(PHYLO)
1619	pa: $(PARSIMONY)
1620	tg: $(TREEGEN)
1621
1622	ifeq ($(OPENGL),1)
1623	3d: RNA3D/RNA3D.dummy
1624	gl: GL/GL.dummy
1625	else
1626	noopengl:
1627	@echo "invalid target for OPENGL=0"
1628	3d: noopengl
1629	gl: noopengl
1630	endif
1631
1632	SL/SL.dummy: com
1633
1634	ds: $(DBSERVER)
1635	pt: $(PROBE)
1636	pst: PROBE_SET/PROBE_SET.dummy
1637	pd: PROBE_DESIGN/PROBE_DESIGN.dummy
1638	na: $(NAMES)
1639	sq: SEQ_QUALITY/SEQ_QUALITY.dummy
1640	cma: $(RNACMA)
1641
1642	sec: SECEDIT/SECEDIT.dummy
1643
1644	e4: $(EDIT4) readseq menus
1645
1646	gi: GENOM_IMPORT/GENOM_IMPORT.dummy
1647	wetc: $(WETC)
1648
1649	xml: XML/XML.dummy
1650	xmlin: XML_IMPORT/XML_IMPORT.dummy# broken
1651	stat: STAT/STAT.dummy $(NTREE) $(EDIT4)
1652	fa: SL/FAST_ALIGNER/FAST_ALIGNER.dummy
1653
1654	#********************************************************************************
1655
1656	up_by_remake: depends proto
1657
1658	up: up_by_remake tags valgrind_update
1659
1660	#********************************************************************************
1661
1662	touch:
1663	SOURCE_TOOLS/touch_modified.pl
1664
1665	modified: touch
1666	$(MAKE) all
1667
1668	#********************************************************************************
1669
1670	libdepends:
1671	$(MAKE) -C "SOURCE_TOOLS" \
1672	"RNA3D_LIB=$(RNA3D_LIB_4_DEPENDS)" \
1673	libdepends
1674
1675	#********************************************************************************
1676
1677	# create generated headers:
1678	genheaders: TEMPLATES/TEMPLATES.dummy
1679
1680	clrdotdepends:
1681	-rm PROBE_COM/.depends
1682	-rm NAMES_COM/.depends
1683	-rm PERL2ARB/.depends
1684
1685	comdepends: comtools clrdotdepends
1686	@echo "$(SEP) Partially build com interface"
1687	$(MAKE) PROBE_COM/PROBE_COM.depends NAMES_COM/NAMES_COM.depends
1688	$(MAKE) PROBE_COM/server.depends NAMES_COM/server.depends
1689
1690	depends: genheaders comdepends
1691	@echo "$(SEP) Updating other dependencies"
1692	$(MAKE) $(subst NAMES_COM/server.depends,,$(subst PROBE_COM/server.depends,,$(ARCHS:.a=.depends))) \
1693	HELP_SOURCE/HELP_SOURCE.depends \
1694	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.depends \
1695
1696	$(MAKE) libdepends
1697
1698	depend: depends
1699
1700	# ------------------------------------------------------------
1701	# dependency generation tests for AISC code
1702	#(all should work w/o creating wrong dependencies;
1703	# neither in XXX_COM/Makefile nor in code using AISC interface)
1704	dependstest1: silent_clean
1705	$(MAKE) depends
1706	dependstest2: silent_clean
1707	$(MAKE) com
1708	dependstest3: silent_clean
1709	$(MAKE) aw
1710	dependstest4: silent_clean
1711	$(MAKE) pt
1712	dependstest5: silent_clean
1713	$(MAKE) na
1714	dependstest6: silent_clean
1715	$(MAKE) nt
1716	dependstest7: silent_clean
1717	$(MAKE) all
1718	# ------------------------------------------------------------
1719
1720	AISC_MKPTPS/AISC_MKPTPS.dummy: links
1721
1722	proto_tools: AISC_MKPTPS/AISC_MKPTPS.dummy
1723
1724	proto: proto_tools
1725	@echo $(SEP) Updating prototypes
1726	$(MAKE) \
1727	ARBDB/ARBDB.proto \
1728	AISC_COM/AISC_COM.proto \
1729	ARB_GDE/ARB_GDE.proto \
1730	CORE/CORE.proto \
1731	CONVERTALN/CONVERTALN.proto \
1732	NTREE/NTREE.proto \
1733	MERGE/MERGE.proto \
1734	$(ARCHS_PT_SERVER:.a=.proto) \
1735	SERVERCNTRL/SERVERCNTRL.proto \
1736	SL/SL.proto \
1737
1738	#********************************************************************************
1739
1740	valgrind_update: links
1741	@echo $(SEP) Updating for valgrind
1742	$(MAKE) -C SOURCE_TOOLS valgrind_update
1743
1744	#********************************************************************************
1745
1746	TAGFILE=TAGS
1747	TAGFILE_TMP=TAGS.tmp
1748
1749	TAG_SOURCE_HEADERS=TAGS.headers
1750	TAG_SOURCE_CODE=TAGS.codefiles
1751	TAG_SOURCE_LISTS=$(TAG_SOURCE_HEADERS) $(TAG_SOURCE_CODE)
1752
1753	ETAGS=ctags -e -f $(TAGFILE_TMP) --sort=no --if0=no --extra=q
1754	ETAGS_TYPES=--C-kinds=cgnsut --C++-kinds=cgnsut
1755	ETAGS_FUN =--C-kinds=fm --C++-kinds=fm
1756	ETAGS_REST =--C-kinds=dev --C++-kinds=dev
1757
1758	FILTER_TAGS_SOURCES= \
1759	$(SED) -e 's/^.\///g' \| \
1760	grep -P -v -i '^HEADERLIBS\|^GDE/\|/GEN[CH]/'
1761
1762	$(TAG_SOURCE_HEADERS): links
1763	find . \( -name '.hxx' -o -name ".h" \) -type f \| $(FILTER_TAGS_SOURCES) > $@
1764
1765	$(TAG_SOURCE_CODE): links
1766	find . \( -name '.cxx' -o -name ".c" \) -type f \| $(FILTER_TAGS_SOURCES) > $@
1767
1768	tags: $(TAG_SOURCE_LISTS)
1769	$(ETAGS) $(ETAGS_TYPES) -L $(TAG_SOURCE_HEADERS)
1770	$(ETAGS) -a $(ETAGS_FUN) -L $(TAG_SOURCE_HEADERS)
1771	$(ETAGS) -a $(ETAGS_REST) -L $(TAG_SOURCE_HEADERS)
1772	$(ETAGS) -a $(ETAGS_TYPES) -L $(TAG_SOURCE_CODE)
1773	$(ETAGS) -a $(ETAGS_FUN) -L $(TAG_SOURCE_CODE)
1774	$(ETAGS) -a $(ETAGS_REST) -L $(TAG_SOURCE_CODE)
1775	mv_if_diff $(TAGFILE_TMP) $(TAGFILE)
1776	rm $(TAG_SOURCE_LISTS)
1777
1778	#********************************************************************************
1779
1780	LINKSTAMP=SOURCE_TOOLS/stamp.generate_all_links
1781
1782	links: checks $(LINKSTAMP) arbmainwrapper
1783	links_no_checks: $(LINKSTAMP) arbmainwrapper
1784
1785	forcelinks:
1786	-rm $(LINKSTAMP)
1787	$(MAKE) links
1788
1789	$(LINKSTAMP): SOURCE_TOOLS/generate_all_links.sh
1790	+SOURCE_TOOLS/generate_all_links.sh
1791	touch $(LINKSTAMP)
1792
1793	clean_links:
1794	# avoid to delete linked pts, nas or arb_tcp.dat:
1795	find . -path './lib' -prune -o -type l -exec rm {} \;
1796	# removed obsolete file - refuses to disappear due to 'prune' above
1797	@rm -f lib/help/GDEHELP
1798	@rm -f $(LINKSTAMP) lib/inputMasks/format.readme
1799
1800	redo_links: clean_links
1801	$(MAKE) links_no_checks
1802
1803	#********************************************************************************
1804
1805	header_libs:
1806	$(MAKE) -C HEADERLIBS all
1807
1808	#********************************************************************************
1809
1810	gde: GDE/GDE.dummy
1811	GDE: gde
1812	agde: ARB_GDE/ARB_GDE.dummy
1813
1814	tools: TOOLS/TOOLS.dummy
1815
1816	convert: $(CONVERT_ALN)
1817	readseq: READSEQ/READSEQ.dummy
1818
1819	#***************************************************************************************
1820	# Some user commands
1821	#***************************************************************************************
1822
1823	menus: binlink links
1824	@(( \
1825	echo "$(SEP) Make GDEHELP"; \
1826	$(MAKE) -C GDEHELP -r all && \
1827	echo "$(SEP) Make GDEHELP [done]"; \
1828	) > GDEHELP.log 2>&1 && (cat GDEHELP.log;rm GDEHELP.log)) \|\| (cat GDEHELP.log;rm GDEHELP.log;false)
1829
1830	ifeq ($(DEBUG),1)
1831	BIN_TARGET=develall
1832	else
1833	BIN_TARGET=all
1834	endif
1835
1836
1837	binlink:
1838	$(MAKE) -C bin $(BIN_TARGET)
1839
1840	preplib:
1841	(cd lib;$(MAKE) all)
1842
1843	# --------------------------------------------------------------------------------
1844	# This section is quite tricky:
1845	#
1846	# make 'perl' is a BIG target, so when it has to be made, it has to be started
1847	# as early as possible to reduce overall compile time. Since 'make' does not
1848	# provide any priotities, i force it to build all 'perl'-prerequisites early, by
1849	# adding artificial dependencies to these prerequisites
1850	#
1851	# That behavior is likely to be system-dependent.
1852	# My goal was only to make it work on my current development system,
1853	# where this saves about 20% of overall build time.
1854
1855	ifeq ($(WITHPERL),1)
1856	links_non_perl: PERLTOOLS/PERLTOOLS.dummy
1857	perltools: links_non_perl
1858	perl: realperl
1859	else
1860	links_non_perl: links
1861	perl:
1862	$(MAKE) "WITHPERL=1" perl
1863	endif
1864
1865	# ---------------------------------------- perl
1866
1867	ifeq ($(ARB_64),$(BUILDHOST_64))
1868	TEST_PERL_SCRIPTS=$(MAKE) -C PERL_SCRIPTS/test test
1869	else
1870	TEST_PERL_SCRIPTS=echo "skipping perl script compilation (when cross-compiling)"
1871	endif
1872
1873	realperl: perltools
1874	(( \
1875	echo "$(SEP) Make PERL2ARB" ; \
1876	$(TIME) $(MAKE) -C PERL2ARB -r -f Makefile.main \
1877	"AUTODEPENDS=1" \
1878	"dflags=$(dflags)" \
1879	"cross_cflags=$(cross_cflags) $(cxxflags) $(dflags)" \
1880	"cross_lflags=$(cross_lflags)" \
1881	"COMPILER_VERSION=$(COMPILER_VERSION)" \
1882	all && \
1883	$(TEST_PERL_SCRIPTS) && \
1884	echo "$(SEP) Make PERL2ARB [done]" ; \
1885	) > PERL2ARB.log 2>&1 && (cat PERL2ARB.log;rm PERL2ARB.log)) \|\| (cat PERL2ARB.log;rm PERL2ARB.log;false)
1886
1887	perl_clean:
1888	@$(MAKE) -C PERL2ARB -r -f Makefile.main \
1889	"AUTODEPENDS=0" \
1890	clean
1891
1892	PERL2ARB/PERL2ARB.clean:
1893	$(MAKE) perl_clean
1894	$(MAKE) -C PERL_SCRIPTS/test clean
1895
1896	# ---------------------------------------- bindings to script languages
1897
1898	bindings: lib/libCORE.so lib/libARBDB.so
1899	$(MAKE) -C BINDINGS all ARBDEPENDS="$(^:%=../%)" DFLAGS="$(dflags)"
1900
1901	bindings_clean:
1902	$(MAKE) -C BINDINGS clean
1903
1904	# ----------------------------------------
1905
1906	CLOC=cloc-1.08.pl
1907	CLOCFLAGS=--no3 --quiet --progress-rate=0
1908	CLOCARB=--exclude-dir=GDE .
1909	CLOCEXT=GDE
1910	CLOCCODE=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.code.def
1911	CLOCREST=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.rest.def
1912	CLOCFILT=tail --lines=+4
1913
1914	cloc:
1915	@echo 'Arb code:'
1916	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCARB) \| $(CLOCFILT)
1917	@echo 'Arb rest:'
1918	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCARB) \| $(CLOCFILT)
1919	@echo 'External code:'
1920	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCEXT) \| $(CLOCFILT)
1921	@echo 'External rest:'
1922	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCEXT) \| $(CLOCFILT)
1923
1924	# ---------------------------------------- check ressources
1925
1926	check_res:
1927	$(ARBHOME)/SOURCE_TOOLS/check_ressources.pl
1928
1929	# ---------------------------------------- cleaning
1930
1931	rmbak:
1932	@echo "Cleanup:"
1933	@find . \( -name '*%' \
1934	-o -name '*.bak' \
1935	-o -name '*~' \) \
1936	-o \( -name 'core' -a \! -type d \) \
1937	-exec rm -v {} \;
1938
1939	bin_reinit:
1940	$(MAKE) bin/bin.clean
1941	$(MAKE) -C "bin" all
1942
1943	clean_directories:
1944	-rm -rf \
1945	$(ARBHOME)/PROBE_SET/bin \
1946	$(ARBHOME)/INCLUDE \
1947
1948	libclean:
1949	-find $(ARBHOME) -type f \( -name '*.a' ! -type l \) -exec rm -f {} \;
1950
1951	objclean:
1952	-find $(ARBHOME) -type f \( -name '*.o' ! -type l \) -exec rm -f {} \;
1953
1954	# bin.clean and HELP_SOURCE.clean interfere
1955	clean3:
1956	$(MAKE) bin/bin.clean
1957	$(MAKE) HELP_SOURCE/HELP_SOURCE.clean
1958
1959	clean2: $(ARCHS:.a=.clean) \
1960	clean3 \
1961	rmbak \
1962	libclean \
1963	objclean \
1964	lib/lib.clean \
1965	GDEHELP/GDEHELP.clean \
1966	HEADERLIBS/HEADERLIBS.clean \
1967	SOURCE_TOOLS/SOURCE_TOOLS.clean \
1968	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.clean \
1969	UNIT_TESTER/UNIT_TESTER.clean \
1970	TEMPLATES/TEMPLATES.clean \
1971	perl_clean \
1972	clean_directories \
1973
1974	rm -f .last_gcc .last_compiler config.makefile.bak
1975
1976	# links are needed for cleanup
1977	clean: redo_links motif_xpm_hack_clean
1978	$(MAKE) clean2
1979	$(MAKE) clean_cov_all clean_links
1980
1981	silent_clean:
1982	$(MAKE) clean >/dev/null
1983
1984	# 'relocated' is about 50% faster than 'rebuild'
1985	reloc_clean: links
1986	@echo "---------------------------------------- Relocation cleanup"
1987	$(MAKE) \
1988	perl_clean \
1989	GDEHELP/GDEHELP.clean \
1990	HELP_SOURCE/genhelp/genhelp.clean \
1991	bin/bin.clean \
1992	libclean \
1993	objclean
1994
1995	relocated: links
1996	$(MAKE) reloc_clean
1997	@echo "---------------------------------------- and remake"
1998	$(MAKE) build
1999
2000	# -----------------------------------
2001	# some stress tests
2002	# (helpful to reveal race conditions with -j)
2003
2004	rebuild4ever: rebuild
2005	$(MAKE) rebuild4ever
2006
2007	build4ever: build
2008	$(MAKE) build4ever
2009
2010	clean4ever: clean
2011	$(MAKE) clean4ever
2012
2013	test4ever: ut
2014	$(MAKE) test4ever
2015
2016	perl4ever: clean
2017	$(MAKE) links
2018	$(MAKE) perl
2019	$(MAKE) perl4ever
2020
2021	help4ever: clean
2022	$(MAKE) help
2023	$(MAKE) help4ever
2024
2025	# -----------------------------------
2026
2027	rebuild: clean
2028	$(MAKE) all
2029
2030	relink: bin/bin.clean libclean
2031	$(MAKE) build
2032
2033	tarfile: rebuild
2034	$(MAKE) prepare_libdir
2035	util/arb_compress
2036
2037	tarfile_quick: build
2038	$(MAKE) prepare_libdir
2039	util/arb_compress
2040
2041	save: sourcetarfile
2042
2043	patch:
2044	SOURCE_TOOLS/arb_create_patch.sh arbPatch
2045
2046	# test early whether save will work
2047	savetest:
2048	@util/arb_srclst.pl >/dev/null
2049
2050	testsave: savetest
2051
2052	sourcetarfile: rmbak
2053	util/arb_save
2054
2055	save2: rmbak
2056	util/arb_save ignore
2057
2058	save_test: rmbak
2059	@echo "Testing source list.."
2060	@util/arb_srclst.pl > /dev/null
2061
2062	save_test_no_error:
2063	@-$(MAKE) save_test
2064
2065	inc_candi:
2066	touch SOURCE_TOOLS/inc_candi.stamp
2067	$(MAKE) do_version_update
2068
2069	inc_patch:
2070	touch SOURCE_TOOLS/inc_patch.stamp
2071	$(MAKE) do_version_update
2072
2073	inc_minor:
2074	touch SOURCE_TOOLS/inc_minor.stamp
2075	$(MAKE) do_version_update
2076
2077	inc_major:
2078	touch SOURCE_TOOLS/inc_major.stamp
2079	$(MAKE) do_version_update
2080
2081	do_version_update:
2082	@echo Incrementing version information
2083	$(MAKE) testsave
2084	$(MAKE) genheaders # auto upgrades version early
2085
2086	show_version:
2087	$(MAKE) genheaders # updates version info
2088	@echo "$(SEP) ARB version info"
2089	@grep ARB_VERSION TEMPLATES/arb_build.h
2090	@echo "$(SEP)"
2091
2092	release_quick:
2093	-rm arb.tgz arbsrc.tgz
2094	$(MAKE) tarfile_quick
2095	$(MAKE) sourcetarfile
2096
2097	# --------------------------------------------------------------------------------
2098
2099	MAKE_IF_COMMITTED=$(MAKE) -C SOURCE_TOOLS -f Makefile.commitbuild
2100
2101	build_CTARGET:
2102	+$(MAKE_IF_COMMITTED) "CTARGET=$(CTARGET)" build_CTARGET
2103
2104	reset_committed_build:
2105	+$(MAKE_IF_COMMITTED) reset
2106
2107	# --------------------------------------------------------------------------------
2108
2109	arbapplications: nt pa e4 wetc pt na nal di ph ds wetc cma
2110
2111	arb_external: convert tools gde readseq tg pst xmlin
2112
2113	arb_no_perl: arbapplications help arb_external
2114
2115	arb: motif_xpm_hack
2116	$(MAKE) "WITHPERL=1" perl arb_no_perl
2117
2118	motif_xpm_hack:
2119	$(MAKE) -r -C "lib/motifHack" all
2120
2121	motif_xpm_hack_clean:
2122	$(MAKE) -r -C "lib/motifHack" clean
2123
2124	# --------------------------------------------------------------------------------
2125	# special targets for SOURCE_TOOLS/remake_after_change.pl
2126
2127	rac_arb_dist: di
2128	rac_arb_edit4: e4
2129	rac_arb_ntree: nt
2130	rac_arb_pars: pa
2131	rac_arb_phylo: ph
2132	rac_arb_wetc: wetc
2133	rac_arb_naligner: nal
2134	rac_arb_pt_server: pt
2135	rac_arb_db_server: ds
2136	rac_arb_name_server: na
2137	rac_arb_convert_aln: convert
2138	rac_arb_treegen: tg
2139	rac_arb_rnacma: cma
2140	rac_arb_help2xml: help
2141
2142	rac_arb_a2ps: tools
2143	rac_arb_consensus_tree: tools
2144	rac_arb_dnarates: tools
2145	rac_arb_export_rates: tools
2146	rac_arb_export_tree: tools
2147	rac_arb_gene_probe: tools
2148	rac_arb_message: tools
2149	rac_arb_notify: tools
2150	rac_arb_primer: tools
2151	rac_arb_probe: tools
2152	rac_arb_read_tree: tools
2153
2154	# --------------------------------------------------------------------------------
2155	# unit testing
2156	# @@@ work in progress
2157	#
2158	# goal is to automatically test all libraries/executables using TESTED_UNITS_AUTO
2159	#
2160	# currently not all test executables link w/o error
2161	# (see UNITS_WORKING, UNITS_UNTESTABLE_ATM and UNITS_NEED_FIX)
2162
2163	# define RNA3D/RNA3D.test
2164	RNA3D_TEST := $(subst .a,.test,$(RNA3D_LIB))
2165
2166	TESTED_UNITS_AUTO = $(ARCHS:.a=.test)
2167
2168	UNITS_WORKING = \
2169	$(RNA3D_TEST) \
2170	AWTI/AWTI.test \
2171	EISPACK/EISPACK.test \
2172	GENOM/GENOM.test \
2173	GL/glAW/libglAW.test \
2174	GL/glpng/libglpng_arb.test \
2175	ISLAND_HOPPING/ISLAND_HOPPING.test \
2176	NALIGNER/NALIGNER.test \
2177	NAMES/NAMES.test \
2178	PHYLO/PHYLO.test \
2179	PRIMER_DESIGN/PRIMER_DESIGN.test \
2180	PROBE_DESIGN/PROBE_DESIGN.test \
2181	SECEDIT/SECEDIT.test \
2182	SEQ_QUALITY/SEQ_QUALITY.test \
2183	SERVERCNTRL/SERVERCNTRL.test \
2184	SL/ALIVIEW/ALIVIEW.test \
2185	SL/AP_TREE/AP_TREE.test \
2186	SL/ARB_TREE/ARB_TREE.test \
2187	SL/AW_HELIX/AW_HELIX.test \
2188	SL/AW_NAME/AW_NAME.test \
2189	SL/DB_SCANNER/DB_SCANNER.test \
2190	SL/GUI_ALIVIEW/GUI_ALIVIEW.test \
2191	SL/HELIX/HELIX.test \
2192	SL/ITEMS/ITEMS.test \
2193	SL/LOCATION/LOCATION.test \
2194	SL/MATRIX/MATRIX.test \
2195	SL/REFENTRIES/REFENTRIES.test \
2196	SL/SEQUENCE/SEQUENCE.test \
2197	SL/TRANSLATE/TRANSLATE.test \
2198	SL/TREE_ADMIN/TREE_ADMIN.test \
2199	SL/TREE_WRITE/TREE_WRITE.test \
2200	STAT/STAT.test \
2201	TREEGEN/TREEGEN.test \
2202	WETC/WETC.test \
2203	XML/XML.test \
2204	SL/ROOTED_TREE/ROOTED_TREE.test \
2205
2206	# untestable units
2207
2208	UNITS_NEED_FIX = \
2209	ptpan/PROBE.test \
2210
2211	UNITS_UNTESTABLE_ATM = \
2212	PROBE_SET/PROBE_SET.test \
2213	XML_IMPORT/XML_IMPORT.test \
2214
2215	# for the moment, put all units containing tests into UNITS_TESTED or UNITS_TESTED_FIRST
2216
2217	UNITS_TESTED_FIRST = \
2218	DIST/DIST.test \
2219	PARSIMONY/PARSIMONY.test \
2220	EDIT4/EDIT4.test \
2221	NTREE/NTREE.test \
2222	MULTI_PROBE/MULTI_PROBE.test \
2223
2224	# plain test-libaries not linked anywhere
2225	TEST_SANDBOXES = \
2226	SL/CB/CB.test \
2227
2228	UNITS_TESTED = \
2229	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.test \
2230	SL/NDS/NDS.test \
2231	ARB_GDE/ARB_GDE.test \
2232	GENOM_IMPORT/GENOM_IMPORT.test \
2233	SL/MACROS/MACROS.test \
2234	SL/REGEXPR/REGEXPR.test \
2235	SL/FILTER/FILTER.test \
2236	ARBDB/libARBDB.test \
2237	CONSENSUS_TREE/CONSENSUS_TREE.test \
2238	TOOLS/arb_consensus_tree.test \
2239	TOOLS/arb_test.test \
2240	TOOLS/arb_probe.test \
2241	PERLTOOLS/arb_proto_2_xsub.test \
2242	AWTC/AWTC.test \
2243	SL/ALILINK/ALILINK.test \
2244	SL/TREE_READ/TREE_READ.test \
2245	DBSERVER/DBSERVER.test \
2246	AWT/libAWT.test \
2247	CORE/libCORE.test \
2248	SL/INSDEL/INSDEL.test \
2249	SL/TREEDISP/TREEDISP.test \
2250	AISC_MKPTPS/mkptypes.test \
2251	MERGE/MERGE.test \
2252	SERVERCNTRL/SERVERCNTRL.test \
2253	SL/FAST_ALIGNER/FAST_ALIGNER.test \
2254	SL/PRONUC/PRONUC.test \
2255	WINDOW/libWINDOW.test \
2256	HELP_SOURCE/arb_help2xml.test \
2257	CONVERTALN/CONVERTALN.test \
2258	SL/SEQIO/SEQIO.test \
2259	SL/PTCLEAN/PTCLEAN.test \
2260	PROBE/PROBE.test \
2261	SL/DB_QUERY/DB_QUERY.test \
2262
2263	TESTED_UNITS_MANUAL = \
2264	$(TEST_SANDBOXES) \
2265	$(UNITS_TESTED_FIRST) \
2266	$(UNITS_TESTED) \
2267
2268	# $(UNITS_WORKING)
2269
2270	# see UNIT_TESTER/sym2testcode.pl@disableErrorOnUnitsWithoutTests
2271
2272	#TESTED_UNITS = $(TESTED_UNITS_AUTO)
2273	TESTED_UNITS = $(TESTED_UNITS_MANUAL)
2274
2275	# ----------------------------------------
2276
2277	TEST_LOG_DIR = UNIT_TESTER/logs
2278	TEST_RUN_SUITE=$(MAKE) $(NODIR) -C UNIT_TESTER -f Makefile.suite -r
2279	TEST_MAKE_FLAGS=
2280	TEST_POST_CLEAN=
2281	ifeq ($(COVERAGE),1)
2282	TEST_POST_CLEAN=$(MAKE) clean_cov
2283	TEST_MAKE_FLAGS+=-j1
2284	endif
2285
2286
2287	%.test:
2288	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
2289	( \
2290	echo "fake[1]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
2291	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
2292	"UNITDIR=$(@D)" \
2293	"UNITLIBNAME=$(@F:.test=)" \
2294	"COVERAGE=$(COVERAGE)" \
2295	"ARB_PID=$(ARB_PID)_$(@F)" \
2296	runtest; \
2297	echo "fake[1]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"; \
2298	$(TEST_POST_CLEAN) \
2299	) >$(TEST_LOG_DIR)/$(@F).log 2>&1; \
2300	UNIT_TESTER/log_result.pl $(TEST_LOG_DIR)/$(@F).log )
2301
2302
2303	test_base: $(UNIT_TESTER_LIB:.a=.dummy) $(subst .test,.dummy,$(TEST_SANDBOXES))
2304
2305	clean_cov:
2306	find . \( -name ".gcda" -o -name ".gcov" -o -name "*.cov" \) -exec rm {} \;
2307
2308	clean_cov_all: clean_cov
2309	find . \( -name "*.gcno" \) -exec rm {} \;
2310
2311	run_tests: test_base clean_cov
2312	$(MAKE) "ARB_PID=UT_$$$$" run_tests_faked_arbpid
2313
2314	cleanup_faked_arbpids:
2315	@-rm ~/.arb_tmp/tmp/arb_pids_${USER}_${ARB_PID}_*
2316
2317	cleanup_faked_arbpids_and_fail: cleanup_faked_arbpids
2318	@false
2319
2320	run_tests_faked_arbpid:
2321	+@$(TEST_RUN_SUITE) init
2322	@echo "fake[2]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2323	$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(TESTED_UNITS) \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2324	@echo "fake[2]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2325	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2326	@$(MAKE) clean_cov >/dev/null
2327	@$(MAKE) cleanup_faked_arbpids
2328
2329	ut:
2330	ifeq ($(UNIT_TESTS),1)
2331	@echo $(MAKE) run_tests
2332	@$(MAKE) run_tests
2333	else
2334	@echo "Not compiled with unit tests"
2335	endif
2336
2337
2338	aut:
2339	+@$(TEST_RUN_SUITE) unskip
2340	$(MAKE) ut
2341
2342	# --------------------------------------------------------------------------------
2343
2344	TIMELOG=$(ARBHOME)/arb_time.log
2345	TIMEARGS=--append --output=$(TIMELOG) --format=" %E(%S+%U) %P [%C]"
2346	TIMECMD=$(TIME) $(TIMEARGS)
2347
2348	time_one:
2349	ifeq ($(ONE_TIMED_TARGET),)
2350	@echo "Error: You have to pass ONE_TIMED_TARGET to $@"
2351	false
2352	else
2353	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET)"
2354	@$(TIMECMD) $(MAKE) $(ONE_TIMED_TARGET)
2355	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET) [done]"
2356	endif
2357
2358	timed_target:
2359	ifeq ($(TIMED_TARGET),)
2360	@echo "Error: You have to pass TIMED_TARGET to $@"
2361	false
2362	else
2363	@echo "Build time:" > $(TIMELOG)
2364	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2365	@cat $(TIMELOG)
2366	@rm $(TIMELOG)
2367	endif
2368
2369	timed_target_tested:
2370	ifeq ($(TIMED_TARGET),)
2371	@echo "Error: You have to pass TIMED_TARGET to $@"
2372	false
2373	else
2374	@echo "Build time:" > $(TIMELOG)
2375	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2376	$(MAKE) "ONE_TIMED_TARGET=ut" time_one
2377	@cat $(TIMELOG)
2378	@rm $(TIMELOG)
2379	endif
2380
2381	clean_timed_target:
2382	ifeq ($(TIMED_TARGET),)
2383	@echo "Error: You have to pass TIMED_TARGET to $@"
2384	false
2385	else
2386	@echo "Build time:" > $(TIMELOG)
2387	$(MAKE) "ONE_TIMED_TARGET=clean" time_one
2388	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2389	@cat $(TIMELOG)
2390	@rm $(TIMELOG)
2391	endif
2392
2393	# --------------------------------------------------------------------------------
2394
2395	CHECKOUT_MODIFIED=0# set to 1 to temporarily skip test for modifications (do not check in if set to 1)
2396
2397	check_svn_does_not_contain_generated:
2398	ifeq ($(CHECKOUT_MODIFIED),0)
2399	@echo "Testing that build does not modify files in SVN"
2400	@test 0 = `svn status \| wc -l` \|\| ( \
2401	echo "The checkout is not/no longer clean:"; \
2402	svn status; \
2403	echo "- if this fails instantly, your checkout is not clean"; \
2404	echo "- if this fails after other targets, these targets modify checked in data"; \
2405	echo " (a common cause may be that depends are not up to date)"; \
2406	false)
2407	else
2408	grep -Hn 'CHECKOUT_MODIFIED' Makefile
2409	endif
2410
2411	check_svn_ignores_generated:
2412	@test 0 = `svn status \| grep '^\?' \| wc -l` \|\| ( \
2413	echo "There are svn-unignored files:"; \
2414	svn status \| grep '^\?'; \
2415	echo "(all generated files should be svn-ignored)"; \
2416	false)
2417
2418	check_svn_state: check_svn_does_not_contain_generated
2419	$(MAKE) check_svn_ignores_generated
2420	$(MAKE) savetest
2421
2422	things_that_always_should_work: depends proto
2423
2424	post_commit_check:
2425	@echo "---------------------------------------- [Initial]"
2426	$(MAKE) check_svn_state
2427
2428	$(MAKE) clean
2429	@echo "---------------------------------------- [After 'make clean']"
2430	$(MAKE) check_svn_state
2431
2432	$(MAKE) things_that_always_should_work
2433	@echo "---------------------------------------- [After 'make things_that_always_should_work']"
2434	$(MAKE) check_svn_state
2435
2436	$(MAKE) all
2437	@echo "---------------------------------------- [After 'make all']"
2438	$(MAKE) check_svn_state
2439
2440	$(MAKE) things_that_always_should_work
2441	@echo "---------------------------------------- [Final]"
2442	$(MAKE) check_svn_state
2443
2444	# --------------------------------------------------------------------------------
2445
2446	build: arb
2447	$(MAKE) binlink preplib compile_compatibility
2448
2449	all:
2450	@echo "Build time" > $(TIMELOG)
2451	@echo "$(SEP) $(MAKE) build"
2452	@$(TIMECMD) $(MAKE) build
2453	@echo $(SEP)
2454	@echo "made 'all' with success."
2455	@echo "to start arb enter 'arb'"
2456	ifeq ($(UNIT_TESTS),1)
2457	@echo $(MAKE) run_tests
2458	@$(TIMECMD) $(MAKE) run_tests
2459	endif
2460	@echo "$(SEP) $(MAKE) build [done]"
2461	ifeq ($(DEBUG),1)
2462	@$(MAKE) save_test_no_error >/dev/null # just show hints
2463	endif
2464	@cat $(TIMELOG)
2465	@rm $(TIMELOG)
2466

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