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Last change on this file was 15966, checked in by westram, 8 years ago
reintegrates 'group' into 'trunk' implements #652 (group search) adds: log:branches/group@15733:15740,15743:15748,15750:15752,15754,15756,15758:15777,15781:15793,15796,15798:15806,15808:15817,15819:15965
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 76.6 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	# Paths for several libraries may be set from config.makefile by using:
22	#
23	# export XLIBS=$(shell pkg-config --libs xpm xerces-c)
24	# export XINCLUDES=$(shell pkg-config --cflags x11)
25	# export XAW_LIBS=$(shell pkg-config --libs xaw7)
26	# export XML_INCLUDES=$(shell pkg-config --cflags xerces-c)
27	#
28	# You make have to explicitely point pkg-config to the *.pc files needed.
29	# For example, Xquartz X11 libraries on macos can be located by adding
30	# the following line before those given above:
31	#
32	# export PKG_CONFIG_PATH=/usr/X11/lib/pkgconfig
33	#
34	# -----------------------------------------------------
35	# ARB Makefile and ARB source code are aware of the following defines:
36	#
37	# $(MACH) name of the machine (LINUX or DARWIN; see config.makefile)
38	# DEBUG compiles the DEBUG sections
39	# DEBUG_GRAPHICS all X-graphics are flushed immediately (for debugging)
40	# ARB_64=0/1 1=>compile 64 bit version
41	# UNIT_TESTS=0/1 1=>compile in unit tests and call them after build
42	# COVERAGE=0/1/2 compile in gcov support (useful together with UNIT_TESTS=1)
43	# 0=no, 1+2=compile in, 1=show
44	# STABS=0/1 force stabs format? (0 = "use default format")
45	# SANITIZE=0/#/all use Sanitizer? (defaults to 0,
46	# 1=AddressSanitizer+LeakSanitizer,
47	# 2=UndefinedBehaviorSanitizer,
48	# combine bit-values to activate multiple Sanitizers,
49	# specify 'all' to activate all)
50	# SHOWTODO=0/1 activate TODO-warnings? (defaults to 0, except for ralf)
51	#
52	# -----------------------------------------------------
53	# The ARB source code is aware of the following defines:
54	#
55	# NDEBUG doesn't compile the DEBUG sections
56	# DEVEL_$(DEVELOPER) developer-dependent flag (enables you to have private sections in code)
57	# DEVELOPER='ANY' (default setting) will be ignored
58	# configurable in config.makefile
59	#
60	# -----------------------------------------------------
61	# Read configuration
62	include config.makefile
63
64	# set defaults for variables commented out in config.makefile:
65	ifndef DARWIN
66	DARWIN:=0
67	endif
68	ifndef LINUX
69	LINUX:=0
70	endif
71	ifndef DEBIAN
72	DEBIAN:=0
73	endif
74	ifndef REDHAT
75	REDHAT:=0
76	endif
77	ifndef ARB_64
78	ARB_64=1#default to 64bit
79	endif
80
81	# compiler settings:
82	ifneq ($(CC),use__A_CC__instead_of__CC)
83	A_CC:=$(CC)# compile C
84	A_CXX:=$(CXX)# compile C++
85
86	# uncomment to ensure no submakefile uses CC and CXX directly
87	override CC:=use__A_CC__instead_of__CC
88	override CXX:=use__A_CXX__instead_of__CXX
89	endif
90
91	export CC CXX A_CC A_CXX
92
93	# unconditionally prepend $(ARBHOME)/lib to LD_LIBRARY_PATH if not found
94	ifeq ($(findstring $(ARBHOME)/lib,$(LD_LIBRARY_PATH)),)
95	LD_LIBRARY_PATH:=${ARBHOME}/lib:$(LD_LIBRARY_PATH)
96	endif
97
98	# store LD_LIBRARY_PATH to circumvent SIP restrictions:
99	ARBBUILD_LIBRARY_PATH:=$(LD_LIBRARY_PATH)
100
101	FORCEMASK = umask 002
102	NODIR=--no-print-directory
103
104	SED:=$(ARBHOME)/SH/arb_sed
105	READLINK:=$(ARBHOME)/SH/arb_readlink
106
107	# ---------------------- compiler version detection
108
109	# supported gcc versions:
110	ALLOWED_gcc_VERSIONS=\
111	4.3.1 4.3.2 4.3.3 4.3.4 \
112	4.4.1 4.4.3 4.4.5 4.4.6 4.4.7 \
113	4.5.2 \
114	4.6.1 4.6.2 4.6.3 4.6.4 \
115	4.7.1 4.7.2 4.7.3 4.7.4 \
116	4.8.0 4.8.1 4.8.2 4.8.3 4.8.4 4.8.5 \
117	4.9.0 4.9.1 4.9.2 4.9.3 4.9.4 \
118	5.1.0 5.2.0 5.3.0 5.3.1 5.4.0 \
119	6.1.0 6.2.0 6.3.0 \
120	7.1.0 \
121
122
123	# ----------------------
124
125	COMPILER_INFO:=$(shell SOURCE_TOOLS/arb_compiler_version.pl $(A_CXX))
126	COMPILER_NAME:=$(word 1,$(COMPILER_INFO))
127	COMPILER_VERSION:=$(word 2,$(COMPILER_INFO))
128
129	USE_CLANG:=0
130	ifneq ($(COMPILER_NAME),gcc)
131	ifeq ($(COMPILER_NAME),clang)
132	USE_CLANG:=1
133	else
134	$(error failed to detect COMPILER_NAME (got '$(COMPILER_NAME)', expected 'clang' or 'gcc'))
135	endif
136	endif
137
138	ifeq ($(USE_CLANG),1)
139	# accept all clang versions:
140	ALLOWED_COMPILER_VERSIONS=$(COMPILER_VERSION)
141	else
142	ALLOWED_COMPILER_VERSIONS=$(ALLOWED_gcc_VERSIONS)
143	endif
144
145	COMPILER_VERSION_ALLOWED=$(strip $(subst ___,,$(foreach version,$(ALLOWED_COMPILER_VERSIONS),$(findstring ___$(version)___,___$(COMPILER_VERSION)___))))
146
147	#---------------------- split gcc version
148
149	SPLITTED_VERSION:=$(subst ., ,$(COMPILER_VERSION))
150
151	USE_GCC_MAJOR:=$(word 1,$(SPLITTED_VERSION))
152	USE_GCC_MINOR:=$(word 2,$(SPLITTED_VERSION))
153	USE_GCC_PATCHLEVEL:=$(word 3,$(SPLITTED_VERSION))
154
155	USE_GCC_452_OR_HIGHER:=
156	USE_GCC_46_OR_HIGHER:=
157	USE_GCC_47_OR_HIGHER:=
158	USE_GCC_48_OR_HIGHER:=
159	USE_GCC_49_OR_HIGHER:=
160	USE_GCC_50_OR_HIGHER:=
161	USE_GCC_60_OR_HIGHER:=
162	USE_GCC_70_OR_HIGHER:=
163
164	ifeq ($(USE_CLANG),0)
165	ifeq ($(USE_GCC_MAJOR),4)
166	ifeq ($(USE_GCC_MINOR),5)
167	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),23456789)','')
168	USE_GCC_452_OR_HIGHER:=yes
169	endif
170	else
171	ifneq ('$(findstring $(USE_GCC_MINOR),6789)','')
172	USE_GCC_452_OR_HIGHER:=yes
173	USE_GCC_46_OR_HIGHER:=yes
174	ifneq ($(USE_GCC_MINOR),6)
175	USE_GCC_47_OR_HIGHER:=yes
176	ifneq ($(USE_GCC_MINOR),7)
177	USE_GCC_48_OR_HIGHER:=yes
178	ifneq ($(USE_GCC_MINOR),8)
179	USE_GCC_49_OR_HIGHER:=yes
180	endif
181	endif
182	endif
183	endif
184	endif
185	else
186	# gcc 5.x or higher
187	USE_GCC_452_OR_HIGHER:=yes
188	USE_GCC_46_OR_HIGHER:=yes
189	USE_GCC_47_OR_HIGHER:=yes
190	USE_GCC_48_OR_HIGHER:=yes
191	USE_GCC_49_OR_HIGHER:=yes
192	USE_GCC_50_OR_HIGHER:=yes
193	ifneq ($(USE_GCC_MAJOR),5)
194	# gcc 6.x or higher
195	USE_GCC_60_OR_HIGHER:=yes
196	ifneq ($(USE_GCC_MAJOR),6)
197	# gcc 7.x or higher
198	USE_GCC_70_OR_HIGHER:=yes
199	endif
200	endif
201	endif
202	endif
203
204	#---------------------- define special directories for non standard builds
205
206	ifeq ($(DARWIN),1)
207	OSX_FW:=/System/Library/Frameworks
208	OSX_FW_OPENGL:=$(OSX_FW)/OpenGL.framework/Versions/A/Libraries
209	OSX_FW_GLUT:=$(OSX_FW)/GLUT.framework/Versions/A/Libraries
210	OSX_FW_IMAGEIO:=$(OSX_FW)/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources
211	endif
212
213	#----------------------
214
215	ifeq ($(DARWIN),1)
216	LINK_STATIC=1# link static
217	else
218	LINK_STATIC=0# link dynamically
219	# LINK_STATIC=1# link static (testing only)
220	endif
221
222	shared_cflags :=# flags for shared lib compilation
223	clflags :=# linker flags (when passed through gcc)
224	extended_warnings :=# warning flags for C and C++-compiler
225	extended_cpp_warnings :=# warning flags for C++-compiler only
226
227	DISABLE_VECTORIZE_CHECK:=0
228
229	ifeq ($(DEBUG),0)
230	dflags := -DNDEBUG# defines
231	ifeq ($(USE_CLANG),1)
232	cflags := -O3# compiler flags (C and C++)
233	else
234	clflags += -Wl,-O2# passthrough linker flags
235	# ------- standard optimization:
236	cflags := -O3# compiler flags (C and C++)
237	# ------- test changed optimization (DISABLE_VECTORIZE_CHECK for -O2 or lower):
238	# cflags := -O2# do not commit uncommented!
239	# DISABLE_VECTORIZE_CHECK:=1
240	endif
241	endif
242
243	ifeq ($(DEBIAN),1)
244	clflags += -Wl,-rpath=/usr/lib/arb/lib -Wl,-z,relro
245	endif
246
247	ifeq ($(DEBUG),1)
248	dflags := -DDEBUG
249
250	gdb_common := -g -g3 -ggdb -ggdb3
251
252	DBGOPTI:=-O0
253	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
254	DBGOPTI:=-Og
255	endif
256
257	ifeq ($(STABS),1)
258	cflags := $(DBGOPTI) $(gdb_common) -gstabs+ # using stabs+ (enable this for bigger debug session: debugs inlines, quick var inspect, BUT valgrind stops working :/)
259	else
260	cflags := $(DBGOPTI) $(gdb_common) # (using dwarf - cant debug inlines here, incredible slow on showing variable content)
261	endif
262
263	# cflags := $(DBGOPTI) $(gdb_common) -gdwarf-3 # (specify explicit dwarf format)
264	# cflags := $(DBGOPTI) $(gdb_common) -gstabs # using stabs (same here IIRC)
265	# cflags := -O2 $(gdb_common) # use this for callgrind (force inlining)
266
267	ifeq ($(DARWIN),0)
268	clflags += -Wl,-g
269	# Note:
270	# Previously '-Wl,-noinhibit-exec' was added to 'clflags' here,
271	# to fix some issues with launchpad binutils (see [12972]).
272	# But that change also caused 'undefined symbols' NOT to be reported as errors
273	# at link time, producing executables that fail at runtime :/
274	endif
275
276	ifeq ($(DEBUG_GRAPHICS),1)
277	dflags += -DDEBUG_GRAPHICS
278	endif
279
280	endif # DEBUG only
281
282	# control how much you get spammed
283	# (please do not change default in SVN, use developer specific setting as below)
284	POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl
285	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --original# dont modify compiler output
286	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --loop-optimization-candi# show candidates for vectorization check
287	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --dump-loop-optimization# useful while optimizing code for vectorization
288	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --hide-Noncopyable-advices
289	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --show-useless-Weff++
290	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --no-warnings
291	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --only-first-error
292	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --no-warnings --only-first-error
293	ifeq ($(DEVELOPER),ELMAR)
294	POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --only-first-error
295	endif
296
297	# Enable extra warnings
298	extended_warnings :=
299	extended_cpp_warnings :=
300
301	# C and C++
302	extended_warnings += -Wwrite-strings -Wunused -Wno-aggregate-return -Wshadow
303
304	# C++ only
305	extended_cpp_warnings += -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute
306	extended_cpp_warnings += -Wctor-dtor-privacy# < gcc 3
307	# extended_cpp_warnings += -Wfloat-equal# gcc 3.0
308
309	# ------- above only warnings available in 3.0
310
311	WEFFC_BROKEN:=0
312	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
313	ifneq ('$(USE_GCC_48_OR_HIGHER)','yes')
314	# -Weffc++ broken in 4.7.x series
315	# gcc 4.7.3 crashes on GenomeImport.cxx when -Weffc++ is active
316	# (bug reported https://gcc.gnu.org/bugzilla/show_bug.cgi?id=56923; apparently wont be fixed for 4.7-series)
317	# gcc 4.7.4 crashes on DBwriter.cxx when -Weffc++ is active
318	WEFFC_BROKEN:=1
319	endif
320	endif
321	ifeq ('$(WEFFC_BROKEN)','0')
322	extended_cpp_warnings += -Weffc++# gcc 3.0.1
323	endif
324
325	extended_cpp_warnings += -Wmissing-noreturn# gcc 3.0.2
326	# extended_cpp_warnings += -Wold-style-cast# gcc 3.0.4 (warn about 28405 old-style casts)
327	extended_cpp_warnings += -Winit-self# gcc 3.4.0
328	extended_cpp_warnings += -Wstrict-aliasing# gcc 3.4
329	extended_cpp_warnings += -Wextra# gcc 3.4.0
330
331	ifeq ($(DEBUG),1)
332	ifeq ($(USE_CLANG),0)
333	# turn off -Wmaybe-uninitialized in debug mode (gets activated with -Wextra). too many bogus warnings
334	extended_cpp_warnings += -Wno-maybe-uninitialized
335	endif
336	endif
337	ifeq ('$(USE_GCC_452_OR_HIGHER)','yes')
338	extended_cpp_warnings += -Wlogical-op# gcc 4.5.2
339	endif
340	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
341	# extended_cpp_warnings += -Wunused-local-typedefs# gcc 4.7 (fails for each STATIC_ASSERT, enable only for Cxx11)
342	# extended_cpp_warnings += -Wzero-as-null-pointer-constant# gcc 4.7 #@@@ activate
343	endif
344	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
345	extended_cpp_warnings += -Wunused-local-typedefs# available since gcc 4.7 (but fails for each STATIC_ASSERT, so enable only for Cxx11)
346	endif
347	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
348	extended_cpp_warnings += -Wswitch-bool
349	extended_cpp_warnings += -Wlogical-not-parentheses
350	extended_cpp_warnings += -Wsizeof-array-argument
351	extended_cpp_warnings += -Wbool-compare
352
353	ifneq ($(DEVELOPER),RELEASE)
354	# suggest final:
355	extended_cpp_warnings += -Wsuggest-final-types
356	extended_cpp_warnings += -Wsuggest-final-methods
357	dflags += -DSUGGESTS_FINAL
358	endif
359	endif
360	ifeq ('$(USE_GCC_60_OR_HIGHER)','yes')
361	# extended_cpp_warnings += -Wshift-negative-value # done by -Wextra
362	extended_cpp_warnings += -Wduplicated-cond
363	endif
364
365	#---------------------- turn off clang bogus warnings
366
367	ifeq ($(USE_CLANG),1)
368	# -Wmismatched-tags warns about struct/class mismatch in forward declarations (which is explicitely allowed)
369	# -Wchar-subscripts reports too many bogus warnings for "array['x']" (when 'x' is known to be in range [0..128])
370	# -Wunused-private-field report too many false positives (currently ~ 2 of 3)
371	# -Wstring-plus-int warns about common ARB coding practice
372	# -Wgnu-static-float-init warns about accepted GNU extension
373	extended_cpp_warnings += -Wno-mismatched-tags -Wno-char-subscripts -Wno-unused-private-field -Wno-string-plus-int
374	ifeq ('$(COMPILER_VERSION)','4.2.1')
375	# jenkins build (doesn't know switch -Wno-gnu-static-float-init)
376	extended_cpp_warnings += -Wno-gnu
377	else
378	extended_cpp_warnings += -Wno-gnu-static-float-init
379	endif
380	endif
381
382	#---------------------- developer
383
384	ifneq ($(DEVELOPER),ANY) # ANY=default setting (skip all developer specific code)
385	dflags += -DDEVEL_$(DEVELOPER)# activate developer/release specific code
386	endif
387
388	#---------------------- activate TODO warnings?
389
390	ifndef SHOWTODO
391	ifeq ($(DEVELOPER),RALF)
392	SHOWTODO:=1
393	else
394	SHOWTODO:=0
395	endif
396	endif
397	ifeq ($(SHOWTODO),1)
398	dflags += -DWARN_TODO# activate "TODO" warnings
399	endif
400
401	#---------------------- activate Sanitizers?
402
403	ASAN_OPTIONS:=handle_segv=0:color=0
404	ASAN_OPTIONS+=:detect_leaks=1 # comment-out to disable leak-detection
405	ASAN_OPTIONS+=:check_initialization_order=1
406	# ASAN_OPTIONS+=:abort_on_error=1
407
408	# suppressions: SOURCE_TOOLS/arb.leaksan.supp
409	LSAN_OPTIONS:=max_leaks=3:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp
410
411
412	ifndef SANITIZE
413	SANITIZE:=0
414	endif
415
416	SANITIZE_ADDRESS:=0
417	SANITIZE_UNDEFINED:=0
418
419	ifneq ($(SANITIZE),0)
420	ifeq ($(SANITIZE),all)
421	SANITIZE:=3
422	endif
423
424	ifeq ($(SANITIZE),1)
425	SANITIZE_ADDRESS:=1
426	else
427	ifeq ($(SANITIZE),2)
428	SANITIZE_UNDEFINED:=1
429	else
430	ifeq ($(SANITIZE),3)
431	SANITIZE_ADDRESS:=1
432	SANITIZE_UNDEFINED:=1
433	else
434	$(error Unknown value '$(SANITIZE)' specified for SANITIZE in config.makefile)
435	endif
436	endif
437	endif
438	endif
439
440	ifeq ($(SANITIZE_ADDRESS),1)
441	ifneq ('$(USE_GCC_48_OR_HIGHER)','yes')
442	$(info AddressSanitizer not usable with gcc $(COMPILER_VERSION) - disabled)
443	SANITIZE_ADDRESS:=0
444	else
445	ifneq ('$(USE_GCC_49_OR_HIGHER)','yes')
446	$(warning note that LeakSanitizer does not work with gcc $(COMPILER_VERSION))
447	endif
448	endif
449	endif
450
451	ifeq ($(SANITIZE_UNDEFINED),1)
452	ifneq ('$(USE_GCC_49_OR_HIGHER)','yes')
453	$(info UndefinedBehaviorSanitizer not usable with gcc $(COMPILER_VERSION) - disabled)
454	SANITIZE_UNDEFINED:=0
455	endif
456	endif
457
458	SANITIZE_ANY:=0
459	ifeq ($(SANITIZE_ADDRESS),1)
460	SANITIZE_ANY:=1
461	endif
462	ifeq ($(SANITIZE_UNDEFINED),1)
463	SANITIZE_ANY:=1
464	endif
465
466	ifeq ($(SANITIZE_ANY),1)
467	DISABLE_VECTORIZE_CHECK:=1
468	endif
469
470	#---------------------- 32 or 64 bit
471
472	ifndef BUILDHOST_64
473	BUILDHOST_64:=$(ARB_64)# assume build host is same as version (see config.makefile)
474	endif
475
476	cross_cflags:=
477	cross_lflags:=
478	cross_clflags:=
479
480	ifeq ($(ARB_64),1)
481	dflags += -DARB_64 #-fPIC
482	shared_cflags += -fPIC
483
484	ifeq ($(BUILDHOST_64),1)
485	# build 64-bit ARB version on 64-bit host
486	CROSS_LIB:=# empty = autodetect below
487	ifeq ($(DARWIN),1)
488	cross_cflags += -arch x86_64
489	cross_lflags += -arch x86_64
490	cross_clflags += -arch x86_64
491	endif
492	else
493	# build 64-bit ARB version on 32-bit host
494	CROSS_LIB:=/lib64
495	cross_cflags += -m64
496	cross_lflags += -m64 -m elf_x86_64
497	cross_clflags += -m64 -Wl,-m64,-m,elf_x86_64
498	endif
499	else
500	ifeq ($(BUILDHOST_64),1)
501	# build 32-bit ARB version on 64-bit host
502	CROSS_LIB:=# empty = autodetect below
503	cross_cflags += -m32
504	cross_lflags += -m32 -m elf_i386
505	cross_clflags += -m32 -Wl,-m32,-m,elf_i386
506	else
507	# build 32-bit ARB version on 32-bit host
508	CROSS_LIB:=/lib
509	endif
510	endif
511
512	cflags += $(cross_cflags)
513	clflags += $(cross_clflags)
514
515	ifeq ('$(CROSS_LIB)','')
516	# autodetect libdir
517	ifeq ($(ARB_64),1)
518	CROSS_LIB:=$(shell (test -d /lib64 && echo lib64) \|\| echo lib)
519	else
520	CROSS_LIB:=$(shell (test -d /lib32 && echo lib32) \|\| echo lib)
521	endif
522	endif
523
524	#---------------------- unit tests
525
526	ifndef UNIT_TESTS
527	UNIT_TESTS=0#default is "no tests"
528	endif
529	ifeq ($(UNIT_TESTS),1)
530	dflags += -DUNIT_TESTS
531	UNIT_TESTER_LIB=UNIT_TESTER/UNIT_TESTER.a
532	else
533	UNIT_TESTER_LIB=
534	endif
535
536	#---------------------- use gcov
537
538	ifndef COVERAGE
539	COVERAGE=0#default is "no"
540	endif
541	ifneq ($(COVERAGE),0)
542	GCOVFLAGS=-ftest-coverage -fprofile-arcs
543	cflags += $(GCOVFLAGS)
544	EXECLIBS=-lgcov
545	else
546	GCOVFLAGS=
547	EXECLIBS=
548	endif
549
550	#---------------------- other flags
551
552	dflags += -D$(MACH) # define machine
553
554	ifeq ($(DARWIN),1)
555	shared_cflags += -fno-common
556	else
557	dflags += $(shell getconf LFS_CFLAGS)
558	endif
559
560	cflags += -pipe
561	cflags += -fmessage-length=0# don't wrap compiler output
562	cflags += -fshow-column# show columns
563	cflags += -funit-at-a-time
564	cflags += -fPIC
565	cflags += -fno-common# link all global data into one namespace
566	cflags += -fstrict-aliasing# gcc 3.4
567	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
568	cflags += -fno-diagnostics-show-caret#gcc 4.8 (4.7.?)
569	endif
570	#cflags += -save-temps# uncomment to see preprocessor output
571
572	#---------------------- various sanitizers
573	# There are some disabled tests in CORE/arb_misc.cxx@sanitizers
574	# which trigger sanitizer reports.
575
576	ifeq ($(SANITIZE_ANY),1)
577	cflags += -ggdb3 -fno-omit-frame-pointer
578	endif
579
580	# activate AddressSanitizer+LeakSanitizer?
581	ifeq ($(SANITIZE_ADDRESS),1)
582	cflags += -fsanitize=address
583	clflags += -fsanitize=address
584	dflags += -DLEAKS_SANITIZED
585	endif
586
587	# activate UndefinedBehaviorSanitizer?
588	ifeq ($(SANITIZE_UNDEFINED),1)
589	cflags += -fsanitize=undefined
590	clflags += -fsanitize=undefined
591	dflags += -DUNDEF_SANITIZED
592	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
593	# abort on runtime errors
594	cflags += -fno-sanitize-recover=all
595	endif
596	#
597	# Note: alignment-sanitizer is deactivated for ARBDB and PROBE!
598	ifeq ('$(DEBUG)','1')
599	ifeq ($(USE_GCC_MAJOR),4)
600	ifeq ($(USE_GCC_MINOR),9)
601	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),01)','')
602	# workaround https://gcc.gnu.org/bugzilla/show_bug.cgi?id=63531 for 4.9.0 + 4.9.1
603	# (problem is fixed in 4.9.2 release)
604	extended_cpp_warnings:=$(subst -Weffc++,,$(extended_cpp_warnings))
605	endif
606	endif
607	endif
608	endif
609	endif
610
611	#---------------------- X11 location
612
613	ifeq ($(DARWIN),1)
614	XHOME:=$(PREFIX)
615	else
616	ifeq ($(DEBIAN),1)
617	XHOME:=$(PREFIX)
618	else
619	XHOME:=/usr/X11R6
620	endif
621	endif
622
623	XINCLUDES ?= -I$(XHOME)/include
624	XLIBS ?= -L$(XHOME)/$(CROSS_LIB)
625	ifeq ($(DARWIN),1)
626	XINCLUDES += -I$(OSX_FW)/GLUT.framework/Headers -I$(OSX_FW)/OpenGL.framework/Headers -I$(OSX_SDK)/usr/include/krb5
627
628	XLIBS += -lXm -lpng -lz -lXt -lX11 -lXext -lXp -lXmu -lXi
629	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGL.dylib:$(OSX_FW_OPENGL)/libGL.dylib
630	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGLU.dylib:$(OSX_FW_OPENGL)/libGLU.dylib
631	else
632	XLIBS += -lXm -lXpm -lXt -lXext -lX11
633	endif
634
635	dflags += -DARB_MOTIF
636
637	#---------------------- open GL
638
639	ifeq ($(OPENGL),1)
640	cflags += -DARB_OPENGL # activate OPENGL code
641	GL := gl # this is the name of the OPENGL base target
642	GL_LIB_SYS := -lGL -lGLU
643	GL_LIB_ARB := -L$(ARBHOME)/GL/glAW -lglAW
644
645	ifeq ($(DARWIN),1)
646	GL_LIB_SYS += -lpthread
647	endif
648
649	GL_PNGLIBS_ARB := -L$(ARBHOME)/GL/glpng -lglpng_arb
650	GL_PNGLIBS_SYS := -lpng
651
652	GLEWLIB := -lGLEW -lGLw
653	ifeq ($(DARWIN),1)
654	GLUTLIB := -glut
655	else
656	GLUTLIB := -lglut
657	endif
658
659	GL_LIBS_SYS := $(GL_LIB_SYS) $(GL_PNGLIBS_SYS) $(GLEWLIB) $(GLUTLIB)
660	GL_LIBS_ARB := $(GL_LIB_ARB) $(GL_PNGLIBS_ARB)
661
662	RNA3D_LIB := RNA3D/RNA3D.a
663	else
664	GL_LIBS_ARB:=# no opengl -> no libs
665	GL_LIBS_SYS:=# no opengl -> no libs
666	GL:=# don't build ARB openGL libs
667
668	RNA3D_LIB :=
669	endif
670
671	RNA3D_LIB_4_DEPENDS := RNA3D/RNA3D.a
672
673	GL_LIBS:=$(GL_LIBS_ARB) $(GL_LIBS_SYS)
674
675	#---------------------- tiff lib:
676
677	TIFFLIBS := -ltiff
678
679	#---------------------- XML lib:
680
681	XMLLIBS := -lxerces-c
682
683	#---------------------- glib:
684
685	ARB_NEEDED_GLIB=glib-2.0
686
687	ARB_GLIB_INCLUDE:=$(strip $(shell pkg-config --cflags $(ARB_NEEDED_GLIB)))
688	ARB_GLIB_LIBS:=$(strip $(shell pkg-config --libs $(ARB_NEEDED_GLIB)))
689
690	#---------------------- basic libs:
691
692	SYSLIBS:=
693	ifeq ($(DARWIN),1)
694	SYSLIBS += -lstdc++
695	else
696	SYSLIBS += -lm $(ARB_GLIB_LIBS)
697	endif
698
699	#---------------------- include symbols?
700
701	ifeq ($(TRACESYM),1)
702	ifeq ($(USE_CLANG),0)
703	cflags += -rdynamic
704	clflags += -rdynamic -Wl,--export-dynamic
705	endif
706	endif
707
708	#---------------------- system dependent commands
709
710	ifeq ($(DARWIN),1)
711	TIME:=gtime
712	else
713	TIME:=/usr/bin/time
714	endif
715
716	#---------------------- SSE vectorizer
717
718	ifeq ('$(USE_GCC_60_OR_HIGHER)','yes')
719	ifeq ('$(USE_GCC_MAJOR)','6')
720	ifneq ('$(findstring $(USE_GCC_MINOR),123)','')
721	# gcc 6.1.x .. 6.3.x
722	# see http://bugs.arb-home.de/ticket/700
723	cflags += -fno-tree-loop-vectorize
724	DISABLE_VECTORIZE_CHECK:=1
725	else
726	ifeq ($(DEBUG),0)
727	$(error vectorizing incompatible? check ticket 700 with this compiler version)
728	endif
729	endif
730	else
731	ifeq ($(DEBUG),0)
732	$(error vectorizing incompatible? check ticket 700 with this compiler version)
733	endif
734	endif
735	endif
736
737	ifeq ($(DEBUG),0)
738	ifeq ($(USE_GCC_49_OR_HIGHER),yes)
739	ifeq ($(DISABLE_VECTORIZE_CHECK),0)
740	# cflags += -fopt-info
741	cflags += -fopt-info-vec
742	# Shows reasons for unsuccessful vectorization:
743	# cflags += -fopt-info-vec-missed
744	POST_COMPILE += --check-loop-optimization
745	endif
746	else
747	ifeq ($(USE_GCC_48_OR_HIGHER),yes)
748	# no automatic vectorization-check for gcc<4.9.0
749	# -> uncomment the next 2 lines and grep the spam it will produce for 'vectorized.*loops'
750	# cflags += -fopt-info -fopt-info-vec-missed
751	# POST_COMPILE += --original
752	endif
753	endif
754	endif
755
756	#---------------------- stop early on broken flags/compiler combination
757
758	ifeq ($(DEBUG),0)
759	ifeq ($(SANITIZE_ANY),1)
760	ifeq ('$(COMPILER_VERSION)','4.9.1')
761	$(error compiling DEBUG=0 + SANITIZE!=0 crashes with gcc $(COMPILER_VERSION) (gcc 4.9.2 works))
762	endif
763	endif
764	endif
765
766	ifeq ('$(USE_GCC_70_OR_HIGHER)', 'yes')
767	$(error compiling with gcc $(COMPILER_VERSION) is considered unstable atm. see http://bugs.arb-home.de/ticket/752 for datails)
768	endif
769
770	#---------------------- differences between linking executables and shared libs:
771
772	# executables:
773	ifeq ($(DARWIN),1)
774	blflags:=$(clflags)
775	else
776	blflags:=$(clflags) -Wl,--no-undefined
777	endif
778
779	# shared libraries
780	llflags:=$(clflags)
781
782	# dont use clflags below
783	clflags:=
784
785	# -------------------------------------------------------------------------
786	# Don't put any machine/version/etc conditionals below!
787	# (instead define variables above)
788	# -------------------------------------------------------------------------
789
790	cflags += -W -Wall $(dflags) $(extended_warnings)
791	cxxflags := $(extended_cpp_warnings)
792
793	# add CFLAGS + CPPFLAGS from environment for DEBIAN build
794	ifeq ($(DEBIAN),1)
795	cflags := $(CFLAGS) $(cflags)
796	cxxflags += $(CPPFLAGS)
797	endif
798
799	ifeq ('$(USE_CLANG)','1')
800	# none of the following standards works with clang3.3 (under linux) => dont use standard (as done before r15516)
801	# cxxflags += -std=gnu++11
802	# cxxflags += -std=gnu++0x
803	else
804	ifeq ('$(USE_GCC_60_OR_HIGHER)','yes')
805	cxxflags += -std=gnu++14# see also TEMPLATES/cxxforward.h@USE_Cxx14
806	else
807	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
808	cxxflags += -std=gnu++11# see also TEMPLATES/cxxforward.h@USE_Cxx11
809	else
810	# gcc versions between 4.3 (lowest supported) and <4.7
811	cxxflags += -std=gnu++0x
812	endif
813	endif
814	endif
815
816	LINK_STATIC_LIB := ar -csq# link static lib
817	LINK_EXECUTABLE := $(A_CXX) $(blflags) -o# link executable (c++)
818
819	ifeq ($(LINK_STATIC),1)
820	SHARED_LIB_SUFFIX = a# static lib suffix
821	LINK_SHARED_LIB := $(LINK_STATIC_LIB)
822	else
823	SHARED_LIB_SUFFIX = so# shared lib suffix
824	LINK_SHARED_LIB := $(A_CXX) $(llflags) -shared $(GCOVFLAGS) -o# link shared lib
825	endif
826
827	ifeq ($(DARWIN),1)
828	lflags4perl:=
829	else
830	lflags4perl:=$(cross_lflags) -shared
831	endif
832
833	# delete variables unused below
834	blflags:=
835	llflags:=
836
837	# other used tools
838	MAKEDEPEND_PLAIN = makedepend
839	MAKEDEPEND = $(FORCEMASK);$(MAKEDEPEND_PLAIN)
840
841	#SEP:=--------------------------------------------------------------------------------
842	SEP=[`date +%M:%S.%N`] ------------------------------------------------
843	# to analyse timings run
844	# make -j9 clean; make -j9 all \| grep '^\[' \| sort
845	# make -j9 "TIMED_TARGET=perl" clean_timed_target \| grep '^\[' \| sort
846
847	CORE_LIB=-lCORE
848	ARBDB_LIB=-lARBDB $(CORE_LIB)
849	LIBS = $(ARBDB_LIB) $(SYSLIBS)
850
851	GUI_LIBS_PREFIX:=
852	ifeq ($(DARWIN),1)
853	# this seem to be added at wrong place, since opengl is only needed to link EDIT4
854	GUI_LIBS_PREFIX:=-framework GLUT -framework OpenGL
855	endif
856
857	GUI_LIBS=$(GUI_LIBS_PREFIX) $(LIBS) -lAWT -lWINDOW
858	GUI_LIBS+=$(XLIBS)
859
860	LIBPATH = -L$(ARBHOME)/lib
861
862	DEST_LIB = lib
863	DEST_BIN = bin
864
865	CC_INCLUDES := -I. -I$(ARBHOME)/INCLUDE $(XINCLUDES) $(ARB_GLIB_INCLUDE)
866	CXX_INCLUDES := $(CC_INCLUDES)
867	MAKEDEPENDFLAGS := -- -DARB_OPENGL -DUNIT_TESTS -D__cplusplus -I. -Y$(ARBHOME)/INCLUDE
868
869	# -------------------------------
870	# old PTSERVER or PTPAN?
871
872	ifeq ($(PTPAN),1)
873	# PTPAN only libs
874	ARCHS_PT_SERVER = \
875	ptpan/PROBE.a
876	else
877	ifeq ($(PTPAN),2)
878	# special mode to compile both servers (developers only!)
879	ARCHS_PT_SERVER = \
880	ptpan/PROBE.a \
881	PROBE/PROBE.a
882	ARCHS_PT_SERVER_LINK = PROBE/PROBE.a# default to old ptserver
883	else
884	# PT-server only libs
885	ARCHS_PT_SERVER = \
886	PROBE/PROBE.a
887	endif
888	endif
889
890	ifndef ARCHS_PT_SERVER_LINK
891	ARCHS_PT_SERVER_LINK = $(ARCHS_PT_SERVER)
892	endif
893
894	# ---------------------------------------
895	# wrap main()
896
897	use_ARB_main=$(ARBHOME)/SOURCE_TOOLS/arb_main_cpp.o
898	use_ARB_main_C=$(ARBHOME)/SOURCE_TOOLS/arb_main_c.o
899
900	# -----------------------------------------
901	# export variables to submakefiles
902
903	include SOURCE_TOOLS/export2sub
904
905	# do not define (exported) variables below this point
906
907	# -------------------------
908	# Main arb targets:
909	# -------------------------
910
911	first_target:
912	$(MAKE) checks
913	@echo $(SEP)
914	@echo 'Main targets:'
915	@echo ''
916	@echo ' all - Compile ARB + TOOLs + and copy shared libs + link foreign software'
917	@echo ' (That is most likely the target you want)'
918	@echo ''
919	@echo ' clean - remove generated files ("SUBDIR/SUBDIR.clean" to clean only SUBDIR)'
920	@echo ' rebuild - clean + all'
921	@echo ' cleanlinked - remove all binaries'
922	@echo ' relink - cleanlinked + all (=relink all from objects)'
923	@echo ''
924	@echo 'Some often used sub targets (make all makes them all):'
925	@echo ''
926	@echo ' arb - Just compile ARB (but none of the integrated tools)'
927	@echo ' menus - create lib/gde/arb.menu from GDEHELP/ARB_GDEmenus.source'
928	@echo ' perl - Compile the PERL XSUBS into lib/ARB.so and create links in lib to perl'
929	@echo ' binlink - Create all links in the bin directory'
930	@echo ''
931	@echo 'Development targets:'
932	@echo ''
933	@echo ' depends - create or update dependencies ("SUBDIR/SUBDIR.depends" to update only SUBDIR)'
934	@echo ' proto - create or update prototypes ("SUBDIR/SUBDIR.proto" to update only SUBDIR)'
935	@echo ' tags - create tags for xemacs'
936	@echo ' show - show available shortcuts (AKA subtargets)'
937	@echo ' up - shortcut for depends+proto+tags'
938	ifeq ($(UNIT_TESTS),1)
939	@echo ' ut - only run tests'
940	endif
941	ifneq ($(SANITIZE),0)
942	@echo ' sanitize - all + run arb_ntree with sanitizer (test.arb + execute _logged)'
943	endif
944	@echo ' modified - rebuild files modified in svn checkout (does touch)'
945	@echo ' touch - touch files modified in svn checkout'
946	@echo ''
947	@echo 'Internal maintenance:'
948	@echo ''
949	@echo ' relinfo - show help on release targets'
950	@echo ' tarfile - make rebuild and create arb version tarfile ("tarfile_quick" to skip rebuild)'
951	@echo ' save - save all basic ARB sources into arbsrc_DATE ("savetest" to check filelist)'
952	@echo ' patch - save svn diff to patchfile'
953	@echo ' source_doc - create doxygen documentation'
954	@echo ' relocated - rebuild partly (use when you have relocated ARBHOME)'
955	@echo ' check_res - check resource usage'
956	@echo ' dep_graph - Build dependency graphs'
957	@echo ' clean_cov - Clean coverage results'
958	@echo ''
959	@echo ' clean_opengl_changed - clean after changing OPENGL setting in config.Makefile'
960	@echo ''
961	@echo ' post_commit_check - Checks whether'
962	@echo ' * main make targets work,'
963	@echo ' * dependencies and prototypes are up to date,'
964	@echo ' * SVN-controlled files remain unaffected by called targets and'
965	@echo ' * all generated files are ignored.'
966	@echo ' (has to be called in a clean SVN checkout)'
967	@echo $(SEP)
968	@echo ''
969
970	relinfo:
971	@echo ''
972	@echo $(SEP)
973	@echo 'Release targets:'
974	@echo ''
975	@echo ' inc_candi - increase RC candidate-number (only possible in "rc" branch, not needed for RC1)'
976	@echo ' inc_patch - increase release patchlevel (only possible in "stable" branch)'
977	@echo ' inc_minor - increase minor version number (only possible in "trunk")'
978	@echo ' inc_major - increase MAJOR version number (only possible in "trunk")'
979	@echo ''
980	@echo ' show_version - show version tag'
981	@echo ''
982	@echo $(SEP)
983	@echo ''
984
985	# auto-generate config.makefile:
986
987	CONFIG_MAKEFILE_FOUND=$(wildcard config.makefile)
988
989	config.makefile : config.makefile.template
990	@echo --------------------------------------------------------------------------------
991	ifeq ($(strip $(CONFIG_MAKEFILE_FOUND)),)
992	@cp $< $@
993	@echo '$(ARBHOME)/$@:1: has been generated.'
994	@echo 'Please edit $@ to configure your system!'
995	@echo --------------------------------------------------------------------------------
996	@false
997	else
998	@echo '$(ARBHOME)/$<:1: is more recent than'
999	@echo '$(ARBHOME)/$@:1:'
1000	@ls -al config.makefile*
1001	@echo --------------------------------------------------------------------------------
1002	@echo "Updating $@ (if this fails, check manually)"
1003	SOURCE_TOOLS/update_config_makefile.pl
1004	@echo "Sucessfully updated $@"
1005	@echo --------------------------------------------------------------------------------
1006	@ls -al config.makefile*
1007	@echo --------------------------------------------------------------------------------
1008	@echo "Diff to your old config.makefile:"
1009	@echo --------------------------------------------------------------------------------
1010	-diff $@.bak $@
1011	@echo --------------------------------------------------------------------------------
1012	endif
1013
1014	# check if everything is configured correctly
1015
1016	check_DEVELOPER:
1017	ifndef DEVELOPER
1018	@echo 'config.makefile:1: DEVELOPER not defined'
1019	@false
1020	endif
1021
1022	check_DEBUG:
1023	ifndef dflags
1024	@echo 'config.makefile:1: DEBUG has to be defined. Valid values are 0 and 1'
1025	@false
1026	endif
1027
1028	check_ARB_64:
1029	ifndef ARB_64
1030	@echo 'config.makefile:1: ARB_64 has to be defined. Valid values are 0 and 1'
1031	@false
1032	endif
1033
1034	# ---------------------------------------- check gcc version
1035
1036	COMPILER_BROKEN:=0
1037
1038	# gcc 4.8.0 produces invalid code (see #617)
1039	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.8.0')
1040	COMPILER_BROKEN:=1
1041	endif
1042
1043	check_same_GCC_VERSION:
1044	$(ARBHOME)/SOURCE_TOOLS/check_same_compiler_version.pl $(COMPILER_NAME) $(COMPILER_VERSION_ALLOWED)
1045
1046	check_GCC_VERSION:
1047	@echo 'Compiler version check:'
1048	# see .@ALLOWED_gcc_VERSIONS
1049	ifeq ('$(COMPILER_VERSION_ALLOWED)', '')
1050	@echo " - Your compiler is '$(COMPILER_NAME)' version '$(COMPILER_VERSION)'"
1051	@echo ' This version is not in the list of supported $(COMPILER_NAME)-versions:'
1052	@$(foreach version,$(ALLOWED_COMPILER_VERSIONS),echo ' * $(version)';)
1053	@echo ' - You may either ..'
1054	@echo ' - add your version to ALLOWED_$(COMPILER_NAME)_VERSIONS in the Makefile and try it out or'
1055	@echo ' - switch to one of the allowed versions (see arb_README_gcc.txt for installing'
1056	@echo ' a different version of gcc)'
1057	$(error Unsupported compiler '$(COMPILER_NAME)' version '$(COMPILER_VERSION)')
1058	else
1059	ifeq ($(COMPILER_BROKEN),1)
1060	$(error $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)' would build a broken ARB version. Compilation refused)
1061	else
1062	@echo " - Supported $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)' detected - fine!"
1063	@echo ''
1064	ifeq ($(USE_CLANG),1)
1065	@echo "Dump clang version:"
1066	$(A_CXX) -v
1067	endif
1068	$(MAKE) check_same_GCC_VERSION
1069	endif
1070	endif
1071
1072	#---------------------- check ARBHOME
1073
1074	# use arb_INSTALL.txt to determine whether ARBHOME points to correct directory
1075	ARB_INSTALL_FOUND=$(wildcard $(ARBHOME)/arb_INSTALL.txt)
1076
1077	check_ARBHOME:
1078	ifeq ($(strip $(ARB_INSTALL_FOUND)),)
1079	@echo ------------------------------------------------------------
1080	@echo "ARBHOME is set to '$(ARBHOME)'"
1081	@echo "The environment variable ARBHOME has to point to the top arb source directory."
1082	@echo "If you use bash enter:"
1083	@echo " export ARBHOME='`pwd`'"
1084	@echo ------------------------------------------------------------
1085	@false
1086	endif
1087
1088	ARB_PATH_SET=$(findstring $(ARBHOME)/bin,$(PATH))
1089
1090	check_PATH: check_ARBHOME
1091	ifeq ($(strip $(ARB_PATH_SET)),)
1092	@echo ------------------------------------------------------------
1093	@echo "The environment variable PATH has to contain $(ARBHOME)/bin"
1094	@echo "If you use bash enter:"
1095	@echo ' export PATH=$$ARBHOME/bin:$$PATH'
1096	@echo ------------------------------------------------------------
1097	@false
1098	endif
1099
1100	check_TOOLS:
1101	@util/arb_check_build_env.pl \
1102	"$(A_CC)" \
1103	"$(A_CXX)" \
1104	"$(MAKEDEPEND_PLAIN)" \
1105	"$(LINK_SHARED_LIB)" \
1106	"$(LINK_SHARED_LIB)" \
1107
1108	check_ENVIRONMENT : check_PATH check_TOOLS
1109	@echo "-------------------- Environment [start]"
1110	@echo "ARBHOME='$(ARBHOME)'"
1111	@echo "PATH='$(PATH)'"
1112	@echo "LD_LIBRARY_PATH='$(LD_LIBRARY_PATH)'"
1113	@echo "-------------------- Environment [end]"
1114
1115	check_tabs: check_setup
1116	ifeq ($(DEBUG),1)
1117	@SOURCE_TOOLS/tabBrake.pl
1118	endif
1119
1120	force_tab_check:
1121	@touch -t 198001010000 SOURCE_TOOLS/stamp.tabBrake
1122	@$(MAKE) check_tabs
1123
1124
1125	# ---------------------
1126
1127	check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION
1128	@echo Your setup seems to be ok.
1129
1130	checks: check_setup check_tabs
1131	@rm -f SOURCE_TOOLS/postcompile.sav
1132
1133
1134	# end test section ------------------------------
1135
1136	# ---------------------------------------
1137	# List of standard top level directories
1138	#
1139	# sub-makefiles have to define the targets
1140	# - 'depends' and
1141	# - 'clean'
1142	#
1143	# when adding new libs here, also add a dependency vs 'links' or 'links_non_perl' in .@DD_links_non_perl
1144
1145	ARCHS = \
1146	$(ARCHS_PT_SERVER) \
1147	AISC/AISC.a \
1148	AISC_MKPTPS/AISC_MKPTPS.a \
1149	ARBDB/libARBDB.a \
1150	CORE/libCORE.a \
1151	ARB_GDE/ARB_GDE.a \
1152	AWT/libAWT.a \
1153	AWTC/AWTC.a \
1154	AWTI/AWTI.a \
1155	CONSENSUS_TREE/CONSENSUS_TREE.a \
1156	CONVERTALN/CONVERTALN.a \
1157	DBSERVER/DBSERVER.a \
1158	DIST/DIST.a \
1159	EDIT4/EDIT4.a \
1160	EISPACK/EISPACK.a \
1161	GDE/GDE.a \
1162	GENOM/GENOM.a \
1163	GENOM_IMPORT/GENOM_IMPORT.a \
1164	GL/GL.a \
1165	ISLAND_HOPPING/ISLAND_HOPPING.a \
1166	MERGE/MERGE.a \
1167	MULTI_PROBE/MULTI_PROBE.a \
1168	NALIGNER/NALIGNER.a \
1169	NAMES/NAMES.a \
1170	NAMES_COM/server.a \
1171	NTREE/NTREE.a \
1172	PARSIMONY/PARSIMONY.a \
1173	PERLTOOLS/PERLTOOLS.a \
1174	PHYLO/PHYLO.a \
1175	PRIMER_DESIGN/PRIMER_DESIGN.a \
1176	PROBE_COM/server.a \
1177	PROBE_DESIGN/PROBE_DESIGN.a \
1178	PROBE_SET/PROBE_SET.a \
1179	READSEQ/READSEQ.a \
1180	RNA3D/RNA3D.a \
1181	RNACMA/RNACMA.a \
1182	SECEDIT/SECEDIT.a \
1183	SEQ_QUALITY/SEQ_QUALITY.a \
1184	SERVERCNTRL/SERVERCNTRL.a \
1185	SL/SL.a \
1186	STAT/STAT.a \
1187	TOOLS/TOOLS.a \
1188	TREEGEN/TREEGEN.a \
1189	UNIT_TESTER/UNIT_TESTER.a \
1190	WETC/WETC.a \
1191	WINDOW/libWINDOW.a \
1192	XML/XML.a \
1193
1194	# -----------------------
1195	# library packets
1196
1197	ARCHS_CLIENT_PROBE = PROBE_COM/client.a
1198	ARCHS_CLIENT_NAMES = NAMES_COM/client.a
1199
1200	ARCHS_MAKEBIN = AISC_MKPTPS/AISC_MKPTPS.a AISC/AISC.a
1201
1202	# communication libs need aisc and aisc_mkpts:
1203
1204	AISC/AISC.dummy: proto_tools
1205
1206	comtools: AISC/AISC.dummy
1207
1208	ARCHS_SEQUENCE = \
1209	SL/SEQUENCE/SEQUENCE.a \
1210	SL/ALIVIEW/ALIVIEW.a \
1211	SL/PRONUC/PRONUC.a \
1212
1213	ARCHS_TREE = \
1214	SL/ARB_TREE/ARB_TREE.a \
1215	SL/FILTER/FILTER.a \
1216	$(ARCHS_SEQUENCE) \
1217
1218	# parsimony tree (used by NTREE, PARSIMONY, STAT(->EDIT4), DIST(obsolete!))
1219	ARCHS_AP_TREE = \
1220	SL/AP_TREE/AP_TREE.a \
1221	$(ARCHS_TREE) \
1222
1223	# --------------------------------------------------------------------------------
1224	# dependencies for linking shared libs
1225
1226	link_core: core
1227	link_db: db link_core
1228	link_aw: aw link_db
1229	link_awt: awt link_aw
1230
1231	#***************************************************************************************
1232	# Individual_Programs_Section
1233	#***************************************************************************************
1234
1235	arbmainwrapper:
1236	$(MAKE) -C SOURCE_TOOLS -r mainwrapper
1237
1238
1239	#********************************* arb_ntree ************************************
1240	NTREE = bin/arb_ntree
1241	ARCHS_NTREE = \
1242	NTREE/NTREE.a \
1243	ARB_GDE/ARB_GDE.a \
1244	SL/GROUP_SEARCH/GROUP_SEARCH.a \
1245	SL/DB_UI/DB_UI.a \
1246	AWTC/AWTC.a \
1247	AWTI/AWTI.a \
1248	CONSENSUS_TREE/CONSENSUS_TREE.a \
1249	GENOM_IMPORT/GENOM_IMPORT.a \
1250	GENOM/GENOM.a \
1251	MERGE/MERGE.a \
1252	MULTI_PROBE/MULTI_PROBE.a \
1253	PRIMER_DESIGN/PRIMER_DESIGN.a \
1254	PROBE_DESIGN/PROBE_DESIGN.a \
1255	SEQ_QUALITY/SEQ_QUALITY.a \
1256	SERVERCNTRL/SERVERCNTRL.a \
1257	SL/ALILINK/ALILINK.a \
1258	SL/AW_NAME/AW_NAME.a \
1259	SL/CONSENSUS/CONSENSUS.a \
1260	SL/DB_SCANNER/DB_SCANNER.a \
1261	SL/DB_QUERY/DB_QUERY.a \
1262	SL/QUERY/QUERY.a \
1263	SL/SEQIO/SEQIO.a \
1264	STAT/STAT.a \
1265	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1266	SL/HELIX/HELIX.a \
1267	SL/REGEXPR/REGEXPR.a \
1268	SL/REFENTRIES/REFENTRIES.a \
1269	SL/NDS/NDS.a \
1270	SL/ITEM_SHADER/ITEM_SHADER.a \
1271	SL/ITEMS/ITEMS.a \
1272	SL/INSDEL/INSDEL.a \
1273	SL/LOCATION/LOCATION.a \
1274	SL/MACROS/MACROS.a \
1275	SL/TRANSLATE/TRANSLATE.a \
1276	SL/TREEDISP/TREEDISP.a \
1277	SL/TREE_ADMIN/TREE_ADMIN.a \
1278	SL/TREE_READ/TREE_READ.a \
1279	SL/TREE_WRITE/TREE_WRITE.a \
1280	XML/XML.a \
1281	$(ARCHS_AP_TREE) \
1282
1283	$(NTREE): $(ARCHS_NTREE:.a=.dummy) link_awt
1284	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NTREE) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1285	echo "$(SEP) Link $@"; \
1286	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(XMLLIBS)" ; \
1287	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(XMLLIBS) && \
1288	echo "$(SEP) Link $@ [done]"; \
1289	)
1290
1291	#********************************* arb_edit4 ************************************
1292	EDIT4 = bin/arb_edit4
1293
1294	ARCHS_EDIT4 := \
1295	EDIT4/EDIT4.a \
1296	ARB_GDE/ARB_GDE.a \
1297	SL/FAST_ALIGNER/FAST_ALIGNER.a \
1298	AWTC/AWTC.a \
1299	ISLAND_HOPPING/ISLAND_HOPPING.a \
1300	SECEDIT/SECEDIT.a \
1301	SERVERCNTRL/SERVERCNTRL.a \
1302	SL/AW_HELIX/AW_HELIX.a \
1303	SL/AW_NAME/AW_NAME.a \
1304	SL/CONSENSUS/CONSENSUS.a \
1305	SL/ITEMS/ITEMS.a \
1306	STAT/STAT.a \
1307	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1308	SL/HELIX/HELIX.a \
1309	SL/TRANSLATE/TRANSLATE.a \
1310	SL/MACROS/MACROS.a \
1311	SL/NDS/NDS.a \
1312	$(ARCHS_AP_TREE) \
1313	XML/XML.a \
1314
1315	ifeq ($(OPENGL),1)
1316	ARCHS_EDIT4 += RNA3D/RNA3D.a
1317	endif
1318
1319	LIBS_EDIT4 := $(GL_LIBS)
1320
1321	$(EDIT4): $(ARCHS_EDIT4:.a=.dummy) link_awt
1322	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_EDIT4) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1323	echo "$(SEP) Link $@"; \
1324	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4)" ; \
1325	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4) && \
1326	echo "$(SEP) Link $@ [done]"; \
1327	)
1328
1329	#********************************* arb_rnacma ************************************
1330	RNACMA = bin/arb_rnacma
1331	ARCHS_RNACMA = \
1332	RNACMA/RNACMA.a \
1333
1334	$(RNACMA) : $(ARCHS_RNACMA:.a=.dummy) link_db
1335	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_RNACMA) \|\| ( \
1336	echo "$(SEP) Link $@"; \
1337	echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_RNACMA) $(LIBS) $(EXECLIBS)"; \
1338	$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_RNACMA) $(LIBS) $(EXECLIBS) && \
1339	echo "$(SEP) Link $@ [done]"; \
1340	)
1341
1342	#********************************* arb_wetc ************************************
1343	WETC = bin/arb_wetc
1344	ARCHS_WETC = \
1345	WETC/WETC.a \
1346	SL/HELIX/HELIX.a \
1347	SL/FILTER/FILTER.a \
1348	XML/XML.a \
1349
1350	$(WETC): $(ARCHS_WETC:.a=.dummy) link_awt
1351	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_WETC) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1352	echo "$(SEP) Link $@"; \
1353	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_WETC) $(GUI_LIBS)" ; \
1354	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_WETC) $(GUI_LIBS) && \
1355	echo "$(SEP) Link $@ [done]"; \
1356	)
1357
1358	#********************************* arb_dist ************************************
1359	DIST = bin/arb_dist
1360	ARCHS_DIST = \
1361	DIST/DIST.a \
1362	CONSENSUS_TREE/CONSENSUS_TREE.a \
1363	EISPACK/EISPACK.a \
1364	SERVERCNTRL/SERVERCNTRL.a \
1365	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1366	SL/HELIX/HELIX.a \
1367	SL/MATRIX/MATRIX.a \
1368	SL/MACROS/MACROS.a \
1369	SL/NDS/NDS.a \
1370	SL/ITEMS/ITEMS.a \
1371	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.a \
1372	XML/XML.a \
1373	$(ARCHS_AP_TREE) \
1374
1375	$(DIST): $(ARCHS_DIST:.a=.dummy) link_awt
1376	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_DIST) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1377	echo "$(SEP) Link $@"; \
1378	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS)" ; \
1379	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) && \
1380	echo "$(SEP) Link $@ [done]"; \
1381	)
1382
1383	#********************************* arb_pars ************************************
1384	PARSIMONY = bin/arb_pars
1385	ARCHS_PARSIMONY = \
1386	PARSIMONY/PARSIMONY.a \
1387	SERVERCNTRL/SERVERCNTRL.a \
1388	SL/AW_NAME/AW_NAME.a \
1389	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1390	SL/HELIX/HELIX.a \
1391	SL/MACROS/MACROS.a \
1392	SL/NDS/NDS.a \
1393	SL/ITEMS/ITEMS.a \
1394	SL/TRANSLATE/TRANSLATE.a \
1395	SL/TREEDISP/TREEDISP.a \
1396	XML/XML.a \
1397	$(ARCHS_AP_TREE) \
1398
1399	$(PARSIMONY): $(ARCHS_PARSIMONY:.a=.dummy) link_awt
1400	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PARSIMONY) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1401	echo "$(SEP) Link $@"; \
1402	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS)" ; \
1403	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) && \
1404	echo "$(SEP) Link $@ [done]"; \
1405	)
1406
1407	#********************************* arb_convert_aln ************************************
1408	CONVERT_ALN = bin/arb_convert_aln
1409	ARCHS_CONVERT_ALN = \
1410	CONVERTALN/CONVERTALN.a \
1411
1412	$(CONVERT_ALN) : $(ARCHS_CONVERT_ALN:.a=.dummy) link_db
1413	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_CONVERT_ALN) $(use_ARB_main) \|\| ( \
1414	echo "$(SEP) Link $@"; \
1415	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_CONVERT_ALN) $(LIBS)"; \
1416	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_CONVERT_ALN) $(LIBS) && \
1417	echo "$(SEP) Link $@ [done]"; \
1418	)
1419
1420	#********************************* arb_treegen ************************************
1421
1422	TREEGEN = bin/arb_treegen
1423	ARCHS_TREEGEN = \
1424	TREEGEN/TREEGEN.a \
1425
1426	$(TREEGEN) : $(ARCHS_TREEGEN:.a=.dummy)
1427	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_TREEGEN) $(use_ARB_main_C) \|\| ( \
1428	echo "$(SEP) Link $@"; \
1429	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(EXECLIBS) $(ARCHS_TREEGEN)" ; \
1430	$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(EXECLIBS) $(ARCHS_TREEGEN) && \
1431	echo "$(SEP) Link $@ [done]"; \
1432	)
1433
1434	#********************************* arb_naligner ************************************
1435	NALIGNER = bin/arb_naligner
1436	ARCHS_NALIGNER = \
1437	NALIGNER/NALIGNER.a \
1438	SERVERCNTRL/SERVERCNTRL.a \
1439	SL/HELIX/HELIX.a \
1440
1441	$(NALIGNER): $(ARCHS_NALIGNER:.a=.dummy) link_db
1442	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NALIGNER) $(use_ARB_main) \|\| ( \
1443	echo "$(SEP) Link $@"; \
1444	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(LIBS)" ; \
1445	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(LIBS) && \
1446	echo "$(SEP) Link $@ [done]"; \
1447	)
1448
1449	#********************************* arb_phylo ************************************
1450	PHYLO = bin/arb_phylo
1451	ARCHS_PHYLO = \
1452	PHYLO/PHYLO.a \
1453	SL/HELIX/HELIX.a \
1454	SL/FILTER/FILTER.a \
1455	SL/MACROS/MACROS.a \
1456	XML/XML.a \
1457
1458	$(PHYLO): $(ARCHS_PHYLO:.a=.dummy) link_awt
1459	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PHYLO) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1460	echo "$(SEP) Link $@"; \
1461	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_PHYLO) $(GUI_LIBS)" ; \
1462	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_PHYLO) $(GUI_LIBS) && \
1463	echo "$(SEP) Link $@ [done]"; \
1464	)
1465
1466	#***************************************************************************************
1467	# SERVER SECTION
1468	#***************************************************************************************
1469
1470	#********************************* arb_db_server ************************************
1471	DBSERVER = bin/arb_db_server
1472	ARCHS_DBSERVER = \
1473	DBSERVER/DBSERVER.a \
1474	SERVERCNTRL/SERVERCNTRL.a \
1475
1476	$(DBSERVER): $(ARCHS_DBSERVER:.a=.dummy) link_db
1477	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_DBSERVER) $(ARBDB_LIB) $(use_ARB_main) \|\| ( \
1478	echo "$(SEP) Link $@"; \
1479	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS)" ; \
1480	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS) && \
1481	echo "$(SEP) Link $@ [done]"; \
1482	)
1483
1484	#********************************* arb_pt_server ************************************
1485	PROBE = bin/arb_pt_server
1486	ARCHS_PROBE_COMMON = \
1487	SL/PTCLEAN/PTCLEAN.a \
1488	SERVERCNTRL/SERVERCNTRL.a \
1489	SL/HELIX/HELIX.a \
1490
1491	ARCHS_PROBE_LINK = \
1492	$(ARCHS_PT_SERVER_LINK) \
1493	$(ARCHS_PROBE_COMMON) \
1494
1495	ARCHS_PROBE_DEPEND = \
1496	$(ARCHS_PT_SERVER) \
1497	$(ARCHS_PROBE_COMMON) \
1498
1499	$(PROBE): $(ARCHS_PROBE_DEPEND:.a=.dummy) link_db
1500	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_SERVER_PROBE) config.makefile $(use_ARB_main) \|\| ( \
1501	echo "$(SEP) Link $@"; \
1502	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_PROBE_LINK) $(ARCHS_CLIENT_PROBE) $(ARBDB_LIB) $(SYSLIBS)" ; \
1503	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_PROBE_LINK) $(ARCHS_CLIENT_PROBE) $(ARBDB_LIB) $(SYSLIBS) && \
1504	echo "$(SEP) Link $@ [done]"; \
1505	)
1506
1507	#********************************* arb_name_server ************************************
1508	NAMES = bin/arb_name_server
1509	ARCHS_NAMES = \
1510	NAMES/NAMES.a \
1511	SERVERCNTRL/SERVERCNTRL.a \
1512
1513	$(NAMES): $(ARCHS_NAMES:.a=.dummy) link_db
1514	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) $(use_ARB_main) \|\| ( \
1515	echo "$(SEP) Link $@"; \
1516	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS)" ; \
1517	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(EXECLIBS) $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS) && \
1518	echo "$(SEP) Link $@ [done]"; \
1519	)
1520
1521	#********************************* SHARED LIBRARIES SECTION ************************************
1522
1523	prepare_libdir: addlibs
1524
1525	addlibs:
1526	(perl $(ARBHOME)/SOURCE_TOOLS/provide_libs.pl \
1527	"arbhome=$(ARBHOME)" \
1528	"opengl=$(OPENGL)" \
1529	"link_static=$(LINK_STATIC)" \
1530	)
1531
1532	#***************************************************************************************
1533	# Recursive calls to sub-makefiles
1534	#***************************************************************************************
1535
1536	%.depends:
1537	@cp -p $(@D)/Makefile $(@D)/Makefile.old # save old Makefile
1538	@$(MAKE) -C $(@D) -r \
1539	"AUTODEPENDS=1" \
1540	"MAIN=nothing" \
1541	"cflags=noCflagsHere_use_MAKEDEPENDFLAGS" \
1542	"cxxflags=noCxxflagsHere_use_MAKEDEPENDFLAGS" \
1543	depends
1544	@grep "^# DO NOT DELETE" $(@D)/Makefile >/dev/null
1545	@cat $(@D)/Makefile \
1546	\| SOURCE_TOOLS/fix_depends.pl "(from main)" \
1547	>$(@D)/Makefile.2
1548	@mv $(@D)/Makefile.old $(@D)/Makefile # restore old Makefile
1549	@$(ARBHOME)/SOURCE_TOOLS/mv_if_diff $(@D)/Makefile.2 $(@D)/Makefile # update Makefile if changed
1550
1551	%.proto:
1552	@($(MAKE) -C $(@D) \
1553	"AUTODEPENDS=0" \
1554	"MAIN=nothing" \
1555	"cflags=noCflags" \
1556	"cxxflags=noCxxflags" \
1557	proto 2>&1 ) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
1558
1559	%.clean:
1560	@$(MAKE) -C $(@D) \
1561	"AUTODEPENDS=0" \
1562	"MAIN=nothing" \
1563	"cflags=noCflags" \
1564	"cxxflags=noCxxflags" \
1565	clean
1566
1567
1568	# stop wrong targets
1569	target_is_missing_lib_prefix:
1570	@echo "Error: Denied to build shared library target with missing 'lib'-prefix"
1571	false
1572
1573	ARBDB/ARBDB.dummy: target_is_missing_lib_prefix
1574	CORE/CORE.dummy: target_is_missing_lib_prefix
1575	AWT/AWT.dummy: target_is_missing_lib_prefix
1576	WINDOW/WINDOW.dummy: target_is_missing_lib_prefix
1577
1578	# rule to generate main target (normally a library):
1579	# @@@ check effect of setting LANG=C below
1580	%.dummy:
1581	@( export ID=$$$$; LANG=C; \
1582	(( \
1583	echo "$(SEP) Make $(@D)"; \
1584	$(MAKE) -C $(@D) -r \
1585	"AUTODEPENDS=1" \
1586	"MAIN=$(@F:.dummy=.a)" \
1587	"cflags=$(cflags) -DIN_ARB_$(subst /,_,$(@D))" \
1588	&& \
1589	echo "$(SEP) Make $(@D) [done]"; \
1590	) >$(@D).$$ID.log 2>&1 && (cat $(@D).$$ID.log;rm $(@D).$$ID.log)) \|\| (cat $(@D).$$ID.log;rm $(@D).$$ID.log;false))
1591
1592	# Additional dependencies for subtargets:
1593
1594	PROBE_COM/PROBE_COM.dummy : comtools
1595	NAMES_COM/NAMES_COM.dummy : comtools
1596
1597	com: PROBE_COM/PROBE_COM.dummy NAMES_COM/NAMES_COM.dummy
1598
1599	PROBE_COM/server.dummy:
1600	@echo Unwanted request to make target $<
1601	false
1602
1603	PROBE_COM/client.dummy:
1604	@echo Unwanted request to make target $<
1605	false
1606
1607	NAMES_COM/server.dummy:
1608	@echo Unwanted request to make target $<
1609	false
1610
1611	NAMES_COM/client.dummy:
1612	@echo Unwanted request to make target $<
1613	false
1614
1615
1616	ARBDB/libARBDB.dummy: links
1617	CORE/libCORE.dummy: links
1618
1619	PERLTOOLS/PERLTOOLS.dummy: core db
1620
1621	# all subdirs perl not depends on go here (ADD_links_non_perl)
1622	AWT/libAWT.dummy: links_non_perl
1623	AWTI/AWTI.dummy: links_non_perl
1624	CONSENSUS_TREE/CONSENSUS_TREE.dummy: links_non_perl
1625	CONVERTALN/CONVERTALN.dummy: links_non_perl
1626	DBSERVER/DBSERVER.dummy: links_non_perl
1627	DIST/DIST.dummy: links_non_perl
1628	EDIT4/EDIT4.dummy: links_non_perl com
1629	EISPACK/EISPACK.dummy: links_non_perl
1630	GDE/GDE.dummy: links_non_perl
1631	GENOM/GENOM.dummy: links_non_perl
1632	GENOM_IMPORT/GENOM_IMPORT.dummy: links_non_perl
1633	ISLAND_HOPPING/ISLAND_HOPPING.dummy: links_non_perl
1634	MERGE/MERGE.dummy: links_non_perl
1635	NTREE/NTREE.dummy: links_non_perl
1636	PARSIMONY/PARSIMONY.dummy: links_non_perl
1637	PHYLO/PHYLO.dummy: links_non_perl
1638	PRIMER_DESIGN/PRIMER_DESIGN.dummy: links_non_perl
1639	PROBE_SET/PROBE_SET.dummy: links_non_perl link_db
1640	READSEQ/READSEQ.dummy: links_non_perl
1641	RNACMA/RNACMA.dummy: links_non_perl header_libs
1642	SECEDIT/SECEDIT.dummy: links_non_perl
1643	SEQ_QUALITY/SEQ_QUALITY.dummy: links_non_perl
1644	SERVERCNTRL/SERVERCNTRL.dummy: links_non_perl com
1645	SL/ALILINK/ALILINK.dummy: links_non_perl
1646	SL/ALIVIEW/ALIVIEW.dummy: links_non_perl
1647	SL/AP_TREE/AP_TREE.dummy: links_non_perl
1648	SL/ARB_TREE/ARB_TREE.dummy: links_non_perl
1649	SL/AW_HELIX/AW_HELIX.dummy: links_non_perl
1650	SL/CONSENSUS/CONSENSUS.dummy: links_non_perl
1651	SL/DB_QUERY/DB_QUERY.dummy: links_non_perl
1652	SL/DB_SCANNER/DB_SCANNER.dummy: links_non_perl
1653	SL/DB_UI/DB_UI.dummy: links_non_perl
1654	SL/FAST_ALIGNER/FAST_ALIGNER.dummy: links_non_perl
1655	SL/FILTER/FILTER.dummy: links_non_perl
1656	SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy: links_non_perl
1657	SL/GROUP_SEARCH/GROUP_SEARCH.dummy: links_non_perl
1658	SL/HELIX/HELIX.dummy: links_non_perl
1659	SL/INSDEL/INSDEL.dummy: links_non_perl
1660	SL/ITEMS/ITEMS.dummy: links_non_perl
1661	SL/ITEM_SHADER/ITEM_SHADER.dummy: links_non_perl
1662	SL/LOCATION/LOCATION.dummy: links_non_perl
1663	SL/MACROS/MACROS.dummy: links_non_perl
1664	SL/MATRIX/MATRIX.dummy: links_non_perl
1665	SL/NDS/NDS.dummy: links_non_perl
1666	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.dummy: links_non_perl
1667	SL/PRONUC/PRONUC.dummy: links_non_perl
1668	SL/PTCLEAN/PTCLEAN.dummy: links_non_perl link_db
1669	SL/QUERY/QUERY.dummy: links_non_perl link_db
1670	SL/REFENTRIES/REFENTRIES.dummy: links_non_perl
1671	SL/REGEXPR/REGEXPR.dummy: links_non_perl
1672	SL/SEQIO/SEQIO.dummy: links_non_perl
1673	SL/SEQUENCE/SEQUENCE.dummy: links_non_perl
1674	SL/TRANSLATE/TRANSLATE.dummy: links_non_perl
1675	SL/TREE_ADMIN/TREE_ADMIN.dummy: links_non_perl
1676	SL/TREE_READ/TREE_READ.dummy: links_non_perl
1677	SL/TREE_WRITE/TREE_WRITE.dummy: links_non_perl
1678	SL/TREEDISP/TREEDISP.dummy: links_non_perl
1679	STAT/STAT.dummy: links_non_perl
1680	TREEGEN/TREEGEN.dummy: links_non_perl
1681	WETC/WETC.dummy: links_non_perl
1682	WINDOW/libWINDOW.dummy: links_non_perl
1683	XML/XML.dummy: links_non_perl
1684
1685	ifeq ($(OPENGL),1)
1686	GL/glAW/glAW.dummy: links_non_perl
1687	GL/glpng/glpng.dummy: links_non_perl
1688	GL/GL.dummy: GL/glAW/glAW.dummy GL/glpng/glpng.dummy
1689	RNA3D/RNA3D.dummy: links_non_perl gl
1690	endif
1691
1692	UNIT_TESTER/UNIT_TESTER.dummy: link_db \
1693	SERVERCNTRL/SERVERCNTRL.dummy \
1694
1695	# see also TOOLS/Makefile@TOOLSLIBDEPENDS
1696	TOOLS/TOOLS.dummy : links_non_perl link_db \
1697	CONSENSUS_TREE/CONSENSUS_TREE.dummy \
1698	SERVERCNTRL/SERVERCNTRL.dummy \
1699	SL/FILTER/FILTER.dummy \
1700	SL/INSDEL/INSDEL.dummy \
1701	SL/REGEXPR/REGEXPR.dummy \
1702	SL/SEQIO/SEQIO.dummy \
1703	SL/TREE_READ/TREE_READ.dummy \
1704	SL/TREE_WRITE/TREE_WRITE.dummy \
1705	XML/XML.dummy \
1706
1707	AWTC/AWTC.dummy : com
1708
1709	NAMES/NAMES.dummy : com
1710	SL/AW_NAME/AW_NAME.dummy : com
1711
1712	PROBE/PROBE.dummy : com
1713	ptpan/PROBE.dummy : com
1714	MULTI_PROBE/MULTI_PROBE.dummy : com
1715	PROBE_DESIGN/PROBE_DESIGN.dummy : com
1716	NALIGNER/NALIGNER.dummy : com
1717
1718	ARB_GDE/ARB_GDE.dummy : proto_tools
1719
1720	compile_compatibility: SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.dummy
1721
1722	#***************************************************************************************
1723	# Short aliases to make targets
1724	#***************************************************************************************
1725
1726	show:
1727	@echo $(SEP)
1728	@echo 'Aliases for often needed targets:'
1729	@echo ''
1730	@echo ' executables:'
1731	@echo ''
1732	@echo ' nt arb_ntree'
1733	@echo ' e4 arb_edit4 (includes secedit)'
1734	@echo ' di arb_dist'
1735	@echo ' ph arb_phylo'
1736	@echo ' pa arb_parsimony'
1737	@echo ' tg arb_treegen'
1738	@echo ' ds arb_dbserver'
1739	@echo ' pt arb_pt_server'
1740	@echo ' na arb_name_server'
1741	@echo ''
1742	@echo ' libraries:'
1743	@echo ''
1744	@echo ' com communication libraries'
1745	@echo ' db ARB database'
1746	@echo ' aw GUI lib'
1747	@echo ' awt GUI toolkit'
1748	@echo ' awtc general purpose library'
1749	@echo ' awti import/export library'
1750	@echo ' mp multi probe library'
1751	@echo ' ge genome library'
1752	@echo ' pd probe design lib'
1753	@echo ' prd primer design lib'
1754	@echo ''
1755	@echo ' other targets:'
1756	@echo ''
1757	@echo ' help recompile help files'
1758	@echo ' tools make small tools used by arb'
1759	@echo ''
1760	@echo ' foreign targets:'
1761	@echo ''
1762	@echo ' gde GDE'
1763	@echo ' agde ARB_GDE'
1764	@echo ''
1765	@echo 'for other targets inspect $(ARBHOME)/Makefile'
1766	@echo ''
1767	@echo $(SEP)
1768
1769	source_doc:
1770	@echo "Remove some links (doxygen crashes otherwise):"
1771	find . \( -name "AISC" -o -name "C" -o -name "GDEHELP" \) -type l -exec rm {} \;
1772	doxygen 2>&1 1>/dev/null
1773	$(MAKE) forcelinks
1774
1775	dep_graph:
1776	@echo "Building some dependency graphs"
1777	SOURCE_TOOLS/dependency_graphs.pl
1778
1779	help: HELP_SOURCE/HELP_SOURCE.dummy
1780
1781	HELP_SOURCE/HELP_SOURCE.dummy: link_core xml menus
1782
1783	db: ARBDB/libARBDB.dummy
1784	core: CORE/libCORE.dummy
1785	aw: WINDOW/libWINDOW.dummy
1786	awt: AWT/libAWT.dummy
1787	awtc: AWTC/AWTC.dummy
1788	awti: AWTI/AWTI.dummy
1789
1790	mp: MULTI_PROBE/MULTI_PROBE.dummy
1791	mg: MERGE/MERGE.dummy
1792	ge: GENOM/GENOM.dummy
1793	prd: PRIMER_DESIGN/PRIMER_DESIGN.dummy
1794
1795	nt: menus $(NTREE)
1796
1797	nal: $(NALIGNER)
1798
1799	di: $(DIST)
1800	ph: $(PHYLO)
1801	pa: $(PARSIMONY)
1802	tg: $(TREEGEN)
1803
1804	ifeq ($(OPENGL),1)
1805	3d: RNA3D/RNA3D.dummy
1806	gl: GL/GL.dummy
1807	else
1808	noopengl:
1809	@echo "invalid target for OPENGL=0"
1810	3d: noopengl
1811	gl: noopengl
1812	endif
1813
1814	SL/SL.dummy: com
1815
1816	ds: $(DBSERVER)
1817	pt: $(PROBE)
1818	pst: PROBE_SET/PROBE_SET.dummy
1819	pd: PROBE_DESIGN/PROBE_DESIGN.dummy
1820	na: $(NAMES)
1821	sq: SEQ_QUALITY/SEQ_QUALITY.dummy
1822	cma: $(RNACMA)
1823
1824	sec: SECEDIT/SECEDIT.dummy
1825
1826	e4: $(EDIT4) readseq menus
1827
1828	gi: GENOM_IMPORT/GENOM_IMPORT.dummy
1829	wetc: $(WETC)
1830
1831	xml: XML/XML.dummy
1832	xmlin: XML_IMPORT/XML_IMPORT.dummy# broken
1833	stat: STAT/STAT.dummy $(NTREE) $(EDIT4)
1834	fa: SL/FAST_ALIGNER/FAST_ALIGNER.dummy
1835
1836	#********************************************************************************
1837
1838	up_by_remake: depends proto vectorize_checks
1839
1840	up: up_by_remake tags valgrind_update
1841
1842	#********************************************************************************
1843
1844	touch:
1845	SOURCE_TOOLS/touch_modified.pl
1846
1847	modified: touch
1848	$(MAKE) all
1849
1850	#********************************************************************************
1851
1852	libdepends:
1853	$(MAKE) -C "SOURCE_TOOLS" \
1854	"RNA3D_LIB=$(RNA3D_LIB_4_DEPENDS)" \
1855	libdepends
1856
1857	#********************************************************************************
1858
1859	# create generated headers:
1860	genheaders: TEMPLATES/TEMPLATES.dummy
1861
1862	clrdotdepends:
1863	rm PROBE_COM/.depends \|\| true
1864	rm NAMES_COM/.depends \|\| true
1865	rm PERL2ARB/.depends \|\| true
1866
1867	comdepends: comtools clrdotdepends
1868	@echo "$(SEP) Partially build com interface"
1869	$(MAKE) PROBE_COM/PROBE_COM.depends NAMES_COM/NAMES_COM.depends
1870	$(MAKE) PROBE_COM/server.depends NAMES_COM/server.depends
1871
1872	depends: genheaders comdepends vectorize_checks
1873	@echo "$(SEP) Updating other dependencies"
1874	$(MAKE) $(subst NAMES_COM/server.depends,,$(subst PROBE_COM/server.depends,,$(ARCHS:.a=.depends))) \
1875	HELP_SOURCE/HELP_SOURCE.depends \
1876	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.depends \
1877
1878	$(MAKE) libdepends
1879
1880	depend: depends
1881
1882	# ------------------------------------------------------------
1883	# dependency generation tests for AISC code
1884	#(all should work w/o creating wrong dependencies;
1885	# neither in XXX_COM/Makefile nor in code using AISC interface)
1886	dependstest1: silent_clean
1887	$(MAKE) depends
1888	dependstest2: silent_clean
1889	$(MAKE) com
1890	dependstest3: silent_clean
1891	$(MAKE) aw
1892	dependstest4: silent_clean
1893	$(MAKE) pt
1894	dependstest5: silent_clean
1895	$(MAKE) na
1896	dependstest6: silent_clean
1897	$(MAKE) nt
1898	dependstest7: silent_clean
1899	$(MAKE) all
1900	# ------------------------------------------------------------
1901
1902	vectorize_checks:
1903	$(MAKE) -C SOURCE_TOOLS -r vectorize_checks
1904
1905	# ------------------------------------------------------------
1906
1907	AISC_MKPTPS/AISC_MKPTPS.dummy: links
1908
1909	proto_tools: AISC_MKPTPS/AISC_MKPTPS.dummy
1910
1911	proto: proto_tools
1912	@echo $(SEP) Updating prototypes
1913	$(MAKE) \
1914	ARBDB/ARBDB.proto \
1915	AISC_COM/AISC_COM.proto \
1916	ARB_GDE/ARB_GDE.proto \
1917	CORE/CORE.proto \
1918	CONVERTALN/CONVERTALN.proto \
1919	NTREE/NTREE.proto \
1920	MERGE/MERGE.proto \
1921	$(ARCHS_PT_SERVER:.a=.proto) \
1922	SERVERCNTRL/SERVERCNTRL.proto \
1923	SL/SL.proto \
1924
1925	#********************************************************************************
1926
1927	valgrind_update: links
1928	@echo $(SEP) Updating for valgrind
1929	$(MAKE) -C SOURCE_TOOLS valgrind_update
1930
1931	#********************************************************************************
1932
1933	TAGFILE=TAGS
1934	TAGFILE_TMP=TAGS.tmp
1935
1936	TAG_SOURCE_HEADERS=TAGS.headers
1937	TAG_SOURCE_CODE=TAGS.codefiles
1938	TAG_SOURCE_LISTS=$(TAG_SOURCE_HEADERS) $(TAG_SOURCE_CODE)
1939
1940	ETAGS_IGNORE_LIST=SOURCE_TOOLS/etags_ignore.lst
1941
1942	ETAGS=ctags -e -I @$(ETAGS_IGNORE_LIST) --sort=no --if0=no --extra=q
1943	ETAGS_TYPES=--C-kinds=cgnsut --C++-kinds=cgnsut
1944	ETAGS_FUN =--C-kinds=fm --C++-kinds=fm
1945	ETAGS_REST =--C-kinds=dev --C++-kinds=dev
1946
1947	FILTER_TAGS_SOURCES= \
1948	$(SED) -e 's/^.\///g' \| \
1949	grep -vi '^HEADERLIBS\\|^GDE/\\|/GEN[CH]/'
1950
1951	$(TAG_SOURCE_HEADERS): links
1952	find . \( -name '.hxx' -o -name ".h" \) -type f \| $(FILTER_TAGS_SOURCES) > $@
1953
1954	$(TAG_SOURCE_CODE): links
1955	find . \( -name '.cxx' -o -name ".c" \) -type f \| $(FILTER_TAGS_SOURCES) > $@
1956
1957	TAGS.1.tmp: $(TAG_SOURCE_HEADERS)
1958	$(ETAGS) -f $@ $(ETAGS_TYPES) -L $<
1959	TAGS.2.tmp: $(TAG_SOURCE_HEADERS)
1960	$(ETAGS) -f $@ $(ETAGS_FUN) -L $<
1961	TAGS.3.tmp: $(TAG_SOURCE_HEADERS)
1962	$(ETAGS) -f $@ $(ETAGS_REST) -L $<
1963	TAGS.4.tmp: $(TAG_SOURCE_CODE)
1964	$(ETAGS) -f $@ $(ETAGS_TYPES) -L $<
1965	TAGS.5.tmp: $(TAG_SOURCE_CODE)
1966	$(ETAGS) -f $@ $(ETAGS_FUN) -L $<
1967	TAGS.6.tmp: $(TAG_SOURCE_CODE)
1968	$(ETAGS) -f $@ $(ETAGS_REST) -L $<
1969
1970	TAGS_ALL_PARTS=TAGS.1.tmp TAGS.2.tmp TAGS.3.tmp TAGS.4.tmp TAGS.5.tmp TAGS.6.tmp
1971
1972	$(TAGFILE_TMP) : $(TAGS_ALL_PARTS)
1973	cat $(TAGS_ALL_PARTS) > $@
1974	rm $(TAGS_ALL_PARTS) $(TAG_SOURCE_LISTS)
1975
1976	tags: $(TAGFILE_TMP)
1977	mv_if_diff $(TAGFILE_TMP) $(TAGFILE)
1978
1979	#********************************************************************************
1980
1981	LINKSTAMP=SOURCE_TOOLS/stamp.generate_all_links
1982
1983	links: checks $(LINKSTAMP) arbmainwrapper
1984	links_no_checks: $(LINKSTAMP) arbmainwrapper
1985
1986	forcelinks:
1987	-rm $(LINKSTAMP)
1988	$(MAKE) links
1989
1990	$(LINKSTAMP): SOURCE_TOOLS/generate_all_links.sh genheaders
1991	+SOURCE_TOOLS/generate_all_links.sh
1992	touch $(LINKSTAMP)
1993
1994	clean_links:
1995	# avoid to delete linked pts, nas or arb_tcp.dat:
1996	find . -path './lib' -prune -o -type l -exec rm {} \;
1997	# removed obsolete file - refuses to disappear due to 'prune' above
1998	@rm -f lib/help/GDEHELP
1999	@rm -f $(LINKSTAMP) lib/inputMasks/format.readme
2000
2001	redo_links: clean_links
2002	$(MAKE) links_no_checks
2003
2004	#********************************************************************************
2005
2006	header_libs:
2007	$(MAKE) -C HEADERLIBS all
2008
2009	#********************************************************************************
2010
2011	gde: GDE/GDE.dummy
2012	GDE: gde
2013	agde: ARB_GDE/ARB_GDE.dummy
2014
2015	tools: TOOLS/TOOLS.dummy
2016
2017	convert: $(CONVERT_ALN)
2018	readseq: READSEQ/READSEQ.dummy
2019
2020	#***************************************************************************************
2021	# Some user commands
2022	#***************************************************************************************
2023
2024	menus: binlink links
2025	@(( \
2026	echo "$(SEP) Make GDEHELP"; \
2027	$(MAKE) -C GDEHELP -r all && \
2028	echo "$(SEP) Make GDEHELP [done]"; \
2029	) > GDEHELP.log 2>&1 && (cat GDEHELP.log;rm GDEHELP.log)) \|\| (cat GDEHELP.log;rm GDEHELP.log;false)
2030
2031	ifeq ($(DEBUG),1)
2032	BIN_TARGET=develall
2033	else
2034	BIN_TARGET=all
2035	endif
2036
2037
2038	binlink:
2039	$(MAKE) -C bin $(BIN_TARGET)
2040
2041	preplib:
2042	(cd lib;$(MAKE) all)
2043
2044	# --------------------------------------------------------------------------------
2045	# This section is quite tricky:
2046	#
2047	# make 'perl' is a BIG target, so when it has to be made, it has to be started
2048	# as early as possible to reduce overall compile time. Since 'make' does not
2049	# provide any priotities, i force it to build all 'perl'-prerequisites early, by
2050	# adding artificial dependencies to these prerequisites
2051	#
2052	# That behavior is likely to be system-dependent.
2053	# My goal was only to make it work on my current development system,
2054	# where this saves about 20% of overall build time.
2055
2056	ifeq ($(WITHPERL),1)
2057	links_non_perl: PERLTOOLS/PERLTOOLS.dummy
2058	perltools: links_non_perl
2059	perl: realperl
2060	else
2061	links_non_perl: links
2062	perl:
2063	$(MAKE) "WITHPERL=1" perl
2064	endif
2065
2066	# ---------------------------------------- perl
2067
2068	ifeq ($(ARB_64),$(BUILDHOST_64))
2069	TEST_PERL_SCRIPTS=$(MAKE) -C PERL_SCRIPTS/test test
2070	else
2071	TEST_PERL_SCRIPTS=echo "skipping perl script compilation (when cross-compiling)"
2072	endif
2073
2074	realperl: perltools
2075	(( \
2076	echo "$(SEP) Make PERL2ARB" ; \
2077	$(TIME) $(MAKE) -C PERL2ARB -r -f Makefile.main \
2078	"AUTODEPENDS=1" \
2079	"dflags=$(dflags)" \
2080	"cflags4perl=$(cflags) $(cxxflags) $(dflags)" \
2081	"lflags4perl=$(lflags4perl)" \
2082	"COMPILER_VERSION=$(COMPILER_VERSION)" \
2083	all && \
2084	$(TEST_PERL_SCRIPTS) && \
2085	echo "$(SEP) Make PERL2ARB [done]" ; \
2086	) > PERL2ARB.log 2>&1 && (cat PERL2ARB.log;rm PERL2ARB.log)) \|\| (cat PERL2ARB.log;rm PERL2ARB.log;false)
2087
2088	perl_clean:
2089	@$(MAKE) -C PERL2ARB -r -f Makefile.main \
2090	"AUTODEPENDS=0" \
2091	clean
2092
2093	PERL2ARB/PERL2ARB.clean:
2094	$(MAKE) perl_clean
2095	$(MAKE) -C PERL_SCRIPTS/test clean
2096
2097	# ---------------------------------------- bindings to script languages
2098
2099	bindings: lib/libCORE.so lib/libARBDB.so
2100	$(MAKE) -C BINDINGS all ARBDEPENDS="$(^:%=../%)" DFLAGS="$(dflags)"
2101
2102	bindings_clean:
2103	$(MAKE) -C BINDINGS clean
2104
2105	# ----------------------------------------
2106
2107	CLOC=cloc-1.08.pl
2108	CLOCFLAGS=--no3 --quiet --progress-rate=0
2109	CLOCARB=--exclude-dir=GDE .
2110	CLOCEXT=GDE
2111	CLOCCODE=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.code.def
2112	CLOCREST=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.rest.def
2113	CLOCFILT=tail --lines=+4
2114
2115	cloc:
2116	@echo 'Arb code:'
2117	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCARB) \| $(CLOCFILT)
2118	@echo 'Arb rest:'
2119	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCARB) \| $(CLOCFILT)
2120	@echo 'External code:'
2121	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCEXT) \| $(CLOCFILT)
2122	@echo 'External rest:'
2123	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCEXT) \| $(CLOCFILT)
2124
2125	# ---------------------------------------- check resources
2126
2127	check_res:
2128	$(ARBHOME)/SOURCE_TOOLS/check_resources.pl
2129
2130	# ---------------------------------------- cleaning
2131
2132	rmbak:
2133	@echo "Cleanup:"
2134	@find . \( -name '*%' \
2135	-o -name '*.bak' \
2136	-o -name '*~' \) \
2137	-o \( -name 'core' -a \! -type d \) \
2138	-exec rm -v {} \;
2139
2140	bin_reinit:
2141	$(MAKE) bin/bin.clean
2142	$(MAKE) -C "bin" all
2143
2144	clean_directories:
2145	-rm -rf \
2146	$(ARBHOME)/PROBE_SET/bin \
2147	$(ARBHOME)/INCLUDE \
2148
2149	libclean:
2150	-find $(ARBHOME) -type f \( -name '*.a' ! -type l \) -exec rm -f {} \;
2151
2152	objclean:
2153	-find $(ARBHOME) -type f \( -name '*.o' ! -type l \) -exec rm -f {} \;
2154
2155	# bin.clean and HELP_SOURCE.clean interfere
2156	clean3:
2157	$(MAKE) bin/bin.clean
2158	$(MAKE) HELP_SOURCE/HELP_SOURCE.clean
2159
2160	clean2: $(ARCHS:.a=.clean) \
2161	clean3 \
2162	rmbak \
2163	libclean \
2164	objclean \
2165	lib/lib.clean \
2166	GDEHELP/GDEHELP.clean \
2167	HEADERLIBS/HEADERLIBS.clean \
2168	SOURCE_TOOLS/SOURCE_TOOLS.clean \
2169	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.clean \
2170	UNIT_TESTER/UNIT_TESTER.clean \
2171	TEMPLATES/TEMPLATES.clean \
2172	perl_clean \
2173	clean_directories \
2174
2175	rm -f .last_gcc .last_compiler config.makefile.bak
2176
2177	# links are needed for cleanup
2178	clean: redo_links motif_xpm_hack_clean
2179	$(MAKE) clean2
2180	$(MAKE) clean_cov_all clean_links
2181
2182	silent_clean:
2183	$(MAKE) clean >/dev/null
2184
2185	# 'relocated' is about 50% faster than 'rebuild'
2186	reloc_clean: links
2187	@echo "---------------------------------------- Relocation cleanup"
2188	$(MAKE) \
2189	perl_clean \
2190	GDEHELP/GDEHELP.clean \
2191	HELP_SOURCE/genhelp/genhelp.clean \
2192	bin/bin.clean \
2193	libclean \
2194	objclean
2195
2196	relocated: links
2197	$(MAKE) reloc_clean
2198	@echo "---------------------------------------- and remake"
2199	$(MAKE) build
2200
2201	# -----------------------------------
2202	# some stress tests
2203	# (helpful to reveal race conditions with -j)
2204
2205	rebuild4ever: rebuild
2206	$(MAKE) rebuild4ever
2207
2208	build4ever: build
2209	$(MAKE) build4ever
2210
2211	clean4ever: clean
2212	$(MAKE) clean4ever
2213
2214	test4ever: ut
2215	$(MAKE) test4ever
2216
2217	perl4ever: clean
2218	$(MAKE) links
2219	$(MAKE) perl
2220	$(MAKE) perl4ever
2221
2222	help4ever: clean
2223	$(MAKE) help
2224	$(MAKE) help4ever
2225
2226	# -----------------------------------
2227
2228	rebuild: clean
2229	$(MAKE) all
2230
2231	cleanlinked: bin/bin.clean libclean
2232
2233	relink: cleanlinked
2234	$(MAKE) all
2235
2236	tarfile: rebuild
2237	$(MAKE) prepare_libdir
2238	util/arb_compress
2239
2240	tarfile_quick: build
2241	$(MAKE) prepare_libdir
2242	util/arb_compress
2243
2244	save: sourcetarfile
2245
2246	patch:
2247	SOURCE_TOOLS/arb_create_patch.sh arbPatch
2248
2249	# test early whether save will work
2250	savetest:
2251	@util/arb_srclst.pl >/dev/null
2252
2253	testsave: savetest
2254
2255	sourcetarfile: rmbak
2256	util/arb_save
2257
2258	save2: rmbak
2259	util/arb_save ignore
2260
2261	save_test: rmbak
2262	@echo "Testing source list.."
2263	@util/arb_srclst.pl > /dev/null
2264
2265	save_test_no_error:
2266	@-$(MAKE) save_test
2267
2268	inc_candi:
2269	touch SOURCE_TOOLS/inc_candi.stamp
2270	$(MAKE) do_version_update
2271
2272	inc_patch:
2273	touch SOURCE_TOOLS/inc_patch.stamp
2274	$(MAKE) do_version_update
2275
2276	inc_minor:
2277	touch SOURCE_TOOLS/inc_minor.stamp
2278	$(MAKE) do_version_update
2279
2280	inc_major:
2281	touch SOURCE_TOOLS/inc_major.stamp
2282	$(MAKE) do_version_update
2283
2284	do_version_update:
2285	@echo Incrementing version information
2286	$(MAKE) savetest
2287	$(MAKE) genheaders # auto upgrades version early
2288
2289	show_version:
2290	$(MAKE) genheaders # updates version info
2291	@echo "$(SEP) ARB version info"
2292	@grep ARB_VERSION TEMPLATES/arb_build.h
2293	@echo "$(SEP)"
2294
2295	release_quick:
2296	-rm arb.tgz arbsrc.tgz
2297	$(MAKE) tarfile_quick
2298	$(MAKE) sourcetarfile
2299
2300	# --------------------------------------------------------------------------------
2301	# special cleanups
2302
2303	clean_opengl_changed: RNA3D/RNA3D.clean EDIT4/EDIT4.clean WINDOW/WINDOW.clean GL/GL.clean
2304
2305	# --------------------------------------------------------------------------------
2306
2307	MAKE_IF_COMMITTED=$(MAKE) -C SOURCE_TOOLS -f Makefile.commitbuild
2308
2309	build_CTARGET:
2310	+$(MAKE_IF_COMMITTED) "CTARGET=$(CTARGET)" build_CTARGET
2311
2312	reset_committed_build:
2313	+$(MAKE_IF_COMMITTED) reset
2314
2315	# --------------------------------------------------------------------------------
2316
2317	arbapplications: nt pa e4 wetc pt na nal di ph ds wetc cma
2318
2319	arb_external: convert tools gde readseq tg pst xmlin
2320
2321	arb_no_perl: arbapplications help arb_external
2322
2323	arb: motif_xpm_hack
2324	$(MAKE) "WITHPERL=1" perl arb_no_perl
2325
2326	motif_xpm_hack:
2327	$(MAKE) -r -C "lib/motifHack" all
2328
2329	motif_xpm_hack_clean:
2330	$(MAKE) -r -C "lib/motifHack" clean
2331
2332	# --------------------------------------------------------------------------------
2333	# special targets for SOURCE_TOOLS/remake_after_change.pl
2334
2335	rac_arb_dist: di
2336	rac_arb_edit4: e4
2337	rac_arb_ntree: nt
2338	rac_arb_pars: pa
2339	rac_arb_phylo: ph
2340	rac_arb_wetc: wetc
2341	rac_arb_naligner: nal
2342	rac_arb_pt_server: pt
2343	rac_arb_db_server: ds
2344	rac_arb_name_server: na
2345	rac_arb_convert_aln: convert
2346	rac_arb_treegen: tg
2347	rac_arb_rnacma: cma
2348	rac_arb_help2xml: help
2349
2350	rac_arb_a2ps: tools
2351	rac_arb_consensus_tree: tools
2352	rac_arb_dnarates: tools
2353	rac_arb_export_rates: tools
2354	rac_arb_export_tree: tools
2355	rac_arb_gene_probe: tools
2356	rac_arb_message: tools
2357	rac_arb_notify: tools
2358	rac_arb_primer: tools
2359	rac_arb_probe: tools
2360	rac_arb_read_tree: tools
2361
2362	# --------------------------------------------------------------------------------
2363	# unit testing
2364	# @@@ work in progress
2365	#
2366	# goal is to automatically test all libraries/executables using TESTED_UNITS_AUTO
2367	#
2368	# currently not all test executables link w/o error
2369	# (see UNITS_WORKING, UNITS_UNTESTABLE_ATM and UNITS_NEED_FIX)
2370
2371	# define RNA3D/RNA3D.test
2372	RNA3D_TEST := $(subst .a,.test,$(RNA3D_LIB))
2373
2374	TESTED_UNITS_AUTO = $(ARCHS:.a=.test)
2375
2376	UNITS_WORKING = \
2377	$(RNA3D_TEST) \
2378	AWTI/AWTI.test \
2379	EISPACK/EISPACK.test \
2380	GENOM/GENOM.test \
2381	GL/glAW/libglAW.test \
2382	GL/glpng/libglpng_arb.test \
2383	ISLAND_HOPPING/ISLAND_HOPPING.test \
2384	NALIGNER/NALIGNER.test \
2385	NAMES/NAMES.test \
2386	PHYLO/PHYLO.test \
2387	PRIMER_DESIGN/PRIMER_DESIGN.test \
2388	PROBE_DESIGN/PROBE_DESIGN.test \
2389	SECEDIT/SECEDIT.test \
2390	SEQ_QUALITY/SEQ_QUALITY.test \
2391	SERVERCNTRL/SERVERCNTRL.test \
2392	SL/ALIVIEW/ALIVIEW.test \
2393	SL/AP_TREE/AP_TREE.test \
2394	SL/ARB_TREE/ARB_TREE.test \
2395	SL/AW_HELIX/AW_HELIX.test \
2396	SL/AW_NAME/AW_NAME.test \
2397	SL/DB_SCANNER/DB_SCANNER.test \
2398	SL/GUI_ALIVIEW/GUI_ALIVIEW.test \
2399	SL/HELIX/HELIX.test \
2400	SL/LOCATION/LOCATION.test \
2401	SL/MATRIX/MATRIX.test \
2402	SL/QUERY/QUERY.test \
2403	SL/REFENTRIES/REFENTRIES.test \
2404	SL/SEQUENCE/SEQUENCE.test \
2405	SL/TRANSLATE/TRANSLATE.test \
2406	SL/TREE_ADMIN/TREE_ADMIN.test \
2407	SL/TREE_WRITE/TREE_WRITE.test \
2408	STAT/STAT.test \
2409	TREEGEN/TREEGEN.test \
2410	WETC/WETC.test \
2411	XML/XML.test \
2412
2413	# untestable units
2414
2415	UNITS_NEED_FIX = \
2416	ptpan/PROBE.test \
2417
2418	UNITS_UNTESTABLE_ATM = \
2419	XML_IMPORT/XML_IMPORT.test \
2420
2421	# for the moment, put all units containing tests into the following 4 sections (see also TESTED_UNITS below)
2422
2423	UNITS_TESTED_FIRST = \
2424	SL/GROUP_SEARCH/GROUP_SEARCH.test \
2425
2426	# plain test-libaries not linked anywhere
2427	TEST_SANDBOXES = \
2428	SL/CB/CB.test \
2429
2430	UNITS_RUNNING_LONG = \
2431	ARBDB/libARBDB.test \
2432	AWTC/AWTC.test \
2433	TOOLS/arb_test.test \
2434
2435	UNITS_TESTED = \
2436	AISC_MKPTPS/mkptypes.test \
2437	ARB_GDE/ARB_GDE.test \
2438	AWT/libAWT.test \
2439	CONSENSUS_TREE/CONSENSUS_TREE.test \
2440	CONVERTALN/CONVERTALN.test \
2441	CORE/libCORE.test \
2442	DBSERVER/DBSERVER.test \
2443	DIST/DIST.test \
2444	EDIT4/EDIT4.test \
2445	GENOM_IMPORT/GENOM_IMPORT.test \
2446	HELP_SOURCE/arb_help2xml.test \
2447	MERGE/MERGE.test \
2448	MULTI_PROBE/MULTI_PROBE.test \
2449	NTREE/NTREE.test \
2450	PARSIMONY/PARSIMONY.test \
2451	PERLTOOLS/arb_proto_2_xsub.test \
2452	PROBE/PROBE.test \
2453	PROBE_SET/fb_test.test \
2454	SERVERCNTRL/SERVERCNTRL.test \
2455	SL/ALILINK/ALILINK.test \
2456	SL/CONSENSUS/CONSENSUS.test \
2457	SL/DB_QUERY/DB_QUERY.test \
2458	SL/FAST_ALIGNER/FAST_ALIGNER.test \
2459	SL/FILTER/FILTER.test \
2460	SL/INSDEL/INSDEL.test \
2461	SL/ITEM_SHADER/ITEM_SHADER.test \
2462	SL/ITEMS/ITEMS.test \
2463	SL/MACROS/MACROS.test \
2464	SL/NDS/NDS.test \
2465	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.test \
2466	SL/PRONUC/PRONUC.test \
2467	SL/PTCLEAN/PTCLEAN.test \
2468	SL/REGEXPR/REGEXPR.test \
2469	SL/SEQIO/SEQIO.test \
2470	SL/TREE_READ/TREE_READ.test \
2471	SL/TREEDISP/TREEDISP.test \
2472	TOOLS/arb_consensus_tree.test \
2473	TOOLS/arb_probe.test \
2474	WINDOW/libWINDOW.test \
2475
2476	TESTED_UNITS = \
2477	$(UNITS_TESTED_FIRST) \
2478	$(TEST_SANDBOXES) \
2479	$(UNITS_RUNNING_LONG) \
2480	$(UNITS_TESTED) \
2481
2482	# see UNIT_TESTER/sym2testcode.pl@disableErrorOnUnitsWithoutTests
2483
2484	# ----------------------------------------
2485
2486	TEST_LOG_DIR = UNIT_TESTER/logs
2487	TEST_RUN_SUITE=$(MAKE) $(NODIR) -C UNIT_TESTER -f Makefile.suite -r
2488	TEST_MAKE_FLAGS=
2489	TEST_POST_CLEAN=
2490	ifeq ($(COVERAGE),1)
2491	TEST_POST_CLEAN=$(MAKE) clean_cov
2492	TEST_MAKE_FLAGS+=-j1
2493	endif
2494
2495
2496	%.test:
2497	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
2498	( \
2499	echo "fake[1]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
2500	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
2501	"UNITDIR=$(@D)" \
2502	"UNITLIBNAME=$(@F:.test=)" \
2503	"COVERAGE=$(COVERAGE)" \
2504	"ARB_PID=$(ARB_PID)_$(@F)" \
2505	runtest; \
2506	echo "fake[1]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"; \
2507	$(TEST_POST_CLEAN) \
2508	) >$(TEST_LOG_DIR)/$(@F).log 2>&1; \
2509	UNIT_TESTER/log_result.pl $(TEST_LOG_DIR)/$(@F).log )
2510
2511
2512	test_base: $(UNIT_TESTER_LIB:.a=.dummy) $(subst .test,.dummy,$(TEST_SANDBOXES))
2513
2514	clean_cov:
2515	find . \( -name ".gcda" -o -name ".gcov" -o -name "*.cov" \) -exec rm {} \;
2516
2517	clean_cov_all: clean_cov
2518	find . \( -name "*.gcno" \) -exec rm {} \;
2519
2520	run_tests: test_base clean_cov
2521	$(MAKE) "ARB_PID=UT_$$$$" run_tests_faked_arbpid
2522
2523	cleanup_faked_arbpids:
2524	@rm ~/.arb_tmp/tmp/arb_pids_${USER}_${ARB_PID}_* \|\| true
2525
2526	cleanup_faked_arbpids_and_fail: cleanup_faked_arbpids
2527	@false
2528
2529	run_tests_faked_arbpid:
2530	+@$(TEST_RUN_SUITE) init
2531	@echo "fake[2]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2532	$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(TESTED_UNITS) \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2533	@echo "fake[2]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2534	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2535	@$(MAKE) clean_cov >/dev/null
2536	@$(MAKE) cleanup_faked_arbpids
2537
2538	ut:
2539	ifeq ($(UNIT_TESTS),1)
2540	@echo $(MAKE) run_tests
2541	@$(MAKE) run_tests
2542	else
2543	@echo "Not compiled with unit tests"
2544	endif
2545
2546
2547	aut:
2548	+@$(TEST_RUN_SUITE) unskip
2549	$(MAKE) ut
2550
2551	# --------------------------------------------------------------------------------
2552
2553	TIMELOG=$(ARBHOME)/arb_time.log
2554	TIMEARGS=--append --output=$(TIMELOG) --format=" %E(%S+%U) %P [%C]"
2555	TIMECMD=$(TIME) $(TIMEARGS)
2556
2557	time_one:
2558	ifeq ($(ONE_TIMED_TARGET),)
2559	@echo "Error: You have to pass ONE_TIMED_TARGET to $@"
2560	false
2561	else
2562	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET)"
2563	@$(TIMECMD) $(MAKE) $(ONE_TIMED_TARGET)
2564	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET) [done]"
2565	endif
2566
2567	timed_target:
2568	ifeq ($(TIMED_TARGET),)
2569	@echo "Error: You have to pass TIMED_TARGET to $@"
2570	false
2571	else
2572	@echo "Build time:" > $(TIMELOG)
2573	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2574	@cat $(TIMELOG)
2575	@rm $(TIMELOG)
2576	endif
2577
2578	timed_target_tested:
2579	ifeq ($(TIMED_TARGET),)
2580	@echo "Error: You have to pass TIMED_TARGET to $@"
2581	false
2582	else
2583	@echo "Build time:" > $(TIMELOG)
2584	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2585	$(MAKE) "ONE_TIMED_TARGET=ut" time_one
2586	@cat $(TIMELOG)
2587	@rm $(TIMELOG)
2588	endif
2589
2590	clean_timed_target:
2591	ifeq ($(TIMED_TARGET),)
2592	@echo "Error: You have to pass TIMED_TARGET to $@"
2593	false
2594	else
2595	@echo "Build time:" > $(TIMELOG)
2596	$(MAKE) "ONE_TIMED_TARGET=clean" time_one
2597	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2598	@cat $(TIMELOG)
2599	@rm $(TIMELOG)
2600	endif
2601
2602	# --------------------------------------------------------------------------------
2603
2604	CHECKOUT_MODIFIED=0# set to 1 to temporarily skip test for modifications (do not check in if set to 1)
2605
2606	check_svn_does_not_contain_generated:
2607	ifeq ($(CHECKOUT_MODIFIED),0)
2608	@echo "Testing that build does not modify files in SVN"
2609	@test 0 = `svn status \| wc -l` \|\| ( \
2610	echo "The checkout is not/no longer clean:"; \
2611	svn status; \
2612	echo "- if this fails instantly, your checkout is not clean"; \
2613	echo "- if this fails after other targets, these targets modify checked in data"; \
2614	echo " (a common cause may be that depends are not up to date)"; \
2615	false)
2616	else
2617	grep -Hn 'CHECKOUT_MODIFIED' Makefile
2618	endif
2619
2620	check_svn_ignores_generated:
2621	@test 0 = `svn status \| grep '^\?' \| wc -l` \|\| ( \
2622	echo "There are svn-unignored files:"; \
2623	svn status \| grep '^\?'; \
2624	echo "(all generated files should be svn-ignored)"; \
2625	false)
2626
2627	check_svn_state: check_svn_does_not_contain_generated
2628	$(MAKE) check_svn_ignores_generated
2629	$(MAKE) savetest
2630
2631	things_that_always_should_work: depends proto
2632
2633	post_commit_check:
2634	@echo "---------------------------------------- [Initial]"
2635	$(MAKE) check_svn_state
2636
2637	$(MAKE) clean
2638	@echo "---------------------------------------- [After 'make clean']"
2639	$(MAKE) check_svn_state
2640
2641	$(MAKE) things_that_always_should_work
2642	@echo "---------------------------------------- [After 'make things_that_always_should_work']"
2643	$(MAKE) check_svn_state
2644
2645	$(MAKE) all
2646	@echo "---------------------------------------- [After 'make all']"
2647	$(MAKE) check_svn_state
2648
2649	$(MAKE) things_that_always_should_work
2650	@echo "---------------------------------------- [Final]"
2651	$(MAKE) check_svn_state
2652
2653	# --------------------------------------------------------------------------------
2654	# sanitize arb_ntree; also works for clients (arb_edit4, ...) started from there.
2655
2656	sanitize: all
2657	( \
2658	export "LSAN_OPTIONS=max_leaks=30:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp"; \
2659	echo "sake[1]: Entering directory \`$(ARBHOME)'"; \
2660	$(ARBHOME)/bin/arb_ntree --execute _logged ~/data/test.arb 2>&1 ; \
2661	echo "sake[1]: Leaving directory \`$(ARBHOME)'" \
2662	) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
2663
2664	# --------------------------------------------------------------------------------
2665
2666	build: arb
2667	$(MAKE) binlink preplib compile_compatibility
2668
2669	all:
2670	@echo "Build time" > $(TIMELOG)
2671	@echo "$(SEP) $(MAKE) build"
2672	@$(TIMECMD) $(MAKE) build
2673	@echo $(SEP)
2674	@echo "made 'all' with success."
2675	@echo "to start arb enter 'arb'"
2676	ifeq ($(UNIT_TESTS),1)
2677	@echo $(MAKE) run_tests
2678	@$(TIMECMD) $(MAKE) run_tests
2679	endif
2680	@echo "$(SEP) $(MAKE) build [done]"
2681	ifeq ($(DEBUG),1)
2682	@$(MAKE) save_test_no_error >/dev/null # just show hints
2683	endif
2684	@cat $(TIMELOG)
2685	@rm $(TIMELOG)
2686

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