Context Navigation

← Previous Revision
Next Revision →
Blame
Revision Log

Makefile

Visit:

Last change on this file was 19918, checked in by westram, 15 hours ago
full update from 'trunk' into 'gcc' adds: log:trunk@19911:19913,19915:19916
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 90.7 KB

Line
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	# [defined by make or env:]
14	#
15	# CC C compiler (cc)
16	# CXX C++ compiler (g++)
17	# AR Linker (ar)
18	#
19	# [defined by config.makefile:]
20	#
21	# DEVELOPER=name special compilation (values: ANY,RELEASE,your name)
22	# OPENGL=0/1 whether OPENGL is available
23	#
24	# -----------------------------------------------------
25	# Paths for several libraries may be set from config.makefile by using:
26	#
27	# export XLIBS=$(shell pkg-config --libs xpm xerces-c)
28	# export XINCLUDES=$(shell pkg-config --cflags x11)
29	# export XAW_LIBS=$(shell pkg-config --libs xaw7)
30	# export XML_INCLUDES=$(shell pkg-config --cflags xerces-c)
31	#
32	# You make have to explicitely point pkg-config to the *.pc files needed.
33	# For example, Xquartz X11 libraries on macOS can be located by adding
34	# the following line before those given above:
35	#
36	# export PKG_CONFIG_PATH=/usr/X11/lib/pkgconfig
37	#
38	# If you introduce a new variable that is handled as described above,
39	# please add to section .@InjectedEnvironment
40	#
41	# -----------------------------------------------------
42	# ARB Makefile and ARB source code are aware of the following defines:
43	#
44	# $(MACH) name of the machine (LINUX or DARWIN; see config.makefile)
45	# DEBUG compiles the DEBUG sections
46	# DEBUG_GRAPHICS all X-graphics are flushed immediately (for debugging)
47	# ARB_64=0/1 1=>compile 64 bit version
48	# UNIT_TESTS=0/1 1=>compile in unit tests and call them after build
49	# COVERAGE=0/1/2 compile in gcov support (useful together with UNIT_TESTS=1)
50	# 0=no, 1+2=compile in, 1=show
51	# STABS=0/1 force stabs format? (0 = "use default format")
52	# SANITIZE=0/#/all use Sanitizer? (defaults to 0,
53	# 1=AddressSanitizer+LeakSanitizer,
54	# 2=UndefinedBehaviorSanitizer,
55	# combine bit-values to activate multiple Sanitizers,
56	# specify 'all' to activate all)
57	# IGNORE_LEAKS=1 does not abort when leaks are detected (while using SANITIZE=1/all)
58	# SHOWTODO=0/1 activate TODO-warnings? (defaults to 0, except for ralf)
59	#
60	# -----------------------------------------------------
61	# The ARB source code is aware of the following defines:
62	#
63	# NDEBUG doesn't compile the DEBUG sections
64	# DEVEL_$(DEVELOPER) developer-dependent flag (enables you to have private sections in code)
65	# DEVELOPER='ANY' (default setting) will be ignored
66	# configurable in config.makefile
67	#
68	# -----------------------------------------------------
69
70	ifndef ARB_ORG_MAKEFLAGS
71	ARB_ORG_MAKEFLAGS=$(MAKEFLAGS)
72	else
73	ifeq ($(ARB_ORG_MAKEFLAGS),)
74	ARB_ORG_MAKEFLAGS=$(MAKEFLAGS)
75	endif
76	endif
77
78	# detect initial (i.e. non-recursive) call:
79	ifndef ARBBID
80	INITIAL_CALL:=yes
81	endif
82
83	# Read configuration
84	include config.makefile
85	CONFIG_MAKEFILE_FOUND=$(strip $(wildcard config.makefile))
86
87	# strip spaces from values defined in config.makefile
88	# (otherwise they easily have spaces appended)
89	ifdef DEVELOPER
90	DEVELOPER := $(strip $(DEVELOPER))
91	endif
92	ifdef OPENGL
93	OPENGL := $(strip $(OPENGL))
94	endif
95	ifdef ISINA
96	ISINA := $(strip $(ISINA))
97	endif
98	ifdef DEBUG
99	DEBUG := $(strip $(DEBUG))
100	endif
101	ifdef UNIT_TESTS
102	UNIT_TESTS := $(strip $(UNIT_TESTS))
103	endif
104	ifdef COVERAGE
105	COVERAGE := $(strip $(COVERAGE))
106	endif
107	ifdef SHOWTODO
108	SHOWTODO := $(strip $(SHOWTODO))
109	endif
110	ifdef STABS
111	STABS := $(strip $(STABS))
112	endif
113	ifdef TRACESYM
114	TRACESYM := $(strip $(TRACESYM))
115	endif
116	ifdef DEBUG_GRAPHICS
117	DEBUG_GRAPHICS := $(strip $(DEBUG_GRAPHICS))
118	endif
119
120	# set defaults for (or strip) variables commented out in config.makefile:
121	ifdef SANITIZE
122	SANITIZE := $(strip $(SANITIZE))
123	else
124	SANITIZE:=0
125	endif
126	ifdef IGNORE_LEAKS
127	IGNORE_LEAKS := $(strip $(IGNORE_LEAKS))
128	else
129	IGNORE_LEAKS:=0
130	endif
131	ifndef DARWIN
132	DARWIN:=0
133	else
134	DARWIN := $(strip $(DARWIN))
135	endif
136	ifndef LINUX
137	LINUX:=0
138	else
139	LINUX := $(strip $(LINUX))
140	endif
141	ifndef DEBIAN
142	DEBIAN:=0
143	else
144	DEBIAN := $(strip $(DEBIAN))
145	endif
146	ifndef ARB_64
147	ARB_64=1#default to 64bit
148	else
149	ARB_64 := $(strip $(ARB_64))
150	endif
151
152	# Variables allowed for injection [InjectedEnvironment]
153	# (alternatively initialize them with '?=', e.g. done for XLIBS and XINCLUDES)
154	# In both cases add them to SOURCE_TOOLS/export2sub
155	ifndef XML_INCLUDES
156	XML_INCLUDES=
157	endif
158	ifndef XAW_LIBS
159	XAW_LIBS=
160	endif
161
162
163	ifneq ($(CONFIG_MAKEFILE_FOUND),)
164	ifneq ($(DARWIN)$(LINUX),10)
165	ifneq ($(DARWIN)$(LINUX),01)
166	$(error exactly one of DARWIN=1 or LINUX=1 has to be defined (got:$(DARWIN)$(LINUX)))
167	endif
168	endif
169	endif
170
171	# compiler settings:
172	ifneq ($(CC),use__A_CC__instead_of__CC)
173	A_CC:=$(CC)# compile C
174	A_CXX:=$(CXX)# compile C++
175
176	# uncomment to ensure no submakefile uses CC and CXX directly
177	override CC:=use__A_CC__instead_of__CC
178	override CXX:=use__A_CXX__instead_of__CXX
179	endif
180
181	# unconditionally prepend $(ARBHOME)/lib to LD_LIBRARY_PATH if not found
182	ifeq ($(findstring $(ARBHOME)/lib,$(LD_LIBRARY_PATH)),)
183	LD_LIBRARY_PATH:=${ARBHOME}/lib:$(LD_LIBRARY_PATH)
184	endif
185
186	# store LD_LIBRARY_PATH to circumvent SIP restrictions:
187	ARBBUILD_LIBRARY_PATH:=$(LD_LIBRARY_PATH)
188
189	FORCEMASK = umask 002
190	NODIR=--no-print-directory
191
192	SED:=$(ARBHOME)/SH/arb_sed
193	READLINK:=$(ARBHOME)/SH/arb_readlink
194
195	# ---------------------- compiler version detection
196
197	# supported gcc versions:
198	ALLOWED_gcc_VERSIONS=\
199	4.4.3 4.4.5 4.4.6 4.4.7 \
200	4.5.2 \
201	4.6.1 4.6.2 4.6.3 4.6.4 \
202	4.7.1 4.7.2 4.7.3 4.7.4 \
203	4.8.0 4.8.1 4.8.2 4.8.3 4.8.4 4.8.5 \
204	4.9.0 4.9.1 4.9.2 4.9.3 4.9.4 \
205	5.1.0 5.2.0 5.3.0 5.4.0 5.5.0 \
206	6.1.0 6.2.0 6.3.0 6.4.0 6.5.0 \
207	7.1.0 7.2.0 7.3.0 7.4.0 7.5.0 \
208	8.1.0 8.2.0 8.3.0 8.4.0 8.5.0 \
209	9.1.0 9.2.0 9.3.0 9.4.0 9.5.0 \
210	10.1.0 10.2.0 10.3.0 10.4.0 10.5.0 \
211	11.3.0 \
212
213	# Note: starting with version 5, arb silently accepts any subversion number
214	# above zero. See SOURCE_TOOLS/arb_compiler_version.pl@acceptSubVersions
215	#
216	# This may cause problems when manually checking for compiler versions in code
217	# (GCC_VERSION_CODE is not affected, GCC_PATCHLEVEL_CODE may cause problems!)
218	# ----------------------
219
220	COMPILER_INFO:=$(shell SOURCE_TOOLS/arb_compiler_version.pl $(A_CXX))
221	COMPILER_NAME:=$(word 1,$(COMPILER_INFO))
222	COMPILER_VERSION:=$(word 2,$(COMPILER_INFO))
223
224	USE_CLANG:=0
225	ifneq ($(COMPILER_NAME),gcc)
226	ifeq ($(COMPILER_NAME),clang)
227	USE_CLANG:=1
228	else
229	ifeq ($(COMPILER_VERSION),4.6.4)
230	# gcc version 4.6.4 segfaults when dumping symbols for detection (silently accept as gcc)
231	COMPILER_NAME:=gcc
232	else
233	$(error failed to detect COMPILER_NAME (got '$(COMPILER_NAME)', expected 'clang' or 'gcc'))
234	endif
235	endif
236	endif
237
238	ifeq ($(USE_CLANG),1)
239	# accept all clang versions:
240	ALLOWED_COMPILER_VERSIONS=$(COMPILER_VERSION)
241	else
242	ALLOWED_COMPILER_VERSIONS=$(ALLOWED_gcc_VERSIONS)
243	endif
244
245	COMPILER_VERSION_ALLOWED=$(strip $(subst ___,,$(foreach version,$(ALLOWED_COMPILER_VERSIONS),$(findstring ___$(version)___,___$(COMPILER_VERSION)___))))
246
247	#---------------------- force no root
248
249	YOU_ARE_ROOT := $(strip $(shell bash -c 'echo $$((EUID == 0))'))
250	ifeq ($(YOU_ARE_ROOT),1)
251	$(error Building arb as root user is not recommended)
252	# To install a custom-compiled arb system-wide, build target 'tarfile' as "normal" user.
253	# Afterwards, use arb_install.sh as root.
254	endif
255
256	#---------------------- split gcc version
257
258	SPLITTED_VERSION:=$(subst ., ,$(COMPILER_VERSION))
259
260	USE_GCC_MAJOR:=$(word 1,$(SPLITTED_VERSION))
261	USE_GCC_MINOR:=$(word 2,$(SPLITTED_VERSION))
262	USE_GCC_PATCHLEVEL:=$(word 3,$(SPLITTED_VERSION))
263
264	USE_GCC_452_OR_HIGHER:=
265	USE_GCC_46_OR_HIGHER:=
266	USE_GCC_47_OR_HIGHER:=
267	USE_GCC_48_OR_HIGHER:=
268	USE_GCC_49_OR_HIGHER:=
269	USE_GCC_50_OR_HIGHER:=
270	USE_GCC_60_OR_HIGHER:=
271	USE_GCC_70_OR_HIGHER:=
272	USE_GCC_80_OR_HIGHER:=
273	USE_GCC_90_OR_HIGHER:=
274	USE_GCC_100_OR_HIGHER:=
275	USE_GCC_110_OR_HIGHER:=
276
277	ifeq ($(USE_CLANG),0)
278	ifeq ($(USE_GCC_MAJOR),4)
279	ifeq ($(USE_GCC_MINOR),5)
280	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),23456789)','')
281	USE_GCC_452_OR_HIGHER:=yes
282	endif
283	else
284	ifneq ('$(findstring $(USE_GCC_MINOR),6789)','')
285	USE_GCC_452_OR_HIGHER:=yes
286	USE_GCC_46_OR_HIGHER:=yes
287	ifneq ($(USE_GCC_MINOR),6)
288	USE_GCC_47_OR_HIGHER:=yes
289	ifneq ($(USE_GCC_MINOR),7)
290	USE_GCC_48_OR_HIGHER:=yes
291	ifneq ($(USE_GCC_MINOR),8)
292	USE_GCC_49_OR_HIGHER:=yes
293	endif
294	endif
295	endif
296	endif
297	endif
298	else
299	# gcc 5.x or higher
300	USE_GCC_452_OR_HIGHER:=yes
301	USE_GCC_46_OR_HIGHER:=yes
302	USE_GCC_47_OR_HIGHER:=yes
303	USE_GCC_48_OR_HIGHER:=yes
304	USE_GCC_49_OR_HIGHER:=yes
305	USE_GCC_50_OR_HIGHER:=yes
306	ifneq ($(USE_GCC_MAJOR),5)
307	# gcc 6.x or higher
308	USE_GCC_60_OR_HIGHER:=yes
309	ifneq ($(USE_GCC_MAJOR),6)
310	# gcc 7.x or higher
311	USE_GCC_70_OR_HIGHER:=yes
312	ifneq ($(USE_GCC_MAJOR),7)
313	# gcc 8.x or higher
314	USE_GCC_80_OR_HIGHER:=yes
315	ifneq ($(USE_GCC_MAJOR),8)
316	# gcc 9.x or higher
317	USE_GCC_90_OR_HIGHER:=yes
318	ifneq ($(USE_GCC_MAJOR),9)
319	# gcc 10.x or higher
320	USE_GCC_100_OR_HIGHER:=yes
321	ifneq ($(USE_GCC_MAJOR),10)
322	# gcc 11.x or higher
323	USE_GCC_110_OR_HIGHER:=yes
324	endif
325	endif
326	endif
327	endif
328	endif
329	endif
330	endif
331	endif
332
333	#---------------------- define special directories for non standard builds
334
335	ifeq ($(DARWIN),1)
336	OSX_FW:=/System/Library/Frameworks
337	OSX_FW_OPENGL:=$(OSX_FW)/OpenGL.framework/Versions/A/Libraries
338	OSX_FW_GLUT:=$(OSX_FW)/GLUT.framework/Versions/A/Libraries
339	OSX_FW_IMAGEIO:=$(OSX_FW)/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources
340	endif
341
342	#---------------------- SSE vectorization
343	# for details about vectorization checks see SOURCE_TOOLS/vectorize.README
344
345	DISABLE_VECTORIZE_CHECK:=0# set to 1 to completely disable vectorization checks
346	TRACE_MISSED_VECTORIZATIONS:=0# set to 1 to activate detailed output about failed vectorizations
347	# (does also show details about successful vectorized loops, which are not optimal)
348	VECTORIZATION_CHECK_CANDIDATES:=0# set to 1 to show vectorizations that may be checked
349	# (for yet unchecked files)
350	# Note: TRACE_MISSED_VECTORIZATIONS and VECTORIZATION_CHECK_CANDIDATES cannot be used together!
351
352	#---------------------- Support for OPENMP
353
354	USE_OPENMP:=1
355	ifeq ($(USE_CLANG),1)
356	USE_OPENMP:=0
357	endif
358
359	#----------------------
360
361	ifeq ($(DARWIN),1)
362	LINK_STATIC=1# link static
363	else
364	LINK_STATIC=0# link dynamically
365	# LINK_STATIC=1# link static (testing only)
366	endif
367
368	shared_cflags :=# flags for shared lib compilation
369	onlyC_flags :=# flags only suitable for C (not C++; see cxxflags).
370	clflags :=# linker flags (when passed through gcc, i.e. used to link binaries and shared libraries)
371	extended_warnings :=# warning flags for C and C++-compiler
372	extended_cpp_warnings :=# warning flags for C++-compiler only
373
374	ifeq ($(DEBUG),0)
375	dflags := -DNDEBUG# defines
376	ifeq ($(USE_CLANG),1)
377	cflags := -O3# compiler flags (C and C++)
378	else
379	clflags += -Wl,-O2# passthrough linker flags
380	# ------- standard optimization:
381	cflags := -O3# compiler flags (C and C++)
382	# ------- test changed optimization (DISABLE_VECTORIZE_CHECK for -O2 or lower):
383	# cflags := -O2# do not commit uncommented!
384	# DISABLE_VECTORIZE_CHECK:=1
385	endif
386	endif
387
388	ifeq ($(DEBIAN),1)
389	clflags += -Wl,-rpath=/usr/lib/arb/lib -Wl,-z,relro
390	endif
391
392	ifeq ($(DEBUG),1)
393	dflags := -DDEBUG
394
395	# [AFAI understand cc doc, the previous setting used here (-g -g3 -ggdb -ggdb3) was same as (-ggdb3)]
396	# GDB_COMMON := -g
397	# GDB_COMMON := -g3
398	GDB_COMMON := -ggdb3
399	# GDB_COMMON := -gdwarf -g3
400
401	DBGOPTI:=-O0
402	ifneq ('$(SANITIZE)','0')
403	# sanitizer report several bogus buffer-overflows when arb is build with -O0 (e.g. with gcc 7.5.0)
404	DBGOPTI:=-O1
405	endif
406	# DBGOPTI:=-O2 # use this for callgrind (to force inlining)
407
408	ifeq ($(STABS),1)
409	$(error STABS no longer supported)
410	endif
411
412	cflags := $(DBGOPTI) $(GDB_COMMON)
413	clflags += $(DBGOPTI) $(GDB_COMMON)
414
415	# to debug link problems uncomment next line:
416	# clflags += -Wl,--verbose
417
418	ifeq ($(DEBUG_GRAPHICS),1)
419	dflags += -DDEBUG_GRAPHICS
420	endif
421
422	endif # DEBUG only
423
424	# ------------------------------ POST_COMPILE - control how much you get spammed
425	# (please do not change default in SVN)
426	POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl
427
428	# POST_COMPILE += --original # dont modify compiler output
429	# POST_COMPILE += --hide-Noncopyable-advices
430	# POST_COMPILE += --show-useless-Weff++
431	# POST_COMPILE += --no-warnings
432	# POST_COMPILE += --only-first-error
433	# POST_COMPILE += --no-warnings --only-first-error
434
435	# always pass used compiler version to postcompile:
436	POST_COMPILE += --compiler=$(COMPILER_VERSION)
437
438	# ------------------------------
439
440	# Enable extra warnings
441	extended_warnings :=
442	extended_cpp_warnings :=
443
444	# C and C++
445	extended_warnings += -Wwrite-strings -Wunused -Wno-aggregate-return
446
447	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
448	# disable shadow warnings for gcc 4.8 (and lower)
449	# (does e.g. warn if a method-name is used as parameter in another method - even for derived classes. unusable!)
450	extended_warnings += -Wshadow
451	endif
452
453	# C++ only
454	extended_cpp_warnings += -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute
455	extended_cpp_warnings += -Wctor-dtor-privacy
456	# extended_cpp_warnings += -Wfloat-equal
457
458	extended_cpp_warnings += -Wmissing-noreturn
459	# extended_cpp_warnings += -Wold-style-cast# (warns about 28405 old-style casts)
460	extended_cpp_warnings += -Winit-self
461	extended_cpp_warnings += -Wstrict-aliasing
462	extended_cpp_warnings += -Wextra
463
464	# ------- above only warning-options already available in gcc 4.4.3
465
466	# -Weffc++ broken in 4.7.x series
467	# gcc 4.7.3 crashes on GenomeImport.cxx when -Weffc++ is active
468	# (bug reported https://gcc.gnu.org/bugzilla/show_bug.cgi?id=56923; apparently wont be fixed for 4.7-series)
469	# gcc 4.7.4 crashes on DBwriter.cxx when -Weffc++ is active
470	WEFFC_BROKEN:=0
471	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
472	ifneq ('$(USE_GCC_48_OR_HIGHER)','yes')
473	WEFFC_BROKEN:=1
474	endif
475	endif
476	ifeq ('$(WEFFC_BROKEN)','0')
477	extended_cpp_warnings += -Weffc++
478	endif
479
480	# turn off -Wmaybe-uninitialized in debug mode (gets activated with -Wextra). too many bogus warnings
481	ifeq ($(DEBUG),1)
482	ifeq ($(USE_CLANG),0)
483	extended_cpp_warnings += -Wno-maybe-uninitialized
484	endif
485	endif
486
487	SUGGEST_FINAL:=
488
489	ifeq ('$(USE_GCC_452_OR_HIGHER)','yes')
490	extended_cpp_warnings += -Wlogical-op# gcc 4.5.2
491	endif
492	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
493	extended_cpp_warnings += -Wzero-as-null-pointer-constant# gcc 4.7
494	endif
495	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
496	extended_cpp_warnings += -Wunused-local-typedefs# available since gcc 4.7 (but fails for each STATIC_ASSERT, so enable only for Cxx11)
497	endif
498	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
499	extended_cpp_warnings += -Wswitch-bool
500	extended_cpp_warnings += -Wlogical-not-parentheses
501	extended_cpp_warnings += -Wsizeof-array-argument
502	extended_cpp_warnings += -Wbool-compare
503
504	SUGGEST_FINAL:=yes
505	endif
506	ifeq ('$(USE_GCC_60_OR_HIGHER)','yes')
507	extended_cpp_warnings += -Wduplicated-cond
508	endif
509	ifeq ('$(USE_GCC_80_OR_HIGHER)','yes')
510	extended_cpp_warnings += -Wmultistatement-macros
511	endif
512
513	# switch off final suggestions for 8.3.0 and 8.4.0:
514	ifeq ('$(COMPILER_VERSION)','8.3.0')
515	SUGGEST_FINAL:=no
516	endif
517	ifeq ('$(COMPILER_VERSION)','8.4.0')
518	SUGGEST_FINAL:=no
519	endif
520
521	ifeq ($(DEVELOPER),RELEASE)
522	# switch off final suggestions in RELEASE:
523	SUGGEST_FINAL:=no
524	endif
525	# suggest final:
526	ifeq ('$(SUGGEST_FINAL)','yes')
527	extended_cpp_warnings += -Wsuggest-final-types
528	extended_cpp_warnings += -Wsuggest-final-methods
529	dflags += -DSUGGESTS_FINAL
530	endif
531
532	#---------------------- turn off clang bogus warnings
533
534	ifeq ($(USE_CLANG),1)
535	# -Wmismatched-tags warns about struct/class mismatch in forward declarations (which is explicitely allowed)
536	# -Wchar-subscripts reports too many bogus warnings for "array['x']" (when 'x' is known to be in range [0..128])
537	# -Wunused-private-field report too many false positives (currently ~ 2 of 3)
538	# -Wstring-plus-int warns about common ARB coding practice
539	# -Wgnu-static-float-init warns about accepted GNU extension
540	extended_cpp_warnings += -Wno-mismatched-tags -Wno-char-subscripts -Wno-unused-private-field -Wno-string-plus-int
541	ifeq ('$(COMPILER_VERSION)','4.2.1')
542	# jenkins build (doesn't know switch -Wno-gnu-static-float-init)
543	extended_cpp_warnings += -Wno-gnu
544	else
545	extended_cpp_warnings += -Wno-gnu-static-float-init
546	endif
547	endif
548
549	#---------------------- developer
550
551	ifneq ($(DEVELOPER),ANY) # ANY=default setting (skip all developer specific code)
552	dflags += -DDEVEL_$(DEVELOPER)# activate developer/release specific code
553	endif
554
555	#---------------------- activate TODO warnings?
556
557	ifndef SHOWTODO
558	ifeq ($(DEVELOPER),RALF)
559	SHOWTODO:=1
560	else
561	SHOWTODO:=0
562	endif
563	endif
564	ifeq ($(SHOWTODO),1)
565	dflags += -DWARN_TODO# activate "TODO" warnings
566	endif
567
568	#---------------------- be strict while building documentation?
569
570	STRICT_DOC:=0
571	ifeq ($(DEVELOPER),RALF)
572	STRICT_DOC:=1
573	endif
574
575	#---------------------- activate threads?
576	# only useful if compiler is able to compile Cxx11 or better
577
578	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
579	# see also ./TEMPLATES/cxxforward.h@USE_Cxx11
580	cflags += -pthread
581	clflags += -pthread
582	endif
583
584	#---------------------- activate Sanitizers?
585
586	ASAN_OPTIONS:=handle_segv=0:color=0
587	ifeq ($(IGNORE_LEAKS),1)
588	ASAN_OPTIONS+=:detect_leaks=0 # disable leak-detection
589	else
590	ASAN_OPTIONS+=:detect_leaks=1 # detect leaks (normal setting)
591	endif
592	ASAN_OPTIONS+=:check_initialization_order=1
593	# ASAN_OPTIONS+=:abort_on_error=1
594
595	# suppressions: SOURCE_TOOLS/arb.leaksan.supp
596	LSAN_OPTIONS:=max_leaks=3:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp
597
598	UBSAN_OPTIONS:=print_stacktrace=1
599
600	SANITIZE_ADDRESS:=0
601	SANITIZE_UNDEFINED:=0
602
603	ifneq ($(SANITIZE),0)
604	ifeq ($(SANITIZE),all)
605	SANITIZE:=3
606	endif
607
608	ifeq ($(SANITIZE),1)
609	SANITIZE_ADDRESS:=1
610	else
611	ifeq ($(SANITIZE),2)
612	SANITIZE_UNDEFINED:=1
613	else
614	ifeq ($(SANITIZE),3)
615	SANITIZE_ADDRESS:=1
616	SANITIZE_UNDEFINED:=1
617	else
618	$(error Unknown value '$(SANITIZE)' specified for SANITIZE in config.makefile)
619	endif
620	endif
621	endif
622	endif
623
624	ifeq ($(SANITIZE_ADDRESS),1)
625	ifneq ('$(USE_GCC_48_OR_HIGHER)','yes')
626	$(info AddressSanitizer not usable with gcc $(COMPILER_VERSION) - disabled)
627	SANITIZE_ADDRESS:=0
628	else
629	ifneq ('$(USE_GCC_49_OR_HIGHER)','yes')
630	$(info LeakSanitizer does not work with gcc $(COMPILER_VERSION) - disabled)
631	# need to disable AddressSanitizer (otherwise build fails; only affects gcc 4.8.x series)
632	SANITIZE_ADDRESS:=0
633	endif
634	endif
635	endif
636
637	ifeq ($(SANITIZE_UNDEFINED),1)
638	ifneq ('$(USE_GCC_49_OR_HIGHER)','yes')
639	$(info UndefinedBehaviorSanitizer not usable with gcc $(COMPILER_VERSION) - disabled)
640	SANITIZE_UNDEFINED:=0
641	endif
642	endif
643
644	SANITIZE_ANY:=0
645	ifeq ($(SANITIZE_ADDRESS),1)
646	SANITIZE_ANY:=1
647	endif
648	ifeq ($(SANITIZE_UNDEFINED),1)
649	SANITIZE_ANY:=1
650	endif
651
652	# vectorization fails if sanitizer active where it normally succeeds -> disable check
653	ifeq ($(SANITIZE_ANY),1)
654	$(info disabling vectorize checks. would fail with sanitized code)
655	DISABLE_VECTORIZE_CHECK:=1
656	else
657	$(info no sanitizer enabled. reset: SANITIZE=0)
658	SANITIZE:=0
659	endif
660
661	# deactivate some bogus warnings occurring when sanitizing NDEBUG version
662	# (do not disable for future gcc-version >= 8.x -> test again when available)
663	ifeq ($(SANITIZE_ANY),1)
664	ifeq ($(DEBUG),0)
665	ifneq ('$(USE_GCC_80_OR_HIGHER)','yes')
666	extended_cpp_warnings += -Wno-format-overflow
667	extended_cpp_warnings += -Wno-maybe-uninitialized
668	endif
669	endif
670	endif
671
672	#---------------------- 32 or 64 bit
673
674	cross_cflags:=
675	cross_lflags:=
676	cross_clflags:=
677
678	ifeq ($(ARB_64),1)
679	dflags += -DARB_64
680	shared_cflags += -fPIC
681	CROSS_LIB:=# empty => autodetect below
682	ifeq ($(DARWIN),1)
683	cross_cflags += -arch x86_64
684	cross_lflags += -arch x86_64
685	cross_clflags += -arch x86_64
686	endif
687	else
688	CROSS_LIB:=/lib
689	endif
690
691	cflags += $(cross_cflags)
692	clflags += $(cross_clflags)
693
694	ifeq ('$(CROSS_LIB)','')
695	# autodetect libdir
696	ifeq ($(ARB_64),1)
697	CROSS_LIB:=$(shell (test -d /lib64 && echo lib64) \|\| echo lib)
698	else
699	CROSS_LIB:=$(shell (test -d /lib32 && echo lib32) \|\| echo lib)
700	endif
701	endif
702
703	#---------------------- unit tests
704
705	ifndef UNIT_TESTS
706	UNIT_TESTS=0#default is "no tests"
707	endif
708	ifeq ($(UNIT_TESTS),1)
709	dflags += -DUNIT_TESTS
710	UNIT_TESTER_LIB=UNIT_TESTER/UNIT_TESTER.a
711	else
712	UNIT_TESTER_LIB=
713	endif
714
715	#---------------------- use gcov
716
717	ifndef COVERAGE
718	COVERAGE=0#default is "no"
719	endif
720	ifneq ($(COVERAGE),0)
721	GCOV_FLAGS=--coverage
722	$(info disabling vectorize checks. would fail with COVERAGE on)
723	DISABLE_VECTORIZE_CHECK:=1
724	else
725	GCOV_FLAGS=
726	endif
727
728	cflags += $(GCOV_FLAGS)
729	clflags += $(GCOV_FLAGS)
730	cross_lflags += $(GCOV_FLAGS)
731
732	#---------------------- disable vectorize checks atm
733
734	ifeq ('$(USE_GCC_110_OR_HIGHER)','yes')
735	ifdef INITIAL_CALL
736	$(warning Note: disabling vectorize checks. has to be fixed for gcc-11 and higher)
737	endif
738	DISABLE_VECTORIZE_CHECK:=1
739	endif
740
741	#---------------------- other flags
742
743	dflags += -D$(MACH) # define machine
744
745	ifeq ($(DARWIN),1)
746	shared_cflags += -fno-common
747	else
748	dflags += $(shell getconf LFS_CFLAGS)
749	endif
750
751	cflags += -pipe
752	cflags += -fmessage-length=0# dont wrap compiler output
753	cflags += -fshow-column# show columns
754	cflags += -funit-at-a-time
755	cflags += -fPIC
756	cflags += -fno-common# link all global data into one namespace
757	cflags += -fstrict-aliasing# gcc 3.4
758
759	onlyC_flags += -Werror-implicit-function-declaration
760
761	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
762	cflags += -fno-diagnostics-show-caret#gcc 4.8 (4.7.?)
763	endif
764	#cflags += -save-temps# uncomment to see preprocessor output
765
766	#---------------------- various sanitizers
767	# There are some disabled tests in CORE/arb_misc.cxx@sanitizers
768	# which trigger sanitizer reports.
769
770	ifeq ($(SANITIZE_ANY),1)
771	cflags += -ggdb3 -fno-omit-frame-pointer
772	endif
773
774	SANI_CFLAGS:=
775	SANI_CLFLAGS:=
776
777	# activate AddressSanitizer+LeakSanitizer?
778	ifeq ($(SANITIZE_ADDRESS),1)
779	SANI_CFLAGS += -fsanitize=address
780	SANI_CLFLAGS += -fsanitize=address
781	dflags += -DLEAKS_SANITIZED
782	endif
783
784	# activate UndefinedBehaviorSanitizer?
785	ifeq ($(SANITIZE_UNDEFINED),1)
786	SANI_CFLAGS += -fsanitize=undefined
787	SANI_CLFLAGS += -fsanitize=undefined
788	dflags += -DUNDEF_SANITIZED
789	ifeq ('$(USE_GCC_50_OR_HIGHER)','yes')
790	# abort on runtime errors
791	SANI_CFLAGS += -fno-sanitize-recover=all
792	endif
793
794	cflags += $(SANI_CFLAGS)
795	clflags += $(SANI_CLFLAGS)
796
797	#
798	# Note: alignment-sanitizer is deactivated for ARBDB and PROBE!
799	ifeq ('$(DEBUG)','1')
800	ifeq ($(USE_GCC_MAJOR),4)
801	ifeq ($(USE_GCC_MINOR),9)
802	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),01)','')
803	# workaround https://gcc.gnu.org/bugzilla/show_bug.cgi?id=63531 for 4.9.0 + 4.9.1
804	# (problem is fixed in 4.9.2 release)
805	extended_cpp_warnings:=$(subst -Weffc++,,$(extended_cpp_warnings))
806	endif
807	endif
808	endif
809	endif
810	endif
811
812	#---------------------- X11 location
813
814	ifeq ($(DARWIN),1)
815	XHOME:=$(PREFIX)
816	else
817	ifeq ($(DEBIAN),1)
818	XHOME:=$(PREFIX)
819	else
820	XHOME:=/usr/X11R6
821	endif
822	endif
823
824	XINCLUDES ?= -I$(XHOME)/include
825	XLIBS ?= -L$(XHOME)/$(CROSS_LIB)
826	ifeq ($(DARWIN),1)
827	XINCLUDES += -I$(OSX_FW)/GLUT.framework/Headers -I$(OSX_FW)/OpenGL.framework/Headers -I$(OSX_SDK)/usr/include/krb5
828
829	XLIBS += -lXm -lpng -lz -lXt -lX11 -lXext -lXp -lXmu -lXi
830	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGL.dylib:$(OSX_FW_OPENGL)/libGL.dylib
831	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGLU.dylib:$(OSX_FW_OPENGL)/libGLU.dylib
832	else
833	XLIBS += -lXm -lXpm -lXt -lXext -lX11
834	endif
835
836	#---------------------- open GL
837
838	ifeq ($(OPENGL),1)
839	cflags += -DARB_OPENGL # activate OPENGL code
840	GL := gl # this is the name of the OPENGL base target
841	GL_LIB_SYS := -lGL -lGLU
842	GL_LIB_ARB := -L$(ARBHOME)/GL/glAW -lglAW
843
844	ifeq ($(DARWIN),1)
845	GL_LIB_SYS += -lpthread
846	endif
847
848	GL_PNGLIBS_ARB := -L$(ARBHOME)/GL/glpng -lglpng_arb
849	GL_PNGLIBS_SYS := -lpng
850
851	GLEWLIB := -lGLEW -lGLw
852	GLUTLIB := -lglut
853
854	GL_LIBS_SYS := $(GL_LIB_SYS) $(GL_PNGLIBS_SYS) $(GLEWLIB) $(GLUTLIB)
855	GL_LIBS_ARB := $(GL_LIB_ARB) $(GL_PNGLIBS_ARB)
856
857	RNA3D_LIB := RNA3D/RNA3D.a
858	else
859	GL_LIBS_SYS:=# no opengl -> no libs
860	GL_LIBS_ARB:=# no opengl -> no libs
861	GL:=# dont build ARB openGL libs
862
863	RNA3D_LIB :=
864	endif
865
866	RNA3D_LIB_4_DEPENDS := RNA3D/RNA3D.a
867
868	GL_LIBS:=$(GL_LIBS_ARB) $(GL_LIBS_SYS)
869
870	#---------------------- sina:
871
872	ifndef ISINA
873	# build sina delivered with arb?
874	ifeq ($(LINUX),1)
875	ifeq ('$(USE_GCC_70_OR_HIGHER)','yes')
876	ISINA := 1# default to 'yes' for linux with gcc>=7
877	endif
878	endif
879	ifndef ISINA
880	ISINA := 0# 'no' otherwise
881	endif
882	endif
883
884	#---------------------- tiff lib:
885
886	TIFFLIBS := -ltiff
887
888	#---------------------- XML lib:
889
890	XMLLIBS := -lxerces-c
891
892	#---------------------- glib:
893
894	ARB_NEEDED_GLIB=glib-2.0
895
896	ARB_GLIB_INCLUDE:=$(strip $(shell pkg-config --cflags $(ARB_NEEDED_GLIB)))
897	ARB_GLIB_LIBS:=$(strip $(shell pkg-config --libs $(ARB_NEEDED_GLIB)))
898
899	#---------------------- sunrpc lib:
900	# Note: sunrpc has been removed from glibc
901	# (e.g. in SuSE Leap 15.3 and Fedora 28)
902	# see https://fedoraproject.org/wiki/Changes/SunRPCRemoval
903	#
904	HAVE_LIBTIRPC=$(strip $(shell pkg-config --exists libtirpc && echo libtirpc))
905	ifeq ($(HAVE_LIBTIRPC),)
906	ARB_RPC_INCLUDE:=
907	ARB_RPC_LIBS:=
908	else
909	ARB_RPC_INCLUDE:=$(strip $(shell pkg-config --cflags $(HAVE_LIBTIRPC)))
910	ARB_RPC_LIBS:=$(strip $(shell pkg-config --libs $(HAVE_LIBTIRPC)))
911	endif
912
913	#---------------------- basic libs:
914
915	ARB_CORE_LIBS:=$(ARB_GLIB_LIBS) $(ARB_RPC_LIBS)
916
917	SYSLIBS:=
918	ifeq ($(DARWIN),1)
919	SYSLIBS += -lstdc++
920	else
921	SYSLIBS += -lm $(ARB_CORE_LIBS)
922	endif
923
924	#---------------------- system dependent commands
925
926	ifeq ($(DARWIN),1)
927	TIME:=gtime
928	else
929	TIME:=/usr/bin/time
930	endif
931
932	#---------------------- SSE vectorizer
933	# for details see SOURCE_TOOLS/vectorize.README
934
935	ifeq ($(DEBUG),0)
936	ifeq ($(USE_GCC_49_OR_HIGHER),yes)
937	ifeq ($(DISABLE_VECTORIZE_CHECK),0)
938	cflags += -fopt-info-vec
939	cflags += -fopt-info-vec-missed
940	ifeq ($(TRACE_MISSED_VECTORIZATIONS),1)
941	# Shows reasons for unsuccessful vectorization:
942	cflags += -ftree-vectorizer-verbose=10
943	POST_COMPILE += --dump-loop-optimization
944	ifeq ($(VECTORIZATION_CHECK_CANDIDATES),1)
945	$(error TRACE_MISSED_VECTORIZATIONS and VECTORIZATION_CHECK_CANDIDATES may not be used together!)
946	endif
947	endif
948	ifeq ($(VECTORIZATION_CHECK_CANDIDATES),1)
949	POST_COMPILE += --loop-optimization-candi
950	endif
951	POST_COMPILE += --check-loop-optimization
952	endif
953	else
954	ifeq ($(USE_GCC_48_OR_HIGHER),yes)
955	# no automatic vectorization-check for gcc<4.9.0
956	# -> uncomment the next 2 lines and grep the spam it will produce for 'vectorized.*loops'
957	# cflags += -fopt-info -fopt-info-vec-missed
958	# POST_COMPILE += --original
959	endif
960	endif
961	endif
962
963	#---------------------- stop early on broken flags/compiler combination
964
965	ifeq ($(DEBUG),0)
966	ifeq ($(SANITIZE_ANY),1)
967	ifeq ('$(COMPILER_VERSION)','4.9.1')
968	$(error compiling DEBUG=0 + SANITIZE!=0 crashes with gcc $(COMPILER_VERSION) (gcc 4.9.2 works))
969	endif
970	endif
971	endif
972
973	#---------------------- include symbols?
974
975	ifeq ($(TRACESYM),1)
976	ifeq ($(USE_CLANG),0)
977	cflags += -rdynamic
978	clflags += -rdynamic -Wl,--export-dynamic
979	endif
980	endif
981
982	#---------------------- warn about duplicate variable definitions
983
984	ifeq ($(DARWIN),1)
985	clflags += -Wl,-warn_commons
986	else
987	clflags += -Wl,--warn-common
988	endif
989
990	#---------------------- differences between linking executables and shared libs:
991
992	# executables:
993	ifeq ($(DARWIN),1)
994	blflags:=$(clflags)
995	else
996	blflags:=$(clflags) -Wl,--no-undefined
997	endif
998
999	# shared libraries
1000	llflags:=$(clflags)
1001
1002	# dont use clflags below
1003	clflags:=
1004
1005	# -------------------------------------------------------------------------
1006	# Don't put any machine/version/etc conditionals below!
1007	# (instead define variables above)
1008	# -------------------------------------------------------------------------
1009
1010	cflags += -W -Wall $(dflags) $(extended_warnings)
1011	cxxflags := $(extended_cpp_warnings)# flags only suitable for C++ (not C; see onlyC_flags).
1012
1013	# add CFLAGS + CPPFLAGS from environment for DEBIAN build
1014	ifeq ($(DEBIAN),1)
1015	cflags := $(CFLAGS) $(cflags)
1016	cxxflags += $(CPPFLAGS)
1017	endif
1018
1019	ifeq ('$(USE_CLANG)','1')
1020	# the following standards also work with clang 6.0.0 (under linux):
1021	# -std=gnu++17 -std=gnu++14 -std=gnu++11 -std=gnu++0x
1022	cxxflags += -std=gnu++17
1023	else
1024	# standard mostly supported by gcc version (according to https://gcc.gnu.org/projects/cxx-status.html)
1025	# C++20 with gcc>=12
1026	# C++23 with gcc>=15 (or 16 for reflection)
1027
1028	ifeq ('$(USE_GCC_80_OR_HIGHER)','yes')
1029	# C++17 mostly supported by gcc>=8
1030	cxxflags += -std=gnu++17 # see also TEMPLATES/cxxforward.h@USE_Cxx17
1031	else
1032	ifeq ('$(USE_GCC_60_OR_HIGHER)','yes')
1033	cxxflags += -std=gnu++14 # see also TEMPLATES/cxxforward.h@USE_Cxx14
1034	else
1035	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
1036	cxxflags += -std=gnu++11 # see also TEMPLATES/cxxforward.h@USE_Cxx11
1037	else
1038	# gcc versions between 4.3 (lowest supported) and <4.7
1039	cxxflags += -std=gnu++0x
1040	endif # 47
1041	endif # 60
1042	endif # 80
1043	endif # USE_CLANG
1044
1045	LINK_STATIC_LIB := $(AR) -csq# link static lib
1046	LINK_EXECUTABLE := $(A_CXX) $(blflags) -o# link executable (c++)
1047
1048	ifeq ($(LINK_STATIC),1)
1049	SHARED_LIB_SUFFIX = a# static lib suffix
1050	LINK_SHARED_LIB := $(LINK_STATIC_LIB)
1051	else
1052	SHARED_LIB_SUFFIX = so# shared lib suffix
1053	LINK_SHARED_LIB := $(A_CXX) $(llflags) -shared -o# link shared lib
1054	endif
1055
1056	ifeq ($(DARWIN),1)
1057	lflags4perl:=
1058	else
1059	lflags4perl:=$(cross_lflags) -shared
1060	endif
1061
1062	# delete variables unused below
1063	blflags:=
1064	llflags:=
1065
1066	# other used tools
1067	MAKEDEPEND_PLAIN = makedepend
1068	MAKEDEPEND = $(FORCEMASK);$(MAKEDEPEND_PLAIN)
1069
1070	SEPNODATE:=--------------------------------------------------------------------------------
1071	SEP=[`date +%M:%S.%N`] ------------------------------------------------
1072	# to analyse timings run
1073	# make -j9 clean; make -j9 all \| grep '^\[' \| sort
1074	# make -j9 "TIMED_TARGET=perl" clean_timed_target \| grep '^\[' \| sort
1075
1076	# ------------------------------------------------------------ DYNLIBDEFS
1077	# various dynamic library definitions for linking executables:
1078	#
1079	# SYSLIBS: system libraries needed by database lib
1080	# ARBDB_LIB: database lib
1081	# DBSYS_LIBS: executable using database (but no GUI)
1082	# GUI_LIBS: executable using database and GUI (arb gui uses database)
1083	#
1084	# Note: definitions exported to sub-makefiles are described in SOURCE_TOOLS/parent_make.txt
1085
1086	CORE_LIB=-lCORE
1087	ARBDB_LIB=-lARBDB $(CORE_LIB)
1088	DBSYS_LIBS = $(ARBDB_LIB) $(SYSLIBS)
1089
1090	GUI_LIBS_PREFIX:=
1091	ifeq ($(DARWIN),1)
1092	# this seem to be added at wrong place, since opengl is only needed to link EDIT4
1093	GUI_LIBS_PREFIX:=-framework GLUT -framework OpenGL
1094	endif
1095
1096	GUI_LIBS=$(GUI_LIBS_PREFIX) $(DBSYS_LIBS) -lWINDOW $(XLIBS)
1097
1098	LIBPATH = -L$(ARBHOME)/lib
1099
1100	DEST_LIB = lib
1101	DEST_BIN = bin
1102
1103	CC_INCLUDES := -I. -I$(ARBHOME)/INCLUDE $(XINCLUDES) $(ARB_GLIB_INCLUDE) $(ARB_RPC_INCLUDE)
1104	CXX_INCLUDES := $(CC_INCLUDES)
1105	MAKEDEPENDFLAGS := -- -DARB_OPENGL -DUNIT_TESTS -D__cplusplus -I. -Y$(ARBHOME)/INCLUDE
1106
1107	# ---------------------------------------
1108	# wrap main()
1109
1110	use_ARB_main=$(ARBHOME)/SOURCE_TOOLS/arb_main_cpp.o
1111	use_ARB_main_C=$(ARBHOME)/SOURCE_TOOLS/arb_main_c.o
1112
1113	# -----------------------------------------
1114	# generate unique IDs:
1115	#
1116	# 1) ARBBID
1117	# - different for different calls of make
1118	# - constant in recursive calls (submake)
1119	#
1120	ifndef ARBBID
1121	ARBBID:=$(shell SOURCE_TOOLS/uniqueID.sh)
1122	endif
1123
1124	# 2) ARBCID
1125	# - identical for multiple calls of make with same gcc and config
1126	# - uses DEBUG, UNIT_TESTS, OPENGL, DEVELOPER, gcc-version
1127
1128	ifndef ARBCID
1129	# Main purpuse is to simply generate filenames based on current config,
1130	# in order to log data and later compare between different versions.
1131	#
1132	# Note: change free at will (i.e. don't rely on content)
1133	ARBCID := $(if $(filter 1,$(DEBUG)),_DEBUG,NDEBUG)
1134	ARBCID := $(ARBCID)$(if $(filter 1,$(UNIT_TESTS)),__TESTS,_NTESTS)
1135	ARBCID := $(ARBCID)$(if $(filter 1,$(OPENGL)),__OPENGL,_NOPENGL)
1136	# ARBCID := $(ARBCID)_$(DEVELOPER)
1137	ARBCID := $(ARBCID)_$(COMPILER_NAME)_$(COMPILER_VERSION)
1138	# $(error ARBCID = $(ARBCID))
1139
1140	endif
1141
1142	# -----------------------------------------
1143	# export variables to submakefiles
1144
1145	include SOURCE_TOOLS/export2sub
1146
1147	# do not define (exported) variables below this point
1148
1149	# -------------------------
1150	# Main arb targets:
1151	# -------------------------
1152
1153	first_target:
1154	$(MAKE) checks
1155	@echo $(SEPNODATE)
1156	@echo 'Main targets:'
1157	@echo ''
1158	@echo ' all - Compile ARB + TOOLs + and copy shared libs + link foreign software'
1159	@echo ' (That is most likely the target you want)'
1160	@echo ''
1161	@echo ' clean - remove generated files ("SUBDIR/SUBDIR.clean" to clean only SUBDIR)'
1162	@echo ' rebuild - clean + all'
1163	@echo ' cleanlinked - remove all binaries'
1164	@echo ' relink - cleanlinked + all (=relink all from objects)'
1165	@echo ''
1166	@echo 'Targets for automated builds:'
1167	@echo ''
1168	@echo ' ALL, REBUILD, TARFILE + TARFILE_QUICK '
1169	@echo ' - same as all, rebuild, tarfile + tarfile_quick'
1170	@echo ' - if errors occur, they are extracted and listed at tail of output'
1171	@echo ''
1172	@echo $(SEPNODATE)
1173	@echo ''
1174	@echo 'Development targets:'
1175	@echo ''
1176	@echo ' depends - create or update dependencies ("SUBDIR/SUBDIR.depends" to update only SUBDIR)'
1177	@echo ' proto - create or update prototypes ("SUBDIR/SUBDIR.proto" to update only SUBDIR)'
1178	@echo ' tags - create tags for xemacs'
1179	@echo ' show - show available shortcuts (AKA subtargets)'
1180	@echo ' up - shortcut for depends+proto+tags'
1181	ifeq ($(UNIT_TESTS),1)
1182	@echo ' ut - only run tests'
1183	@echo ' "UNIT=..." oneunit - build one unit and run tests (see also UNIT_TESTER/Makefile.setup.local)'
1184	endif
1185	ifneq ($(SANITIZE),0)
1186	@echo ' sanitize - all + run arb_ntree with sanitizer (test.arb + execute _logged)'
1187	endif
1188	@echo ' modified - rebuild files modified in svn checkout (does touch)'
1189	@echo ' touch - touch files modified in svn checkout'
1190	@echo ''
1191	@echo 'Some often used sub targets:'
1192	@echo ''
1193	@echo ' arb - Just compile ARB (but none of the integrated tools)'
1194	@echo ' menus - create lib/gde/arb.menu from GDEHELP/ARB_GDEmenus.source'
1195	@echo ' perl - Compile the PERL XSUBS into lib/ARB.so and create links in lib to perl'
1196	@echo ' binlink - Create all links in the bin directory'
1197	@echo ''
1198	@echo 'Internal maintenance:'
1199	@echo ''
1200	@echo ' relinfo - show help on release targets'
1201	@echo ' tarfile - make rebuild and create arb version tarfile ("tarfile_quick" to skip rebuild)'
1202	@echo ' save - save all basic ARB sources into arbsrc_DATE ("savetest" to check filelist)'
1203	@echo ' patch - save svn diff to patchfile'
1204	@echo ' source_doc - create doxygen documentation'
1205	@echo ' relocated - rebuild partly (use when you have relocated ARBHOME)'
1206	@echo ' check_res - check resource usage'
1207	@echo ' dep_graph - Build dependency graphs'
1208	@echo ' clean_cov - Clean coverage results'
1209	@echo ''
1210	@echo ' clean_opengl_changed - clean after changing OPENGL setting in config.Makefile'
1211	@echo ' clean_checked_vect - clean units containing vectorization checks'
1212	@echo ' cleanRelinkable - similar to cleanlinked (but skips raxml8 to avoid rebuild)'
1213	@echo ''
1214	@echo ' post_commit_check - Checks whether'
1215	@echo ' * main make targets work,'
1216	@echo ' * dependencies and prototypes are up to date,'
1217	@echo ' * SVN-controlled files remain unaffected by called targets and'
1218	@echo ' * all generated files are ignored.'
1219	@echo ' (has to be called in a clean SVN checkout)'
1220	@echo $(SEPNODATE)
1221	@echo ''
1222
1223	relinfo:
1224	@echo ''
1225	@echo $(SEPNODATE)
1226	@echo 'Release targets:'
1227	@echo ''
1228	@echo ' inc_candi - increase RC candidate-number (only possible in "rc" branch, not needed for RC1)'
1229	@echo ' inc_patch - increase release patchlevel (only possible in "stable" branch)'
1230	@echo ' inc_minor - increase minor version number (only possible in "trunk")'
1231	@echo ' inc_major - increase MAJOR version number (only possible in "trunk")'
1232	@echo ''
1233	@echo ' show_version - show version tag'
1234	@echo ''
1235	@echo $(SEPNODATE)
1236	@echo ''
1237
1238	# auto-generate config.makefile:
1239
1240	config.makefile : config.makefile.template
1241	@echo --------------------------------------------------------------------------------
1242	ifeq ($(CONFIG_MAKEFILE_FOUND),)
1243	@cp $< $@
1244	@echo '$(ARBHOME)/$@:1: has been generated.'
1245	@echo 'Please edit $@ to configure your system!'
1246	@echo --------------------------------------------------------------------------------
1247	@false
1248	else
1249	@echo '$(ARBHOME)/$<:1: is more recent than'
1250	@echo '$(ARBHOME)/$@:1:'
1251	@ls -al config.makefile*
1252	@echo --------------------------------------------------------------------------------
1253	@echo "Updating $@ (if this fails, check manually)"
1254	SOURCE_TOOLS/update_config_makefile.pl
1255	@echo "Sucessfully updated $@"
1256	@echo --------------------------------------------------------------------------------
1257	@ls -al config.makefile*
1258	@echo --------------------------------------------------------------------------------
1259	@echo "Diff to your old config.makefile:"
1260	@echo --------------------------------------------------------------------------------
1261	-diff $@.bak $@
1262	@echo --------------------------------------------------------------------------------
1263	endif
1264
1265	# check if everything is configured correctly
1266
1267	check_DEVELOPER:
1268	ifndef DEVELOPER
1269	@echo 'config.makefile:1: DEVELOPER not defined'
1270	@false
1271	endif
1272
1273	check_DEBUG:
1274	ifndef dflags
1275	@echo 'config.makefile:1: DEBUG has to be defined. Valid values are 0 and 1'
1276	@false
1277	endif
1278
1279	check_ARB_64:
1280	ifndef ARB_64
1281	@echo 'config.makefile:1: ARB_64 has to be defined. Valid values are 0 and 1'
1282	@false
1283	endif
1284
1285	# ---------------------------------------- check gcc version
1286
1287	COMPILER_BROKEN:=0
1288
1289	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.6.4')
1290	COMPILER_BROKEN:=1
1291	endif
1292	ifeq ('$(COMPILER_VERSION_ALLOWED)', '4.8.0')
1293	COMPILER_BROKEN:=1
1294	endif
1295
1296	check_same_GCC_VERSION:
1297	$(ARBHOME)/SOURCE_TOOLS/check_same_compiler_version.pl $(COMPILER_NAME) $(COMPILER_VERSION_ALLOWED)
1298
1299	check_GCC_VERSION:
1300	@echo 'Compiler version check:'
1301	# see .@ALLOWED_gcc_VERSIONS
1302	ifeq ('$(COMPILER_VERSION_ALLOWED)', '')
1303	@echo " - Your compiler is '$(COMPILER_NAME)' version '$(COMPILER_VERSION)'"
1304	@echo ' This version is not in the list of supported $(COMPILER_NAME)-versions:'
1305	@$(foreach version,$(ALLOWED_COMPILER_VERSIONS),echo ' * $(version)';)
1306	@echo ' - You may either ..'
1307	@echo ' - add your version to ALLOWED_$(COMPILER_NAME)_VERSIONS in the Makefile and try it out or'
1308	@echo ' - switch to one of the allowed versions (see arb_README_gcc.txt for installing'
1309	@echo ' a different version of gcc)'
1310	$(error Unsupported compiler '$(COMPILER_NAME)' version '$(COMPILER_VERSION)')
1311	else
1312	ifeq ($(COMPILER_BROKEN),1)
1313	$(error compilation refused for $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)'. Refer to http://bugs.arb-home.de/wiki/GccVersionInfo for details.)
1314	else
1315	@echo " - Supported $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)' detected - fine!"
1316	@echo ''
1317	$(MAKE) check_same_GCC_VERSION
1318	endif
1319	endif
1320
1321	#---------------------- check ARBHOME
1322
1323	# use arb_INSTALL.txt to determine whether ARBHOME points to correct directory
1324	ARB_INSTALL_FOUND=$(wildcard $(ARBHOME)/arb_INSTALL.txt)
1325
1326	check_ARBHOME:
1327	ifeq ($(strip $(ARB_INSTALL_FOUND)),)
1328	@echo ------------------------------------------------------------
1329	@echo "ARBHOME is set to '$(ARBHOME)'"
1330	@echo "The environment variable ARBHOME has to point to the top arb source directory."
1331	@echo "If you use bash enter:"
1332	@echo " export ARBHOME='`pwd`'"
1333	@echo ------------------------------------------------------------
1334	@false
1335	endif
1336
1337	ARB_PATH_SET=$(findstring $(ARBHOME)/bin,$(PATH))
1338
1339	check_PATH: check_ARBHOME
1340	ifeq ($(strip $(ARB_PATH_SET)),)
1341	@echo ------------------------------------------------------------
1342	@echo "The environment variable PATH has to contain $(ARBHOME)/bin"
1343	@echo "If you use bash enter:"
1344	@echo ' export PATH=$$ARBHOME/bin:$$PATH'
1345	@echo ------------------------------------------------------------
1346	@false
1347	endif
1348
1349	check_TOOLS:
1350	@util/arb_check_build_env.pl \
1351	"$(A_CC)" \
1352	"$(A_CXX)" \
1353	"$(LINK_SHARED_LIB)" \
1354
1355	have_makedepend:
1356	@util/arb_check_build_env.pl --check-only "$(MAKEDEPEND_PLAIN)"
1357
1358	check_ENVIRONMENT : check_PATH check_TOOLS
1359	@echo "-------------------- Environment [start]"
1360	@echo "ARBHOME='$(ARBHOME)'"
1361	@echo "PATH='$(PATH)'"
1362	@echo "LD_LIBRARY_PATH='$(LD_LIBRARY_PATH)'"
1363	@echo "-------------------- Environment [end]"
1364
1365	check_tabs: check_setup
1366	ifeq ($(DEBUG),1)
1367	@SOURCE_TOOLS/tabBrake.pl
1368	endif
1369
1370	force_tab_check:
1371	@touch -t 198001010000 SOURCE_TOOLS/stamp.tabBrake
1372	@$(MAKE) check_tabs
1373
1374
1375	# ---------------------
1376
1377	check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION
1378	@echo Your setup seems to be ok.
1379
1380	checks: check_setup check_tabs
1381	@rm -f SOURCE_TOOLS/postcompile.sav
1382
1383
1384	# end test section ------------------------------
1385
1386	# ---------------------------------------
1387	# List of standard top level directories
1388	#
1389	# sub-makefiles have to define the targets
1390	# - 'depends' and
1391	# - 'clean'
1392	#
1393	# when adding new libraries/subdirs here, also add a dependency vs 'links' or 'links_non_perl' in .@DD_links_non_perl
1394
1395	TL_ARCHIVES = \
1396	AISC/AISC.a \
1397	ARB_GDE/ARB_GDE.a \
1398	AWTC/AWTC.a \
1399	AWTI/AWTI.a \
1400	CONSENSUS_TREE/CONSENSUS_TREE.a \
1401	CONVERTALN/CONVERTALN.a \
1402	DBSERVER/DBSERVER.a \
1403	DIST/DIST.a \
1404	EDIT4/EDIT4.a \
1405	EISPACK/EISPACK.a \
1406	GENOM/GENOM.a \
1407	GENOM_IMPORT/GENOM_IMPORT.a \
1408	ISLAND_HOPPING/ISLAND_HOPPING.a \
1409	MERGE/MERGE.a \
1410	MULTI_PROBE/MULTI_PROBE.a \
1411	NALIGNER/NALIGNER.a \
1412	NAMES/NAMES.a \
1413	NAMES_COM/server.a \
1414	NTREE/NTREE.a \
1415	PARSIMONY/PARSIMONY.a \
1416	PHYLO/PHYLO.a \
1417	PRIMER_DESIGN/PRIMER_DESIGN.a \
1418	PROBE/PROBE.a \
1419	PROBE_COM/server.a \
1420	PROBE_DESIGN/PROBE_DESIGN.a \
1421	$(RNA3D_LIB) \
1422	RNACMA/RNACMA.a \
1423	SECEDIT/SECEDIT.a \
1424	SEQ_QUALITY/SEQ_QUALITY.a \
1425	SERVERCNTRL/SERVERCNTRL.a \
1426	STAT/STAT.a \
1427	TREEGEN/TREEGEN.a \
1428	WETC/WETC.a \
1429	XML/XML.a \
1430
1431	TL_SHARED_ARCHIVES = \
1432	ARBDB/libARBDB.so \
1433	CORE/libCORE.so \
1434	WINDOW/libWINDOW.so \
1435
1436	TL_ARCHIV_COLLECTIONS = \
1437	SL/SL.archColl \
1438
1439	TL_TOOLS_COLLECTIONS = \
1440	AISC_MKPTPS/AISC_MKPTPS.toolColl \
1441	TOOLS/TOOLS.toolColl \
1442	PERLTOOLS/PERLTOOLS.toolColl \
1443	PROBE_SET/PROBE_SET.toolColl \
1444	READSEQ/READSEQ.toolColl \
1445
1446	RECURSIVE_SUBS = \
1447	GDE/GDE.sub \
1448	UNIT_TESTER/UNIT_TESTER.sub \
1449
1450	SUBDIRS = \
1451	$(RECURSIVE_SUBS) \
1452	$(TL_ARCHIVES:.a=.sub) \
1453	$(TL_SHARED_ARCHIVES:.so=.sub) \
1454	$(TL_ARCHIV_COLLECTIONS:.archColl=.sub) \
1455	$(TL_TOOLS_COLLECTIONS:.toolColl=.sub) \
1456
1457	# sub directories inside TL_ARCHIV_COLLECTIONS
1458	CL_ARCH_DIRS = $(foreach coll,$(TL_ARCHIV_COLLECTIONS),$(shell find $(dir $(coll)) -maxdepth 1 -mindepth 1 -type d))
1459
1460	# archives inside CL_ARCH_DIRS:
1461	CL_ARCHIVES = $(foreach adir,$(CL_ARCH_DIRS),$(dir $(adir))$(notdir $(adir))/$(notdir $(adir)).a)
1462
1463	# -----------------------
1464	# library packets
1465
1466	ARCHS_CLIENT_PROBE = PROBE_COM/client.a
1467	ARCHS_CLIENT_NAMES = NAMES_COM/client.a
1468
1469	ARCHS_MAKEBIN = AISC_MKPTPS/AISC_MKPTPS.a AISC/AISC.a
1470
1471	# communication libs need aisc and aisc_mkpts:
1472
1473	AISC/AISC.dummy: proto_tools
1474
1475	comtools: AISC/AISC.dummy
1476
1477	ARCHS_SEQUENCE = \
1478	SL/SEQUENCE/SEQUENCE.a \
1479	SL/ALIVIEW/ALIVIEW.a \
1480	SL/PRONUC/PRONUC.a \
1481
1482	ARCHS_TREE = \
1483	SL/ARB_TREE/ARB_TREE.a \
1484	SL/FILTER/FILTER.a \
1485	$(ARCHS_SEQUENCE) \
1486
1487	# parsimony tree (used by NTREE, PARSIMONY, STAT(->EDIT4), DIST(obsolete!))
1488	ARCHS_AP_TREE = \
1489	SL/AP_TREE/AP_TREE.a \
1490	$(ARCHS_TREE) \
1491
1492	# --------------------------------------------------------------------------------
1493	# dependencies for linking shared libs
1494
1495	link_core: core
1496	link_db: db link_core
1497	link_aw: aw link_db
1498
1499	#***************************************************************************************
1500	# Individual_Programs_Section
1501	#***************************************************************************************
1502
1503	arbmainwrapper:
1504	$(MAKE) -C SOURCE_TOOLS -r mainwrapper
1505
1506
1507	#********************************* arb_ntree ************************************
1508	NTREE = bin/arb_ntree
1509	ARCHS_NTREE = \
1510	NTREE/NTREE.a \
1511	ARB_GDE/ARB_GDE.a \
1512	SL/SPECSEL/SPECSEL.a \
1513	SL/GROUP_SEARCH/GROUP_SEARCH.a \
1514	SL/SAICALC/SAICALC.a \
1515	SL/DB_UI/DB_UI.a \
1516	SL/ARB_SPEC/ARB_SPEC.a \
1517	SL/MASKS/MASKS.a \
1518	AWTC/AWTC.a \
1519	AWTI/AWTI.a \
1520	CONSENSUS_TREE/CONSENSUS_TREE.a \
1521	GENOM_IMPORT/GENOM_IMPORT.a \
1522	GENOM/GENOM.a \
1523	MERGE/MERGE.a \
1524	MULTI_PROBE/MULTI_PROBE.a \
1525	PRIMER_DESIGN/PRIMER_DESIGN.a \
1526	PROBE_DESIGN/PROBE_DESIGN.a \
1527	SEQ_QUALITY/SEQ_QUALITY.a \
1528	SERVERCNTRL/SERVERCNTRL.a \
1529	SL/ALILINK/ALILINK.a \
1530	SL/AW_NAME/AW_NAME.a \
1531	SL/APP/APP.a \
1532	SL/CONSENSUS/CONSENSUS.a \
1533	SL/CANVAS/CANVAS.a \
1534	SL/DB_SCANNER/DB_SCANNER.a \
1535	SL/DB_QUERY/DB_QUERY.a \
1536	SL/QUERY/QUERY.a \
1537	SL/SEQIO/SEQIO.a \
1538	STAT/STAT.a \
1539	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1540	SL/GUI_TK/GUI_TK.a \
1541	SL/HELIX/HELIX.a \
1542	SL/REGEXPR/REGEXPR.a \
1543	SL/REFENTRIES/REFENTRIES.a \
1544	SL/NDS/NDS.a \
1545	SL/ITEM_SHADER/ITEM_SHADER.a \
1546	SL/ITEMS/ITEMS.a \
1547	SL/INSDEL/INSDEL.a \
1548	SL/LOCATION/LOCATION.a \
1549	SL/MACROS/MACROS.a \
1550	SL/PVP/PVP.a \
1551	SL/TRANSLATE/TRANSLATE.a \
1552	SL/TREEDISP/TREEDISP.a \
1553	SL/TREE_ADMIN/TREE_ADMIN.a \
1554	SL/TREE_READ/TREE_READ.a \
1555	SL/TREE_WRITE/TREE_WRITE.a \
1556	SL/XFERGUI/XFERGUI.a \
1557	SL/XFERSET/XFERSET.a \
1558	XML/XML.a \
1559	$(ARCHS_AP_TREE) \
1560
1561	ARCHS_NTREE_ALL = $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(XMLLIBS)
1562
1563	$(NTREE): $(ARCHS_NTREE:.a=.dummy) link_aw
1564	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NTREE_ALL) \|\| ( \
1565	echo "$(SEP) Link $@"; \
1566	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE_ALL)" ; \
1567	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE_ALL) && \
1568	echo "$(SEP) Link $@ [done]"; \
1569	)
1570
1571	#********************************* arb_edit4 ************************************
1572	EDIT4 = bin/arb_edit4
1573
1574	ARCHS_EDIT4 := \
1575	EDIT4/EDIT4.a \
1576	ARB_GDE/ARB_GDE.a \
1577	SL/FAST_ALIGNER/FAST_ALIGNER.a \
1578	AWTC/AWTC.a \
1579	ISLAND_HOPPING/ISLAND_HOPPING.a \
1580	SECEDIT/SECEDIT.a \
1581	SERVERCNTRL/SERVERCNTRL.a \
1582	SL/APP/APP.a \
1583	SL/GUI_TK/GUI_TK.a \
1584	SL/ARB_SPEC/ARB_SPEC.a \
1585	SL/AW_HELIX/AW_HELIX.a \
1586	SL/AW_NAME/AW_NAME.a \
1587	SL/CONSENSUS/CONSENSUS.a \
1588	SL/CANVAS/CANVAS.a \
1589	SL/ITEMS/ITEMS.a \
1590	STAT/STAT.a \
1591	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1592	SL/HELIX/HELIX.a \
1593	SL/TRANSLATE/TRANSLATE.a \
1594	SL/MACROS/MACROS.a \
1595	SL/MAPKEY/MAPKEY.a \
1596	SL/NDS/NDS.a \
1597	$(ARCHS_AP_TREE) \
1598	XML/XML.a \
1599
1600	ifeq ($(OPENGL),1)
1601	ARCHS_EDIT4 += RNA3D/RNA3D.a
1602	endif
1603
1604	ARCHS_EDIT4_ALL = $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4)
1605
1606	LIBS_EDIT4 := $(GL_LIBS)
1607
1608	$(EDIT4): $(ARCHS_EDIT4:.a=.dummy) link_aw
1609	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_EDIT4_ALL) \|\| ( \
1610	echo "$(SEP) Link $@"; \
1611	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4_ALL)" ; \
1612	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4_ALL) && \
1613	echo "$(SEP) Link $@ [done]"; \
1614	)
1615
1616	#********************************* arb_rnacma ************************************
1617	RNACMA = bin/arb_rnacma
1618	ARCHS_RNACMA = \
1619	RNACMA/RNACMA.a \
1620
1621	ARCHS_RNACMA_ALL = $(ARCHS_RNACMA) $(DBSYS_LIBS)
1622
1623	$(RNACMA) : $(ARCHS_RNACMA:.a=.dummy) link_db
1624	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_RNACMA_ALL) \|\| ( \
1625	echo "$(SEP) Link $@"; \
1626	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_RNACMA_ALL)"; \
1627	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_RNACMA_ALL) && \
1628	echo "$(SEP) Link $@ [done]"; \
1629	)
1630
1631	#********************************* arb_wetc ************************************
1632	WETC = bin/arb_wetc
1633	ARCHS_WETC = \
1634	WETC/WETC.a \
1635	SL/APP/APP.a \
1636	SL/MACROS/MACROS.a \
1637	SL/GUI_TK/GUI_TK.a \
1638	SL/HELIX/HELIX.a \
1639	SL/FILTER/FILTER.a \
1640	XML/XML.a \
1641
1642	ARCHS_WETC_ALL = $(ARCHS_WETC) $(GUI_LIBS)
1643
1644	$(WETC): $(ARCHS_WETC:.a=.dummy) link_aw
1645	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_WETC_ALL) \|\| ( \
1646	echo "$(SEP) Link $@"; \
1647	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC_ALL)" ; \
1648	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC_ALL) && \
1649	echo "$(SEP) Link $@ [done]"; \
1650	)
1651
1652	#********************************* arb_dist ************************************
1653	DIST = bin/arb_dist
1654	ARCHS_DIST = \
1655	DIST/DIST.a \
1656	CONSENSUS_TREE/CONSENSUS_TREE.a \
1657	EISPACK/EISPACK.a \
1658	SERVERCNTRL/SERVERCNTRL.a \
1659	SL/APP/APP.a \
1660	SL/GUI_TK/GUI_TK.a \
1661	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1662	SL/HELIX/HELIX.a \
1663	SL/MATRIX/MATRIX.a \
1664	SL/MACROS/MACROS.a \
1665	SL/NDS/NDS.a \
1666	SL/ITEMS/ITEMS.a \
1667	SL/ARB_SPEC/ARB_SPEC.a \
1668	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.a \
1669	XML/XML.a \
1670	$(ARCHS_AP_TREE) \
1671
1672	ARCHS_DIST_ALL = $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS)
1673
1674	$(DIST): $(ARCHS_DIST:.a=.dummy) link_aw
1675	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_DIST_ALL) \|\| ( \
1676	echo "$(SEP) Link $@"; \
1677	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST_ALL)" ; \
1678	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST_ALL) && \
1679	echo "$(SEP) Link $@ [done]"; \
1680	)
1681
1682	#********************************* arb_pars ************************************
1683	PARSIMONY = bin/arb_pars
1684	ARCHS_PARSIMONY = \
1685	PARSIMONY/PARSIMONY.a \
1686	SERVERCNTRL/SERVERCNTRL.a \
1687	SL/APP/APP.a \
1688	SL/GUI_TK/GUI_TK.a \
1689	SL/AW_NAME/AW_NAME.a \
1690	SL/CANVAS/CANVAS.a \
1691	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1692	SL/HELIX/HELIX.a \
1693	SL/MACROS/MACROS.a \
1694	SL/NDS/NDS.a \
1695	SL/ITEMS/ITEMS.a \
1696	SL/TRANSLATE/TRANSLATE.a \
1697	SL/TREEDISP/TREEDISP.a \
1698	XML/XML.a \
1699	$(ARCHS_AP_TREE) \
1700
1701	ARCHS_PARSIMONY_ALL = $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS)
1702
1703	$(PARSIMONY): $(ARCHS_PARSIMONY:.a=.dummy) link_aw
1704	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_PARSIMONY_ALL) \|\| ( \
1705	echo "$(SEP) Link $@"; \
1706	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY_ALL)" ; \
1707	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY_ALL) && \
1708	echo "$(SEP) Link $@ [done]"; \
1709	)
1710
1711	#********************************* arb_convert_aln ************************************
1712	CONVERT_ALN = bin/arb_convert_aln
1713	ARCHS_CONVERT_ALN = \
1714	CONVERTALN/CONVERTALN.a \
1715
1716	ARCHS_CONVERT_ALN_ALL = $(ARCHS_CONVERT_ALN) $(DBSYS_LIBS)
1717
1718	$(CONVERT_ALN) : $(ARCHS_CONVERT_ALN:.a=.dummy) link_db
1719	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_CONVERT_ALN_ALL) \|\| ( \
1720	echo "$(SEP) Link $@"; \
1721	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN_ALL)"; \
1722	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN_ALL) && \
1723	echo "$(SEP) Link $@ [done]"; \
1724	)
1725
1726	#********************************* arb_treegen ************************************
1727
1728	TREEGEN = bin/arb_treegen
1729	ARCHS_TREEGEN = \
1730	TREEGEN/TREEGEN.a \
1731
1732	ARCHS_TREEGEN_ALL = $(ARCHS_TREEGEN)
1733
1734	$(TREEGEN) : $(ARCHS_TREEGEN:.a=.dummy)
1735	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main_C) $(ARCHS_TREEGEN_ALL) \|\| ( \
1736	echo "$(SEP) Link $@"; \
1737	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN_ALL)" ; \
1738	$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN_ALL) && \
1739	echo "$(SEP) Link $@ [done]"; \
1740	)
1741
1742	#********************************* arb_naligner ************************************
1743	NALIGNER = bin/arb_naligner
1744	ARCHS_NALIGNER = \
1745	NALIGNER/NALIGNER.a \
1746	SERVERCNTRL/SERVERCNTRL.a \
1747	SL/HELIX/HELIX.a \
1748
1749	ARCHS_NALIGNER_ALL = $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(DBSYS_LIBS)
1750
1751	$(NALIGNER): $(ARCHS_NALIGNER:.a=.dummy) link_db
1752	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NALIGNER_ALL) \|\| ( \
1753	echo "$(SEP) Link $@"; \
1754	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER_ALL)" ; \
1755	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER_ALL) && \
1756	echo "$(SEP) Link $@ [done]"; \
1757	)
1758
1759	#********************************* arb_phylo ************************************
1760	PHYLO = bin/arb_phylo
1761	ARCHS_PHYLO = \
1762	PHYLO/PHYLO.a \
1763	SL/APP/APP.a \
1764	SL/GUI_TK/GUI_TK.a \
1765	SL/HELIX/HELIX.a \
1766	SL/FILTER/FILTER.a \
1767	SL/MACROS/MACROS.a \
1768	XML/XML.a \
1769
1770	ARCHS_PHYLO_ALL = $(ARCHS_PHYLO) $(GUI_LIBS)
1771
1772	$(PHYLO): $(ARCHS_PHYLO:.a=.dummy) link_aw
1773	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_PHYLO_ALL) \|\| ( \
1774	echo "$(SEP) Link $@"; \
1775	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO_ALL)" ; \
1776	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO_ALL) && \
1777	echo "$(SEP) Link $@ [done]"; \
1778	)
1779
1780	#***************************************************************************************
1781	# SERVER SECTION
1782	#***************************************************************************************
1783
1784	#********************************* arb_db_server ************************************
1785	DBSERVER = bin/arb_db_server
1786	ARCHS_DBSERVER = \
1787	DBSERVER/DBSERVER.a \
1788	SERVERCNTRL/SERVERCNTRL.a \
1789
1790	ARCHS_DBSERVER_ALL = $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS)
1791
1792	$(DBSERVER): $(ARCHS_DBSERVER:.a=.dummy) link_db
1793	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_DBSERVER_ALL) \|\| ( \
1794	echo "$(SEP) Link $@"; \
1795	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER_ALL)" ; \
1796	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER_ALL) && \
1797	echo "$(SEP) Link $@ [done]"; \
1798	)
1799
1800	#********************************* arb_pt_server ************************************
1801	PROBE = bin/arb_pt_server
1802
1803	ARCHS_PROBE_DEPEND = \
1804	PROBE/PROBE.a \
1805	SL/PTCLEAN/PTCLEAN.a \
1806	SERVERCNTRL/SERVERCNTRL.a \
1807	SL/HELIX/HELIX.a \
1808
1809	ARCHS_PROBE_ALL = $(ARCHS_PROBE_DEPEND) $(ARCHS_CLIENT_PROBE) $(ARBDB_LIB) $(SYSLIBS)
1810
1811	$(PROBE): $(ARCHS_PROBE_DEPEND:.a=.dummy) link_db
1812	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) config.makefile $(ARCHS_PROBE_ALL) \|\| ( \
1813	echo "$(SEP) Link $@"; \
1814	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_ALL)" ; \
1815	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_ALL) && \
1816	echo "$(SEP) Link $@ [done]"; \
1817	)
1818
1819	#********************************* arb_name_server ************************************
1820	NAMES = bin/arb_name_server
1821	ARCHS_NAMES = \
1822	NAMES/NAMES.a \
1823	SERVERCNTRL/SERVERCNTRL.a \
1824
1825	ARCHS_NAMES_ALL = $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS)
1826
1827	$(NAMES): $(ARCHS_NAMES:.a=.dummy) link_db
1828	@SOURCE_TOOLS/binuptodate.pl $@ $(use_ARB_main) $(ARCHS_NAMES_ALL) \|\| ( \
1829	echo "$(SEP) Link $@"; \
1830	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES_ALL)" ; \
1831	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES_ALL) && \
1832	echo "$(SEP) Link $@ [done]"; \
1833	)
1834
1835	#********************************* SHARED LIBRARIES SECTION ************************************
1836
1837	prepare_libdir: addlibs
1838
1839	addlibs:
1840	(perl $(ARBHOME)/SOURCE_TOOLS/provide_libs.pl \
1841	"arbhome=$(ARBHOME)" \
1842	"opengl=$(OPENGL)" \
1843	"link_static=$(LINK_STATIC)" \
1844	)
1845
1846	#***************************************************************************************
1847	# Recursive calls to sub-makefiles
1848	#***************************************************************************************
1849
1850	%.depends: have_makedepend
1851	@cp -p $(@D)/Makefile $(@D)/Makefile.old # save old Makefile
1852	@$(MAKE) -C $(@D) -r \
1853	"AUTODEPENDS=1" \
1854	"MAIN=nothing" \
1855	"cflags=noCflagsHere_use_MAKEDEPENDFLAGS" \
1856	"cxxflags=noCxxflagsHere_use_MAKEDEPENDFLAGS" \
1857	depends
1858	@grep "^# DO NOT DELETE" $(@D)/Makefile >/dev/null
1859	@cat $(@D)/Makefile \
1860	\| SOURCE_TOOLS/fix_depends.pl "(from main)" \
1861	>$(@D)/Makefile.2
1862	@mv $(@D)/Makefile.old $(@D)/Makefile # restore old Makefile
1863	@$(ARBHOME)/SOURCE_TOOLS/mv_if_diff $(@D)/Makefile.2 $(@D)/Makefile # update Makefile if changed
1864
1865	%.proto:
1866	@($(MAKE) -C $(@D) \
1867	"AUTODEPENDS=0" \
1868	"MAIN=nothing" \
1869	"cflags=noCflags" \
1870	"cxxflags=noCxxflags" \
1871	proto 2>&1 ) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
1872
1873	%.clean:
1874	@$(MAKE) -C $(@D) \
1875	"AUTODEPENDS=0" \
1876	"MAIN=nothing" \
1877	"cflags=noCflags" \
1878	"cxxflags=noCxxflags" \
1879	clean
1880
1881
1882	# stop wrong targets:
1883	target_is_missing_lib_prefix:
1884	@echo "Error: Denied to build shared library target with missing 'lib'-prefix"
1885	false
1886
1887	ARBDB/ARBDB.dummy: target_is_missing_lib_prefix
1888	CORE/CORE.dummy: target_is_missing_lib_prefix
1889	AWT/AWT.dummy: target_is_missing_lib_prefix
1890	WINDOW/WINDOW.dummy: target_is_missing_lib_prefix
1891
1892	# rule to generate main target (normally a library):
1893	# @@@ check effect of setting LANG=C below
1894	%.dummy:
1895	@( export ID=$$$$; LANG=C; \
1896	(( \
1897	echo "$(SEP) Make $(@D)"; \
1898	$(MAKE) -C $(@D) -r \
1899	"AUTODEPENDS=1" \
1900	"MAIN=$(@F:.dummy=.a)" \
1901	"cflags=$(cflags) -DIN_ARB_$(subst /,_,$(@D))" \
1902	&& \
1903	echo "$(SEP) Make $(@D) [done]"; \
1904	) >$(@D).$$ID.log 2>&1 && (cat $(@D).$$ID.log;rm $(@D).$$ID.log)) \|\| (cat $(@D).$$ID.log;rm $(@D).$$ID.log;false))
1905
1906	# Additional dependencies for subtargets:
1907
1908	PROBE_COM/PROBE_COM.dummy : comtools
1909	NAMES_COM/NAMES_COM.dummy : comtools
1910
1911	com: PROBE_COM/PROBE_COM.dummy NAMES_COM/NAMES_COM.dummy
1912
1913	# stop wrong more targets:
1914	PROBE_COM/server.dummy:
1915	@echo Unwanted request to make target $<
1916	false
1917
1918	PROBE_COM/client.dummy:
1919	@echo Unwanted request to make target $<
1920	false
1921
1922	NAMES_COM/server.dummy:
1923	@echo Unwanted request to make target $<
1924	false
1925
1926	NAMES_COM/client.dummy:
1927	@echo Unwanted request to make target $<
1928	false
1929
1930
1931	ARBDB/libARBDB.dummy: links
1932	CORE/libCORE.dummy: links
1933
1934	PERLTOOLS/PERLTOOLS.dummy: core db
1935
1936	# all subdirs perl not depends on go here (ADD_links_non_perl)
1937	AWTI/AWTI.dummy: links_non_perl
1938	CONSENSUS_TREE/CONSENSUS_TREE.dummy: links_non_perl
1939	CONVERTALN/CONVERTALN.dummy: links_non_perl
1940	DBSERVER/DBSERVER.dummy: links_non_perl
1941	DIST/DIST.dummy: links_non_perl
1942	EDIT4/EDIT4.dummy: links_non_perl com
1943	EISPACK/EISPACK.dummy: links_non_perl
1944	GDE/GDE.dummy: links_non_perl
1945	GENOM/GENOM.dummy: links_non_perl
1946	GENOM_IMPORT/GENOM_IMPORT.dummy: links_non_perl
1947	ISLAND_HOPPING/ISLAND_HOPPING.dummy: links_non_perl
1948	MERGE/MERGE.dummy: links_non_perl
1949	NTREE/NTREE.dummy: links_non_perl
1950	PARSIMONY/PARSIMONY.dummy: links_non_perl
1951	PHYLO/PHYLO.dummy: links_non_perl
1952	PRIMER_DESIGN/PRIMER_DESIGN.dummy: links_non_perl
1953	PROBE_SET/PROBE_SET.dummy: links_non_perl link_db
1954	READSEQ/READSEQ.dummy: links_non_perl
1955	RNACMA/RNACMA.dummy: links_non_perl header_libs
1956	SECEDIT/SECEDIT.dummy: links_non_perl
1957	SEQ_QUALITY/SEQ_QUALITY.dummy: links_non_perl
1958	SERVERCNTRL/SERVERCNTRL.dummy: links_non_perl com
1959	SL/ALILINK/ALILINK.dummy: links_non_perl
1960	SL/ALIVIEW/ALIVIEW.dummy: links_non_perl
1961	SL/AP_TREE/AP_TREE.dummy: links_non_perl
1962	SL/APP/APP.dummy: links_non_perl
1963	SL/ARB_SPEC/ARB_SPEC.dummy: links_non_perl
1964	SL/ARB_TREE/ARB_TREE.dummy: links_non_perl
1965	SL/AW_HELIX/AW_HELIX.dummy: links_non_perl
1966	SL/CONSENSUS/CONSENSUS.dummy: links_non_perl
1967	SL/CANVAS/CANVAS.dummy: links_non_perl
1968	SL/DB_QUERY/DB_QUERY.dummy: links_non_perl
1969	SL/DB_SCANNER/DB_SCANNER.dummy: links_non_perl
1970	SL/DB_UI/DB_UI.dummy: links_non_perl
1971	SL/FAST_ALIGNER/FAST_ALIGNER.dummy: links_non_perl
1972	SL/FILTER/FILTER.dummy: links_non_perl
1973	SL/FILTSEQEXP/FILTSEQEXP.dummy: links_non_perl
1974	SL/GROUP_SEARCH/GROUP_SEARCH.dummy: links_non_perl
1975	SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy: links_non_perl
1976	SL/GUI_TK/GUI_TK.dummy: links_non_perl
1977	SL/HEADERTESTS/HEADERTESTS.dummy: links_non_perl
1978	SL/HELIX/HELIX.dummy: links_non_perl
1979	SL/INSDEL/INSDEL.dummy: links_non_perl
1980	SL/ITEM_SHADER/ITEM_SHADER.dummy: links_non_perl
1981	SL/ITEMS/ITEMS.dummy: links_non_perl
1982	SL/LOCATION/LOCATION.dummy: links_non_perl
1983	SL/MACROS/MACROS.dummy: links_non_perl
1984	SL/MASKS/MASKS.dummy: links_non_perl
1985	SL/MATRIX/MATRIX.dummy: links_non_perl
1986	SL/MAPKEY/MAPKEY.dummy: links_non_perl
1987	SL/NDS/NDS.dummy: links_non_perl
1988	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.dummy: links_non_perl
1989	SL/PRONUC/PRONUC.dummy: links_non_perl
1990	SL/PTCLEAN/PTCLEAN.dummy: links_non_perl link_db
1991	SL/PVP/PVP.dummy: links_non_perl
1992	SL/QUERY/QUERY.dummy: links_non_perl link_db
1993	SL/REFENTRIES/REFENTRIES.dummy: links_non_perl
1994	SL/REGEXPR/REGEXPR.dummy: links_non_perl
1995	SL/SAICALC/SAICALC.dummy: links_non_perl
1996	SL/SPECSEL/SPECSEL.dummy: links_non_perl
1997	SL/SEQIO/SEQIO.dummy: links_non_perl
1998	SL/SEQUENCE/SEQUENCE.dummy: links_non_perl
1999	SL/TRANSLATE/TRANSLATE.dummy: links_non_perl
2000	SL/TREE_ADMIN/TREE_ADMIN.dummy: links_non_perl
2001	SL/TREE_READ/TREE_READ.dummy: links_non_perl
2002	SL/TREE_WRITE/TREE_WRITE.dummy: links_non_perl
2003	SL/TREEDISP/TREEDISP.dummy: links_non_perl
2004	SL/XFERGUI/XFERGUI.dummy: links_non_perl
2005	SL/XFERSET/XFERSET.dummy: links_non_perl
2006	STAT/STAT.dummy: links_non_perl
2007	TREEGEN/TREEGEN.dummy: links_non_perl
2008	WETC/WETC.dummy: links_non_perl
2009	WINDOW/libWINDOW.dummy: links_non_perl
2010	XML/XML.dummy: links_non_perl
2011
2012	ifeq ($(OPENGL),1)
2013	GL/glAW/glAW.dummy: links_non_perl
2014	GL/glpng/glpng.dummy: links_non_perl
2015	GL/GL.dummy: GL/glAW/glAW.dummy GL/glpng/glpng.dummy
2016	RNA3D/RNA3D.dummy: links_non_perl gl
2017	endif
2018
2019	UNIT_TESTER/UNIT_TESTER.dummy: link_db \
2020	SERVERCNTRL/SERVERCNTRL.dummy \
2021
2022	# see also TOOLS/Makefile@TOOLSLIBDEPENDS
2023	TOOLS/TOOLS.dummy : links_non_perl link_db com \
2024	CONSENSUS_TREE/CONSENSUS_TREE.dummy \
2025	SERVERCNTRL/SERVERCNTRL.dummy \
2026	SL/FILTER/FILTER.dummy \
2027	SL/FILTSEQEXP/FILTSEQEXP.dummy \
2028	SL/INSDEL/INSDEL.dummy \
2029	SL/PRONUC/PRONUC.dummy \
2030	SL/PVP/PVP.dummy \
2031	SL/REGEXPR/REGEXPR.dummy \
2032	SL/SEQIO/SEQIO.dummy \
2033	SL/TREE_READ/TREE_READ.dummy \
2034	SL/TREE_WRITE/TREE_WRITE.dummy \
2035	SL/XFERSET/XFERSET.dummy \
2036	XML/XML.dummy \
2037
2038	AWTC/AWTC.dummy : com
2039
2040	NAMES/NAMES.dummy : com
2041	SL/AW_NAME/AW_NAME.dummy : com
2042
2043	PROBE/PROBE.dummy : com
2044	MULTI_PROBE/MULTI_PROBE.dummy : com
2045	PROBE_DESIGN/PROBE_DESIGN.dummy : com
2046	NALIGNER/NALIGNER.dummy : com
2047
2048	ARB_GDE/ARB_GDE.dummy : proto_tools menus
2049
2050	compile_compatibility: SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.dummy
2051
2052	#***************************************************************************************
2053	# Short aliases to make targets
2054	#***************************************************************************************
2055
2056	show:
2057	@echo $(SEP)
2058	@echo 'Aliases for often needed targets:'
2059	@echo ''
2060	@echo ' executables:'
2061	@echo ''
2062	@echo ' nt arb_ntree'
2063	@echo ' e4 arb_edit4 (includes secedit)'
2064	@echo ' di arb_dist'
2065	@echo ' ph arb_phylo'
2066	@echo ' pa arb_parsimony'
2067	@echo ' tg arb_treegen'
2068	@echo ' ds arb_dbserver'
2069	@echo ' pt arb_pt_server'
2070	@echo ' na arb_name_server'
2071	@echo ''
2072	@echo ' libraries:'
2073	@echo ''
2074	@echo ' com communication libraries'
2075	@echo ' db ARB database'
2076	@echo ' aw GUI lib'
2077	@echo ' awt GUI toolkit'
2078	@echo ' awtc general purpose library'
2079	@echo ' awti import/export library'
2080	@echo ' mp multi probe library'
2081	@echo ' ge genome library'
2082	@echo ' pd probe design lib'
2083	@echo ' prd primer design lib'
2084	@echo ''
2085	@echo ' other targets:'
2086	@echo ''
2087	@echo ' help recompile help files'
2088	@echo ' tools make small tools used by arb'
2089	@echo ''
2090	@echo ' foreign targets:'
2091	@echo ''
2092	@echo ' gde GDE'
2093	@echo ' agde ARB_GDE'
2094	@echo ''
2095	@echo 'for other targets inspect $(ARBHOME)/Makefile'
2096	@echo ''
2097	@echo $(SEP)
2098
2099	source_doc:
2100	@echo "Remove some links (doxygen crashes otherwise):"
2101	find . $ -name "AISC" -o -name "C" -o -name "GDEHELP" $ -type l -exec rm {} \;
2102	doxygen 2>&1 1>/dev/null
2103	$(MAKE) forcelinks
2104
2105	dep_graph:
2106	@echo "Building some dependency graphs"
2107	SOURCE_TOOLS/dependency_graphs.pl
2108
2109	help: HELP_SOURCE/HELP_SOURCE.dummy
2110
2111	HELP_SOURCE/HELP_SOURCE.dummy: link_core xml menus
2112
2113	db: ARBDB/libARBDB.dummy
2114	core: CORE/libCORE.dummy
2115	aw: WINDOW/libWINDOW.dummy
2116	awtc: AWTC/AWTC.dummy
2117	awti: AWTI/AWTI.dummy
2118
2119	mp: MULTI_PROBE/MULTI_PROBE.dummy
2120	mg: MERGE/MERGE.dummy
2121	ge: GENOM/GENOM.dummy
2122	prd: PRIMER_DESIGN/PRIMER_DESIGN.dummy
2123
2124	nt: menus $(NTREE)
2125
2126	nal: $(NALIGNER)
2127
2128	di: $(DIST)
2129	ph: $(PHYLO)
2130	pa: $(PARSIMONY)
2131	tg: $(TREEGEN)
2132
2133	ifeq ($(OPENGL),1)
2134	3d: RNA3D/RNA3D.dummy
2135	gl: GL/GL.dummy
2136	else
2137	noopengl:
2138	@echo "invalid target for OPENGL=0"
2139	3d: noopengl
2140	gl: noopengl
2141	endif
2142
2143	SL/SL.dummy: com
2144
2145	ds: $(DBSERVER)
2146	pt: $(PROBE)
2147	pst: PROBE_SET/PROBE_SET.dummy
2148	pd: PROBE_DESIGN/PROBE_DESIGN.dummy
2149	na: $(NAMES)
2150	sq: SEQ_QUALITY/SEQ_QUALITY.dummy
2151	cma: $(RNACMA)
2152
2153	sec: SECEDIT/SECEDIT.dummy
2154
2155	e4: $(EDIT4) readseq menus
2156
2157	gi: GENOM_IMPORT/GENOM_IMPORT.dummy
2158	wetc: $(WETC)
2159
2160	xml: XML/XML.dummy
2161	stat: STAT/STAT.dummy $(NTREE) $(EDIT4)
2162	fa: SL/FAST_ALIGNER/FAST_ALIGNER.dummy
2163
2164	#********************************************************************************
2165
2166	up_by_remake: depends proto vectorize_checks
2167
2168	up: up_by_remake tags valgrind_update
2169
2170	#********************************************************************************
2171
2172	touch:
2173	SOURCE_TOOLS/touch_modified.pl
2174
2175	modified: touch
2176	$(MAKE) all
2177
2178	#********************************************************************************
2179
2180	libdepends:
2181	$(MAKE) -C "SOURCE_TOOLS" \
2182	"RNA3D_LIB=$(RNA3D_LIB_4_DEPENDS)" \
2183	libdepends
2184
2185	#********************************************************************************
2186
2187	# create generated headers:
2188	genheaders: TEMPLATES/TEMPLATES.dummy
2189
2190	clrdotdepends:
2191	rm PROBE_COM/.depends \|\| true
2192	rm NAMES_COM/.depends \|\| true
2193	rm PERL2ARB/.depends \|\| true
2194
2195	comdepends: comtools clrdotdepends have_makedepend
2196	@echo "$(SEP) Partially build com interface"
2197	$(MAKE) PROBE_COM/PROBE_COM.depends NAMES_COM/NAMES_COM.depends
2198	$(MAKE) PROBE_COM/server.depends NAMES_COM/server.depends
2199
2200	depends: genheaders comdepends vectorize_checks have_makedepend
2201	@echo "$(SEP) Updating other dependencies"
2202	$(MAKE) $(subst NAMES_COM/server.depends,,$(subst PROBE_COM/server.depends,,$(SUBDIRS:.sub=.depends))) \
2203	HELP_SOURCE/HELP_SOURCE.depends \
2204	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.depends \
2205
2206	$(MAKE) libdepends
2207
2208	depend: depends
2209
2210	# ------------------------------------------------------------
2211	# dependency generation tests for AISC code
2212	#(all should work w/o creating wrong dependencies;
2213	# neither in XXX_COM/Makefile nor in code using AISC interface)
2214	dependstest1: silent_clean
2215	$(MAKE) depends
2216	dependstest2: silent_clean
2217	$(MAKE) com
2218	dependstest3: silent_clean
2219	$(MAKE) aw
2220	dependstest4: silent_clean
2221	$(MAKE) pt
2222	dependstest5: silent_clean
2223	$(MAKE) na
2224	dependstest6: silent_clean
2225	$(MAKE) nt
2226	dependstest7: silent_clean
2227	$(MAKE) all
2228	# ------------------------------------------------------------
2229
2230	vectorize_checks:
2231	$(MAKE) -C SOURCE_TOOLS -r vectorize_checks
2232
2233	clean_checked_vect: lib/lib.clean
2234	SOURCE_TOOLS/clean_checked_vectorizations.sh
2235
2236	# ------------------------------------------------------------
2237
2238	AISC_MKPTPS/AISC_MKPTPS.dummy: links
2239
2240	proto_tools: AISC_MKPTPS/AISC_MKPTPS.dummy
2241
2242	proto: proto_tools
2243	@echo $(SEP) Updating prototypes
2244	$(MAKE) \
2245	ARBDB/ARBDB.proto \
2246	AISC_COM/AISC_COM.proto \
2247	ARB_GDE/ARB_GDE.proto \
2248	CORE/CORE.proto \
2249	CONVERTALN/CONVERTALN.proto \
2250	NTREE/NTREE.proto \
2251	MERGE/MERGE.proto \
2252	PROBE/PROBE.proto \
2253	SERVERCNTRL/SERVERCNTRL.proto \
2254	SL/SL.proto \
2255
2256	#********************************************************************************
2257
2258	valgrind_update: links
2259	@echo $(SEP) Updating for valgrind
2260	$(MAKE) -C SOURCE_TOOLS valgrind_update
2261
2262	#********************************************************************************
2263
2264	TAGFILE=TAGS
2265	UTAGS=TAGS.$(ARBBID)
2266	TAGFILE_TMP=$(UTAGS).tmp
2267
2268	TAG_SOURCE_HEADERS=$(UTAGS).headers.tmp
2269	TAG_SOURCE_CODE=$(UTAGS).codefiles.tmp
2270	TAG_SOURCE_LISTS=$(TAG_SOURCE_HEADERS) $(TAG_SOURCE_CODE)
2271
2272	ETAGS_IGNORE_LIST=SOURCE_TOOLS/etags_ignore.lst
2273
2274	ETAGS=ctags -e -I @$(ETAGS_IGNORE_LIST) --sort=no --if0=no --extra=q
2275	ETAGS_TYPES=--C-kinds=cgnsut --C++-kinds=cgnsut
2276	ETAGS_FUN =--C-kinds=fm --C++-kinds=fm
2277	ETAGS_REST =--C-kinds=dev --C++-kinds=dev
2278
2279	FILTER_TAGS_SOURCES= \
2280	$(SED) -e 's/^.\///g' \| \
2281	grep -Pvi '^HEADERLIBS/\|^GDE/\|^UNIT_TESTER/tests(?:\.slow)?/' \| \
2282	grep -Pvi '/GEN[CH]/'
2283
2284	$(TAG_SOURCE_HEADERS): links
2285	@find . $ -name '.hxx' -o -name ".h" $ -type f \| $(FILTER_TAGS_SOURCES) > $@
2286
2287	$(TAG_SOURCE_CODE): links
2288	@find . $ -name '.cxx' -o -name ".c" $ -type f \| $(FILTER_TAGS_SOURCES) > $@
2289
2290	$(UTAGS).1.tmp: $(TAG_SOURCE_HEADERS)
2291	@$(ETAGS) -f $@ $(ETAGS_TYPES) -L $<
2292	$(UTAGS).2.tmp: $(TAG_SOURCE_HEADERS)
2293	@$(ETAGS) -f $@ $(ETAGS_FUN) -L $<
2294	$(UTAGS).3.tmp: $(TAG_SOURCE_HEADERS)
2295	@$(ETAGS) -f $@ $(ETAGS_REST) -L $<
2296	$(UTAGS).4.tmp: $(TAG_SOURCE_CODE)
2297	@$(ETAGS) -f $@ $(ETAGS_TYPES) -L $<
2298	$(UTAGS).5.tmp: $(TAG_SOURCE_CODE)
2299	@$(ETAGS) -f $@ $(ETAGS_FUN) -L $<
2300	$(UTAGS).6.tmp: $(TAG_SOURCE_CODE)
2301	@$(ETAGS) -f $@ $(ETAGS_REST) -L $<
2302
2303	TAGS_ALL_PARTS=$(UTAGS).1.tmp $(UTAGS).2.tmp $(UTAGS).3.tmp $(UTAGS).4.tmp $(UTAGS).5.tmp $(UTAGS).6.tmp
2304
2305	$(TAGFILE_TMP) : $(TAGS_ALL_PARTS)
2306	@cat $(TAGS_ALL_PARTS) > $@
2307	@rm $(TAGS_ALL_PARTS) $(TAG_SOURCE_LISTS)
2308
2309	cleanOldTags:
2310	@find $(ARBHOME) -name 'TAGS.*.tmp' -ctime +2 -exec rm {} \;
2311
2312	tags: $(TAGFILE_TMP) cleanOldTags
2313	@mv_if_diff $(TAGFILE_TMP) $(TAGFILE)
2314
2315	#********************************************************************************
2316
2317	LINKSTAMP=SOURCE_TOOLS/stamp.generate_all_links
2318
2319	links: checks $(LINKSTAMP) arbmainwrapper
2320	links_no_checks: $(LINKSTAMP) arbmainwrapper
2321
2322	forcelinks:
2323	-rm $(LINKSTAMP)
2324	$(MAKE) links
2325
2326	$(LINKSTAMP): SOURCE_TOOLS/generate_all_links.sh genheaders
2327	+SOURCE_TOOLS/generate_all_links.sh
2328	touch $(LINKSTAMP)
2329
2330	clean_links:
2331	# avoid to delete linked pts, nas or arb_tcp.dat:
2332	find . -path './lib' -prune -o -type l -exec rm {} \;
2333	# removed obsolete file - refuses to disappear due to 'prune' above
2334	@rm -f lib/help/GDEHELP
2335	@rm -f $(LINKSTAMP) lib/inputMasks/format.readme
2336
2337	redo_links: clean_links
2338	$(MAKE) links_no_checks
2339
2340	#********************************************************************************
2341
2342	header_libs:
2343	@(( \
2344	echo "$(SEP) Make HEADERLIBS"; \
2345	$(MAKE) -C HEADERLIBS all && \
2346	echo "$(SEP) Make HEADERLIBS [done]"; \
2347	) > HEADERLIBS.log 2>&1 && (cat HEADERLIBS.log;rm HEADERLIBS.log)) \|\| (cat HEADERLIBS.log;rm HEADERLIBS.log;false)
2348
2349	#********************************************************************************
2350
2351	gde: GDE/GDE.dummy
2352	GDE: gde
2353	agde: ARB_GDE/ARB_GDE.dummy
2354	tools: TOOLS/TOOLS.dummy
2355	convert: $(CONVERT_ALN)
2356	readseq: READSEQ/READSEQ.dummy
2357
2358	#***************************************************************************************
2359	# Some user commands
2360	#***************************************************************************************
2361
2362	menus: binlink links
2363	@(( \
2364	echo "$(SEP) Make GDEHELP"; \
2365	$(MAKE) -C GDEHELP -r all && \
2366	echo "$(SEP) Make GDEHELP [done]"; \
2367	) > GDEHELP.log 2>&1 && (cat GDEHELP.log;rm GDEHELP.log)) \|\| (cat GDEHELP.log;rm GDEHELP.log;false)
2368
2369	ifeq ($(DEBUG),1)
2370	BIN_TARGET=develall
2371	else
2372	BIN_TARGET=all
2373	endif
2374
2375
2376	binlink:
2377	$(MAKE) -C bin $(BIN_TARGET)
2378
2379	check_bin_dep: binlink
2380	SOURCE_TOOLS/check_bin_dependencies.pl
2381
2382	fig_cure:
2383	SOURCE_TOOLS/sortfig.pl doit
2384
2385	preplib:
2386	(cd lib;$(MAKE) all)
2387
2388	# --------------------------------------------------------------------------------
2389	# This section is quite tricky:
2390	#
2391	# make 'perl' is a BIG target, so when it has to be made, it has to be started
2392	# as early as possible to reduce overall compile time. Since 'make' does not
2393	# provide any priorities, i force it to build all 'perl'-prerequisites early, by
2394	# adding artificial dependencies to these prerequisites
2395	#
2396	# That behavior is likely to be system-dependent.
2397	# My goal was only to make it work on my current development system,
2398	# where this saves about 20% of overall build time.
2399
2400	ifeq ($(WITHPERL),1)
2401	links_non_perl: PERLTOOLS/PERLTOOLS.dummy
2402	perltools: links_non_perl
2403	perl: realperl
2404	else
2405	links_non_perl: links
2406	perl: links
2407	$(MAKE) "WITHPERL=1" perl
2408	endif
2409
2410	# ---------------------------------------- perl
2411
2412	realperl: perltools
2413	(( \
2414	echo "$(SEP) Make PERL2ARB" ; \
2415	$(TIME) $(MAKE) -C PERL2ARB -r -f Makefile.main \
2416	"AUTODEPENDS=1" \
2417	"dflags=$(dflags)" \
2418	"cflags4perl=$(cflags) $(cxxflags) $(dflags)" \
2419	"lflags4perl=$(lflags4perl)" \
2420	"COMPILER_VERSION=$(COMPILER_VERSION)" \
2421	all && \
2422	$(MAKE) -C PERL_SCRIPTS/test test && \
2423	echo "$(SEP) Make PERL2ARB [done]" ; \
2424	) > PERL2ARB.log 2>&1 && (cat PERL2ARB.log;rm PERL2ARB.log)) \|\| (cat PERL2ARB.log;rm PERL2ARB.log;false)
2425
2426	perl_clean:
2427	@$(MAKE) -C PERL2ARB -r -f Makefile.main \
2428	"AUTODEPENDS=0" \
2429	clean
2430
2431	PERL2ARB/PERL2ARB.clean:
2432	$(MAKE) perl_clean
2433	$(MAKE) -C PERL_SCRIPTS/test clean
2434
2435	# ---------------------------------------- bindings to script languages
2436
2437	bindings: lib/libCORE.so lib/libARBDB.so
2438	$(MAKE) -C BINDINGS all ARBDEPENDS="$(^:%=../%)" DFLAGS="$(dflags)"
2439
2440	bindings_clean:
2441	$(MAKE) -C BINDINGS clean
2442
2443	# ---------------------------------------- check resources
2444
2445	check_res:
2446	$(ARBHOME)/SOURCE_TOOLS/check_resources.pl
2447
2448	# ---------------------------------------- cleaning
2449
2450	rmbak:
2451	@echo "[cleanup backup/core files]"
2452	@find . \( -name '*%' \
2453	-o -name '*.bak' \
2454	-o -name '*~' \) \
2455	-o $ -name 'core' -a \! -type d $ \
2456	-exec rm -v {} \; \|\| \
2457	echo "Warning: target 'rmbak' reported problems when removing misc. backup files (ignored)"
2458	@echo "[cleanup done]"
2459
2460	bin_reinit:
2461	$(MAKE) bin/bin.clean
2462	$(MAKE) -C "bin" all
2463
2464	clean_directories:
2465	-rm -rf \
2466	$(ARBHOME)/PROBE_SET/bin \
2467	$(ARBHOME)/INCLUDE \
2468
2469	libclean:
2470	-find $(ARBHOME) -type f $ -name '*.a' ! -type l $ -exec rm -f {} \;
2471	-find $(ARBHOME) -type f $ -name 'lib*.so' ! -type l $ -exec rm -f {} \;
2472
2473	objclean:
2474	-find $(ARBHOME) -type f $ -name '*.o' ! -type l $ -exec rm -f {} \;
2475
2476	# bin.clean and HELP_SOURCE.clean interfere
2477	clean3:
2478	$(MAKE) bin/bin.clean
2479	$(MAKE) HELP_SOURCE/HELP_SOURCE.clean
2480
2481
2482	# delete all binaries (similar to 'cleanlinked')
2483	cleanRelinkable: libclean UNIT_TESTER/UNIT_TESTER.clean
2484	$(MAKE) -C bin cleanbinariesRelinkable
2485	$(MAKE) -C PROBE_SET cleanLinked
2486
2487
2488	clean2: $(SUBDIRS:.sub=.clean) \
2489	clean3 \
2490	rmbak \
2491	libclean \
2492	objclean \
2493	lib/lib.clean \
2494	GDEHELP/GDEHELP.clean \
2495	HEADERLIBS/HEADERLIBS.clean \
2496	SOURCE_TOOLS/SOURCE_TOOLS.clean \
2497	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.clean \
2498	UNIT_TESTER/UNIT_TESTER.clean \
2499	TEMPLATES/TEMPLATES.clean \
2500	perl_clean \
2501
2502	rm -f .last_gcc .last_compiler config.makefile.bak
2503	$(MAKE) clean_directories
2504
2505	# links are needed for cleanup
2506	clean: redo_links motif_xpm_hack_clean
2507	$(MAKE) clean2
2508	$(MAKE) clean_cov_all clean_links
2509
2510	silent_clean:
2511	$(MAKE) clean >/dev/null
2512
2513	# 'relocated' is about 50% faster than 'rebuild'
2514	reloc_clean: links
2515	@echo "---------------------------------------- Relocation cleanup"
2516	$(MAKE) \
2517	perl_clean \
2518	GDEHELP/GDEHELP.clean \
2519	HELP_SOURCE/genhelp/genhelp.clean \
2520	bin/bin.clean \
2521	libclean \
2522	objclean
2523
2524	relocated: links
2525	$(MAKE) reloc_clean
2526	@echo "---------------------------------------- and remake"
2527	$(MAKE) build
2528
2529	# -----------------------------------
2530	# some stress tests
2531	# (helpful to reveal race conditions with -j)
2532
2533	rebuild4ever: rebuild
2534	$(MAKE) rebuild4ever
2535
2536	build4ever: build
2537	$(MAKE) build4ever
2538
2539	clean4ever: clean
2540	$(MAKE) clean4ever
2541
2542	test4ever: ut
2543	$(MAKE) test4ever
2544
2545	perl4ever: clean
2546	$(MAKE) links
2547	$(MAKE) perl
2548	$(MAKE) perl4ever
2549
2550	help4ever: clean
2551	$(MAKE) help
2552	$(MAKE) help4ever
2553
2554	# -----------------------------------
2555
2556	cleanlinked: bin/bin.clean libclean
2557
2558	relink: cleanlinked
2559	$(MAKE) all
2560
2561	# --------------------------------------------------------------------------------
2562	# source related targets
2563
2564	CLOC=cloc
2565	CLOCFLAGS=--no3 --quiet --progress-rate=0
2566	CLOCARB=--exclude-dir=GDE .
2567	CLOCEXT=GDE
2568	CLOCCODE=--force-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.code.def
2569	CLOCREST=--force-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.rest.def
2570	CLOCFILT=tail --lines=+4
2571
2572	cloc:
2573	@echo 'Arb code:'
2574	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCARB) \| $(CLOCFILT)
2575	@echo 'Arb rest:'
2576	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCARB) \| $(CLOCFILT)
2577	@echo 'External code:'
2578	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCEXT) \| $(CLOCFILT)
2579	@echo 'External rest:'
2580	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCEXT) \| $(CLOCFILT)
2581
2582
2583	# patch generation
2584	patch:
2585	SOURCE_TOOLS/arb_create_patch.sh arbPatch --svn
2586
2587	# source tarball generation
2588	save: sourcetarfile
2589
2590	sourcetarfile: rmbak
2591	util/arb_save
2592
2593	# test early whether save will work
2594	savetest:
2595	@util/arb_srclst.pl >/dev/null
2596
2597	testsave: savetest
2598
2599	save2: rmbak
2600	util/arb_save ignore
2601
2602	save_test: rmbak
2603	@echo "Testing source list.."
2604	@util/arb_srclst.pl > /dev/null
2605
2606	save_test_no_error:
2607	@-$(MAKE) save_test
2608
2609	# --------------------------------------------------------------------------------
2610	# version management
2611
2612	inc_candi:
2613	touch SOURCE_TOOLS/inc_candi.stamp
2614	$(MAKE) do_version_update
2615
2616	inc_patch:
2617	touch SOURCE_TOOLS/inc_patch.stamp
2618	$(MAKE) do_version_update
2619
2620	inc_minor:
2621	touch SOURCE_TOOLS/inc_minor.stamp
2622	$(MAKE) do_version_update
2623
2624	inc_major:
2625	touch SOURCE_TOOLS/inc_major.stamp
2626	$(MAKE) do_version_update
2627
2628	do_version_update:
2629	@echo Incrementing version information
2630	$(MAKE) savetest
2631	$(MAKE) genheaders # auto upgrades version early
2632
2633	show_version:
2634	$(MAKE) genheaders # updates version info
2635	@echo "$(SEP) ARB version info"
2636	@grep ARB_VERSION TEMPLATES/arb_build.h
2637	@echo "$(SEP)"
2638
2639	# --------------------------------------------------------------------------------
2640	# special cleanups
2641
2642	clean_opengl_changed: RNA3D/RNA3D.clean EDIT4/EDIT4.clean WINDOW/WINDOW.clean GL/GL.clean
2643
2644	# --------------------------------------------------------------------------------
2645
2646	arbapplications: nt pa e4 wetc pt na nal di ph ds wetc cma
2647
2648	arb_external: convert tools gde readseq tg pst
2649
2650	arb_no_perl: arbapplications help arb_external
2651
2652	arb: motif_xpm_hack
2653	$(MAKE) "WITHPERL=1" perl arb_no_perl
2654
2655	motif_xpm_hack:
2656	$(MAKE) -r -C "lib/motifHack" all
2657
2658	motif_xpm_hack_clean:
2659	$(MAKE) -r -C "lib/motifHack" clean
2660
2661	# --------------------------------------------------------------------------------
2662	# special targets for SOURCE_TOOLS/remake_after_change.pl
2663
2664	rac_arb_dist: di
2665	rac_arb_edit4: e4
2666	rac_arb_ntree: nt
2667	rac_arb_pars: pa
2668	rac_arb_phylo: ph
2669	rac_arb_wetc: wetc
2670	rac_arb_naligner: nal
2671	rac_arb_pt_server: pt
2672	rac_arb_db_server: ds
2673	rac_arb_name_server: na
2674	rac_arb_convert_aln: convert
2675	rac_arb_treegen: tg
2676	rac_arb_rnacma: cma
2677	rac_arb_help2xml: help
2678
2679	rac_arb_a2ps: tools
2680	rac_arb_consensus_tree: tools
2681	rac_arb_dnarates: tools
2682	rac_arb_export_rates: tools
2683	rac_arb_export_tree: tools
2684	rac_arb_gene_probe: tools
2685	rac_arb_message: tools
2686	rac_arb_primer: tools
2687	rac_arb_probe: tools
2688	rac_arb_read_tree: tools
2689
2690	# --------------------------------------------------------------------------------
2691	# unit testing
2692	# @@@ work in progress
2693	#
2694	# goal is to automatically test all libraries/executables using TESTED_UNITS_AUTO
2695	# currently not all test executables link w/o error.
2696	# therefor units are organized in three sets:
2697	#
2698	# TESTED_UNITS = testable and contain tests
2699	# UNTESTED_UNITS = testable, but no tests written yet
2700	# UNTESTABLE_UNITS = not testable
2701
2702	# always define OPENGL units manually:
2703	OPENGL_TESTS :=
2704	ifeq ($(OPENGL),1)
2705	# this section defines RNA3D.test
2706	OPENGL_TESTS += \
2707	$(subst .a,.test,$(RNA3D_LIB)) \
2708	GL/glAW/libglAW.test \
2709	GL/glpng/libglpng_arb.test \
2710
2711	endif
2712
2713	UNITS_NOT_AUTODETECTED = \
2714	HELP_SOURCE/HELP_SOURCE.tooltests
2715
2716	TESTED_UNITS_AUTO = \
2717	$(OPENGL_TESTS) \
2718	$(TL_ARCHIVES:.a=.test) \
2719	$(TL_SHARED_ARCHIVES:.so=.test) \
2720	$(CL_ARCHIVES:.a=.test) \
2721	$(TL_TOOLS_COLLECTIONS:.toolColl=.tooltests) \
2722	$(UNITS_NOT_AUTODETECTED) \
2723
2724	UNTESTED_UNITS = \
2725	$(OPENGL_TESTS) \
2726	EISPACK/EISPACK.test \
2727	GENOM/GENOM.test \
2728	ISLAND_HOPPING/ISLAND_HOPPING.test \
2729	NALIGNER/NALIGNER.test \
2730	NAMES/NAMES.test \
2731	PHYLO/PHYLO.test \
2732	PRIMER_DESIGN/PRIMER_DESIGN.test \
2733	READSEQ/READSEQ.tooltests \
2734	SECEDIT/SECEDIT.test \
2735	SEQ_QUALITY/SEQ_QUALITY.test \
2736	SERVERCNTRL/SERVERCNTRL.test \
2737	SL/ALIVIEW/ALIVIEW.test \
2738	SL/AP_TREE/AP_TREE.test \
2739	SL/ARB_SPEC/ARB_SPEC.test \
2740	SL/ARB_TREE/ARB_TREE.test \
2741	SL/AW_HELIX/AW_HELIX.test \
2742	SL/AW_NAME/AW_NAME.test \
2743	SL/CANVAS/CANVAS.test \
2744	SL/DB_SCANNER/DB_SCANNER.test \
2745	SL/DB_UI/DB_UI.test \
2746	SL/GUI_ALIVIEW/GUI_ALIVIEW.test \
2747	SL/GUI_TK/GUI_TK.test \
2748	SL/HELIX/HELIX.test \
2749	SL/MASKS/MASKS.test \
2750	SL/MAPKEY/MAPKEY.test \
2751	SL/QUERY/QUERY.test \
2752	SL/REFENTRIES/REFENTRIES.test \
2753	SL/SEQUENCE/SEQUENCE.test \
2754	SL/TREE_ADMIN/TREE_ADMIN.test \
2755	SL/TREE_WRITE/TREE_WRITE.test \
2756	SL/XFERGUI/XFERGUI.test \
2757	STAT/STAT.test \
2758	TREEGEN/TREEGEN.test \
2759	WETC/WETC.test \
2760	XML/XML.test \
2761
2762	# untestable units
2763
2764	UNTESTABLE_UNITS = \
2765	AISC/AISC.test \
2766	NAMES_COM/server.test \
2767	PROBE_COM/server.test \
2768
2769	# --------------------
2770	# put all units containing tests into the following 4 sections (see also TESTED_UNITS below)
2771
2772	# recent development
2773	UNITS_TESTED_FIRST = \
2774	SL/SPECSEL/SPECSEL.test \
2775	SL/MATRIX/MATRIX.test \
2776	AWTI/AWTI.test \
2777	SL/FILTSEQEXP/FILTSEQEXP.test \
2778	SL/GROUP_SEARCH/GROUP_SEARCH.test \
2779	SL/PVP/PVP.test \
2780	SL/SAICALC/SAICALC.test \
2781	SL/TRANSLATE/TRANSLATE.test \
2782	SL/XFERSET/XFERSET.test \
2783
2784	# start units with long duration early
2785	UNITS_RUNNING_LONG = \
2786	ARBDB/libARBDB.test \
2787	AWTC/AWTC.test \
2788	TOOLS/TOOLS.tooltests \
2789
2790	# plain test-libaries that are not linked anywhere
2791	TEST_SANDBOXES = \
2792	SL/CB/CB.test \
2793	SL/HEADERTESTS/HEADERTESTS.test \
2794
2795	UNITS_TESTED = \
2796	AISC_MKPTPS/AISC_MKPTPS.tooltests \
2797	ARB_GDE/ARB_GDE.test \
2798	CONSENSUS_TREE/CONSENSUS_TREE.test \
2799	CONVERTALN/CONVERTALN.test \
2800	CORE/libCORE.test \
2801	DBSERVER/DBSERVER.test \
2802	DIST/DIST.test \
2803	EDIT4/EDIT4.test \
2804	GENOM_IMPORT/GENOM_IMPORT.test \
2805	HELP_SOURCE/HELP_SOURCE.tooltests \
2806	MERGE/MERGE.test \
2807	MULTI_PROBE/MULTI_PROBE.test \
2808	NTREE/NTREE.test \
2809	PARSIMONY/PARSIMONY.test \
2810	PERLTOOLS/PERLTOOLS.tooltests \
2811	PROBE/PROBE.test \
2812	PROBE_DESIGN/PROBE_DESIGN.test \
2813	PROBE_SET/PROBE_SET.tooltests \
2814	RNACMA/RNACMA.test \
2815	SL/ALILINK/ALILINK.test \
2816	SL/APP/APP.test \
2817	SL/CONSENSUS/CONSENSUS.test \
2818	SL/DB_QUERY/DB_QUERY.test \
2819	SL/FAST_ALIGNER/FAST_ALIGNER.test \
2820	SL/FILTER/FILTER.test \
2821	SL/INSDEL/INSDEL.test \
2822	SL/ITEM_SHADER/ITEM_SHADER.test \
2823	SL/ITEMS/ITEMS.test \
2824	SL/LOCATION/LOCATION.test \
2825	SL/MACROS/MACROS.test \
2826	SL/NDS/NDS.test \
2827	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.test \
2828	SL/PRONUC/PRONUC.test \
2829	SL/PTCLEAN/PTCLEAN.test \
2830	SL/REGEXPR/REGEXPR.test \
2831	SL/SEQIO/SEQIO.test \
2832	SL/TREE_READ/TREE_READ.test \
2833	SL/TREEDISP/TREEDISP.test \
2834	WINDOW/libWINDOW.test \
2835
2836	TESTED_UNITS = \
2837	$(UNITS_TESTED_FIRST) \
2838	$(UNITS_RUNNING_LONG) \
2839	$(TEST_SANDBOXES) \
2840	$(UNITS_TESTED) \
2841
2842	# ----------------------------------------
2843
2844	ifeq ($(DEVELOPER),RALF)
2845
2846	DEFINED_TEST_UNITS = \
2847	$(TESTED_UNITS) \
2848	$(UNTESTED_UNITS) \
2849	$(UNTESTABLE_UNITS) \
2850
2851	list_undefined_units:
2852	@UNIT_TESTER/list_undefined_units.pl $(DEFINED_TEST_UNITS) -- $(TESTED_UNITS_AUTO)
2853
2854	else
2855
2856	list_undefined_units:
2857
2858	endif
2859
2860	# ----------------------------------------
2861
2862	TEST_LOG_DIR = UNIT_TESTER/logs
2863	TEST_RUN_SUITE=$(MAKE) $(NODIR) -C UNIT_TESTER -f Makefile.suite -r
2864	# -> UNIT_TESTER/Makefile.suite
2865	TEST_MAKE_FLAGS=
2866	TEST_POST_CLEAN=
2867	ifeq ($(COVERAGE),1)
2868	TEST_POST_CLEAN=$(MAKE) clean_cov
2869	TEST_MAKE_FLAGS+=-j1
2870	endif
2871
2872
2873	%.test:
2874	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
2875	( \
2876	echo "take[1]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
2877	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
2878	"UNITDIR=$(@D)" \
2879	"UNITLIBNAME=$(@F:.test=)" \
2880	"COVERAGE=$(COVERAGE)" \
2881	"ARB_PID=$(ARB_PID)_$(@F)" \
2882	"DEVELOPER=$(DEVELOPER)" \
2883	runtest; \
2884	echo "take[1]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"; \
2885	$(TEST_POST_CLEAN) \
2886	) >$(TEST_LOG_DIR)/$(@F).log 2>&1; \
2887	UNIT_TESTER/log_result.pl $(TEST_LOG_DIR)/$(@F).log )
2888
2889	%.notest:
2890	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
2891	( \
2892	echo "take[4]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
2893	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
2894	"UNITDIR=$(@D)" \
2895	"UNITLIBNAME=$(@F:.notest=)" \
2896	"COVERAGE=0" \
2897	"ARB_PID=$(ARB_PID)_$(@F)" \
2898	"DEVELOPER=$(DEVELOPER)" \
2899	check_no_test; \
2900	echo "take[4]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'" \
2901	) >$(TEST_LOG_DIR)/$(@F).log 2>&1 )
2902
2903
2904	# tool test aliases (used to test one or multiple executable(s) in a single subdir):
2905	%.tooltests:
2906	$(error please define an explicit tooltest alias for $@)
2907
2908	AISC_MKPTPS/AISC_MKPTPS.tooltests : AISC_MKPTPS/mkptypes.test
2909	@echo "aliasing $@ -> $^"
2910	PERLTOOLS/PERLTOOLS.tooltests : PERLTOOLS/arb_proto_2_xsub.test
2911	@echo "aliasing $@ -> $^"
2912	PROBE_SET/PROBE_SET.tooltests : PROBE_SET/fb_test.test
2913	@echo "aliasing $@ -> $^"
2914	HELP_SOURCE/HELP_SOURCE.tooltests : HELP_SOURCE/arb_help2xml.test
2915	@echo "aliasing $@ -> $^"
2916	TOOLS/TOOLS.tooltests : TOOLS/arb_consensus_tree.test TOOLS/arb_probe.test TOOLS/arb_test.test
2917	@echo "aliasing $@ -> $^"
2918
2919	# aliases for tools w/o tests:
2920	READSEQ/READSEQ.tooltests:
2921	@echo "Note: no tests for $@"
2922
2923
2924	test_base: $(UNIT_TESTER_LIB:.a=.dummy) $(subst .test,.dummy,$(TEST_SANDBOXES))
2925
2926	clean_cov:
2927	find . $ -name ".gcda" -o -name ".gcov" -o -name "*.cov" $ -exec rm {} \;
2928
2929	clean_cov_all: clean_cov
2930	find . $ -name "*.gcno" $ -exec rm {} \;
2931
2932	cleanup_faked_arbpids:
2933	@rm ~/.arb_tmp/tmp/arb_pids_${USER}_${ARB_PID}_* \|\| true
2934
2935	cleanup_faked_arbpids_and_fail: cleanup_faked_arbpids
2936	@false
2937
2938	NOTESTS_IN_UNTESTED = $(subst .test,.notest,$(UNTESTED_UNITS))
2939
2940	run_tests_faked_arbpid:
2941	+@$(TEST_RUN_SUITE) init
2942	@echo "take[2]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2943	@$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(TESTED_UNITS) $(NOTESTS_IN_UNTESTED) \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2944	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2945	@echo "take[2]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2946	@$(MAKE) clean_cov >/dev/null
2947	@$(MAKE) cleanup_faked_arbpids
2948
2949	# @@@ instead of only running UNIT, this should as well run all tests this unit depends on? according to 'needs_libs'
2950	# @@@ 'run_tests_faked_arbpid' does not work for UNIT=ARBDB/libARBDB or UNIT=PARS/PARS -> could be solved via extra suffix, e.g. ARBDB/libARBDB.unit
2951
2952	run_onetest_faked_arbpid:
2953	+@$(TEST_RUN_SUITE) init
2954	@echo "take[3]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2955	@test -n "$(UNIT)" \|\| (echo "Error: UNIT has to be defined for target 'run_onetest_faked_arbpid'!"; false)
2956	$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(UNIT).test \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2957	@echo "take[3]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2958	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2959	@$(MAKE) clean_cov >/dev/null
2960	@$(MAKE) cleanup_faked_arbpids
2961
2962	run_tests: test_base clean_cov
2963	$(MAKE) "ARB_PID=UT_$$$$" run_tests_faked_arbpid list_undefined_units
2964
2965	run_oneunitstests: test_base
2966	$(MAKE) "ARB_PID=UT_$$$$" run_onetest_faked_arbpid
2967
2968
2969	ut:
2970	ifeq ($(UNIT_TESTS),1)
2971	@echo $(MAKE) run_tests
2972	@$(MAKE) run_tests
2973	else
2974	@echo "Not compiled with unit tests"
2975	endif
2976
2977
2978	aut:
2979	+@$(TEST_RUN_SUITE) unskip
2980	$(MAKE) ut
2981
2982	# --------------------------------------------------------------------------------
2983
2984	TIMELOG=$(ARBHOME)/arb_time.log
2985	TIMEARGS=--append --output=$(TIMELOG) --format=" * %E(%S+%U) %P [%C]"
2986	TIMECMD=$(TIME) $(TIMEARGS)
2987
2988	time_one:
2989	ifeq ($(ONE_TIMED_TARGET),)
2990	@echo "Error: You have to pass ONE_TIMED_TARGET to $@"
2991	false
2992	else
2993	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET)"
2994	@$(TIMECMD) $(MAKE) $(ONE_TIMED_TARGET)
2995	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET) [done]"
2996	endif
2997
2998	timed_target:
2999	ifeq ($(TIMED_TARGET),)
3000	@echo "Error: You have to pass TIMED_TARGET to $@"
3001	false
3002	else
3003	@echo "Build time:" > $(TIMELOG)
3004	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
3005	@cat $(TIMELOG)
3006	@rm $(TIMELOG)
3007	endif
3008
3009	timed_target_tested:
3010	ifeq ($(TIMED_TARGET),)
3011	@echo "Error: You have to pass TIMED_TARGET to $@"
3012	false
3013	else
3014	@echo "Build time:" > $(TIMELOG)
3015	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
3016	$(MAKE) "ONE_TIMED_TARGET=ut" time_one
3017	@cat $(TIMELOG)
3018	@rm $(TIMELOG)
3019	endif
3020
3021	clean_timed_target:
3022	ifeq ($(TIMED_TARGET),)
3023	@echo "Error: You have to pass TIMED_TARGET to $@"
3024	false
3025	else
3026	@echo "Build time:" > $(TIMELOG)
3027	$(MAKE) "ONE_TIMED_TARGET=clean" time_one
3028	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
3029	@cat $(TIMELOG)
3030	@rm $(TIMELOG)
3031	endif
3032
3033	# --------------------------------------------------------------------------------
3034
3035	CHECKOUT_MODIFIED=0# set to 1 to temporarily skip test for modifications (do not check in if set to 1)
3036
3037	check_svn_does_not_contain_generated:
3038	ifeq ($(CHECKOUT_MODIFIED),0)
3039	@echo "Testing that build does not modify files in SVN"
3040	@test 0 = `svn status \| wc -l` \|\| ( \
3041	echo "The checkout is not/no longer clean:"; \
3042	svn status; \
3043	echo "- if this fails instantly, your checkout is not clean"; \
3044	echo "- if this fails after other targets, these targets modify checked in data"; \
3045	echo " (a common cause may be that depends are not up to date)"; \
3046	false)
3047	else
3048	grep -Hn 'CHECKOUT_MODIFIED' Makefile
3049	endif
3050
3051	check_svn_ignores_generated:
3052	@test 0 = `svn status \| grep '^\?' \| wc -l` \|\| ( \
3053	echo "There are svn-unignored files:"; \
3054	svn status \| grep '^\?'; \
3055	echo "(all generated files should be svn-ignored)"; \
3056	false)
3057
3058	check_svn_state: check_svn_does_not_contain_generated
3059	$(MAKE) check_svn_ignores_generated
3060	$(MAKE) savetest
3061
3062	things_that_always_should_work: depends proto
3063
3064	post_commit_check:
3065	@echo "---------------------------------------- [Initial]"
3066	$(MAKE) check_svn_state
3067
3068	$(MAKE) clean
3069	@echo "---------------------------------------- [After 'make clean']"
3070	$(MAKE) check_svn_state
3071
3072	$(MAKE) things_that_always_should_work
3073	@echo "---------------------------------------- [After 'make things_that_always_should_work']"
3074	$(MAKE) check_svn_state
3075
3076	$(MAKE) all
3077	@echo "---------------------------------------- [After 'make all']"
3078	$(MAKE) check_svn_state
3079
3080	$(MAKE) things_that_always_should_work
3081	@echo "---------------------------------------- [Final]"
3082	$(MAKE) check_svn_state
3083
3084	# --------------------------------------------------------------------------------
3085	# sanitize arb_ntree; also works for clients (arb_edit4, ...) started from there.
3086
3087	sanitize: all
3088	( \
3089	export "LSAN_OPTIONS=max_leaks=30:suppressions=$(ARBHOME)/SOURCE_TOOLS/arb.leaksan.supp"; \
3090	echo "sake[1]: Entering directory \`$(ARBHOME)'"; \
3091	$(ARBHOME)/bin/arb_ntree --execute _logged ~/data/test.arb 2>&1 ; \
3092	echo "sake[1]: Leaving directory \`$(ARBHOME)'" \
3093	) \| $(ARBHOME)/SOURCE_TOOLS/asan2msg.pl
3094
3095	# --------------------------------------------------------------------------------
3096	# build and test one unit:
3097
3098	build_oneunit:
3099	$(MAKE) "WITHPERL=1" $(UNIT).dummy
3100
3101	oneunit:
3102	ifndef UNIT
3103	@echo "Please define UNIT, e.g. using"
3104	@echo " make \"UNIT=ARBDB/libARBDB\" oneunit"
3105	@echo " make \"UNIT=SL/TREEDISP/TREEDISP\" oneunit"
3106	@echo "(Note: 1st is a shared library, 2nd isn't)"
3107	false
3108	else
3109	@echo "Build time" > $(TIMELOG)
3110	@echo "$(SEP) $(MAKE) build_oneunit"
3111	@$(TIMECMD) $(MAKE) build_oneunit
3112	ifeq ($(UNIT_TESTS),1)
3113	@echo "$(SEP) $(MAKE) run_oneunitstests"
3114	@$(TIMECMD) $(MAKE) run_oneunitstests
3115	endif
3116	@cat $(TIMELOG)
3117	@rm $(TIMELOG)
3118	endif
3119
3120	# --------------------------------------------------------------------------------
3121	# Main targets:
3122
3123	tarfile: rebuild
3124	$(MAKE) prepare_libdir
3125	util/arb_compress
3126
3127	tarfile_quick: all
3128	$(MAKE) prepare_libdir
3129	util/arb_compress
3130
3131	# -----------------------------------
3132
3133	build: arb
3134	$(MAKE) check_bin_dep preplib compile_compatibility fig_cure
3135
3136	all:
3137	@echo "Build time" > $(TIMELOG)
3138	# $(MAKE) clean_checked_vect # uncomment to rebuild sources where expected vectorization gets tested
3139	@echo "$(SEP) $(MAKE) all"
3140	@$(TIMECMD) $(MAKE) build
3141	@echo $(SEP)
3142	@echo "made 'all' with success."
3143	@echo "to start arb enter 'arb'"
3144	ifeq ($(UNIT_TESTS),1)
3145	@echo "$(SEP) $(MAKE) run_tests"
3146	@$(TIMECMD) $(MAKE) run_tests
3147	endif
3148	@echo "$(SEP) $(MAKE) all [done]"
3149	ifeq ($(DEBUG),1)
3150	@$(MAKE) save_test_no_error >/dev/null # just show hints
3151	endif
3152	@cat $(TIMELOG)
3153	@rm $(TIMELOG)
3154
3155	rebuild: clean
3156	$(MAKE) all
3157
3158	# --------------------------------------------------------------------------------
3159	# special targets showing obvious error at bottom
3160	# (intended to be used from automated builds)
3161
3162	BUILD_LOG=build.log
3163	SHELL=bash
3164	REDIRECT_KEEP_EXITCODE = tee $(BUILD_LOG) ; exit "$${PIPESTATUS[0]}"
3165	EXTRACT_ERROR_SUMMARY = (./SOURCE_TOOLS/short_error_summary.pl $(BUILD_LOG); false)
3166
3167	REEXTRACT:
3168	@echo "Note: Re-extracting errors from $(BUILD_LOG):"
3169	@$(EXTRACT_ERROR_SUMMARY)
3170
3171	ALL:
3172	@(($(MAKE) all 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
3173
3174	REBUILD:
3175	@(($(MAKE) rebuild 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
3176
3177	TARFILE:
3178	@(($(MAKE) tarfile 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
3179
3180	TARFILE_QUICK:
3181	@(($(MAKE) tarfile_quick 2>&1) \| $(REDIRECT_KEEP_EXITCODE)) \|\| $(EXTRACT_ERROR_SUMMARY)
3182

Note: See TracBrowser for help on using the repository browser.

Context Navigation

source: branches/gcc/Makefile

Download in other formats: