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Last change on this file was 10105, checked in by westram, 11 years ago
tested and enabled gcc 4.8.0 and 4.8.1
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 58.9 KB

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1	# =============================================================== #
2	# #
3	# File : Makefile #
4	# #
5	# Institute of Microbiology (Technical University Munich) #
6	# http://www.arb-home.de/ #
7	# #
8	# =============================================================== #
9
10	# -----------------------------------------------------
11	# The ARB Makefile is aware of the following defines:
12	#
13	# BUILDHOST_64=0/1 1=>compile on 64 bit platform (defaults to ARB_64)
14	# DEVELOPER=name special compilation (values: ANY,RELEASE,your name)
15	# OPENGL=0/1 whether OPENGL is available
16	#
17	# -----------------------------------------------------
18	# ARB Makefile and ARB source code are aware of the following defines:
19	#
20	# $(MACH) name of the machine (LINUX or DARWIN; see config.makefile)
21	# DEBUG compiles the DEBUG sections
22	# DEBUG_GRAPHICS all X-graphics are flushed immediately (for debugging)
23	# ARB_64=0/1 1=>compile 64 bit version
24	# UNIT_TESTS=0/1 1=>compile in unit tests and call them after build
25	# COVERAGE=0/1/2 compile in gcov support (useful together with UNIT_TESTS=1)
26	# 0=no, 1+2=compile in, 1=show
27	#
28	# -----------------------------------------------------
29	# The ARB source code is aware of the following defines:
30	#
31	# NDEBUG doesn't compile the DEBUG sections
32	# DEVEL_$(DEVELOPER) developer-dependent flag (enables you to have private sections in code)
33	# DEVELOPER='ANY' (default setting) will be ignored
34	# configurable in config.makefile
35	#
36	# -----------------------------------------------------
37	# Read configuration
38	include config.makefile
39
40	ifeq ($(LD_LIBRARY_PATH),'')
41	LD_LIBRARY_PATH:=${ARBHOME}/lib
42	endif
43
44	FORCEMASK = umask 002
45	NODIR=--no-print-directory
46
47	SED:=$(ARBHOME)/SH/arb_sed
48	READLINK:=$(ARBHOME)/SH/arb_readlink
49
50	# ---------------------- [basic compiler setting]
51
52	GCC ?= $(CC)
53	GPP ?= $(CXX)
54
55	# ---------------------- compiler version detection
56
57	# supported compiler versions:
58
59	ALLOWED_GCC_4xx_VERSIONS=\
60	4.2.1 \
61	4.3.1 4.3.2 4.3.3 4.3.4 \
62	4.4.1 4.4.3 4.4.5 4.4.6 4.4.7 \
63	4.5.2 \
64	4.6.1 4.6.2 4.6.3 \
65	4.7.1 4.7.2 4.7.3 \
66	4.8.0 4.8.1
67
68	ALLOWED_GCC_VERSIONS=$(ALLOWED_GCC_4xx_VERSIONS)
69
70	GCC_VERSION_FOUND=$(shell SOURCE_TOOLS/arb_gcc_version.pl)
71	GCC_VERSION_ALLOWED=$(strip $(subst ___,,$(foreach version,$(ALLOWED_GCC_VERSIONS),$(findstring ___$(version)___,___$(GCC_VERSION_FOUND)___))))
72
73	#---------------------- split gcc version
74
75	SPLITTED_VERSION:=$(subst ., ,$(GCC_VERSION_FOUND))
76
77	USE_GCC_MAJOR:=$(word 1,$(SPLITTED_VERSION))
78	USE_GCC_MINOR:=$(word 2,$(SPLITTED_VERSION))
79	USE_GCC_PATCHLEVEL:=$(word 3,$(SPLITTED_VERSION))
80
81	USE_GCC_452_OR_HIGHER:=
82	USE_GCC_47_OR_HIGHER:=
83	USE_GCC_48_OR_HIGHER:=
84
85	ifeq ($(USE_GCC_MAJOR),4)
86	ifeq ($(USE_GCC_MINOR),5)
87	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),23456789)','')
88	USE_GCC_452_OR_HIGHER:=yes
89	endif
90	else
91	ifneq ('$(findstring $(USE_GCC_MINOR),6789)','')
92	USE_GCC_452_OR_HIGHER:=yes
93	ifneq ($(USE_GCC_MINOR),6)
94	USE_GCC_47_OR_HIGHER:=yes
95	ifneq ($(USE_GCC_MINOR),7)
96	USE_GCC_48_OR_HIGHER:=yes
97	endif
98	endif
99	endif
100	endif
101	else
102	USE_GCC_452_OR_HIGHER:=yes
103	USE_GCC_47_OR_HIGHER:=yes
104	USE_GCC_48_OR_HIGHER:=yes
105	endif
106
107	#---------------------- define special directories for non standard builds
108
109	ifdef DARWIN
110	OSX_FW:=/System/Library/Frameworks
111	OSX_FW_OPENGL:=$(OSX_FW)/OpenGL.framework/Versions/A/Libraries
112	OSX_FW_GLUT:=$(OSX_FW)/GLUT.framework/Versions/A/Libraries
113	OSX_FW_IMAGEIO:=$(OSX_FW)/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources
114	endif
115
116	#----------------------
117
118	ifdef DARWIN
119	LINK_STATIC=1# link static
120	else
121	LINK_STATIC=0# link dynamically
122	endif
123
124	shared_cflags :=# flags for shared lib compilation
125	lflags :=# linker flags
126	extended_warnings :=# warning flags for C and C++-compiler
127	extended_cpp_warnings :=# warning flags for C++-compiler only
128
129
130	ifeq ($(DEBUG),0)
131	dflags := -DNDEBUG# defines
132	ifdef DARWIN
133	cflags := -O3# compiler flags (C and C++)
134	else
135	cflags := -O4# compiler flags (C and C++)
136	lflags += -O99# linker flags
137	endif
138	endif
139
140	ifeq ($(DEBUG),1)
141	dflags := -DDEBUG
142
143	gdb_common := -g -g3 -ggdb -ggdb3
144
145	cflags := -O0 $(gdb_common) # (using dwarf - cant debug inlines here, incredible slow on showing variable content)
146	# cflags := -O0 $(gdb_common) -gdwarf-3 # (specify explicit dwarf format)
147	# cflags := -O0 $(gdb_common) -gstabs+ # using stabs+ (enable this for bigger debug session: debugs inlines, quick var inspect, BUT valgrind stops working :/)
148	# cflags := -O0 $(gdb_common) -gstabs # using stabs (same here IIRC)
149	# cflags := -O2 $(gdb_common) # use this for callgrind (force inlining)
150	ifndef DARWIN
151	lflags += -g
152	endif
153
154	# control how much you get spammed
155	POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl
156	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --original# dont modify compiler output
157	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --hide-Noncopyable-advices
158	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --show-useless-Weff++
159	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --no-warnings
160	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --only-first-error
161	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --no-warnings --only-first-error
162
163	# Enable extra warnings
164	extended_warnings :=
165	extended_cpp_warnings :=
166
167	# C and C++
168	extended_warnings += -Wwrite-strings -Wunused -Wno-aggregate-return -Wshadow
169
170	# C++ only
171	extended_cpp_warnings += -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute
172	extended_cpp_warnings += -Wctor-dtor-privacy# < gcc 3
173	# extended_cpp_warnings += -Wfloat-equal# gcc 3.0
174
175	# ------- above only warnings available in 3.0
176
177	ifneq ('$(GCC_VERSION_FOUND)','4.7.3') # g++ crashes on GenomeImport.cxx when -Weffc++ is active (bug reported)
178	extended_cpp_warnings += -Weffc++# gcc 3.0.1
179	endif
180	extended_cpp_warnings += -Wmissing-noreturn# gcc 3.0.2
181	# extended_cpp_warnings += -Wold-style-cast# gcc 3.0.4 (warn about 28405 old-style casts)
182	extended_cpp_warnings += -Winit-self# gcc 3.4.0
183	extended_cpp_warnings += -Wstrict-aliasing# gcc 3.4
184	extended_cpp_warnings += -Wextra# gcc 3.4.0
185	ifeq ('$(USE_GCC_452_OR_HIGHER)','yes')
186	extended_cpp_warnings += -Wlogical-op# gcc 4.5.2
187	endif
188
189	ifeq ($(DEBUG_GRAPHICS),1)
190	dflags += -DDEBUG_GRAPHICS
191	endif
192	endif
193
194	#---------------------- developer
195
196	ifneq ($(DEVELOPER),ANY) # ANY=default setting (skip all developer specific code)
197	ifdef dflags
198	dflags += -DDEVEL_$(DEVELOPER)# activate developer/release specific code
199	endif
200	endif
201
202	ifndef SHOWTODO
203	ifeq ($(DEVELOPER),RALF)
204	SHOWTODO:=1
205	else
206	SHOWTODO:=0
207	endif
208	endif
209	ifeq ($(SHOWTODO),1)
210	dflags += -DWARN_TODO# activate "TODO" warnings
211	endif
212
213	#---------------------- 32 or 64 bit
214
215	ifndef ARB_64
216	ARB_64=0#default to 32bit
217	endif
218	ifndef BUILDHOST_64
219	BUILDHOST_64:=$(ARB_64)# assume build host is same as version (see config.makefile)
220	endif
221
222	cross_cflags:=
223	cross_lflags:=
224
225	ifeq ($(ARB_64),1)
226	dflags += -DARB_64 #-fPIC
227	lflags +=
228	shared_cflags += -fPIC
229
230	ifeq ($(BUILDHOST_64),1)
231	# build 64-bit ARB version on 64-bit host
232	CROSS_LIB:=# empty = autodetect below
233	ifdef DARWIN
234	cross_cflags += -arch x86_64
235	cross_lflags += -arch x86_64
236	endif
237	else
238	# build 64-bit ARB version on 32-bit host
239	CROSS_LIB:=/lib64
240	cross_cflags += -m64
241	cross_lflags += -m64 -m elf_x86_64
242	endif
243	else
244	ifeq ($(BUILDHOST_64),1)
245	# build 32-bit ARB version on 64-bit host
246	CROSS_LIB:=# empty = autodetect below
247	cross_cflags += -m32
248	cross_lflags += -m32 -m elf_i386
249	else
250	# build 32-bit ARB version on 32-bit host
251	CROSS_LIB:=/lib
252	endif
253	endif
254
255	cflags += $(cross_cflags)
256	lflags += $(cross_lflags)
257
258	ifeq ('$(CROSS_LIB)','')
259	# autodetect libdir
260	ifeq ($(ARB_64),1)
261	CROSS_LIB:=$(shell (test -d /lib64 && echo lib64) \|\| echo lib)
262	else
263	CROSS_LIB:=$(shell (test -d /lib32 && echo lib32) \|\| echo lib)
264	endif
265	endif
266
267	#---------------------- unit tests
268
269	ifndef UNIT_TESTS
270	UNIT_TESTS=0#default is "no tests"
271	endif
272	ifeq ($(UNIT_TESTS),1)
273	dflags += -DUNIT_TESTS
274	UNIT_TESTER_LIB=UNIT_TESTER/UNIT_TESTER.a
275	else
276	UNIT_TESTER_LIB=
277	endif
278
279	#---------------------- use gcov
280
281	ifndef COVERAGE
282	COVERAGE=0#default is "no"
283	endif
284	ifneq ($(COVERAGE),0)
285	GCOVFLAGS=-ftest-coverage -fprofile-arcs
286	cflags += $(GCOVFLAGS)
287	EXECLIBS=-lgcov
288	else
289	GCOVFLAGS=
290	EXECLIBS=
291	endif
292
293	#---------------------- other flags
294
295	dflags += -D$(MACH) # define machine
296
297	ifdef DARWIN
298	shared_cflags += -fno-common
299	else
300	dflags += $(shell getconf LFS_CFLAGS)
301	endif
302
303	cflags += -pipe
304	cflags += -fmessage-length=0# don't wrap compiler output
305	cflags += -fshow-column# show columns
306	cflags += -funit-at-a-time
307	cflags += -fPIC
308	cflags += -fno-common# link all global data into one namespace
309	cflags += -fstrict-aliasing# gcc 3.4
310	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
311	cflags += -fno-diagnostics-show-caret#gcc 4.8 (4.7.?)
312	endif
313	#cflags += -save-temps# uncomment to see preprocessor output
314
315	#---------------------- X11 location
316
317	ifdef DARWIN
318	XHOME:=$(PREFIX)
319	else
320	XHOME:=/usr/X11R6
321	endif
322
323	XINCLUDES:=-I$(XHOME)/include
324	ifdef DARWIN
325	XINCLUDES += -I$(OSX_FW)/GLUT.framework/Headers -I$(OSX_FW)/OpenGL.framework/Headers -I$(OSX_SDK)/usr/include/krb5
326
327	XLIBS := -L$(XHOME)/lib -lXm -lpng -lz -lXt -lX11 -lXext -lXp -lXmu -lXi
328	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGL.dylib:$(OSX_FW_OPENGL)/libGL.dylib
329	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGLU.dylib:$(OSX_FW_OPENGL)/libGLU.dylib
330	else
331	XLIBS:=-L$(XHOME)/$(CROSS_LIB) -lXm -lXpm -lXt -lXext -lX11
332	endif
333
334	#---------------------- open GL
335
336	ifeq ($(OPENGL),1)
337	cflags += -DARB_OPENGL # activate OPENGL code
338	GL := gl # this is the name of the OPENGL base target
339	GL_LIB_SYS := -lGL -lGLU
340	GL_LIB_ARB := -L$(ARBHOME)/GL/glAW -lglAW
341
342	ifdef DEBIAN
343	GL_LIB_SYS += -lpthread
344	endif
345
346	GL_PNGLIBS_ARB := -L$(ARBHOME)/GL/glpng -lglpng_arb
347	GL_PNGLIBS_SYS := -lpng
348
349	GLEWLIB := -lGLEW -lGLw
350	ifdef DARWIN
351	GLUTLIB := -glut
352	else
353	GLUTLIB := -lglut
354	endif
355
356	GL_LIBS_SYS := $(GL_LIB_SYS) $(GL_PNGLIBS_SYS) $(GLEWLIB) $(GLUTLIB)
357	GL_LIBS_ARB := $(GL_LIB_ARB) $(GL_PNGLIBS_ARB)
358
359	RNA3D_LIB := RNA3D/RNA3D.a
360
361	else
362
363	GL_LIBS_ARB:=# no opengl -> no libs
364	GL_LIBS_SYS:=# no opengl -> no libs
365	GL:=# don't build ARB openGL libs
366
367	RNA3D_LIB :=
368
369	endif
370
371	RNA3D_LIB_4_DEPENDS := RNA3D/RNA3D.a
372
373	GL_LIBS:=$(GL_LIBS_ARB) $(GL_LIBS_SYS)
374
375	#---------------------- tiff lib:
376
377	TIFFLIBS := -ltiff
378
379	#---------------------- basic libs:
380
381	SYSLIBS:=
382
383	ifdef DARWIN
384	SYSLIBS += -lstdc++
385	else
386	SYSLIBS += -lm
387	endif
388
389	#---------------------- include symbols?
390
391	ifeq ($(TRACESYM),1)
392	ifdef DARWIN
393	cdynamic =
394	ldynamic =
395	else
396	cdynamic = -rdynamic -Wl,--export-dynamic
397	ldynamic = --export-dynamic
398	endif
399	endif
400
401	#---------------------- system dependent commands
402
403	ifdef DARWIN
404	TIME:=gtime
405	else
406	TIME:=/usr/bin/time
407	endif
408
409	# -------------------------------------------------------------------------
410	# Don't put any machine/version/etc conditionals below!
411	# (instead define variables above)
412	# -------------------------------------------------------------------------
413
414	cflags += -W -Wall $(dflags) $(extended_warnings) $(cdynamic)
415
416	cppflags := $(extended_cpp_warnings)
417
418	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
419	cppflags += -std=gnu++11# see also TEMPLATES/cxxforward.h@USE_Cxx11
420	else
421	# only use for gcc versions between 4.3 and <4.7 (4.7++ adds -Wc++11-compat above)
422	HAVE_GNUPP0X=`SOURCE_TOOLS/requireVersion.pl 4.3 $(GCC_VERSION_FOUND)`
423	ifeq ($(HAVE_GNUPP0X),1)
424	# ensure compatibility with upcoming C++ standard
425	cppflags += -std=gnu++0x
426	endif
427	endif
428
429	# compiler settings:
430
431	ACC := $(GCC)# compile C
432	CPP := $(GPP) $(cppflags)# compile C++
433	ACCLIB := $(ACC) $(shared_cflags)# compile C (shared libs)
434	CPPLIB := $(CPP) $(shared_cflags)# compile C++ (shared libs)
435
436	LINK_STATIC_LIB := ld $(lflags) $(ldynamic) -r -o# link static lib
437	LINK_EXECUTABLE := $(GPP) $(lflags) $(cdynamic) -o# link executable (c++)
438
439	ifeq ($(LINK_STATIC),1)
440	SHARED_LIB_SUFFIX = a# static lib suffix
441	LINK_SHARED_LIB := $(LINK_STATIC_LIB)
442	else
443	SHARED_LIB_SUFFIX = so# shared lib suffix
444	LINK_SHARED_LIB := $(GPP) $(lflags) $(cdynamic) -shared $(GCOVFLAGS) -o# link shared lib
445	endif
446
447	# other used tools
448
449
450	ifdef DARWIN
451	XMKMF := $(PREFIX)/bin/xmkmf
452	else
453	XMKMF := xmkmf
454	endif
455
456	MAKEDEPEND_PLAIN = makedepend
457
458	MAKEDEPEND = $(FORCEMASK);$(MAKEDEPEND_PLAIN)
459
460	#SEP:=--------------------------------------------------------------------------------
461	SEP=[`date +%M:%S.%N`] ------------------------------------------------
462	# to analyse timings run
463	# make -j9 clean; make -j9 all \| grep '^\[' \| sort
464	# make -j9 "TIMED_TARGET=perl" clean_timed_target \| grep '^\[' \| sort
465
466
467
468	# delete variables unused below
469
470	lflags:=
471
472	# -------------------------
473	# Main arb targets:
474	# -------------------------
475
476	first_target:
477	$(MAKE) checks
478	@echo $(SEP)
479	@echo 'Main targets:'
480	@echo ''
481	@echo ' all - Compile ARB + TOOLs + and copy shared libs + link foreign software'
482	@echo ' (That is most likely the target you want)'
483	@echo ''
484	@echo ' clean - remove generated files ("SUBDIR/SUBDIR.clean" to clean only SUBDIR)'
485	@echo ' rebuild - clean + all'
486	@echo ' relink - remove all binaries and relink them from objects'
487	@echo ''
488	@echo 'Some often used sub targets (make all makes them all):'
489	@echo ''
490	@echo ' arb - Just compile ARB (but none of the integrated tools)'
491	@echo ' menus - create GDEHELP/ARB_GDEmenus from GDEHELP/ARB_GDEmenus.source'
492	@echo ' perl - Compile the PERL XSUBS into lib/ARB.so and create links in lib to perl'
493	@echo ' binlink - Create all links in the bin directory'
494	@echo ''
495	@echo 'Development targets:'
496	@echo ''
497	@echo ' depends - create or update dependencies ("SUBDIR/SUBDIR.depends" to update only SUBDIR)'
498	@echo ' proto - create or update prototypes ("SUBDIR/SUBDIR.proto" to update only SUBDIR)'
499	@echo ' tags - create tags for xemacs'
500	@echo ' show - show available shortcuts (AKA subtargets)'
501	@echo ' up - shortcut for depends+proto+tags'
502	ifeq ($(UNIT_TESTS),1)
503	@echo ' ut - only run tests'
504	endif
505	@echo ' modified - rebuild files modified in svn checkout (does touch)'
506	@echo ' touch - touch files modified in svn checkout'
507	@echo ''
508	@echo 'Internal maintenance:'
509	@echo ''
510	@echo ' rel_minor - build a release (increases minor version number)'
511	@echo ' rel_major - build a release (increases MAJOR version number)'
512	@echo ' tarfile - make rebuild and create arb version tarfile ("tarfile_quick" to skip rebuild)'
513	@echo ' save - save all basic ARB sources into arbsrc_DATE ("savetest" to check filelist)'
514	@echo ' patch - save svn diff to patchfile'
515	@echo ' source_doc - create doxygen documentation'
516	@echo ' relocated - rebuild partly (use when you have relocated ARBHOME)'
517	@echo ' check_res - check ressource usage'
518	@echo ' dep_graph - Build dependency graphs'
519	@echo ' clean_cov - Clean coverage results'
520	@echo ''
521	@echo $(SEP)
522	@echo ''
523
524
525	# auto-generate config.makefile:
526
527	CONFIG_MAKEFILE_FOUND=$(wildcard config.makefile)
528
529	config.makefile : config.makefile.template
530	@echo --------------------------------------------------------------------------------
531	ifeq ($(strip $(CONFIG_MAKEFILE_FOUND)),)
532	@cp $< $@
533	@echo '$(ARBHOME)/$@:1: has been generated.'
534	@echo 'Please edit $@ to configure your system!'
535	@echo --------------------------------------------------------------------------------
536	@false
537	else
538	@echo '$(ARBHOME)/$<:1: is more recent than'
539	@echo '$(ARBHOME)/$@:1:'
540	@ls -al config.makefile*
541	@echo --------------------------------------------------------------------------------
542	@echo "Updating $@ (if this fails, check manually)"
543	SOURCE_TOOLS/update_config_makefile.pl
544	@echo "Sucessfully updated $@"
545	@echo --------------------------------------------------------------------------------
546	@ls -al config.makefile*
547	@echo --------------------------------------------------------------------------------
548	@echo "Diff to your old config.makefile:"
549	@echo --------------------------------------------------------------------------------
550	-diff $@.bak $@
551	@echo --------------------------------------------------------------------------------
552	endif
553
554	# check if everything is configured correctly
555
556	check_DEVELOPER:
557	ifndef DEVELOPER
558	@echo 'config.makefile:1: DEVELOPER not defined'
559	@false
560	endif
561
562	check_DEBUG:
563	ifndef dflags
564	@echo 'config.makefile:1: DEBUG has to be defined. Valid values are 0 and 1'
565	@false
566	endif
567
568	check_ARB_64:
569	ifndef ARB_64
570	@echo 'config.makefile:1: ARB_64 has to be defined. Valid values are 0 and 1'
571	@false
572	endif
573
574	# ---------------------------------------- check gcc version
575
576	check_same_GCC_VERSION:
577	$(ARBHOME)/SOURCE_TOOLS/check_same_gcc_version.pl $(GCC_VERSION_ALLOWED)
578
579	check_GCC_VERSION:
580	@echo 'GCC version check:'
581	@echo " - Your version is '$(GCC_VERSION_FOUND)'"
582	ifeq ('$(GCC_VERSION_ALLOWED)', '')
583	@echo ' - This version is not in the list of supported gcc-versions:'
584	@$(foreach version,$(ALLOWED_GCC_VERSIONS),echo ' * $(version)';)
585	@echo ' - You may either ..'
586	@echo ' - add your version to ALLOWED_GCC_VERSIONS in the Makefile and try it out or'
587	@echo ' - switch to one of the allowed versions (see arb_README_gcc.txt for installing'
588	@echo ' a different version of gcc)'
589	@echo ''
590	@false
591	else
592	@echo " - Supported gcc version '$(GCC_VERSION_ALLOWED)' detected - fine!"
593	@echo ''
594	$(MAKE) check_same_GCC_VERSION
595
596	endif
597
598	GCC_WITH_VTABLE_AFTER_CLASS=#occurred only with no longer supported $(ALLOWED_GCC_295_VERSIONS)
599	HAVE_GCC_WITH_VTABLE_AFTER_CLASS=$(strip $(foreach version,$(GCC_WITH_VTABLE_AFTER_CLASS),$(findstring $(version),$(GCC_VERSION_ALLOWED))))
600
601	# depending on the version of gcc the location of the vtable pointer differs.
602	ifeq ('$(HAVE_GCC_WITH_VTABLE_AFTER_CLASS)', '')
603	VTABLE_INFRONTOF_CLASS=1
604	else
605	VTABLE_INFRONTOF_CLASS=0
606	endif
607
608	#---------------------- check ARBHOME
609
610	# use arb_INSTALL.txt to determine whether ARBHOME points to correct directory
611	ARB_INSTALL_FOUND=$(wildcard $(ARBHOME)/arb_INSTALL.txt)
612
613	check_ARBHOME:
614	ifeq ($(strip $(ARB_INSTALL_FOUND)),)
615	@echo ------------------------------------------------------------
616	@echo "ARBHOME is set to '$(ARBHOME)'"
617	@echo "The environment variable ARBHOME has to point to the top arb source directory."
618	@echo "If you use bash enter:"
619	@echo " export ARBHOME='`pwd`'"
620	@echo ------------------------------------------------------------
621	@false
622	endif
623
624	ARB_PATH_SET=$(findstring $(ARBHOME)/bin,$(PATH))
625
626	check_PATH: check_ARBHOME
627	ifeq ($(strip $(ARB_PATH_SET)),)
628	@echo ------------------------------------------------------------
629	@echo "The environment variable PATH has to contain $(ARBHOME)/bin"
630	@echo "If you use bash enter:"
631	@echo ' export PATH=$$ARBHOME/bin:$$PATH'
632	@echo ------------------------------------------------------------
633	@false
634	endif
635
636	check_TOOLS:
637	@util/arb_check_build_env.pl \
638	"$(ACC)" \
639	"$(CPP)" \
640	"$(GPP)" \
641	"$(GCC)" \
642	"$(ACCLIB)" \
643	"$(CPPLIB)" \
644	"$(XMKMF)" \
645	"$(MAKEDEPEND_PLAIN)" \
646	"$(LINK_SHARED_LIB)" \
647	"$(LINK_SHARED_LIB)" \
648
649
650	check_ENVIRONMENT : check_PATH check_TOOLS
651
652	check_tabs: check_setup
653	ifeq ($(DEBUG),1)
654	@SOURCE_TOOLS/tabBrake.pl
655	endif
656
657	force_tab_check:
658	@touch -t 198001010000 SOURCE_TOOLS/stamp.tabBrake
659	@$(MAKE) check_tabs
660
661
662	# ---------------------
663
664	check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION
665	@echo Your setup seems to be ok.
666
667	checks: check_setup check_tabs
668	@rm -f SOURCE_TOOLS/postcompile.sav
669
670
671	# end test section ------------------------------
672
673	CORE_LIB=-lCORE
674	ARBDB_LIB=-lARBDB $(CORE_LIB)
675	LIBS = $(ARBDB_LIB) $(SYSLIBS)
676
677	GUI_LIBS_PREFIX:=
678	ifdef DARWIN
679	# this seem to be added at wrong place, since opengl is only needed to link EDIT4
680	GUI_LIBS_PREFIX:=-framework GLUT -framework OpenGL
681	endif
682
683	GUI_LIBS = $(GUI_LIBS_PREFIX) $(LIBS) -lWINDOW -lAWT $(XLIBS)
684	LIBPATH = -L$(ARBHOME)/lib
685
686	DEST_LIB = lib
687	DEST_BIN = bin
688
689	AINCLUDES := -I. -I$(ARBHOME)/INCLUDE $(XINCLUDES)
690	CPPINCLUDES := -I. -I$(ARBHOME)/INCLUDE $(XINCLUDES)
691	MAKEDEPENDFLAGS := -- -DARB_OPENGL -DUNIT_TESTS -D__cplusplus -I. -Y$(ARBHOME)/INCLUDE
692
693	ifeq ($(VTABLE_INFRONTOF_CLASS),1)
694	# Some code in ARB depends on the location of the vtable pointer
695	# (it does a cast from class AP_tree to struct GBT_TREE). In order to
696	# work around that hack properly, we define FAKE_VTAB_PTR
697	# if the vtable is located at the beginning of class.
698	# We are really sorry for that hack.
699	cflags:=$(cflags) -DFAKE_VTAB_PTR=char
700	endif
701
702	# -------------------------------
703	# old PTSERVER or PTPAN?
704
705	ifeq ($(PTPAN),1)
706	# PTPAN only libs
707	ARCHS_PT_SERVER = \
708	ptpan/PROBE.a
709	else
710	ifeq ($(PTPAN),2)
711	# special mode to compile both servers (developers only!)
712	ARCHS_PT_SERVER = \
713	ptpan/PROBE.a \
714	PROBE/PROBE.a
715	ARCHS_PT_SERVER_LINK = PROBE/PROBE.a# default to old ptserver
716	else
717	# PT-server only libs
718	ARCHS_PT_SERVER = \
719	PROBE/PROBE.a
720	endif
721	endif
722
723	ifndef ARCHS_PT_SERVER_LINK
724	ARCHS_PT_SERVER_LINK = $(ARCHS_PT_SERVER)
725	endif
726
727	# ---------------------------------------
728	# wrap main()
729
730	use_ARB_main=$(ARBHOME)/SOURCE_TOOLS/arb_main_cpp.o
731	use_ARB_main_C=$(ARBHOME)/SOURCE_TOOLS/arb_main_c.o
732
733	arbmainwrapper:
734	$(MAKE) -C SOURCE_TOOLS -r "cflags = $(cflags)" mainwrapper
735
736	# ---------------------------------------
737	# List of standard top level directories
738	#
739	# sub-makefiles have to define the targets
740	# - 'depends' and
741	# - 'clean'
742	#
743	# when adding new libs here, also add a dependency vs 'links' or 'links_non_perl' in .@DD_links_non_perl
744
745	ARCHS = \
746	$(ARCHS_PT_SERVER) \
747	AISC/AISC.a \
748	AISC_MKPTPS/AISC_MKPTPS.a \
749	ARBDB/libARBDB.a \
750	CORE/libCORE.a \
751	ARB_GDE/ARB_GDE.a \
752	AWT/libAWT.a \
753	AWTC/AWTC.a \
754	AWTI/AWTI.a \
755	CONSENSUS_TREE/CONSENSUS_TREE.a \
756	CONVERTALN/CONVERTALN.a \
757	DBSERVER/DBSERVER.a \
758	DIST/DIST.a \
759	EDIT4/EDIT4.a \
760	EISPACK/EISPACK.a \
761	GDE/GDE.a \
762	GENOM/GENOM.a \
763	GENOM_IMPORT/GENOM_IMPORT.a \
764	GL/GL.a \
765	ISLAND_HOPPING/ISLAND_HOPPING.a \
766	MERGE/MERGE.a \
767	MULTI_PROBE/MULTI_PROBE.a \
768	NALIGNER/NALIGNER.a \
769	NAMES/NAMES.a \
770	NAMES_COM/server.a \
771	NTREE/NTREE.a \
772	PARSIMONY/PARSIMONY.a \
773	PERLTOOLS/PERLTOOLS.a \
774	PGT/PGT.a \
775	PHYLO/PHYLO.a \
776	PRIMER_DESIGN/PRIMER_DESIGN.a \
777	PROBE_COM/server.a \
778	PROBE_DESIGN/PROBE_DESIGN.a \
779	PROBE_SET/PROBE_SET.a \
780	READSEQ/READSEQ.a \
781	RNA3D/RNA3D.a \
782	RNACMA/RNACMA.a \
783	SECEDIT/SECEDIT.a \
784	SEQ_QUALITY/SEQ_QUALITY.a \
785	SERVERCNTRL/SERVERCNTRL.a \
786	SL/SL.a \
787	STAT/STAT.a \
788	TOOLS/TOOLS.a \
789	TREEGEN/TREEGEN.a \
790	UNIT_TESTER/UNIT_TESTER.a \
791	WETC/WETC.a \
792	WINDOW/libWINDOW.a \
793	XML/XML.a \
794
795	# -----------------------
796	# library packets
797
798	ARCHS_CLIENT_PROBE = PROBE_COM/client.a
799	ARCHS_CLIENT_NAMES = NAMES_COM/client.a
800	ARCHS_MAKEBIN = AISC_MKPTPS/AISC_MKPTPS.a AISC/AISC.a
801
802	# communication libs need aisc and aisc_mkpts:
803
804	AISC/AISC.dummy: proto_tools
805
806	comtools: AISC/AISC.dummy
807
808	ARCHS_SEQUENCE = \
809	SL/SEQUENCE/SEQUENCE.a \
810	SL/ALIVIEW/ALIVIEW.a \
811	SL/PRONUC/PRONUC.a \
812
813	ARCHS_TREE = \
814	$(ARCHS_SEQUENCE) \
815	SL/FILTER/FILTER.a \
816	SL/ARB_TREE/ARB_TREE.a \
817
818	# parsimony tree (used by NTREE, PARSIMONY, STAT(->EDIT4), DIST(obsolete!))
819	ARCHS_AP_TREE = \
820	$(ARCHS_TREE) \
821	SL/AP_TREE/AP_TREE.a \
822
823	# --------------------------------------------------------------------------------
824	# dependencies for linking shared libs
825
826	link_core: core
827	link_db: db link_core
828	link_aw: aw link_db
829	link_awt: awt link_aw
830
831	#***************************************************************************************
832	# Individual_Programs_Section
833	#***************************************************************************************
834
835	#********************************* arb_ntree ************************************
836	NTREE = bin/arb_ntree
837	ARCHS_NTREE = \
838	NTREE/NTREE.a \
839	$(ARCHS_AP_TREE) \
840	ARB_GDE/ARB_GDE.a \
841	AWTC/AWTC.a \
842	AWTI/AWTI.a \
843	CONSENSUS_TREE/CONSENSUS_TREE.a \
844	GENOM/GENOM.a \
845	GENOM_IMPORT/GENOM_IMPORT.a \
846	MERGE/MERGE.a \
847	MULTI_PROBE/MULTI_PROBE.a \
848	PRIMER_DESIGN/PRIMER_DESIGN.a \
849	PROBE_DESIGN/PROBE_DESIGN.a \
850	SEQ_QUALITY/SEQ_QUALITY.a \
851	SERVERCNTRL/SERVERCNTRL.a \
852	SL/AW_NAME/AW_NAME.a \
853	SL/DB_UI/DB_UI.a \
854	SL/DB_SCANNER/DB_SCANNER.a \
855	SL/DB_QUERY/DB_QUERY.a \
856	SL/SEQIO/SEQIO.a \
857	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
858	SL/HELIX/HELIX.a \
859	SL/REGEXPR/REGEXPR.a \
860	SL/REFENTRIES/REFENTRIES.a \
861	SL/NDS/NDS.a \
862	SL/ITEMS/ITEMS.a \
863	SL/INSDEL/INSDEL.a \
864	SL/LOCATION/LOCATION.a \
865	SL/MACROS/MACROS.a \
866	SL/TRANSLATE/TRANSLATE.a \
867	SL/TREEDISP/TREEDISP.a \
868	SL/TREE_ADMIN/TREE_ADMIN.a \
869	SL/TREE_READ/TREE_READ.a \
870	SL/TREE_WRITE/TREE_WRITE.a \
871	STAT/STAT.a \
872	XML/XML.a \
873
874	$(NTREE): $(ARCHS_NTREE:.a=.dummy) link_awt
875	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NTREE) $(GUI_LIBS) \|\| ( \
876	echo "$(SEP) Link $@"; \
877	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS)" ; \
878	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS) && \
879	echo "$(SEP) Link $@ [done]"; \
880	)
881
882	#********************************* arb_edit4 ************************************
883	EDIT4 = bin/arb_edit4
884
885	ARCHS_EDIT4 := \
886	EDIT4/EDIT4.a \
887	$(ARCHS_AP_TREE) \
888	ARB_GDE/ARB_GDE.a \
889	AWTC/AWTC.a \
890	ISLAND_HOPPING/ISLAND_HOPPING.a \
891	SECEDIT/SECEDIT.a \
892	SERVERCNTRL/SERVERCNTRL.a \
893	SL/AW_HELIX/AW_HELIX.a \
894	SL/AW_NAME/AW_NAME.a \
895	SL/FAST_ALIGNER/FAST_ALIGNER.a \
896	SL/ITEMS/ITEMS.a \
897	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
898	SL/HELIX/HELIX.a \
899	SL/TRANSLATE/TRANSLATE.a \
900	SL/MACROS/MACROS.a \
901	STAT/STAT.a \
902	XML/XML.a \
903
904	ifeq ($(OPENGL),1)
905	ARCHS_EDIT4 += RNA3D/RNA3D.a
906	endif
907
908	LIBS_EDIT4 := $(GL_LIBS)
909
910	$(EDIT4): $(ARCHS_EDIT4:.a=.dummy) link_awt
911	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_EDIT4) $(GUI_LIBS) \|\| ( \
912	echo "$(SEP) Link $@"; \
913	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4) $(EXECLIBS)" ; \
914	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4) $(EXECLIBS) && \
915	echo "$(SEP) Link $@ [done]"; \
916	)
917
918	#********************************* arb_rnacma ************************************
919	RNACMA = bin/arb_rnacma
920	ARCHS_RNACMA = \
921	RNACMA/RNACMA.a \
922
923	$(RNACMA) : $(ARCHS_RNACMA:.a=.dummy) link_db
924	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_RNACMA) \|\| ( \
925	echo "$(SEP) Link $@"; \
926	echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_RNACMA) $(LIBS) $(EXECLIBS)"; \
927	$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_RNACMA) $(LIBS) $(EXECLIBS) && \
928	echo "$(SEP) Link $@ [done]"; \
929	)
930
931	#********************************* arb_pgt ************************************
932
933	PGT = bin/arb_pgt
934	ARCHS_PGT = \
935	PGT/PGT.a \
936
937	PGT_SYS_LIBS=$(XLIBS) $(TIFFLIBS) $(LIBS)
938
939	$(PGT) : $(ARCHS_PGT:.a=.dummy) link_db
940	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PGT) \|\| ( \
941	echo "$(SEP) Link $@"; \
942	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PGT) $(PGT_SYS_LIBS) $(EXECLIBS) "; \
943	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PGT) $(PGT_SYS_LIBS) $(EXECLIBS) && \
944	echo "$(SEP) Link $@ [done]"; \
945	)
946
947
948	#********************************* arb_wetc ************************************
949	WETC = bin/arb_wetc
950	ARCHS_WETC = \
951	WETC/WETC.a \
952	SL/HELIX/HELIX.a \
953	SL/FILTER/FILTER.a \
954	XML/XML.a \
955
956	$(WETC): $(ARCHS_WETC:.a=.dummy) link_awt
957	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_WETC) $(GUI_LIBS) \|\| ( \
958	echo "$(SEP) Link $@"; \
959	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC) $(GUI_LIBS) $(EXECLIBS)" ; \
960	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC) $(GUI_LIBS) $(EXECLIBS) && \
961	echo "$(SEP) Link $@ [done]"; \
962	)
963
964	#********************************* arb_dist ************************************
965	DIST = bin/arb_dist
966	ARCHS_DIST = \
967	$(ARCHS_AP_TREE) \
968	CONSENSUS_TREE/CONSENSUS_TREE.a \
969	DIST/DIST.a \
970	EISPACK/EISPACK.a \
971	SERVERCNTRL/SERVERCNTRL.a \
972	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
973	SL/HELIX/HELIX.a \
974	SL/MATRIX/MATRIX.a \
975	SL/MACROS/MACROS.a \
976	SL/NDS/NDS.a \
977	SL/ITEMS/ITEMS.a \
978	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.a \
979	XML/XML.a \
980
981	$(DIST): $(ARCHS_DIST:.a=.dummy) link_awt
982	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_DIST) $(GUI_LIBS) \|\| ( \
983	echo "$(SEP) Link $@"; \
984	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS)" ; \
985	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS) && \
986	echo "$(SEP) Link $@ [done]"; \
987	)
988
989	#********************************* arb_pars ************************************
990	PARSIMONY = bin/arb_pars
991	ARCHS_PARSIMONY = \
992	$(ARCHS_AP_TREE) \
993	PARSIMONY/PARSIMONY.a \
994	SERVERCNTRL/SERVERCNTRL.a \
995	SL/AW_NAME/AW_NAME.a \
996	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
997	SL/HELIX/HELIX.a \
998	SL/MACROS/MACROS.a \
999	SL/NDS/NDS.a \
1000	SL/ITEMS/ITEMS.a \
1001	SL/TRANSLATE/TRANSLATE.a \
1002	SL/TREEDISP/TREEDISP.a \
1003	XML/XML.a \
1004
1005	$(PARSIMONY): $(ARCHS_PARSIMONY:.a=.dummy) link_awt
1006	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PARSIMONY) $(GUI_LIBS) \|\| ( \
1007	echo "$(SEP) Link $@"; \
1008	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(EXECLIBS)" ; \
1009	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(EXECLIBS) && \
1010	echo "$(SEP) Link $@ [done]"; \
1011	)
1012
1013	#********************************* arb_convert_aln ************************************
1014	CONVERT_ALN = bin/arb_convert_aln
1015	ARCHS_CONVERT_ALN = \
1016	CONVERTALN/CONVERTALN.a \
1017
1018	$(CONVERT_ALN) : $(ARCHS_CONVERT_ALN:.a=.dummy) link_db
1019	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_CONVERT_ALN) \|\| ( \
1020	echo "$(SEP) Link $@"; \
1021	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN) $(LIBS) $(ARBDB_LIB) $(EXECLIBS)"; \
1022	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN) $(LIBS) $(ARBDB_LIB) $(EXECLIBS) && \
1023	echo "$(SEP) Link $@ [done]"; \
1024	)
1025
1026	#********************************* arb_treegen ************************************
1027
1028	TREEGEN = bin/arb_treegen
1029	ARCHS_TREEGEN = \
1030	TREEGEN/TREEGEN.a \
1031
1032	$(TREEGEN) : $(ARCHS_TREEGEN:.a=.dummy)
1033	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_TREEGEN) \|\| ( \
1034	echo "$(SEP) Link $@"; \
1035	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN) $(EXECLIBS)" ; \
1036	$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN) $(EXECLIBS) && \
1037	echo "$(SEP) Link $@ [done]"; \
1038	)
1039
1040	#********************************* arb_naligner ************************************
1041	NALIGNER = bin/arb_naligner
1042	ARCHS_NALIGNER = \
1043	NALIGNER/NALIGNER.a \
1044	SERVERCNTRL/SERVERCNTRL.a \
1045	SL/HELIX/HELIX.a \
1046
1047	$(NALIGNER): $(ARCHS_NALIGNER:.a=.dummy) link_db
1048	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NALIGNER) \|\| ( \
1049	echo "$(SEP) Link $@"; \
1050	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(LIBS) $(EXECLIBS)" ; \
1051	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(LIBS) $(EXECLIBS) && \
1052	echo "$(SEP) Link $@ [done]"; \
1053	)
1054
1055	#********************************* arb_phylo ************************************
1056	PHYLO = bin/arb_phylo
1057	ARCHS_PHYLO = \
1058	PHYLO/PHYLO.a \
1059	SL/HELIX/HELIX.a \
1060	SL/FILTER/FILTER.a \
1061	SL/MATRIX/MATRIX.a \
1062	SL/MACROS/MACROS.a \
1063	XML/XML.a \
1064
1065	$(PHYLO): $(ARCHS_PHYLO:.a=.dummy) link_awt
1066	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PHYLO) $(GUI_LIBS) \|\| ( \
1067	echo "$(SEP) Link $@"; \
1068	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO) $(GUI_LIBS) $(EXECLIBS)" ; \
1069	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO) $(GUI_LIBS) $(EXECLIBS) && \
1070	echo "$(SEP) Link $@ [done]"; \
1071	)
1072
1073	#***************************************************************************************
1074	# SERVER SECTION
1075	#***************************************************************************************
1076
1077	#********************************* arb_db_server ************************************
1078	DBSERVER = bin/arb_db_server
1079	ARCHS_DBSERVER = \
1080	DBSERVER/DBSERVER.a \
1081	SERVERCNTRL/SERVERCNTRL.a \
1082
1083	$(DBSERVER): $(ARCHS_DBSERVER:.a=.dummy) link_db
1084	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_DBSERVER) $(ARBDB_LIB) \|\| ( \
1085	echo "$(SEP) Link $@"; \
1086	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER) $(ARBDB_LIB) PROBE_COM/client.a $(SYSLIBS) $(EXECLIBS)" ; \
1087	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER) $(ARBDB_LIB) PROBE_COM/client.a $(SYSLIBS) $(EXECLIBS) && \
1088	echo "$(SEP) Link $@ [done]"; \
1089	)
1090
1091	#********************************* arb_pt_server ************************************
1092	PROBE = bin/arb_pt_server
1093	ARCHS_PROBE_COMMON = \
1094	SERVERCNTRL/SERVERCNTRL.a \
1095	SL/HELIX/HELIX.a \
1096	SL/PTCLEAN/PTCLEAN.a \
1097
1098	ARCHS_PROBE_LINK = \
1099	$(ARCHS_PROBE_COMMON) \
1100	$(ARCHS_PT_SERVER_LINK) \
1101
1102	ARCHS_PROBE_DEPEND = \
1103	$(ARCHS_PROBE_COMMON) \
1104	$(ARCHS_PT_SERVER) \
1105
1106	$(PROBE): $(ARCHS_PROBE_DEPEND:.a=.dummy) link_db
1107	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) config.makefile \|\| ( \
1108	echo "$(SEP) Link $@"; \
1109	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) PROBE_COM/server.a $(SYSLIBS) $(EXECLIBS)" ; \
1110	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) PROBE_COM/server.a $(SYSLIBS) $(EXECLIBS) && \
1111	echo "$(SEP) Link $@ [done]"; \
1112	)
1113
1114	#********************************* arb_name_server ************************************
1115	NAMES = bin/arb_name_server
1116	ARCHS_NAMES = \
1117	NAMES/NAMES.a \
1118	SERVERCNTRL/SERVERCNTRL.a \
1119
1120	$(NAMES): $(ARCHS_NAMES:.a=.dummy) link_db
1121	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) \|\| ( \
1122	echo "$(SEP) Link $@"; \
1123	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS) $(EXECLIBS)" ; \
1124	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS) $(EXECLIBS) && \
1125	echo "$(SEP) Link $@ [done]"; \
1126	)
1127
1128	#********************************* SHARED LIBRARIES SECTION ************************************
1129
1130	prepare_libdir: addlibs
1131
1132	addlibs:
1133	(perl $(ARBHOME)/SOURCE_TOOLS/provide_libs.pl \
1134	"arbhome=$(ARBHOME)" \
1135	"opengl=$(OPENGL)" \
1136	"link_static=$(LINK_STATIC)" \
1137	)
1138
1139	#***************************************************************************************
1140	# Recursive calls to sub-makefiles
1141	#***************************************************************************************
1142
1143	include SOURCE_TOOLS/export2sub
1144
1145	%.depends:
1146	@cp -p $(@D)/Makefile $(@D)/Makefile.old # save old Makefile
1147	@$(MAKE) -C $(@D) -r \
1148	"AUTODEPENDS=1" \
1149	"MAIN=nothing" \
1150	"cflags=noCflagsHere_use_MAKEDEPENDFLAGS" \
1151	depends
1152	@grep "^# DO NOT DELETE" $(@D)/Makefile >/dev/null
1153	@cat $(@D)/Makefile \
1154	\| SOURCE_TOOLS/fix_depends.pl "(from main)" \
1155	>$(@D)/Makefile.2
1156	@mv $(@D)/Makefile.old $(@D)/Makefile # restore old Makefile
1157	@$(ARBHOME)/SOURCE_TOOLS/mv_if_diff $(@D)/Makefile.2 $(@D)/Makefile # update Makefile if changed
1158
1159	%.proto:
1160	@$(MAKE) -C $(@D) \
1161	"AUTODEPENDS=0" \
1162	"MAIN=nothing" \
1163	"cflags=noCflags" \
1164	proto
1165
1166	%.clean:
1167	@$(MAKE) -C $(@D) \
1168	"AUTODEPENDS=0" \
1169	"MAIN=nothing" \
1170	"cflags=noCflags" \
1171	clean
1172
1173
1174	# stop wrong targets
1175	target_is_missing_lib_prefix:
1176	@echo "Error: Denied to build shared library target with missing 'lib'-prefix"
1177	false
1178
1179	ARBDB/ARBDB.dummy: target_is_missing_lib_prefix
1180	CORE/CORE.dummy: target_is_missing_lib_prefix
1181	AWT/AWT.dummy: target_is_missing_lib_prefix
1182	WINDOW/WINDOW.dummy: target_is_missing_lib_prefix
1183
1184	# rule to generate main target (normally a library):
1185	%.dummy:
1186	@( export ID=$$$$; LANG=C; \
1187	(( \
1188	echo "$(SEP) Make $(@D)"; \
1189	$(MAKE) -C $(@D) -r \
1190	"AUTODEPENDS=1" \
1191	"MAIN = $(@F:.dummy=.a)" \
1192	"cflags = $(cflags) -DIN_ARB_$(subst /,_,$(@D))" && \
1193	echo "$(SEP) Make $(@D) [done]"; \
1194	) >$(@D).$$ID.log 2>&1 && (cat $(@D).$$ID.log;rm $(@D).$$ID.log)) \|\| (cat $(@D).$$ID.log;rm $(@D).$$ID.log;false))
1195
1196	# Additional dependencies for subtargets:
1197
1198	PROBE_COM/PROBE_COM.dummy : comtools
1199	NAMES_COM/NAMES_COM.dummy : comtools
1200
1201	com: PROBE_COM/PROBE_COM.dummy NAMES_COM/NAMES_COM.dummy
1202
1203	PROBE_COM/server.dummy:
1204	@echo Unwanted request to make target $<
1205	false
1206
1207	PROBE_COM/client.dummy:
1208	@echo Unwanted request to make target $<
1209	false
1210
1211	NAMES_COM/server.dummy:
1212	@echo Unwanted request to make target $<
1213	false
1214
1215	NAMES_COM/client.dummy:
1216	@echo Unwanted request to make target $<
1217	false
1218
1219
1220	ARBDB/libARBDB.dummy: links
1221	CORE/libCORE.dummy: links
1222
1223	PERLTOOLS/PERLTOOLS.dummy: core db
1224
1225	# all subdirs perl not depends on go here (ADD_links_non_perl)
1226	AWT/libAWT.dummy: links_non_perl
1227	AWTI/AWTI.dummy: links_non_perl
1228	CONSENSUS_TREE/CONSENSUS_TREE.dummy: links_non_perl
1229	CONVERTALN/CONVERTALN.dummy: links_non_perl
1230	DBSERVER/DBSERVER.dummy: links_non_perl
1231	DIST/DIST.dummy: links_non_perl
1232	EDIT4/EDIT4.dummy: links_non_perl genheaders com
1233	EISPACK/EISPACK.dummy: links_non_perl
1234	GDE/GDE.dummy: links_non_perl
1235	GENOM/GENOM.dummy: links_non_perl
1236	GENOM_IMPORT/GENOM_IMPORT.dummy: links_non_perl
1237	ISLAND_HOPPING/ISLAND_HOPPING.dummy: links_non_perl
1238	MERGE/MERGE.dummy: links_non_perl
1239	NTREE/NTREE.dummy: links_non_perl genheaders
1240	PARSIMONY/PARSIMONY.dummy: links_non_perl
1241	PGT/PGT.dummy: links_non_perl
1242	PHYLO/PHYLO.dummy: links_non_perl
1243	PRIMER_DESIGN/PRIMER_DESIGN.dummy: links_non_perl
1244	PROBE_SET/PROBE_SET.dummy: links_non_perl link_db
1245	READSEQ/READSEQ.dummy: links_non_perl
1246	RNACMA/RNACMA.dummy: links_non_perl header_libs
1247	SECEDIT/SECEDIT.dummy: links_non_perl
1248	SEQ_QUALITY/SEQ_QUALITY.dummy: links_non_perl
1249	SERVERCNTRL/SERVERCNTRL.dummy: links_non_perl com
1250	SL/ALIVIEW/ALIVIEW.dummy: links_non_perl
1251	SL/AP_TREE/AP_TREE.dummy: links_non_perl
1252	SL/ARB_TREE/ARB_TREE.dummy: links_non_perl
1253	SL/AW_HELIX/AW_HELIX.dummy: links_non_perl
1254	SL/DB_QUERY/DB_QUERY.dummy: links_non_perl
1255	SL/DB_SCANNER/DB_SCANNER.dummy: links_non_perl
1256	SL/DB_UI/DB_UI.dummy: links_non_perl
1257	SL/FAST_ALIGNER/FAST_ALIGNER.dummy: links_non_perl
1258	SL/FILTER/FILTER.dummy: links_non_perl
1259	SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy: links_non_perl
1260	SL/HELIX/HELIX.dummy: links_non_perl
1261	SL/INSDEL/INSDEL.dummy: links_non_perl
1262	SL/ITEMS/ITEMS.dummy: links_non_perl
1263	SL/LOCATION/LOCATION.dummy: links_non_perl
1264	SL/MACROS/MACROS.dummy: links_non_perl
1265	SL/MATRIX/MATRIX.dummy: links_non_perl
1266	SL/NDS/NDS.dummy: links_non_perl
1267	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.dummy: links_non_perl
1268	SL/PRONUC/PRONUC.dummy: links_non_perl
1269	SL/PTCLEAN/PTCLEAN.dummy: links_non_perl link_db
1270	SL/REFENTRIES/REFENTRIES.dummy: links_non_perl
1271	SL/REGEXPR/REGEXPR.dummy: links_non_perl
1272	SL/SEQIO/SEQIO.dummy: links_non_perl
1273	SL/SEQUENCE/SEQUENCE.dummy: links_non_perl
1274	SL/TRANSLATE/TRANSLATE.dummy: links_non_perl
1275	SL/TREE_ADMIN/TREE_ADMIN.dummy: links_non_perl
1276	SL/TREE_READ/TREE_READ.dummy: links_non_perl
1277	SL/TREE_WRITE/TREE_WRITE.dummy: links_non_perl
1278	SL/TREEDISP/TREEDISP.dummy: links_non_perl
1279	STAT/STAT.dummy: links_non_perl
1280	TREEGEN/TREEGEN.dummy: links_non_perl
1281	WETC/WETC.dummy: links_non_perl
1282	WINDOW/libWINDOW.dummy: links_non_perl
1283	XML/XML.dummy: links_non_perl
1284
1285	ifeq ($(OPENGL),1)
1286	GL/glAW/glAW.dummy: links_non_perl
1287	GL/glpng/glpng.dummy: links_non_perl
1288	GL/GL.dummy: GL/glAW/glAW.dummy GL/glpng/glpng.dummy
1289	RNA3D/RNA3D.dummy: links_non_perl gl
1290	endif
1291
1292	UNIT_TESTER/UNIT_TESTER.dummy: link_db \
1293	SERVERCNTRL/SERVERCNTRL.dummy \
1294
1295	TOOLS/TOOLS.dummy : links_non_perl link_db \
1296	SERVERCNTRL/SERVERCNTRL.dummy \
1297	SL/TREE_WRITE/TREE_WRITE.dummy \
1298	SL/TREE_READ/TREE_READ.dummy \
1299	CONSENSUS_TREE/CONSENSUS_TREE.dummy \
1300	XML/XML.dummy \
1301
1302	AWTC/AWTC.dummy : com
1303
1304	NAMES/NAMES.dummy : com
1305	SL/AW_NAME/AW_NAME.dummy : com
1306
1307	PROBE/PROBE.dummy : com
1308	ptpan/PROBE.dummy : com
1309	MULTI_PROBE/MULTI_PROBE.dummy : com
1310	PROBE_DESIGN/PROBE_DESIGN.dummy : com
1311	NALIGNER/NALIGNER.dummy : com
1312
1313	ARB_GDE/ARB_GDE.dummy : proto_tools
1314
1315	#***************************************************************************************
1316	# Short aliases to make targets
1317	#***************************************************************************************
1318
1319	show:
1320	@echo $(SEP)
1321	@echo 'Aliases for often needed targets:'
1322	@echo ''
1323	@echo ' executables:'
1324	@echo ''
1325	@echo ' nt arb_ntree'
1326	@echo ' e4 arb_edit4 (includes secedit)'
1327	@echo ' di arb_dist'
1328	@echo ' ph arb_phylo'
1329	@echo ' pa arb_parsimony'
1330	@echo ' tg arb_treegen'
1331	@echo ' ds arb_dbserver'
1332	@echo ' pt arb_pt_server'
1333	@echo ' na arb_name_server'
1334	@echo ''
1335	@echo ' libraries:'
1336	@echo ''
1337	@echo ' com communication libraries'
1338	@echo ' db ARB database'
1339	@echo ' aw GUI lib'
1340	@echo ' awt GUI toolkit'
1341	@echo ' awtc general purpose library'
1342	@echo ' awti import/export library'
1343	@echo ' mp multi probe library'
1344	@echo ' ge genome library'
1345	@echo ' pd probe design lib'
1346	@echo ' prd primer design lib'
1347	@echo ''
1348	@echo ' other targets:'
1349	@echo ''
1350	@echo ' help recompile help files'
1351	@echo ' tools make small tools used by arb'
1352	@echo ''
1353	@echo ' foreign targets:'
1354	@echo ''
1355	@echo ' gde GDE'
1356	@echo ' agde ARB_GDE'
1357	@echo ''
1358	@echo 'for other targets inspect $(ARBHOME)/Makefile'
1359	@echo ''
1360	@echo $(SEP)
1361
1362	source_doc:
1363	@echo "Remove some links (doxygen crashes otherwise):"
1364	find . \( -name "AISC" -o -name "C" -o -name "GDEHELP" \) -type l -exec rm {} \;
1365	doxygen
1366	$(MAKE) forcelinks
1367
1368	dep_graph:
1369	@echo "Building some dependency graphs"
1370	SOURCE_TOOLS/dependency_graphs.pl
1371
1372	help: HELP_SOURCE/HELP_SOURCE.dummy
1373
1374	# @@@ when backtracing code is in libCORE, link vs ARBDB is no longer needed
1375	HELP_SOURCE/HELP_SOURCE.dummy: link_db xml menus
1376
1377	db: ARBDB/libARBDB.dummy
1378	core: CORE/libCORE.dummy
1379	aw: WINDOW/libWINDOW.dummy
1380	awt: AWT/libAWT.dummy
1381	awtc: AWTC/AWTC.dummy
1382	awti: AWTI/AWTI.dummy
1383
1384	mp: MULTI_PROBE/MULTI_PROBE.dummy
1385	mg: MERGE/MERGE.dummy
1386	ge: GENOM/GENOM.dummy
1387	prd: PRIMER_DESIGN/PRIMER_DESIGN.dummy
1388
1389	nt: menus $(NTREE)
1390
1391	nal: $(NALIGNER)
1392
1393	di: $(DIST)
1394	ph: $(PHYLO)
1395	pa: $(PARSIMONY)
1396	tg: $(TREEGEN)
1397
1398	ifeq ($(OPENGL),1)
1399	3d: RNA3D/RNA3D.dummy
1400	gl: GL/GL.dummy
1401	else
1402	noopengl:
1403	@echo "invalid target for OPENGL=0"
1404	3d: noopengl
1405	gl: noopengl
1406	endif
1407
1408	SL/SL.dummy: com
1409
1410	ds: $(DBSERVER)
1411	pt: $(PROBE)
1412	pst: PROBE_SET/PROBE_SET.dummy
1413	pd: PROBE_DESIGN/PROBE_DESIGN.dummy
1414	na: $(NAMES)
1415	sq: SEQ_QUALITY/SEQ_QUALITY.dummy
1416	cma: $(RNACMA)
1417
1418	sec: SECEDIT/SECEDIT.dummy
1419
1420	e4: $(EDIT4) readseq menus
1421
1422	gi: GENOM_IMPORT/GENOM_IMPORT.dummy
1423	wetc: $(WETC)
1424
1425	pgt: $(PGT)
1426	xml: XML/XML.dummy
1427	xmlin: XML_IMPORT/XML_IMPORT.dummy# broken
1428	stat: STAT/STAT.dummy $(NTREE) $(EDIT4)
1429	fa: SL/FAST_ALIGNER/FAST_ALIGNER.dummy
1430
1431	#********************************************************************************
1432
1433	up_by_remake: depends proto
1434
1435	up: up_by_remake tags valgrind_update
1436
1437	#********************************************************************************
1438
1439	touch:
1440	SOURCE_TOOLS/touch_modified.pl
1441
1442	modified: touch
1443	$(MAKE) all
1444
1445	#********************************************************************************
1446
1447	libdepends:
1448	$(MAKE) -C "SOURCE_TOOLS" \
1449	"RNA3D_LIB=$(RNA3D_LIB_4_DEPENDS)" \
1450	libdepends
1451
1452	#********************************************************************************
1453
1454	# create generated headers:
1455	genheaders: TEMPLATES/TEMPLATES.dummy
1456
1457	clrdotdepends:
1458	-rm PROBE_COM/.depends
1459	-rm NAMES_COM/.depends
1460	-rm PERL2ARB/.depends
1461
1462	comdepends: comtools clrdotdepends
1463	@echo "$(SEP) Partially build com interface"
1464	$(MAKE) PROBE_COM/PROBE_COM.depends
1465	$(MAKE) NAMES_COM/NAMES_COM.depends
1466
1467	depends: genheaders comdepends
1468	@echo "$(SEP) Updating other dependencies"
1469	$(MAKE) $(ARCHS:.a=.depends) \
1470	HELP_SOURCE/HELP_SOURCE.depends
1471	$(MAKE) libdepends
1472
1473	depend: depends
1474
1475	AISC_MKPTPS/AISC_MKPTPS.dummy: links
1476
1477	proto_tools: AISC_MKPTPS/AISC_MKPTPS.dummy
1478
1479	proto: proto_tools
1480	@echo $(SEP) Updating prototypes
1481	$(MAKE) \
1482	ARBDB/ARBDB.proto \
1483	AISC_COM/AISC_COM.proto \
1484	ARB_GDE/ARB_GDE.proto \
1485	CORE/CORE.proto \
1486	CONVERTALN/CONVERTALN.proto \
1487	NTREE/NTREE.proto \
1488	MERGE/MERGE.proto \
1489	$(ARCHS_PT_SERVER:.a=.proto) \
1490	SERVERCNTRL/SERVERCNTRL.proto \
1491	SL/SL.proto \
1492
1493	#********************************************************************************
1494
1495	valgrind_update: links
1496	@echo $(SEP) Updating for valgrind
1497	$(MAKE) -C SOURCE_TOOLS valgrind_update
1498
1499	#********************************************************************************
1500
1501	TAGFILE=TAGS
1502	TAGFILE_TMP=TAGS.tmp
1503
1504	TAG_SOURCE_HEADERS=TAGS.headers
1505	TAG_SOURCE_CODE=TAGS.codefiles
1506
1507	TAG_SOURCE_LISTS=$(TAG_SOURCE_HEADERS) $(TAG_SOURCE_CODE)
1508
1509	ETAGS=ctags -e -f $(TAGFILE_TMP) --sort=no --if0=no --extra=q
1510	ETAGS_TYPES=--C-kinds=cgnsut --C++-kinds=cgnsut
1511	ETAGS_FUN =--C-kinds=fm --C++-kinds=fm
1512	ETAGS_REST =--C-kinds=dev --C++-kinds=dev
1513
1514	$(TAG_SOURCE_HEADERS): links
1515	# find . \( -name '.[ch]xx' -o -name ".[ch]" \) -type f \| grep -v -i perl5 > $@
1516	# workaround a bug in ctags 5.8:
1517	find . \( -name '.hxx' -o -name ".h" \) -type f \| grep -v -i perl5 \| $(SED) -e 's/^.\///g' > $@
1518
1519	$(TAG_SOURCE_CODE): links
1520	# find . \( -name '.[ch]xx' -o -name ".[ch]" \) -type f \| grep -v -i perl5 > $@
1521	# workaround a bug in ctags 5.8:
1522	find . \( -name '.cxx' -o -name ".c" \) -type f \| grep -v -i perl5 \| $(SED) -e 's/^.\///g' > $@
1523
1524	tags: $(TAG_SOURCE_LISTS)
1525	$(ETAGS) $(ETAGS_TYPES) -L $(TAG_SOURCE_HEADERS)
1526	$(ETAGS) -a $(ETAGS_FUN) -L $(TAG_SOURCE_HEADERS)
1527	$(ETAGS) -a $(ETAGS_REST) -L $(TAG_SOURCE_HEADERS)
1528	$(ETAGS) -a $(ETAGS_TYPES) -L $(TAG_SOURCE_CODE)
1529	$(ETAGS) -a $(ETAGS_FUN) -L $(TAG_SOURCE_CODE)
1530	$(ETAGS) -a $(ETAGS_REST) -L $(TAG_SOURCE_CODE)
1531	mv_if_diff $(TAGFILE_TMP) $(TAGFILE)
1532	rm $(TAG_SOURCE_LISTS)
1533
1534	#********************************************************************************
1535
1536	LINKSTAMP=SOURCE_TOOLS/stamp.generate_all_links
1537
1538	links: checks $(LINKSTAMP) arbmainwrapper
1539	links_no_checks: $(LINKSTAMP) arbmainwrapper
1540
1541	forcelinks:
1542	-rm $(LINKSTAMP)
1543	$(MAKE) links
1544
1545	$(LINKSTAMP): SOURCE_TOOLS/generate_all_links.sh
1546	+SOURCE_TOOLS/generate_all_links.sh
1547	touch $(LINKSTAMP)
1548
1549	clean_links:
1550	# avoid to delete linked pts, nas or arb_tcp.dat:
1551	find . -path './lib' -prune -o -type l -exec rm {} \;
1552	@rm -f $(LINKSTAMP) lib/inputMasks/format.readme
1553
1554	redo_links: clean_links
1555	$(MAKE) links_no_checks
1556
1557	#********************************************************************************
1558
1559	header_libs:
1560	$(MAKE) -C HEADERLIBS all
1561
1562	#********************************************************************************
1563
1564	gde: GDE/GDE.dummy
1565	GDE: gde
1566	agde: ARB_GDE/ARB_GDE.dummy
1567
1568	tools: TOOLS/TOOLS.dummy
1569
1570	convert: $(CONVERT_ALN)
1571	readseq: READSEQ/READSEQ.dummy
1572
1573	#***************************************************************************************
1574	# Some user commands
1575	#***************************************************************************************
1576
1577	menus: binlink links
1578	@(( \
1579	echo "$(SEP) Make GDEHELP"; \
1580	$(MAKE) -C GDEHELP -r all && \
1581	echo "$(SEP) Make GDEHELP [done]"; \
1582	) > GDEHELP.log 2>&1 && (cat GDEHELP.log;rm GDEHELP.log)) \|\| (cat GDEHELP.log;rm GDEHELP.log;false)
1583
1584	ifeq ($(DEBUG),1)
1585	BIN_TARGET=develall
1586	else
1587	BIN_TARGET=all
1588	endif
1589
1590
1591	binlink:
1592	$(MAKE) -C bin $(BIN_TARGET)
1593
1594	preplib:
1595	(cd lib;$(MAKE) all)
1596
1597	# --------------------------------------------------------------------------------
1598	# This section is quite tricky:
1599	#
1600	# make 'perl' is a BIG target, so when it has to be made, it has to be started
1601	# as early as possible to reduce overall compile time. Since 'make' does not
1602	# provide any priotities, i force it to build all 'perl'-prerequisites early, by
1603	# adding artificial dependencies to these prerequisites
1604	#
1605	# That behavior is likely to be system-dependent.
1606	# My goal was only to make it work on my current development system,
1607	# where this saves about 20% of overall build time.
1608
1609	ifeq ($(WITHPERL),1)
1610	links_non_perl: PERLTOOLS/PERLTOOLS.dummy
1611	perltools: links_non_perl
1612	perl: realperl
1613	else
1614	links_non_perl: links
1615	perl:
1616	$(MAKE) "WITHPERL=1" perl
1617	endif
1618
1619	# ---------------------------------------- perl
1620
1621	ifeq ($(ARB_64),$(BUILDHOST_64))
1622	TEST_PERL_SCRIPTS=$(MAKE) -C PERL_SCRIPTS/test test
1623	else
1624	TEST_PERL_SCRIPTS=echo "skipping perl script compilation (when cross-compiling)"
1625	endif
1626
1627	realperl: perltools
1628	(( \
1629	echo "$(SEP) Make PERL2ARB" ; \
1630	$(TIME) $(MAKE) -C PERL2ARB -r -f Makefile.main \
1631	"AUTODEPENDS=1" \
1632	"dflags=$(dflags)" \
1633	"cross_cflags=$(cross_cflags) $(dflags)" \
1634	"cross_lflags=$(cross_lflags)" \
1635	all && \
1636	$(TEST_PERL_SCRIPTS) && \
1637	echo "$(SEP) Make PERL2ARB [done]" ; \
1638	) > PERL2ARB.log 2>&1 && (cat PERL2ARB.log;rm PERL2ARB.log)) \|\| (cat PERL2ARB.log;rm PERL2ARB.log;false)
1639
1640	perl_clean:
1641	@$(MAKE) -C PERL2ARB -r -f Makefile.main \
1642	"AUTODEPENDS=0" \
1643	clean
1644
1645	PERL2ARB/PERL2ARB.clean:
1646	$(MAKE) perl_clean
1647
1648	# ---------------------------------------- bindings to script languages
1649
1650	bindings: lib/libCORE.so lib/libARBDB.so
1651	$(MAKE) -C BINDINGS all ARBDEPENDS="$(^:%=../%)" DFLAGS="$(dflags)"
1652
1653	bindings_clean:
1654	$(MAKE) -C BINDINGS clean
1655
1656	# ----------------------------------------
1657
1658	CLOC=cloc-1.08.pl
1659	CLOCFLAGS=--no3 --quiet --progress-rate=0
1660	CLOCARB=--exclude-dir=GDE .
1661	CLOCEXT=GDE
1662	CLOCCODE=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.code.def
1663	CLOCREST=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.rest.def
1664	CLOCFILT=tail --lines=+4
1665
1666	cloc:
1667	@echo 'Arb code:'
1668	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCARB) \| $(CLOCFILT)
1669	@echo 'Arb rest:'
1670	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCARB) \| $(CLOCFILT)
1671	@echo 'External code:'
1672	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCEXT) \| $(CLOCFILT)
1673	@echo 'External rest:'
1674	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCEXT) \| $(CLOCFILT)
1675
1676	# ---------------------------------------- check ressources
1677
1678	check_res:
1679	$(ARBHOME)/SOURCE_TOOLS/check_ressources.pl
1680
1681	# ---------------------------------------- cleaning
1682
1683	rmbak:
1684	@echo "Cleanup:"
1685	@find . \( -name '*%' \
1686	-o -name '*.bak' \
1687	-o -name '*~' \) \
1688	-o -name 'core' \
1689	-exec rm -v {} \;
1690
1691	bin_reinit:
1692	$(MAKE) bin/bin.clean
1693	$(MAKE) -C "bin" all
1694
1695	clean_directories:
1696	-rm -rf \
1697	$(ARBHOME)/PROBE_SET/bin \
1698	$(ARBHOME)/INCLUDE \
1699
1700	libclean:
1701	-find $(ARBHOME) -type f \( -name '*.a' ! -type l \) -exec rm -f {} \;
1702
1703	objclean:
1704	-find $(ARBHOME) -type f \( -name '*.o' ! -type l \) -exec rm -f {} \;
1705
1706	# bin.clean and HELP_SOURCE.clean interfere
1707	clean3:
1708	$(MAKE) bin/bin.clean
1709	$(MAKE) HELP_SOURCE/HELP_SOURCE.clean
1710
1711	clean2: $(ARCHS:.a=.clean) \
1712	clean3 \
1713	rmbak \
1714	libclean \
1715	objclean \
1716	lib/lib.clean \
1717	GDEHELP/GDEHELP.clean \
1718	HEADERLIBS/HEADERLIBS.clean \
1719	SOURCE_TOOLS/SOURCE_TOOLS.clean \
1720	UNIT_TESTER/UNIT_TESTER.clean \
1721	TEMPLATES/TEMPLATES.clean \
1722	perl_clean \
1723	clean_directories \
1724
1725	rm -f *.last_gcc config.makefile.bak
1726
1727	# links are needed for cleanup
1728	clean: redo_links motif_xpm_hack_clean
1729	$(MAKE) clean2
1730	$(MAKE) clean_cov_all clean_links
1731
1732	# 'relocated' is about 50% faster than 'rebuild'
1733	reloc_clean: links
1734	@echo "---------------------------------------- Relocation cleanup"
1735	$(MAKE) \
1736	perl_clean \
1737	GDEHELP/GDEHELP.clean \
1738	HELP_SOURCE/genhelp/genhelp.clean \
1739	bin/bin.clean \
1740	libclean \
1741	objclean
1742
1743	relocated: links
1744	$(MAKE) reloc_clean
1745	@echo "---------------------------------------- and remake"
1746	$(MAKE) build
1747
1748	# -----------------------------------
1749	# some stress tests:
1750
1751	rebuild4ever: rebuild
1752	$(MAKE) rebuild4ever
1753
1754	build4ever: build
1755	$(MAKE) build4ever
1756
1757	clean4ever: clean
1758	$(MAKE) clean4ever
1759
1760	test4ever: ut
1761	$(MAKE) test4ever
1762
1763	perl4ever: clean
1764	$(MAKE) links
1765	$(MAKE) perl
1766	$(MAKE) perl4ever
1767
1768
1769	# -----------------------------------
1770
1771	rebuild: clean
1772	$(MAKE) all
1773
1774	relink: bin/bin.clean libclean
1775	$(MAKE) build
1776
1777	tarfile: rebuild
1778	$(MAKE) prepare_libdir
1779	util/arb_compress
1780
1781	tarfile_quick: build
1782	$(MAKE) prepare_libdir
1783	util/arb_compress
1784
1785	save: sourcetarfile
1786
1787	patch:
1788	SOURCE_TOOLS/arb_create_patch.sh arbPatch
1789
1790	# test early whether save will work
1791	savetest:
1792	@util/arb_srclst.pl >/dev/null
1793
1794	testsave: savetest
1795
1796	sourcetarfile: rmbak
1797	util/arb_save
1798
1799	save2: rmbak
1800	util/arb_save ignore
1801
1802	save_test: rmbak
1803	@echo "Testing source list.."
1804	@util/arb_srclst.pl > /dev/null
1805
1806	save_test_no_error:
1807	@-$(MAKE) save_test
1808
1809	rel_minor:
1810	touch SOURCE_TOOLS/inc_minor.stamp
1811	$(MAKE) do_release
1812
1813	rel_major:
1814	touch SOURCE_TOOLS/inc_major.stamp
1815	$(MAKE) do_release
1816
1817	do_release:
1818	@echo Building release
1819	@echo PATH=$(PATH)
1820	@echo ARBHOME=$(ARBHOME)
1821	-rm arb.tgz arbsrc.tgz
1822	$(MAKE) testsave
1823	$(MAKE) genheaders # auto upgrades version early
1824	$(MAKE) tarfile
1825	$(MAKE) sourcetarfile
1826
1827	release_quick:
1828	-rm arb.tgz arbsrc.tgz
1829	$(MAKE) tarfile_quick
1830	$(MAKE) sourcetarfile
1831
1832	# --------------------------------------------------------------------------------
1833
1834	MAKE_IF_COMMITTED=$(MAKE) -C SOURCE_TOOLS -f Makefile.commitbuild
1835
1836	build_CTARGET:
1837	+$(MAKE_IF_COMMITTED) "CTARGET=$(CTARGET)" build_CTARGET
1838
1839	reset_committed_build:
1840	+$(MAKE_IF_COMMITTED) reset
1841
1842	# --------------------------------------------------------------------------------
1843
1844	arbapplications: nt pa e4 wetc pt na nal di ph ds pgt wetc cma
1845
1846	arb_external: convert tools gde readseq tg pst xmlin
1847
1848	arb_no_perl: arbapplications help arb_external
1849
1850	arb: motif_xpm_hack
1851	$(MAKE) "WITHPERL=1" perl arb_no_perl
1852
1853	motif_xpm_hack:
1854	$(MAKE) -r -C "lib/motifHack" all
1855
1856	motif_xpm_hack_clean:
1857	$(MAKE) -r -C "lib/motifHack" clean
1858
1859	# --------------------------------------------------------------------------------
1860	# special targets for SOURCE_TOOLS/remake_after_change.pl
1861
1862	rac_arb_dist: di
1863	rac_arb_edit4: e4
1864	rac_arb_ntree: nt
1865	rac_arb_pars: pa
1866	rac_arb_phylo: ph
1867	rac_arb_wetc: wetc
1868	rac_arb_naligner: nal
1869	rac_arb_pt_server: pt
1870	rac_arb_db_server: ds
1871	rac_arb_name_server: na
1872	rac_arb_pgt: pgt
1873	rac_arb_convert_aln: convert
1874	rac_arb_treegen: tg
1875	rac_arb_rnacma: cma
1876
1877	# --------------------------------------------------------------------------------
1878	# unit testing
1879	# @@@ work in progress
1880	#
1881	# goal is to automatically test all libraries/executables using TESTED_UNITS_AUTO
1882	#
1883	# currently not all test executables link w/o error
1884	# (see UNITS_WORKING, UNITS_UNTESTABLE_ATM and UNITS_NEED_FIX)
1885
1886	# define RNA3D/RNA3D.test
1887	RNA3D_TEST := $(subst .a,.test,$(RNA3D_LIB))
1888
1889	TESTED_UNITS_AUTO = $(ARCHS:.a=.test)
1890
1891	UNITS_WORKING = \
1892	$(RNA3D_TEST) \
1893	ARB_GDE/ARB_GDE.test \
1894	AWTI/AWTI.test \
1895	DIST/DIST.test \
1896	EISPACK/EISPACK.test \
1897	GENOM/GENOM.test \
1898	GENOM_IMPORT/GENOM_IMPORT.test \
1899	GL/glAW/libglAW.test \
1900	GL/glpng/libglpng_arb.test \
1901	ISLAND_HOPPING/ISLAND_HOPPING.test \
1902	NALIGNER/NALIGNER.test \
1903	NAMES/NAMES.test \
1904	PARSIMONY/PARSIMONY.test \
1905	PGT/PGT.test \
1906	PHYLO/PHYLO.test \
1907	PRIMER_DESIGN/PRIMER_DESIGN.test \
1908	PROBE_DESIGN/PROBE_DESIGN.test \
1909	SECEDIT/SECEDIT.test \
1910	SEQ_QUALITY/SEQ_QUALITY.test \
1911	SERVERCNTRL/SERVERCNTRL.test \
1912	SL/ALIVIEW/ALIVIEW.test \
1913	SL/AP_TREE/AP_TREE.test \
1914	SL/ARB_TREE/ARB_TREE.test \
1915	SL/AW_HELIX/AW_HELIX.test \
1916	SL/AW_NAME/AW_NAME.test \
1917	SL/DB_SCANNER/DB_SCANNER.test \
1918	SL/GUI_ALIVIEW/GUI_ALIVIEW.test \
1919	SL/HELIX/HELIX.test \
1920	SL/ITEMS/ITEMS.test \
1921	SL/LOCATION/LOCATION.test \
1922	SL/MATRIX/MATRIX.test \
1923	SL/NDS/NDS.test \
1924	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.test \
1925	SL/REFENTRIES/REFENTRIES.test \
1926	SL/SEQUENCE/SEQUENCE.test \
1927	SL/TRANSLATE/TRANSLATE.test \
1928	SL/TREE_ADMIN/TREE_ADMIN.test \
1929	SL/TREE_READ/TREE_READ.test \
1930	SL/TREE_WRITE/TREE_WRITE.test \
1931	STAT/STAT.test \
1932	TREEGEN/TREEGEN.test \
1933	WETC/WETC.test \
1934	XML/XML.test \
1935
1936	# untestable units
1937
1938	UNITS_NEED_FIX = \
1939	ptpan/PROBE.test \
1940
1941	UNITS_UNTESTABLE_ATM = \
1942	PROBE_SET/PROBE_SET.test \
1943	XML_IMPORT/XML_IMPORT.test \
1944
1945	# for the moment, put all units containing tests into UNITS_TESTED or UNITS_TESTED_FIRST
1946
1947	UNITS_TESTED_FIRST = \
1948	SL/MACROS/MACROS.test \
1949	SL/REGEXPR/REGEXPR.test \
1950	SL/FILTER/FILTER.test \
1951	ARBDB/libARBDB.test \
1952	CONSENSUS_TREE/CONSENSUS_TREE.test \
1953	TOOLS/arb_consensus_tree.test \
1954	TOOLS/arb_test.test \
1955	TOOLS/arb_probe.test \
1956	PERLTOOLS/arb_proto_2_xsub.test \
1957	AWTC/AWTC.test \
1958
1959	UNITS_TESTED = \
1960	DBSERVER/DBSERVER.test \
1961	AWT/libAWT.test \
1962	CORE/libCORE.test \
1963	SL/INSDEL/INSDEL.test \
1964	SL/TREEDISP/TREEDISP.test \
1965	NTREE/NTREE.test \
1966	AISC_MKPTPS/mkptypes.test \
1967	EDIT4/EDIT4.test \
1968	MERGE/MERGE.test \
1969	MULTI_PROBE/MULTI_PROBE.test \
1970	SERVERCNTRL/SERVERCNTRL.test \
1971	SL/FAST_ALIGNER/FAST_ALIGNER.test \
1972	SL/PRONUC/PRONUC.test \
1973	WINDOW/libWINDOW.test \
1974	HELP_SOURCE/arb_help2xml.test \
1975	CONVERTALN/CONVERTALN.test \
1976	SL/SEQIO/SEQIO.test \
1977	SL/PTCLEAN/PTCLEAN.test \
1978	PROBE/PROBE.test \
1979	SL/DB_QUERY/DB_QUERY.test \
1980
1981	TESTED_UNITS_MANUAL = \
1982	$(UNITS_TESTED_FIRST) \
1983	$(UNITS_TESTED) \
1984
1985	# $(UNITS_WORKING)
1986
1987	# see UNIT_TESTER/sym2testcode.pl@disableErrorOnUnitsWithoutTests
1988
1989	#TESTED_UNITS = $(TESTED_UNITS_AUTO)
1990	TESTED_UNITS = $(TESTED_UNITS_MANUAL)
1991
1992	# ----------------------------------------
1993
1994	TEST_LOG_DIR = UNIT_TESTER/logs
1995	TEST_RUN_SUITE=$(MAKE) $(NODIR) -C UNIT_TESTER -f Makefile.suite -r
1996	TEST_MAKE_FLAGS=
1997	TEST_POST_CLEAN=
1998	ifeq ($(COVERAGE),1)
1999	TEST_POST_CLEAN=$(MAKE) clean_cov
2000	TEST_MAKE_FLAGS+=-j1
2001	endif
2002
2003
2004	%.test: %.dummy
2005	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
2006	( \
2007	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
2008	"UNITDIR=$(@D)" \
2009	"UNITLIBNAME=$(@F:.test=)" \
2010	"COVERAGE=$(COVERAGE)" \
2011	"cflags=$(cflags)" \
2012	"ARB_PID=$(ARB_PID)_$(@F)" \
2013	runtest; \
2014	$(TEST_POST_CLEAN) \
2015	) >$(TEST_LOG_DIR)/$(@F).log 2>&1; echo "- $(@F)")
2016
2017
2018	test_base: $(UNIT_TESTER_LIB:.a=.dummy)
2019
2020	clean_cov:
2021	find . \( -name ".gcda" -o -name ".gcov" -o -name "*.cov" \) -exec rm {} \;
2022
2023	clean_cov_all: clean_cov
2024	find . \( -name "*.gcno" \) -exec rm {} \;
2025
2026	run_tests: test_base clean_cov
2027	$(MAKE) "ARB_PID=UT_$$$$" run_tests_faked_arbpid
2028
2029	run_tests_faked_arbpid:
2030	+@$(TEST_RUN_SUITE) init
2031	@echo "fake[1]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2032	$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(TESTED_UNITS)
2033	@echo "fake[1]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2034	+@$(TEST_RUN_SUITE) cleanup
2035	@$(MAKE) clean_cov >/dev/null
2036
2037	ut:
2038	ifeq ($(UNIT_TESTS),1)
2039	@echo $(MAKE) run_tests
2040	@$(MAKE) run_tests
2041	else
2042	@echo "Not compiled with unit tests"
2043	endif
2044
2045
2046	aut:
2047	+@$(TEST_RUN_SUITE) unskip
2048	$(MAKE) ut
2049
2050	# --------------------------------------------------------------------------------
2051
2052	TIMELOG=$(ARBHOME)/arb_time.log
2053	TIMEARGS=--append --output=$(TIMELOG) --format=" %E(%S+%U) %P [%C]"
2054	TIMECMD=$(TIME) $(TIMEARGS)
2055
2056	time_one:
2057	ifeq ($(ONE_TIMED_TARGET),)
2058	@echo "Error: You have to pass ONE_TIMED_TARGET to $@"
2059	false
2060	else
2061	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET)"
2062	@$(TIMECMD) $(MAKE) $(ONE_TIMED_TARGET)
2063	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET) [done]"
2064	endif
2065
2066	timed_target:
2067	ifeq ($(TIMED_TARGET),)
2068	@echo "Error: You have to pass TIMED_TARGET to $@"
2069	false
2070	else
2071	@echo "Build time:" > $(TIMELOG)
2072	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2073	@cat $(TIMELOG)
2074	@rm $(TIMELOG)
2075	endif
2076
2077	timed_target_tested:
2078	ifeq ($(TIMED_TARGET),)
2079	@echo "Error: You have to pass TIMED_TARGET to $@"
2080	false
2081	else
2082	@echo "Build time:" > $(TIMELOG)
2083	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2084	$(MAKE) "ONE_TIMED_TARGET=ut" time_one
2085	@cat $(TIMELOG)
2086	@rm $(TIMELOG)
2087	endif
2088
2089	clean_timed_target:
2090	ifeq ($(TIMED_TARGET),)
2091	@echo "Error: You have to pass TIMED_TARGET to $@"
2092	false
2093	else
2094	@echo "Build time:" > $(TIMELOG)
2095	$(MAKE) "ONE_TIMED_TARGET=clean" time_one
2096	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2097	@cat $(TIMELOG)
2098	@rm $(TIMELOG)
2099	endif
2100
2101	# --------------------------------------------------------------------------------
2102
2103	build: arb
2104	$(MAKE) binlink preplib
2105
2106	all:
2107	@echo "Build time" > $(TIMELOG)
2108	@echo "$(SEP) $(MAKE) build"
2109	@$(TIMECMD) $(MAKE) build
2110	@echo $(SEP)
2111	@echo "made 'all' with success."
2112	@echo "to start arb enter 'arb'"
2113	ifeq ($(UNIT_TESTS),1)
2114	@echo $(MAKE) run_tests
2115	@$(TIMECMD) $(MAKE) run_tests
2116	endif
2117	@echo "$(SEP) $(MAKE) build [done]"
2118	@$(MAKE) save_test_no_error >/dev/null # just show hints
2119	@cat $(TIMELOG)
2120	@rm $(TIMELOG)
2121
2122

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