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Last change on this file was 8327, checked in by westram, 12 years ago
clang static analyzer working
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 56.7 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	# ---------------------- [basic compiler setting]
48
49	GCC:=$(CC)
50	GPP:=$(CXX)
51	CPPreal:=cpp
52
53	# to use clang-static-analyzer, call make like this:
54	# setenv CLANG_STATIC_CHECKER 1 ; scan-build make -j5 build
55	ifeq ($(CLANG_STATIC_CHECKER),1)
56	CCC_ANALYZER_CPLUSPLUS=1
57	endif
58
59	# ---------------------- compiler version detection
60
61	# supported compiler versions:
62
63	ALLOWED_GCC_4xx_VERSIONS=\
64	4.3 4.3.1 4.3.2 4.3.3 4.3.4 \
65	4.4 4.4.1 4.4.3 4.4.5 \
66	4.5.2 \
67	4.6 4.6.1
68
69	ALLOWED_GCC_VERSIONS=$(ALLOWED_GCC_4xx_VERSIONS)
70
71	GCC_VERSION_FOUND=$(shell $(GCC) -dumpversion)
72	GCC_VERSION_ALLOWED=$(strip $(subst ___,,$(foreach version,$(ALLOWED_GCC_VERSIONS),$(findstring ___$(version)___,___$(GCC_VERSION_FOUND)___))))
73
74	#---------------------- split gcc version
75
76	SPLITTED_VERSION:=$(subst ., ,$(GCC_VERSION_FOUND))
77
78	USE_GCC_MAJOR:=$(word 1,$(SPLITTED_VERSION))
79	USE_GCC_MINOR:=$(word 2,$(SPLITTED_VERSION))
80	USE_GCC_PATCHLEVEL:=$(word 3,$(SPLITTED_VERSION))
81
82	USE_GCC_452_OR_HIGHER:=
83	ifeq ($(USE_GCC_MAJOR),4)
84	ifeq ($(USE_GCC_MINOR),5)
85	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),23456789)','')
86	USE_GCC_452_OR_HIGHER:=yes
87	endif
88	else
89	ifneq ('$(findstring $(USE_GCC_MINOR),6789)','')
90	USE_GCC_452_OR_HIGHER:=yes
91	endif
92	endif
93	else
94	USE_GCC_452_OR_HIGHER:=yes
95	endif
96
97	#---------------------- define special directories for non standard builds
98
99	ifdef DARWIN
100	OSX_SDK:=/Developer/SDKs/MacOSX10.5.sdk
101	OSX_FW:=/System/Library/Frameworks
102	OSX_FW_OPENGL:=$(OSX_FW)/OpenGL.framework/Versions/A/Libraries
103	OSX_FW_IMAGEIO:=$(OSX_FW)/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources
104	endif
105
106	#----------------------
107
108	ifdef DARWIN
109	LINK_STATIC=1# link static
110	else
111	LINK_STATIC=0# link dynamically
112	endif
113
114	shared_cflags :=# flags for shared lib compilation
115	lflags :=# linker flags
116	extended_warnings :=# warning flags for C and C++-compiler
117	extended_cpp_warnings :=# warning flags for C++-compiler only
118
119
120	ifeq ($(DEBUG),0)
121	dflags := -DNDEBUG# defines
122	cflags := -O4# compiler flags (C and C++)
123	ifndef DARWIN
124	lflags += -O99# linker flags
125	endif
126	endif
127
128	ifeq ($(DEBUG),1)
129	dflags := -DDEBUG
130	cflags := -O0 -g -g3 -ggdb -ggdb3
131	# cflags := -O2 -g -g3 -ggdb -ggdb3 # use this for callgrind (force inlining)
132	ifndef DARWIN
133	lflags += -g
134	endif
135
136	# control how much you get spammed
137	POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl
138	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --original# dont modify compiler output
139	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --hide-Noncopyable-advices
140	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --show-useless-Weff++
141	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --no-warnings
142	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --only-first-error
143	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --no-warnings --only-first-error
144
145	# Enable extra warnings
146	extended_warnings :=
147	extended_cpp_warnings :=
148
149	# C and C++
150	extended_warnings += -Wwrite-strings -Wunused -Wno-aggregate-return -Wshadow
151
152	# C++ only
153	extended_cpp_warnings += -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute
154	extended_cpp_warnings += -Wctor-dtor-privacy# < gcc 3
155	# extended_cpp_warnings += -Wfloat-equal# gcc 3.0
156
157	# ------- above only warnings available in 3.0
158
159	extended_cpp_warnings += -Weffc++# gcc 3.0.1
160	extended_cpp_warnings += -Wmissing-noreturn# gcc 3.0.2
161	# extended_cpp_warnings += -Wold-style-cast# gcc 3.0.4 (warn about 28405 old-style casts)
162	extended_cpp_warnings += -Winit-self# gcc 3.4.0
163	extended_cpp_warnings += -Wstrict-aliasing# gcc 3.4
164	extended_cpp_warnings += -Wextra# gcc 3.4.0
165	ifeq ('$(USE_GCC_452_OR_HIGHER)','yes')
166	extended_cpp_warnings += -Wlogical-op# gcc 4.5.2
167	endif
168
169	ifeq ($(DEBUG_GRAPHICS),1)
170	dflags += -DDEBUG_GRAPHICS
171	endif
172	endif
173
174	#---------------------- developer
175
176	ifneq ($(DEVELOPER),ANY) # ANY=default setting (skip all developer specific code)
177	ifdef dflags
178	dflags += -DDEVEL_$(DEVELOPER)# activate developer/release specific code
179	endif
180	endif
181
182	ifndef SHOWTODO
183	ifeq ($(DEVELOPER),RALF)
184	SHOWTODO:=1
185	else
186	SHOWTODO:=0
187	endif
188	endif
189	ifeq ($(SHOWTODO),1)
190	dflags += -DWARN_TODO# activate "TODO" warnings
191	endif
192
193	#---------------------- 32 or 64 bit
194
195	ifndef ARB_64
196	ARB_64=0#default to 32bit
197	endif
198	ifndef BUILDHOST_64
199	BUILDHOST_64:=$(ARB_64)# assume build host is same as version (see config.makefile)
200	endif
201
202	cross_cflags:=
203	cross_lflags:=
204
205	ifeq ($(ARB_64),1)
206	dflags += -DARB_64 #-fPIC
207	lflags +=
208	shared_cflags += -fPIC
209
210	ifeq ($(BUILDHOST_64),1)
211	# build 64-bit ARB version on 64-bit host
212	CROSS_LIB:=# empty = autodetect below
213	ifdef DARWIN
214	cross_cflags += -arch x86_64
215	cross_lflags += -arch x86_64
216	endif
217	else
218	# build 64-bit ARB version on 32-bit host
219	CROSS_LIB:=/lib64
220	cross_cflags += -m64
221	cross_lflags += -m64 -m elf_x86_64
222	endif
223	else
224	ifeq ($(BUILDHOST_64),1)
225	# build 32-bit ARB version on 64-bit host
226	CROSS_LIB:=# empty = autodetect below
227	cross_cflags += -m32
228	cross_lflags += -m32 -m elf_i386
229	else
230	# build 32-bit ARB version on 32-bit host
231	CROSS_LIB:=/lib
232	endif
233	endif
234
235	cflags += $(cross_cflags)
236	lflags += $(cross_lflags)
237
238	ifeq ('$(CROSS_LIB)','')
239	# autodetect libdir
240	ifeq ($(ARB_64),1)
241	CROSS_LIB:=$(shell (test -d /lib64 && echo lib64) \|\| echo lib)
242	else
243	CROSS_LIB:=$(shell (test -d /lib32 && echo lib32) \|\| echo lib)
244	endif
245	endif
246
247	#---------------------- unit tests
248
249	ifndef UNIT_TESTS
250	UNIT_TESTS=0#default is "no tests"
251	endif
252	ifeq ($(UNIT_TESTS),1)
253	dflags += -DUNIT_TESTS
254	UNIT_TESTER_LIB=UNIT_TESTER/UNIT_TESTER.a
255	else
256	UNIT_TESTER_LIB=
257	endif
258
259	#---------------------- use gcov
260
261	ifndef COVERAGE
262	COVERAGE=0#default is "no"
263	endif
264	ifneq ($(COVERAGE),0)
265	GCOVFLAGS=-ftest-coverage -fprofile-arcs
266	cflags += $(GCOVFLAGS)
267	EXECLIBS=-lgcov
268	else
269	GCOVFLAGS=
270	EXECLIBS=
271	endif
272
273	#---------------------- other flags
274
275	dflags += -D$(MACH) # define machine
276
277	ifdef DARWIN
278	cflags += -no-cpp-precomp
279	shared_cflags += -fno-common
280	else
281	dflags += $(shell getconf LFS_CFLAGS)
282	endif
283
284	cflags += -pipe
285	cflags += -fmessage-length=0# don't wrap compiler output
286	cflags += -fshow-column# show columns
287	cflags += -funit-at-a-time
288	cflags += -fPIC
289	cflags += -fno-common# link all global data into one namespace
290	cflags += -fstrict-aliasing# gcc 3.4
291
292	#---------------------- X11 location
293
294	XHOME:=/usr/X11R6
295	XINCLUDES:=-I$(XHOME)/include
296
297	ifdef DARWIN
298	XINCLUDES := -I/sw/include -I$(OSX_SDK)/usr/X11/include -I$(OSX_SDK)/usr/include/krb5 -I/usr/OpenMotif/include #Snow Leopard couldn't find OpenMotif
299	endif
300
301	ifdef DARWIN
302	XLIBS := -L/usr/OpenMotif/lib -lXm -L$(XHOME)/lib -lpng -lXt -lX11 -lXext -lc -lXmu -lXi
303	XLIBS += -lGLU -lGL -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGL.dylib:$(OSX_FW_OPENGL)/libGL.dylib
304	else
305	XLIBS:=-L$(XHOME)/$(CROSS_LIB) -lXm -lXpm -lXt -lXext -lX11
306	endif
307
308	#---------------------- open GL
309
310	ifeq ($(OPENGL),1)
311	cflags += -DARB_OPENGL # activate OPENGL code
312	GL := gl # this is the name of the OPENGL base target
313	GL_LIB_SYS := -lGL -lGLU
314	GL_LIB_ARB := -L$(ARBHOME)/GL/glAW -lglAW
315
316	ifdef DEBIAN
317	GL_LIB_SYS += -lpthread
318	endif
319
320	GL_PNGLIBS_ARB := -L$(ARBHOME)/GL/glpng -lglpng_arb
321	GL_PNGLIBS_SYS := -lpng
322
323	ifdef DARWIN
324	GLEWLIB := -L/usr/lib -lGLEW -L$(OSX_SDK)/usr/X11/lib -lGLw
325	GLUTLIB := -L$(XHOME)/lib -lglut
326	else
327	GLEWLIB := -lGLEW -lGLw
328	GLUTLIB := -lglut
329	endif
330
331	GL_LIBS_SYS := $(GL_LIB_SYS) $(GL_PNGLIBS_SYS) $(GLEWLIB) $(GLUTLIB)
332	GL_LIBS_ARB := $(GL_LIB_ARB) $(GL_PNGLIBS_ARB)
333
334	RNA3D_LIB := RNA3D/RNA3D.a
335
336	else
337	# OPENGL=0
338
339	GL_LIBS_ARB:=# no opengl -> no libs
340	GL_LIBS_SYS:=# no opengl -> no libs
341	GL:=# don't build ARB openGL libs
342
343	RNA3D_LIB :=
344
345	endif
346
347
348
349	GL_LIBS:=$(GL_LIBS_ARB) $(GL_LIBS_SYS)
350
351	#---------------------- tiff lib:
352
353	ifdef DARWIN
354	TIFFLIBS := -L/usr/local/lib -ltiff -L$(OSX_FW_IMAGEIO) -lTIFF
355	else
356	TIFFLIBS := -ltiff
357	endif
358
359	#---------------------- basic libs:
360
361	SYSLIBS:=
362
363	ifdef DARWIN
364	SYSLIBS += -lstdc++
365	else
366	SYSLIBS += -lm
367	endif
368
369	#---------------------- include symbols?
370
371	ifeq ($(TRACESYM),1)
372	ifdef DARWIN
373	cdynamic =
374	ldynamic =
375	else
376	cdynamic = -rdynamic -Wl,--export-dynamic
377	ldynamic = --export-dynamic
378	endif
379	endif
380
381	# -------------------------------------------------------------------------
382	# Don't put any machine/version/etc conditionals below!
383	# (instead define variables above)
384	# -------------------------------------------------------------------------
385
386	cflags += -W -Wall $(dflags) $(extended_warnings) $(cdynamic)
387
388	cppflags := $(extended_cpp_warnings)
389
390	ifeq ($(DEVELOPER),RALF)
391	HAVE_GNUPP0X=`SOURCE_TOOLS/requireVersion.pl 4.3 $(GCC_VERSION_FOUND)`
392	ifeq ($(HAVE_GNUPP0X),1)
393	# ensure compatibility with upcoming C++ standard
394	cppflags += -std=gnu++0x
395	endif
396	endif
397
398	# compiler settings:
399
400	ACC := $(GCC)# compile C
401	CPP := $(GPP) $(cppflags)# compile C++
402	ACCLIB := $(ACC) $(shared_cflags)# compile C (shared libs)
403	CPPLIB := $(CPP) $(shared_cflags)# compile C++ (shared libs)
404
405	PP := $(CPPreal)# preprocessor
406
407	LINK_STATIC_LIB := ld $(lflags) $(ldynamic) -r -o# link static lib
408	LINK_EXECUTABLE := $(GPP) $(lflags) $(cdynamic) -o# link executable (c++)
409
410	ifeq ($(LINK_STATIC),1)
411	SHARED_LIB_SUFFIX = a# static lib suffix
412	LINK_SHARED_LIB := $(LINK_STATIC_LIB)
413	else
414	SHARED_LIB_SUFFIX = so# shared lib suffix
415	LINK_SHARED_LIB := $(GPP) $(lflags) $(cdynamic) -shared $(GCOVFLAGS) -o# link shared lib
416	endif
417
418	# other used tools
419
420	ifdef DARWIN
421	XMKMF := /usr/X11/bin/xmkmf
422	else
423	XMKMF := /usr/bin/X11/xmkmf
424	endif
425	MAKEDEPEND_PLAIN = makedepend
426
427	MAKEDEPEND = $(FORCEMASK);$(MAKEDEPEND_PLAIN)
428
429	#SEP:=--------------------------------------------------------------------------------
430	SEP=[`date +%M:%S.%N`] ------------------------------------------------
431	# to analyse timings run
432	# make -j9 clean; make -j9 all \| grep '^\[' \| sort
433	# make -j9 "TIMED_TARGET=perl" clean_timed_target \| grep '^\[' \| sort
434
435
436
437	# delete variables unused below
438
439	lflags:=
440
441	# -------------------------
442	# Main arb targets:
443	# -------------------------
444
445	first_target:
446	$(MAKE) checks
447	@echo $(SEP)
448	@echo 'Main targets:'
449	@echo ''
450	@echo ' all - Compile ARB + TOOLs + and copy shared libs + link foreign software'
451	@echo ' (That is most likely the target you want)'
452	@echo ''
453	@echo ' clean - remove generated files ("SUBDIR/SUBDIR.clean" to clean only SUBDIR)'
454	@echo ' rebuild - clean + all'
455	@echo ' relink - remove all binaries and relink them from objects'
456	@echo ''
457	@echo 'Some often used sub targets (make all makes them all):'
458	@echo ''
459	@echo ' arb - Just compile ARB (but none of the integrated tools)'
460	@echo ' menus - create GDEHELP/ARB_GDEmenus from GDEHELP/ARB_GDEmenus.source'
461	@echo ' perl - Compile the PERL XSUBS into lib/ARB.so and create links in lib to perl'
462	@echo ' binlink - Create all links in the bin directory'
463	@echo ''
464	@echo 'Development targets:'
465	@echo ''
466	@echo ' depends - create or update dependencies ("SUBDIR/SUBDIR.depends" to update only SUBDIR)'
467	@echo ' proto - create or update prototypes ("SUBDIR/SUBDIR.proto" to update only SUBDIR)'
468	@echo ' tags - create tags for xemacs'
469	@echo ' show - show available shortcuts (AKA subtargets)'
470	@echo ' up - shortcut for depends+proto+tags'
471	ifeq ($(UNIT_TESTS),1)
472	@echo ' ut - only run tests'
473	endif
474	@echo ' modified - rebuild files modified in svn checkout (does touch)'
475	@echo ' touch - touch files modified in svn checkout'
476	@echo ''
477	@echo 'Internal maintenance:'
478	@echo ''
479	@echo ' rel_minor - build a release (increases minor version number)'
480	@echo ' rel_major - build a release (increases MAJOR version number)'
481	@echo ' tarfile - make rebuild and create arb version tarfile ("tarfile_quick" to skip rebuild)'
482	@echo ' save - save all basic ARB sources into arbsrc_DATE ("savetest" to check filelist)'
483	@echo ' patch - save svn diff to patchfile'
484	@echo ' source_doc - create doxygen documentation'
485	@echo ' relocated - rebuild partly (use when you have relocated ARBHOME)'
486	@echo ' check_res - check ressource usage'
487	@echo ' dep_graph - Build dependency graphs'
488	@echo ' clean_cov - Clean coverage results'
489	@echo ''
490	@echo $(SEP)
491	@echo ''
492
493
494	# auto-generate config.makefile:
495
496	CONFIG_MAKEFILE_FOUND=$(wildcard config.makefile)
497
498	config.makefile : config.makefile.template
499	@echo --------------------------------------------------------------------------------
500	ifeq ($(strip $(CONFIG_MAKEFILE_FOUND)),)
501	@cp $< $@
502	@echo '$(ARBHOME)/$@:1: has been generated.'
503	@echo 'Please edit $@ to configure your system!'
504	@echo --------------------------------------------------------------------------------
505	@false
506	else
507	@echo '$(ARBHOME)/$<:1: is more recent than'
508	@echo '$(ARBHOME)/$@:1:'
509	@ls -al config.makefile*
510	@echo --------------------------------------------------------------------------------
511	@echo "Updating $@ (if this fails, check manually)"
512	SOURCE_TOOLS/update_config_makefile.pl
513	@echo "Sucessfully updated $@"
514	@echo --------------------------------------------------------------------------------
515	@ls -al config.makefile*
516	@echo --------------------------------------------------------------------------------
517	@echo "Diff to your old config.makefile:"
518	@echo --------------------------------------------------------------------------------
519	-diff $@.bak $@
520	@echo --------------------------------------------------------------------------------
521	endif
522
523	# check if everything is configured correctly
524
525	check_DEVELOPER:
526	ifndef DEVELOPER
527	@echo 'config.makefile:1: DEVELOPER not defined'
528	@false
529	endif
530
531	check_DEBUG:
532	ifndef dflags
533	@echo 'config.makefile:1: DEBUG has to be defined. Valid values are 0 and 1'
534	@false
535	endif
536
537	check_ARB_64:
538	ifndef ARB_64
539	@echo 'config.makefile:1: ARB_64 has to be defined. Valid values are 0 and 1'
540	@false
541	endif
542
543	# ---------------------------------------- check gcc version
544
545	check_same_GCC_VERSION:
546	$(ARBHOME)/SOURCE_TOOLS/check_same_gcc_version.pl $(GCC_VERSION_ALLOWED)
547
548	check_GCC_VERSION:
549	@echo 'GCC version check:'
550	@echo " - Your version is '$(GCC_VERSION_FOUND)'"
551	ifeq ('$(GCC_VERSION_ALLOWED)', '')
552	@echo ' - This version is not in the list of supported gcc-versions:'
553	@$(foreach version,$(ALLOWED_GCC_VERSIONS),echo ' * $(version)';)
554	@echo ' - You may either ..'
555	@echo ' - add your version to ALLOWED_GCC_VERSIONS in the Makefile and try it out or'
556	@echo ' - switch to one of the allowed versions (see arb_README_gcc.txt for installing'
557	@echo ' a different version of gcc)'
558	@echo ''
559	@false
560	else
561	@echo " - Supported gcc version '$(GCC_VERSION_ALLOWED)' detected - fine!"
562	@echo ''
563	$(MAKE) check_same_GCC_VERSION
564
565	endif
566
567	GCC_WITH_VTABLE_AFTER_CLASS=#occurred only with no longer supported $(ALLOWED_GCC_295_VERSIONS)
568	HAVE_GCC_WITH_VTABLE_AFTER_CLASS=$(strip $(foreach version,$(GCC_WITH_VTABLE_AFTER_CLASS),$(findstring $(version),$(GCC_VERSION_ALLOWED))))
569
570	# depending on the version of gcc the location of the vtable pointer differs.
571	ifeq ('$(HAVE_GCC_WITH_VTABLE_AFTER_CLASS)', '')
572	VTABLE_INFRONTOF_CLASS=1
573	else
574	VTABLE_INFRONTOF_CLASS=0
575	endif
576
577	#---------------------- check ARBHOME
578
579	# use arb_INSTALL.txt to determine whether ARBHOME points to correct directory
580	ARB_INSTALL_FOUND=$(wildcard $(ARBHOME)/arb_INSTALL.txt)
581
582	check_ARBHOME:
583	ifeq ($(strip $(ARB_INSTALL_FOUND)),)
584	@echo ------------------------------------------------------------
585	@echo "ARBHOME is set to '$(ARBHOME)'"
586	@echo "The environment variable ARBHOME has to point to the top arb source directory."
587	@echo "If you use bash enter:"
588	@echo " export ARBHOME='`pwd`'"
589	@echo ------------------------------------------------------------
590	@false
591	endif
592
593	ARB_PATH_SET=$(findstring $(ARBHOME)/bin,$(PATH))
594
595	check_PATH: check_ARBHOME
596	ifeq ($(strip $(ARB_PATH_SET)),)
597	@echo ------------------------------------------------------------
598	@echo "The environment variable PATH has to contain $(ARBHOME)/bin"
599	@echo "If you use bash enter:"
600	@echo ' export PATH=$$ARBHOME/bin:$$PATH'
601	@echo ------------------------------------------------------------
602	@false
603	endif
604
605	check_TOOLS:
606	@util/arb_check_build_env.pl \
607	"$(ACC)" \
608	"$(CPP)" \
609	"$(GPP)" \
610	"$(PP)" \
611	"$(ACCLIB)" \
612	"$(CPPLIB)" \
613	"$(XMKMF)" \
614	"$(MAKEDEPEND_PLAIN)" \
615	"$(LINK_SHARED_LIB)" \
616	"$(LINK_SHARED_LIB)" \
617
618
619	check_ENVIRONMENT : check_PATH check_TOOLS
620
621	check_tabs: check_setup
622	ifeq ($(DEBUG),1)
623	@SOURCE_TOOLS/tabBrake.pl
624	endif
625
626	force_tab_check:
627	@touch -t 198001010000 SOURCE_TOOLS/tabBrake.stamp
628	@$(MAKE) check_tabs
629
630
631	# ---------------------
632
633	check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION
634	@echo Your setup seems to be ok.
635
636	checks: check_setup check_tabs
637	@rm -f SOURCE_TOOLS/postcompile.sav
638
639
640	# end test section ------------------------------
641
642	CORE_LIB=-lCORE
643	ARBDB_LIB=-lARBDB $(CORE_LIB)
644
645	LIBS = $(ARBDB_LIB) $(SYSLIBS)
646	GUI_LIBS = $(LIBS) -lWINDOW -lAWT $(XLIBS)
647
648	LIBPATH = -L$(ARBHOME)/LIBLINK
649
650	DEST_LIB = lib
651	DEST_BIN = bin
652
653	AINCLUDES := -I. -I$(ARBHOME)/INCLUDE $(XINCLUDES)
654	CPPINCLUDES := -I. -I$(ARBHOME)/INCLUDE $(XINCLUDES)
655	MAKEDEPENDFLAGS := -- $(cflags) -- -DARB_OPENGL -DUNIT_TESTS -D__cplusplus -I. -Y$(ARBHOME)/INCLUDE
656
657	ifeq ($(VTABLE_INFRONTOF_CLASS),1)
658	# Some code in ARB depends on the location of the vtable pointer
659	# (it does a cast from class AP_tree to struct GBT_TREE). In order to
660	# work around that hack properly, we define FAKE_VTAB_PTR
661	# if the vtable is located at the beginning of class.
662	# We are really sorry for that hack.
663	cflags:=$(cflags) -DFAKE_VTAB_PTR=char
664	endif
665
666	# -------------------------------
667	# old PTSERVER or PTPAN?
668
669	ifeq ($(PTPAN),1)
670	# PTPAN only libs
671	ARCHS_PT_SERVER = \
672	ptpan/PROBE.a
673	else
674	ifeq ($(PTPAN),2)
675	# special mode to compile both servers (developers only!)
676	ARCHS_PT_SERVER = \
677	ptpan/PROBE.a \
678	PROBE/PROBE.a
679	ARCHS_PT_SERVER_LINK = PROBE/PROBE.a# default to old ptserver
680	else
681	# PT-server only libs
682	ARCHS_PT_SERVER = \
683	PROBE/PROBE.a
684	endif
685	endif
686
687	ifndef ARCHS_PT_SERVER_LINK
688	ARCHS_PT_SERVER_LINK = $(ARCHS_PT_SERVER)
689	endif
690
691	# ---------------------------------------
692	# wrap main()
693
694	use_ARB_main=$(ARBHOME)/SOURCE_TOOLS/arb_main_cpp.o
695	use_ARB_main_C=$(ARBHOME)/SOURCE_TOOLS/arb_main_c.o
696
697	arbmainwrapper:
698	$(MAKE) -C SOURCE_TOOLS -r "cflags = $(cflags)" mainwrapper
699
700	# ---------------------------------------
701	# List of standard top level directories
702	#
703	# sub-makefiles have to define the targets
704	# - 'depends' and
705	# - 'clean'
706	#
707	# when adding new libs here, also add a dependency vs 'links' or 'links_non_perl' below
708
709	ARCHS = \
710	$(ARCHS_PT_SERVER) \
711	AISC/AISC.a \
712	AISC_MKPTPS/AISC_MKPTPS.a \
713	ARBDB/libARBDB.a \
714	CORE/libCORE.a \
715	ARB_GDE/ARB_GDE.a \
716	AWT/libAWT.a \
717	AWTC/AWTC.a \
718	AWTI/AWTI.a \
719	CONSENSUS_TREE/CONSENSUS_TREE.a \
720	CONVERTALN/CONVERTALN.a \
721	DBSERVER/DBSERVER.a \
722	DIST/DIST.a \
723	EDIT4/EDIT4.a \
724	EISPACK/EISPACK.a \
725	GDE/GDE.a \
726	GENOM/GENOM.a \
727	GENOM_IMPORT/GENOM_IMPORT.a \
728	GL/GL.a \
729	ISLAND_HOPPING/ISLAND_HOPPING.a \
730	MERGE/MERGE.a \
731	MULTI_PROBE/MULTI_PROBE.a \
732	NALIGNER/NALIGNER.a \
733	NAMES/NAMES.a \
734	NAMES_COM/server.a \
735	NTREE/NTREE.a \
736	PARSIMONY/PARSIMONY.a \
737	PERLTOOLS/PERLTOOLS.a \
738	PGT/PGT.a \
739	PHYLO/PHYLO.a \
740	PRIMER_DESIGN/PRIMER_DESIGN.a \
741	PROBE_COM/server.a \
742	PROBE_DESIGN/PROBE_DESIGN.a \
743	PROBE_SET/PROBE_SET.a \
744	READSEQ/READSEQ.a \
745	RNA3D/RNA3D.a \
746	RNACMA/RNACMA.a \
747	SECEDIT/SECEDIT.a \
748	SEQ_QUALITY/SEQ_QUALITY.a \
749	SERVERCNTRL/SERVERCNTRL.a \
750	SL/SL.a \
751	STAT/STAT.a \
752	TOOLS/TOOLS.a \
753	TREEGEN/TREEGEN.a \
754	UNIT_TESTER/UNIT_TESTER.a \
755	WETC/WETC.a \
756	WINDOW/libWINDOW.a \
757	XML/XML.a \
758
759	# -----------------------
760	# library packets
761
762	ARCHS_CLIENT_PROBE = PROBE_COM/client.a
763	ARCHS_CLIENT_NAMES = NAMES_COM/client.a
764	ARCHS_MAKEBIN = AISC_MKPTPS/AISC_MKPTPS.a AISC/AISC.a
765
766	# communication libs need aisc and aisc_mkpts:
767
768	AISC/AISC.dummy: proto_tools
769
770	comtools: AISC/AISC.dummy
771
772	ARCHS_SEQUENCE = \
773	SL/SEQUENCE/SEQUENCE.a \
774	SL/ALIVIEW/ALIVIEW.a \
775	SL/PRONUC/PRONUC.a \
776
777	ARCHS_TREE = \
778	$(ARCHS_SEQUENCE) \
779	SL/FILTER/FILTER.a \
780	SL/ARB_TREE/ARB_TREE.a \
781
782	# parsimony tree (used by NTREE, PARSIMONY, STAT(->EDIT4), DIST(obsolete!))
783	ARCHS_AP_TREE = \
784	$(ARCHS_TREE) \
785	SL/AP_TREE/AP_TREE.a \
786
787	# --------------------------------------------------------------------------------
788	# dependencies for linking shared libs
789
790	link_core: core
791	link_db: db link_core
792	link_aw: aw link_db
793	link_awt: awt link_aw
794
795	#***************************************************************************************
796	# Individual Programs Section
797	#***************************************************************************************
798
799	#********************************* arb_ntree ************************************
800	NTREE = bin/arb_ntree
801	ARCHS_NTREE = \
802	NTREE/NTREE.a \
803	$(ARCHS_AP_TREE) \
804	ARB_GDE/ARB_GDE.a \
805	AWTC/AWTC.a \
806	AWTI/AWTI.a \
807	GENOM/GENOM.a \
808	GENOM_IMPORT/GENOM_IMPORT.a \
809	MERGE/MERGE.a \
810	MULTI_PROBE/MULTI_PROBE.a \
811	PRIMER_DESIGN/PRIMER_DESIGN.a \
812	PROBE_DESIGN/PROBE_DESIGN.a \
813	SEQ_QUALITY/SEQ_QUALITY.a \
814	SERVERCNTRL/SERVERCNTRL.a \
815	SL/AW_NAME/AW_NAME.a \
816	SL/DB_UI/DB_UI.a \
817	SL/DB_SCANNER/DB_SCANNER.a \
818	SL/DB_QUERY/DB_QUERY.a \
819	SL/SEQIO/SEQIO.a \
820	SL/FILE_BUFFER/FILE_BUFFER.a \
821	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
822	SL/HELIX/HELIX.a \
823	SL/REGEXPR/REGEXPR.a \
824	SL/REFENTRIES/REFENTRIES.a \
825	SL/NDS/NDS.a \
826	SL/ITEMS/ITEMS.a \
827	SL/LOCATION/LOCATION.a \
828	SL/TRANSLATE/TRANSLATE.a \
829	SL/TREEDISP/TREEDISP.a \
830	SL/TREE_READ/TREE_READ.a \
831	SL/TREE_WRITE/TREE_WRITE.a \
832	STAT/STAT.a \
833	XML/XML.a \
834
835	$(NTREE): $(ARCHS_NTREE:.a=.dummy) link_awt
836	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NTREE) $(GUI_LIBS) \|\| ( \
837	echo "$(SEP) Link $@"; \
838	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS)" ; \
839	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS) && \
840	echo "$(SEP) Link $@ [done]"; \
841	)
842
843	#********************************* arb_edit4 ************************************
844	EDIT4 = bin/arb_edit4
845
846	ARCHS_EDIT4 := \
847	EDIT4/EDIT4.a \
848	$(ARCHS_AP_TREE) \
849	ARB_GDE/ARB_GDE.a \
850	AWTC/AWTC.a \
851	ISLAND_HOPPING/ISLAND_HOPPING.a \
852	SECEDIT/SECEDIT.a \
853	SERVERCNTRL/SERVERCNTRL.a \
854	SL/AW_HELIX/AW_HELIX.a \
855	SL/AW_NAME/AW_NAME.a \
856	SL/FAST_ALIGNER/FAST_ALIGNER.a \
857	SL/FILE_BUFFER/FILE_BUFFER.a \
858	SL/ITEMS/ITEMS.a \
859	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
860	SL/HELIX/HELIX.a \
861	SL/TRANSLATE/TRANSLATE.a \
862	STAT/STAT.a \
863	XML/XML.a \
864
865	ifeq ($(OPENGL),1)
866	ARCHS_EDIT4 += RNA3D/RNA3D.a
867	endif
868
869	LIBS_EDIT4 := $(GL_LIBS)
870
871	$(EDIT4): $(ARCHS_EDIT4:.a=.dummy) link_awt
872	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_EDIT4) $(GUI_LIBS) \|\| ( \
873	echo "$(SEP) Link $@"; \
874	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4) $(EXECLIBS)" ; \
875	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4) $(EXECLIBS) && \
876	echo "$(SEP) Link $@ [done]"; \
877	)
878
879	#********************************* arb_rnacma ************************************
880	RNACMA = bin/arb_rnacma
881	ARCHS_RNACMA = \
882	RNACMA/RNACMA.a \
883
884	$(RNACMA) : $(ARCHS_RNACMA:.a=.dummy) link_db
885	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_RNACMA) \|\| ( \
886	echo "$(SEP) Link $@"; \
887	echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_RNACMA) $(LIBS) $(EXECLIBS)"; \
888	$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_RNACMA) $(LIBS) $(EXECLIBS) && \
889	echo "$(SEP) Link $@ [done]"; \
890	)
891
892	#********************************* arb_pgt ************************************
893
894	PGT = bin/arb_pgt
895	ARCHS_PGT = \
896	PGT/PGT.a \
897
898	PGT_SYS_LIBS=$(XLIBS) $(TIFFLIBS) $(LIBS)
899
900	$(PGT) : $(ARCHS_PGT:.a=.dummy) link_db
901	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PGT) \|\| ( \
902	echo "$(SEP) Link $@"; \
903	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PGT) $(PGT_SYS_LIBS) $(EXECLIBS) "; \
904	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PGT) $(PGT_SYS_LIBS) $(EXECLIBS) && \
905	echo "$(SEP) Link $@ [done]"; \
906	)
907
908
909	#********************************* arb_wetc ************************************
910	WETC = bin/arb_wetc
911	ARCHS_WETC = \
912	WETC/WETC.a \
913	SL/HELIX/HELIX.a \
914	SL/FILTER/FILTER.a \
915	XML/XML.a \
916
917	$(WETC): $(ARCHS_WETC:.a=.dummy) link_awt
918	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_WETC) $(GUI_LIBS) \|\| ( \
919	echo "$(SEP) Link $@"; \
920	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC) $(GUI_LIBS) $(EXECLIBS)" ; \
921	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC) $(GUI_LIBS) $(EXECLIBS) && \
922	echo "$(SEP) Link $@ [done]"; \
923	)
924
925	#********************************* arb_dist ************************************
926	DIST = bin/arb_dist
927	ARCHS_DIST = \
928	$(ARCHS_AP_TREE) \
929	CONSENSUS_TREE/CONSENSUS_TREE.a \
930	DIST/DIST.a \
931	EISPACK/EISPACK.a \
932	SERVERCNTRL/SERVERCNTRL.a \
933	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
934	SL/HELIX/HELIX.a \
935	SL/MATRIX/MATRIX.a \
936	SL/NDS/NDS.a \
937	SL/ITEMS/ITEMS.a \
938	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.a \
939	XML/XML.a \
940
941	$(DIST): $(ARCHS_DIST:.a=.dummy) link_awt
942	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_DIST) $(GUI_LIBS) \|\| ( \
943	echo "$(SEP) Link $@"; \
944	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS)" ; \
945	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS) && \
946	echo "$(SEP) Link $@ [done]"; \
947	)
948
949	#********************************* arb_pars ************************************
950	PARSIMONY = bin/arb_pars
951	ARCHS_PARSIMONY = \
952	$(ARCHS_AP_TREE) \
953	PARSIMONY/PARSIMONY.a \
954	SERVERCNTRL/SERVERCNTRL.a \
955	SL/AW_NAME/AW_NAME.a \
956	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
957	SL/HELIX/HELIX.a \
958	SL/NDS/NDS.a \
959	SL/ITEMS/ITEMS.a \
960	SL/TRANSLATE/TRANSLATE.a \
961	SL/TREEDISP/TREEDISP.a \
962	XML/XML.a \
963
964	$(PARSIMONY): $(ARCHS_PARSIMONY:.a=.dummy) link_awt
965	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PARSIMONY) $(GUI_LIBS) \|\| ( \
966	echo "$(SEP) Link $@"; \
967	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(EXECLIBS)" ; \
968	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(EXECLIBS) && \
969	echo "$(SEP) Link $@ [done]"; \
970	)
971
972	#********************************* arb_convert_aln ************************************
973	CONVERT_ALN = bin/arb_convert_aln
974	ARCHS_CONVERT_ALN = \
975	CONVERTALN/CONVERTALN.a \
976	SL/FILE_BUFFER/FILE_BUFFER.a \
977
978	$(CONVERT_ALN) : $(ARCHS_CONVERT_ALN:.a=.dummy) link_db
979	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_CONVERT_ALN) \|\| ( \
980	echo "$(SEP) Link $@"; \
981	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN) $(LIBS) $(ARBDB_LIB) $(EXECLIBS)"; \
982	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN) $(LIBS) $(ARBDB_LIB) $(EXECLIBS) && \
983	echo "$(SEP) Link $@ [done]"; \
984	)
985
986	#********************************* arb_treegen ************************************
987
988	TREEGEN = bin/arb_treegen
989	ARCHS_TREEGEN = \
990	TREEGEN/TREEGEN.a \
991
992	$(TREEGEN) : $(ARCHS_TREEGEN:.a=.dummy)
993	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_TREEGEN) \|\| ( \
994	echo "$(SEP) Link $@"; \
995	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN) $(EXECLIBS)" ; \
996	$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN) $(EXECLIBS) && \
997	echo "$(SEP) Link $@ [done]"; \
998	)
999
1000	#********************************* arb_naligner ************************************
1001	NALIGNER = bin/arb_naligner
1002	ARCHS_NALIGNER = \
1003	NALIGNER/NALIGNER.a \
1004	SERVERCNTRL/SERVERCNTRL.a \
1005	SL/HELIX/HELIX.a \
1006
1007	$(NALIGNER): $(ARCHS_NALIGNER:.a=.dummy) link_db
1008	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NALIGNER) \|\| ( \
1009	echo "$(SEP) Link $@"; \
1010	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(LIBS) $(EXECLIBS)" ; \
1011	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(LIBS) $(EXECLIBS) && \
1012	echo "$(SEP) Link $@ [done]"; \
1013	)
1014
1015	#********************************* arb_phylo ************************************
1016	PHYLO = bin/arb_phylo
1017	ARCHS_PHYLO = \
1018	PHYLO/PHYLO.a \
1019	SL/HELIX/HELIX.a \
1020	SL/FILTER/FILTER.a \
1021	SL/MATRIX/MATRIX.a \
1022	XML/XML.a \
1023
1024	$(PHYLO): $(ARCHS_PHYLO:.a=.dummy) link_awt
1025	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PHYLO) $(GUI_LIBS) \|\| ( \
1026	echo "$(SEP) Link $@"; \
1027	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO) $(GUI_LIBS) $(EXECLIBS)" ; \
1028	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO) $(GUI_LIBS) $(EXECLIBS) && \
1029	echo "$(SEP) Link $@ [done]"; \
1030	)
1031
1032	#***************************************************************************************
1033	# SERVER SECTION
1034	#***************************************************************************************
1035
1036	#********************************* arb_db_server ************************************
1037	DBSERVER = bin/arb_db_server
1038	ARCHS_DBSERVER = \
1039	DBSERVER/DBSERVER.a \
1040	SERVERCNTRL/SERVERCNTRL.a \
1041
1042	$(DBSERVER): $(ARCHS_DBSERVER:.a=.dummy) link_db
1043	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_DBSERVER) $(ARBDB_LIB) \|\| ( \
1044	echo "$(SEP) Link $@"; \
1045	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER) $(ARBDB_LIB) PROBE_COM/client.a $(SYSLIBS) $(EXECLIBS)" ; \
1046	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER) $(ARBDB_LIB) PROBE_COM/client.a $(SYSLIBS) $(EXECLIBS) && \
1047	echo "$(SEP) Link $@ [done]"; \
1048	)
1049
1050	#********************************* arb_pt_server ************************************
1051	PROBE = bin/arb_pt_server
1052	ARCHS_PROBE_COMMON = \
1053	SERVERCNTRL/SERVERCNTRL.a \
1054	SL/HELIX/HELIX.a \
1055	SL/PTCLEAN/PTCLEAN.a \
1056
1057	ARCHS_PROBE_LINK = \
1058	$(ARCHS_PROBE_COMMON) \
1059	$(ARCHS_PT_SERVER_LINK) \
1060
1061	ARCHS_PROBE_DEPEND = \
1062	$(ARCHS_PROBE_COMMON) \
1063	$(ARCHS_PT_SERVER) \
1064
1065	$(PROBE): $(ARCHS_PROBE_DEPEND:.a=.dummy) link_db
1066	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) config.makefile \|\| ( \
1067	echo "$(SEP) Link $@"; \
1068	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) PROBE_COM/server.a $(SYSLIBS) $(EXECLIBS)" ; \
1069	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) PROBE_COM/server.a $(SYSLIBS) $(EXECLIBS) && \
1070	echo "$(SEP) Link $@ [done]"; \
1071	)
1072
1073	#********************************* arb_name_server ************************************
1074	NAMES = bin/arb_name_server
1075	ARCHS_NAMES = \
1076	NAMES/NAMES.a \
1077	SERVERCNTRL/SERVERCNTRL.a \
1078
1079	$(NAMES): $(ARCHS_NAMES:.a=.dummy) link_db
1080	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) \|\| ( \
1081	echo "$(SEP) Link $@"; \
1082	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS) $(EXECLIBS)" ; \
1083	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS) $(EXECLIBS) && \
1084	echo "$(SEP) Link $@ [done]"; \
1085	)
1086
1087	#********************************* SHARED LIBRARIES SECTION ************************************
1088
1089	prepare_libdir: libs addlibs
1090
1091	addlibs:
1092	(perl $(ARBHOME)/SOURCE_TOOLS/provide_libs.pl \
1093	"arbhome=$(ARBHOME)" \
1094	"opengl=$(OPENGL)" \
1095	"link_static=$(LINK_STATIC)" \
1096	)
1097
1098	lib/libCORE.$(SHARED_LIB_SUFFIX): core
1099	lib/libARBDB.$(SHARED_LIB_SUFFIX): db
1100	lib/libWINDOW.$(SHARED_LIB_SUFFIX): aw
1101	lib/libAWT.$(SHARED_LIB_SUFFIX): awt
1102
1103	libs: lib/libCORE.$(SHARED_LIB_SUFFIX) \
1104	lib/libARBDB.$(SHARED_LIB_SUFFIX) \
1105	lib/libWINDOW.$(SHARED_LIB_SUFFIX) \
1106	lib/libAWT.$(SHARED_LIB_SUFFIX)
1107
1108	lib/lib%.$(SHARED_LIB_SUFFIX): LIBLINK/lib%.$(SHARED_LIB_SUFFIX)
1109	cp $< $@
1110
1111	#***************************************************************************************
1112	# Recursive calls to sub-makefiles
1113	#***************************************************************************************
1114
1115	include SOURCE_TOOLS/export2sub
1116
1117	%.depends:
1118	@cp -p $(@D)/Makefile $(@D)/Makefile.old # save old Makefile
1119	@$(MAKE) -C $(@D) -r \
1120	"AUTODEPENDS=1" \
1121	"MAIN=nothing" \
1122	"cflags=noCflagsHere_use_MAKEDEPENDFLAGS" \
1123	depends;
1124	@grep "^# DO NOT DELETE" $(@D)/Makefile >/dev/null
1125	@cat $(@D)/Makefile \
1126	\| SOURCE_TOOLS/fix_depends.pl \
1127	>$(@D)/Makefile.2
1128	@mv $(@D)/Makefile.old $(@D)/Makefile # restore old Makefile
1129	@$(ARBHOME)/SOURCE_TOOLS/mv_if_diff $(@D)/Makefile.2 $(@D)/Makefile # update Makefile if changed
1130
1131	%.proto:
1132	@$(MAKE) -C $(@D) \
1133	"AUTODEPENDS=0" \
1134	"MAIN=nothing" \
1135	"cflags=noCflags" \
1136	proto
1137
1138	%.clean:
1139	@$(MAKE) -C $(@D) \
1140	"AUTODEPENDS=0" \
1141	"MAIN=nothing" \
1142	"cflags=noCflags" \
1143	clean
1144
1145	# rule to generate main target (normally a library):
1146	%.dummy:
1147	@( export ID=$$$$; LANG=C; \
1148	(( \
1149	echo "$(SEP) Make $(@D)"; \
1150	$(MAKE) -C $(@D) -r \
1151	"AUTODEPENDS=1" \
1152	"MAIN = $(@F:.dummy=.a)" \
1153	"cflags = $(cflags) -DIN_ARB_$(subst /,_,$(@D))" && \
1154	echo "$(SEP) Make $(@D) [done]"; \
1155	) >$(@D).$$ID.log 2>&1 && (cat $(@D).$$ID.log;rm $(@D).$$ID.log)) \|\| (cat $(@D).$$ID.log;rm $(@D).$$ID.log;false))
1156
1157	# Additional dependencies for subtargets:
1158
1159	PROBE_COM/PROBE_COM.dummy : comtools
1160	NAMES_COM/NAMES_COM.dummy : comtools
1161
1162	com: PROBE_COM/PROBE_COM.dummy NAMES_COM/NAMES_COM.dummy
1163
1164	PROBE_COM/server.dummy:
1165	@echo Unwanted request to make target $<
1166	false
1167
1168	PROBE_COM/client.dummy:
1169	@echo Unwanted request to make target $<
1170	false
1171
1172	NAMES_COM/server.dummy:
1173	@echo Unwanted request to make target $<
1174	false
1175
1176	NAMES_COM/client.dummy:
1177	@echo Unwanted request to make target $<
1178	false
1179
1180
1181	ARBDB/libARBDB.dummy: links
1182	CORE/libCORE.dummy: links
1183
1184	SL/FILE_BUFFER/FILE_BUFFER.dummy: links
1185	PERLTOOLS/PERLTOOLS.dummy: core db SL/FILE_BUFFER/FILE_BUFFER.dummy
1186
1187	# all subdirs perl not depends on go here:
1188	AWT/libAWT.dummy: links_non_perl
1189	AWTI/AWTI.dummy: links_non_perl
1190	CONSENSUS_TREE/CONSENSUS_TREE.dummy: links_non_perl
1191	CONVERTALN/CONVERTALN.dummy: links_non_perl
1192	DBSERVER/DBSERVER.dummy: links_non_perl
1193	DIST/DIST.dummy: links_non_perl
1194	EDIT4/EDIT4.dummy: links_non_perl templ com
1195	EISPACK/EISPACK.dummy: links_non_perl
1196	GDE/GDE.dummy: links_non_perl
1197	GENOM/GENOM.dummy: links_non_perl
1198	GENOM_IMPORT/GENOM_IMPORT.dummy: links_non_perl
1199	ISLAND_HOPPING/ISLAND_HOPPING.dummy: links_non_perl
1200	MERGE/MERGE.dummy: links_non_perl
1201	NTREE/NTREE.dummy: links_non_perl templ
1202	PARSIMONY/PARSIMONY.dummy: links_non_perl
1203	PGT/PGT.dummy: links_non_perl
1204	PHYLO/PHYLO.dummy: links_non_perl
1205	PRIMER_DESIGN/PRIMER_DESIGN.dummy: links_non_perl
1206	PROBE_SET/PROBE_SET.dummy: links_non_perl link_db
1207	READSEQ/READSEQ.dummy: links_non_perl
1208	RNACMA/RNACMA.dummy: links_non_perl headerlibs
1209	SECEDIT/SECEDIT.dummy: links_non_perl
1210	SEQ_QUALITY/SEQ_QUALITY.dummy: links_non_perl
1211	SERVERCNTRL/SERVERCNTRL.dummy: links_non_perl com
1212	SL/ALIVIEW/ALIVIEW.dummy: links_non_perl
1213	SL/AP_TREE/AP_TREE.dummy: links_non_perl
1214	SL/ARB_TREE/ARB_TREE.dummy: links_non_perl
1215	SL/AW_HELIX/AW_HELIX.dummy: links_non_perl
1216	SL/DB_QUERY/DB_QUERY.dummy: links_non_perl
1217	SL/DB_SCANNER/DB_SCANNER.dummy: links_non_perl
1218	SL/DB_UI/DB_UI.dummy: links_non_perl
1219	SL/FAST_ALIGNER/FAST_ALIGNER.dummy: links_non_perl
1220	SL/FILTER/FILTER.dummy: links_non_perl
1221	SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy: links_non_perl
1222	SL/HELIX/HELIX.dummy: links_non_perl
1223	SL/ITEMS/ITEMS.dummy: links_non_perl
1224	SL/LOCATION/LOCATION.dummy: links_non_perl
1225	SL/MATRIX/MATRIX.dummy: links_non_perl
1226	SL/NDS/NDS.dummy: links_non_perl
1227	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.dummy: links_non_perl
1228	SL/PRONUC/PRONUC.dummy: links_non_perl
1229	SL/PTCLEAN/PTCLEAN.dummy: links_non_perl link_db
1230	SL/REFENTRIES/REFENTRIES.dummy: links_non_perl
1231	SL/REGEXPR/REGEXPR.dummy: links_non_perl
1232	SL/SEQIO/SEQIO.dummy: links_non_perl
1233	SL/SEQUENCE/SEQUENCE.dummy: links_non_perl
1234	SL/TRANSLATE/TRANSLATE.dummy: links_non_perl
1235	SL/TREE_READ/TREE_READ.dummy: links_non_perl
1236	SL/TREE_WRITE/TREE_WRITE.dummy: links_non_perl
1237	SL/TREEDISP/TREEDISP.dummy: links_non_perl
1238	STAT/STAT.dummy: links_non_perl
1239	TREEGEN/TREEGEN.dummy: links_non_perl
1240	WETC/WETC.dummy: links_non_perl
1241	WINDOW/libWINDOW.dummy: links_non_perl
1242	XML/XML.dummy: links_non_perl
1243
1244	ifeq ($(OPENGL),1)
1245	GL/glAW/glAW.dummy: links_non_perl
1246	GL/glpng/glpng.dummy: links_non_perl
1247	GL/GL.dummy: GL/glAW/glAW.dummy GL/glpng/glpng.dummy
1248	RNA3D/RNA3D.dummy: links_non_perl gl
1249	endif
1250
1251	UNIT_TESTER/UNIT_TESTER.dummy: link_db \
1252	SERVERCNTRL/SERVERCNTRL.dummy \
1253
1254	TOOLS/TOOLS.dummy : links_non_perl link_db \
1255	SL/FILE_BUFFER/FILE_BUFFER.dummy \
1256	SERVERCNTRL/SERVERCNTRL.dummy \
1257	SL/TREE_WRITE/TREE_WRITE.dummy \
1258	SL/TREE_READ/TREE_READ.dummy \
1259	XML/XML.dummy \
1260
1261	AWTC/AWTC.dummy : com
1262
1263	NAMES/NAMES.dummy : com
1264	SL/AW_NAME/AW_NAME.dummy : com
1265
1266	PROBE/PROBE.dummy : com
1267	ptpan/PROBE.dummy : com
1268	MULTI_PROBE/MULTI_PROBE.dummy : com
1269	PROBE_DESIGN/PROBE_DESIGN.dummy : com
1270	NALIGNER/NALIGNER.dummy : com
1271
1272	ARB_GDE/ARB_GDE.dummy : proto_tools
1273
1274	# synonyms for some dummy targets
1275
1276	ARBDB/ARBDB.dummy: ARBDB/libARBDB.dummy
1277	CORE/CORE.dummy: CORE/libCORE.dummy
1278	AWT/AWT.dummy: AWT/libAWT.dummy
1279	WINDOW/WINDOW.dummy: WINDOW/libWINDOW.dummy
1280
1281	#***************************************************************************************
1282	# Short aliases to make targets
1283	#***************************************************************************************
1284
1285	show:
1286	@echo $(SEP)
1287	@echo 'Aliases for often needed targets:'
1288	@echo ''
1289	@echo ' executables:'
1290	@echo ''
1291	@echo ' nt arb_ntree'
1292	@echo ' e4 arb_edit4 (includes secedit)'
1293	@echo ' di arb_dist'
1294	@echo ' ph arb_phylo'
1295	@echo ' pa arb_parsimony'
1296	@echo ' tg arb_treegen'
1297	@echo ' ds arb_dbserver'
1298	@echo ' pt arb_pt_server'
1299	@echo ' na arb_name_server'
1300	@echo ''
1301	@echo ' libraries:'
1302	@echo ''
1303	@echo ' com communication libraries'
1304	@echo ' db ARB database'
1305	@echo ' aw GUI lib'
1306	@echo ' awt GUI toolkit'
1307	@echo ' awtc general purpose library'
1308	@echo ' awti import/export library'
1309	@echo ' mp multi probe library'
1310	@echo ' ge genome library'
1311	@echo ' pd probe design lib'
1312	@echo ' prd primer design lib'
1313	@echo ''
1314	@echo ' other targets:'
1315	@echo ''
1316	@echo ' help recompile help files'
1317	@echo ' tools make small tools used by arb'
1318	@echo ''
1319	@echo ' foreign targets:'
1320	@echo ''
1321	@echo ' gde GDE'
1322	@echo ' agde ARB_GDE'
1323	@echo ''
1324	@echo 'for other targets inspect $(ARBHOME)/Makefile'
1325	@echo ''
1326	@echo $(SEP)
1327
1328	source_doc:
1329	@echo "Remove some links (doxygen crashes otherwise):"
1330	find . \( -name "AISC" -o -name "C" -o -name "GDEHELP" \) -type l -exec rm {} \;
1331	doxygen
1332	$(MAKE) forcelinks
1333
1334	dep_graph:
1335	@echo "Building some dependency graphs"
1336	SOURCE_TOOLS/dependency_graphs.pl
1337
1338	help: HELP_SOURCE/HELP_SOURCE.dummy
1339
1340	# @@@ when backtracing code is in libCORE, link vs ARBDB is no longer needed
1341	HELP_SOURCE/HELP_SOURCE.dummy: link_db xml menus
1342
1343	db: ARBDB/libARBDB.dummy
1344	core: CORE/libCORE.dummy
1345	aw: WINDOW/libWINDOW.dummy
1346	awt: AWT/libAWT.dummy
1347	awtc: AWTC/AWTC.dummy
1348	awti: AWTI/AWTI.dummy
1349
1350	mp: MULTI_PROBE/MULTI_PROBE.dummy
1351	mg: MERGE/MERGE.dummy
1352	ge: GENOM/GENOM.dummy
1353	prd: PRIMER_DESIGN/PRIMER_DESIGN.dummy
1354
1355	nt: menus $(NTREE)
1356
1357	nal: $(NALIGNER)
1358
1359	di: $(DIST)
1360	ph: $(PHYLO)
1361	pa: $(PARSIMONY)
1362	tg: $(TREEGEN)
1363
1364	ifeq ($(OPENGL),1)
1365	3d: RNA3D/RNA3D.dummy
1366	gl: GL/GL.dummy
1367	else
1368	noopengl:
1369	@echo "invalid target for OPENGL=0"
1370	3d: noopengl
1371	gl: noopengl
1372	endif
1373
1374	SL/SL.dummy: com
1375
1376	ds: $(DBSERVER)
1377	pt: $(PROBE)
1378	pst: PROBE_SET/PROBE_SET.dummy
1379	pd: PROBE_DESIGN/PROBE_DESIGN.dummy
1380	na: $(NAMES)
1381	sq: SEQ_QUALITY/SEQ_QUALITY.dummy
1382	cma: $(RNACMA)
1383
1384	sec: SECEDIT/SECEDIT.dummy
1385
1386	e4: $(EDIT4) readseq menus
1387
1388	gi: GENOM_IMPORT/GENOM_IMPORT.dummy
1389	wetc: $(WETC)
1390
1391	pgt: $(PGT)
1392	xml: XML/XML.dummy
1393	xmlin: XML_IMPORT/XML_IMPORT.dummy# broken
1394	templ: TEMPLATES/TEMPLATES.dummy
1395	stat: STAT/STAT.dummy $(NTREE) $(EDIT4)
1396	fa: SL/FAST_ALIGNER/FAST_ALIGNER.dummy
1397
1398	#********************************************************************************
1399
1400	up_by_remake: depends proto libdepends
1401
1402	up: up_by_remake tags valgrind_update
1403
1404	#********************************************************************************
1405
1406	touch:
1407	SOURCE_TOOLS/touch_modified.pl
1408
1409	modified: touch
1410	$(MAKE) all
1411
1412	#********************************************************************************
1413
1414	libdepends:
1415	$(MAKE) -C "SOURCE_TOOLS" libdepends
1416
1417	#********************************************************************************
1418
1419	depends: templ comtools
1420	@echo "$(SEP) Partially build com interface"
1421	-rm PROBE_COM/.depends
1422	-rm NAMES_COM/.depends
1423	-rm PERL2ARB/.depends
1424	$(MAKE) PROBE_COM/PROBE_COM.depends
1425	$(MAKE) NAMES_COM/NAMES_COM.depends
1426	@echo $(SEP) Updating dependencies
1427	$(MAKE) $(ARCHS:.a=.depends) \
1428	HELP_SOURCE/HELP_SOURCE.depends \
1429
1430	depend: depends
1431
1432	AISC_MKPTPS/AISC_MKPTPS.dummy: links
1433
1434	proto_tools: AISC_MKPTPS/AISC_MKPTPS.dummy
1435
1436	proto: proto_tools
1437	@echo $(SEP) Updating prototypes
1438	$(MAKE) \
1439	ARBDB/ARBDB.proto \
1440	ARB_GDE/ARB_GDE.proto \
1441	CORE/CORE.proto \
1442	CONVERTALN/CONVERTALN.proto \
1443	NTREE/NTREE.proto \
1444	$(ARCHS_PT_SERVER:.a=.proto) \
1445	SERVERCNTRL/SERVERCNTRL.proto \
1446	SL/SL.proto \
1447
1448	#********************************************************************************
1449
1450	valgrind_update: links
1451	@echo $(SEP) Updating for valgrind
1452	$(MAKE) -C SOURCE_TOOLS valgrind_update
1453
1454	#********************************************************************************
1455
1456	TAGFILE=TAGS
1457	TAGFILE_TMP=TAGS.tmp
1458
1459	TAG_SOURCE_HEADERS=TAGS.headers
1460	TAG_SOURCE_CODE=TAGS.codefiles
1461
1462	TAG_SOURCE_LISTS=$(TAG_SOURCE_HEADERS) $(TAG_SOURCE_CODE)
1463
1464	ETAGS=ctags -e -f $(TAGFILE_TMP) --sort=no --if0=no --extra=q
1465	ETAGS_TYPES=--C-kinds=cgnsut --C++-kinds=cgnsut
1466	ETAGS_FUN =--C-kinds=fm --C++-kinds=fm
1467	ETAGS_REST =--C-kinds=dev --C++-kinds=dev
1468
1469	$(TAG_SOURCE_HEADERS): links
1470	# find . \( -name '.[ch]xx' -o -name ".[ch]" \) -type f \| grep -v -i perl5 > $@
1471	# workaround a bug in ctags 5.8:
1472	find . \( -name '.hxx' -o -name ".h" \) -type f \| grep -v -i perl5 \| sed -e 's/^.\///g' > $@
1473
1474	$(TAG_SOURCE_CODE): links
1475	# find . \( -name '.[ch]xx' -o -name ".[ch]" \) -type f \| grep -v -i perl5 > $@
1476	# workaround a bug in ctags 5.8:
1477	find . \( -name '.cxx' -o -name ".c" \) -type f \| grep -v -i perl5 \| sed -e 's/^.\///g' > $@
1478
1479	tags: $(TAG_SOURCE_LISTS)
1480	$(ETAGS) $(ETAGS_TYPES) -L $(TAG_SOURCE_HEADERS)
1481	$(ETAGS) -a $(ETAGS_FUN) -L $(TAG_SOURCE_HEADERS)
1482	$(ETAGS) -a $(ETAGS_REST) -L $(TAG_SOURCE_HEADERS)
1483	$(ETAGS) -a $(ETAGS_TYPES) -L $(TAG_SOURCE_CODE)
1484	$(ETAGS) -a $(ETAGS_FUN) -L $(TAG_SOURCE_CODE)
1485	$(ETAGS) -a $(ETAGS_REST) -L $(TAG_SOURCE_CODE)
1486	mv $(TAGFILE_TMP) $(TAGFILE)
1487	rm $(TAG_SOURCE_LISTS)
1488
1489	#********************************************************************************
1490
1491	LINKSTAMP=SOURCE_TOOLS/generate_all_links.stamp
1492
1493	links: checks $(LINKSTAMP) arbmainwrapper
1494
1495	forcelinks:
1496	-rm $(LINKSTAMP)
1497	$(MAKE) links
1498
1499	$(LINKSTAMP): SOURCE_TOOLS/generate_all_links.sh
1500	+SOURCE_TOOLS/generate_all_links.sh
1501	touch $(LINKSTAMP)
1502
1503	clean_links:
1504	# avoid to delete linked pts, nas or arb_tcp.dat:
1505	find . -path './lib' -prune -o -type l -exec rm {} \;
1506	@rm -f $(LINKSTAMP) lib/inputMasks/format.readme
1507
1508	redo_links: clean_links
1509	$(MAKE) links
1510
1511	#********************************************************************************
1512
1513	headerlibs:
1514	$(MAKE) -C HEADERLIBS all
1515
1516	#********************************************************************************
1517
1518	gde: GDE/GDE.dummy
1519	GDE: gde
1520	agde: ARB_GDE/ARB_GDE.dummy
1521
1522	tools: TOOLS/TOOLS.dummy
1523
1524	convert: $(CONVERT_ALN)
1525	readseq: READSEQ/READSEQ.dummy
1526
1527	#***************************************************************************************
1528	# Some user commands
1529	#***************************************************************************************
1530
1531	menus: binlink links
1532	@(( \
1533	echo "$(SEP) Make GDEHELP"; \
1534	$(MAKE) -C GDEHELP -r "PP=$(PP)" all && \
1535	echo "$(SEP) Make GDEHELP [done]"; \
1536	) > GDEHELP.log 2>&1 && (cat GDEHELP.log;rm GDEHELP.log)) \|\| (cat GDEHELP.log;rm GDEHELP.log;false)
1537
1538	ifeq ($(DEBUG),1)
1539	BIN_TARGET=develall
1540	else
1541	BIN_TARGET=all
1542	endif
1543
1544
1545	binlink:
1546	$(MAKE) -C bin $(BIN_TARGET)
1547
1548	preplib:
1549	(cd lib;$(MAKE) all)
1550
1551	# --------------------------------------------------------------------------------
1552	# This section is quite tricky:
1553	#
1554	# make 'perl' is a BIG target, so when it has to be made, it has to be started
1555	# as early as possible to reduce overall compile time. Since 'make' does not
1556	# provide any priotities, i force it to build all 'perl'-prerequisites early, by
1557	# adding artificial dependencies to these prerequisites
1558	#
1559	# That behavior is likely to be system-dependent.
1560	# My goal was only to make it work on my current development system,
1561	# where this saves about 20% of overall build time.
1562
1563	ifeq ($(WITHPERL),1)
1564	links_non_perl: PERLTOOLS/PERLTOOLS.dummy
1565	perltools: links_non_perl
1566	perl: realperl
1567	else
1568	links_non_perl: links
1569	perl:
1570	$(MAKE) "WITHPERL=1" perl
1571	endif
1572
1573	# ---------------------------------------- perl
1574
1575	ifeq ($(ARB_64),$(BUILDHOST_64))
1576	TEST_PERL_SCRIPTS=$(MAKE) -C PERL_SCRIPTS/test test
1577	else
1578	TEST_PERL_SCRIPTS=echo "skipping perl script compilation (when cross-compiling)"
1579	endif
1580
1581	realperl: perltools
1582	(( \
1583	echo "$(SEP) Make PERL2ARB" ; \
1584	time $(MAKE) -C PERL2ARB -r -f Makefile.main \
1585	"AUTODEPENDS=1" \
1586	"dflags=$(dflags)" \
1587	"cross_cflags=$(cross_cflags) $(dflags)" \
1588	"cross_lflags=$(cross_lflags)" \
1589	all && \
1590	$(TEST_PERL_SCRIPTS) && \
1591	echo "$(SEP) Make PERL2ARB [done]" ; \
1592	) > PERL2ARB.log 2>&1 && (cat PERL2ARB.log;rm PERL2ARB.log)) \|\| (cat PERL2ARB.log;rm PERL2ARB.log;false)
1593
1594	perl_clean:
1595	@$(MAKE) -C PERL2ARB -r -f Makefile.main \
1596	"AUTODEPENDS=0" \
1597	clean
1598
1599	PERL2ARB/PERL2ARB.clean:
1600	$(MAKE) perl_clean
1601
1602
1603	# ----------------------------------------
1604
1605	CLOC=cloc-1.08.pl
1606	CLOCFLAGS=--no3 --quiet --progress-rate=0
1607	CLOCARB=--exclude-dir=GDE .
1608	CLOCEXT=GDE
1609	CLOCCODE=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.code.def
1610	CLOCREST=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.rest.def
1611	CLOCFILT=tail --lines=+4
1612
1613	cloc:
1614	@echo 'Arb code:'
1615	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCARB) \| $(CLOCFILT)
1616	@echo 'Arb rest:'
1617	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCARB) \| $(CLOCFILT)
1618	@echo 'External code:'
1619	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCEXT) \| $(CLOCFILT)
1620	@echo 'External rest:'
1621	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCEXT) \| $(CLOCFILT)
1622
1623	# ---------------------------------------- check ressources
1624
1625	check_res:
1626	$(ARBHOME)/SOURCE_TOOLS/check_ressources.pl
1627
1628	# ---------------------------------------- cleaning
1629
1630	rmbak:
1631	@echo "Cleanup:"
1632	@find . \( -name '*%' \
1633	-o -name '*.bak' \
1634	-o -name '*~' \) \
1635	-o -name 'core' \
1636	-exec rm -v {} \;
1637
1638	bin_reinit:
1639	$(MAKE) bin/bin.clean
1640	$(MAKE) -C "bin" all
1641
1642	clean_directories:
1643	-rm -rf \
1644	$(ARBHOME)/PROBE_SET/bin \
1645	$(ARBHOME)/INCLUDE \
1646	$(ARBHOME)/LIBLINK \
1647
1648	libclean:
1649	-find $(ARBHOME) -type f \( -name '*.a' ! -type l \) -exec rm -f {} \;
1650
1651	objclean:
1652	-find $(ARBHOME) -type f \( -name '*.o' ! -type l \) -exec rm -f {} \;
1653
1654	# bin.clean and HELP_SOURCE.clean interfere
1655	clean3:
1656	$(MAKE) bin/bin.clean
1657	$(MAKE) HELP_SOURCE/HELP_SOURCE.clean
1658
1659	clean2: $(ARCHS:.a=.clean) \
1660	clean3 \
1661	rmbak \
1662	libclean \
1663	objclean \
1664	lib/lib.clean \
1665	GDEHELP/GDEHELP.clean \
1666	HEADERLIBS/HEADERLIBS.clean \
1667	SOURCE_TOOLS/SOURCE_TOOLS.clean \
1668	UNIT_TESTER/UNIT_TESTER.clean \
1669	TEMPLATES/TEMPLATES.clean \
1670	perl_clean \
1671	clean_directories \
1672
1673	rm -f *.last_gcc config.makefile.bak TAGS
1674
1675	# links are needed for cleanup
1676	clean: redo_links
1677	$(MAKE) clean2
1678	$(MAKE) clean_cov_all clean_links
1679
1680	# 'relocated' is about 50% faster than 'rebuild'
1681	reloc_clean: links
1682	@echo "---------------------------------------- Relocation cleanup"
1683	$(MAKE) \
1684	perl_clean \
1685	GDEHELP/GDEHELP.clean \
1686	HELP_SOURCE/genhelp/genhelp.clean \
1687	bin/bin.clean \
1688	libclean \
1689	objclean
1690
1691	relocated: links
1692	$(MAKE) reloc_clean
1693	@echo "---------------------------------------- and remake"
1694	$(MAKE) build
1695
1696	# -----------------------------------
1697	# some stress tests:
1698
1699	rebuild4ever: rebuild
1700	$(MAKE) rebuild4ever
1701
1702	build4ever: build
1703	$(MAKE) build4ever
1704
1705	clean4ever: clean
1706	$(MAKE) clean4ever
1707
1708	test4ever: ut
1709	$(MAKE) test4ever
1710
1711	perl4ever: clean
1712	$(MAKE) links
1713	$(MAKE) perl
1714	$(MAKE) perl4ever
1715
1716
1717	# -----------------------------------
1718
1719	rebuild: clean
1720	$(MAKE) all
1721
1722	relink: bin/bin.clean libclean
1723	$(MAKE) build
1724
1725	tarfile: rebuild
1726	$(MAKE) prepare_libdir
1727	util/arb_compress
1728
1729	tarfile_quick: build
1730	$(MAKE) prepare_libdir
1731	util/arb_compress
1732
1733	save: sourcetarfile
1734
1735	patch:
1736	SOURCE_TOOLS/arb_create_patch.sh arbPatch
1737
1738	# test early whether save will work
1739	savetest:
1740	@util/arb_srclst.pl >/dev/null
1741
1742	testsave: savetest
1743
1744	sourcetarfile: rmbak
1745	util/arb_save
1746
1747	save2: rmbak
1748	util/arb_save ignore
1749
1750	save_test: rmbak
1751	@echo "Testing source list.."
1752	@util/arb_srclst.pl > /dev/null
1753
1754	rel_minor:
1755	touch SOURCE_TOOLS/inc_minor.stamp
1756	$(MAKE) do_release
1757
1758	rel_major:
1759	touch SOURCE_TOOLS/inc_major.stamp
1760	$(MAKE) do_release
1761
1762	do_release:
1763	@echo Building release
1764	@echo PATH=$(PATH)
1765	@echo ARBHOME=$(ARBHOME)
1766	-rm arb.tgz arbsrc.tgz
1767	$(MAKE) testsave
1768	$(MAKE) templ # auto upgrades version early
1769	$(MAKE) tarfile sourcetarfile
1770
1771	release_quick:
1772	-rm arb.tgz arbsrc.tgz
1773	$(MAKE) tarfile_quick sourcetarfile
1774
1775	# --------------------------------------------------------------------------------
1776
1777	MAKE_IF_COMMITTED=$(MAKE) -C SOURCE_TOOLS -f Makefile.commitbuild
1778
1779	build_CTARGET:
1780	+$(MAKE_IF_COMMITTED) "CTARGET=$(CTARGET)" build_CTARGET
1781
1782	reset_committed_build:
1783	+$(MAKE_IF_COMMITTED) reset
1784
1785	# --------------------------------------------------------------------------------
1786
1787	arbapplications: nt pa e4 wetc pt na nal di ph ds pgt wetc cma
1788
1789	arb_external: convert tools gde readseq tg pst xmlin
1790
1791	arb_no_perl: arbapplications help arb_external
1792
1793	arb:
1794	$(MAKE) "WITHPERL=1" perl arb_no_perl
1795
1796	# --------------------------------------------------------------------------------
1797	# special targets for SOURCE_TOOLS/remake_after_change.pl
1798
1799	rac_arb_dist: di
1800	rac_arb_edit4: e4
1801	rac_arb_ntree: nt
1802	rac_arb_pars: pa
1803	rac_arb_phylo: ph
1804	rac_arb_wetc: wetc
1805	rac_arb_naligner: nal
1806	rac_arb_pt_server: pt
1807	rac_arb_db_server: ds
1808	rac_arb_name_server: na
1809	rac_arb_pgt: pgt
1810	rac_arb_convert_aln: convert
1811	rac_arb_treegen: tg
1812	rac_arb_rnacma: cma
1813
1814	# --------------------------------------------------------------------------------
1815	# unit testing
1816	# @@@ work in progress
1817	#
1818	# goal is to automatically test all libraries/executables using TESTED_UNITS_AUTO
1819	#
1820	# currently not all test executables link w/o error
1821	# (see UNITS_WORKING, UNITS_UNTESTABLE_ATM and UNITS_NEED_FIX)
1822
1823	# define RNA3D/RNA3D.test
1824	RNA3D_TEST := $(subst .a,.test,$(RNA3D_LIB))
1825
1826	TESTED_UNITS_AUTO = $(ARCHS:.a=.test)
1827
1828	UNITS_WORKING = \
1829	$(RNA3D_TEST) \
1830	ARB_GDE/ARB_GDE.test \
1831	AWTI/AWTI.test \
1832	CONSENSUS_TREE/CONSENSUS_TREE.test \
1833	DIST/DIST.test \
1834	EISPACK/EISPACK.test \
1835	GENOM/GENOM.test \
1836	GENOM_IMPORT/GENOM_IMPORT.test \
1837	GL/glAW/libglAW.test \
1838	GL/glpng/libglpng_arb.test \
1839	ISLAND_HOPPING/ISLAND_HOPPING.test \
1840	NALIGNER/NALIGNER.test \
1841	NAMES/NAMES.test \
1842	PARSIMONY/PARSIMONY.test \
1843	PGT/PGT.test \
1844	PHYLO/PHYLO.test \
1845	PRIMER_DESIGN/PRIMER_DESIGN.test \
1846	PROBE_DESIGN/PROBE_DESIGN.test \
1847	SECEDIT/SECEDIT.test \
1848	SEQ_QUALITY/SEQ_QUALITY.test \
1849	SERVERCNTRL/SERVERCNTRL.test \
1850	SL/ALIVIEW/ALIVIEW.test \
1851	SL/AP_TREE/AP_TREE.test \
1852	SL/ARB_TREE/ARB_TREE.test \
1853	SL/AW_HELIX/AW_HELIX.test \
1854	SL/AW_NAME/AW_NAME.test \
1855	SL/DB_QUERY/DB_QUERY.test \
1856	SL/DB_SCANNER/DB_SCANNER.test \
1857	SL/FILE_BUFFER/FILE_BUFFER.test \
1858	SL/FILTER/FILTER.test \
1859	SL/GUI_ALIVIEW/GUI_ALIVIEW.test \
1860	SL/HELIX/HELIX.test \
1861	SL/ITEMS/ITEMS.test \
1862	SL/LOCATION/LOCATION.test \
1863	SL/MATRIX/MATRIX.test \
1864	SL/NDS/NDS.test \
1865	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.test \
1866	SL/REFENTRIES/REFENTRIES.test \
1867	SL/REGEXPR/REGEXPR.test \
1868	SL/SEQUENCE/SEQUENCE.test \
1869	SL/TRANSLATE/TRANSLATE.test \
1870	SL/TREE_READ/TREE_READ.test \
1871	SL/TREE_WRITE/TREE_WRITE.test \
1872	STAT/STAT.test \
1873	TREEGEN/TREEGEN.test \
1874	WETC/WETC.test \
1875	XML/XML.test \
1876
1877	# untestable units
1878
1879	UNITS_NEED_FIX = \
1880	ptpan/PROBE.test \
1881
1882	UNITS_UNTESTABLE_ATM = \
1883	PROBE_SET/PROBE_SET.test \
1884	XML_IMPORT/XML_IMPORT.test \
1885
1886	# for the moment, put all units containing tests into UNITS_TESTED or UNITS_TESTED_FIRST
1887
1888	UNITS_TESTED_FIRST = \
1889	ARBDB/ARBDB.test \
1890	TOOLS/arb_test.test \
1891	TOOLS/arb_probe.test \
1892	AWTC/AWTC.test \
1893
1894	UNITS_TESTED = \
1895	DBSERVER/DBSERVER.test \
1896	AWT/AWT.test \
1897	CORE/CORE.test \
1898	SL/TREEDISP/TREEDISP.test \
1899	NTREE/NTREE.test \
1900	AISC_MKPTPS/mkptypes.test \
1901	EDIT4/EDIT4.test \
1902	MERGE/MERGE.test \
1903	MULTI_PROBE/MULTI_PROBE.test \
1904	SERVERCNTRL/SERVERCNTRL.test \
1905	SL/FAST_ALIGNER/FAST_ALIGNER.test \
1906	SL/PRONUC/PRONUC.test \
1907	WINDOW/WINDOW.test \
1908	HELP_SOURCE/arb_help2xml.test \
1909	CONVERTALN/CONVERTALN.test \
1910	SL/SEQIO/SEQIO.test \
1911	SL/PTCLEAN/PTCLEAN.test \
1912	PROBE/PROBE.test \
1913
1914	TESTED_UNITS_MANUAL = \
1915	$(UNITS_TESTED_FIRST) \
1916	$(UNITS_TESTED) \
1917
1918	# $(UNITS_WORKING)
1919
1920	# see UNIT_TESTER/sym2testcode.pl@disableErrorOnUnitsWithoutTests
1921
1922	#TESTED_UNITS = $(TESTED_UNITS_AUTO)
1923	TESTED_UNITS = $(TESTED_UNITS_MANUAL)
1924
1925	# ----------------------------------------
1926
1927	TEST_LOG_DIR = UNIT_TESTER/logs
1928	TEST_RUN_SUITE=$(MAKE) $(NODIR) -C UNIT_TESTER -f Makefile.suite -r
1929	TEST_MAKE_FLAGS=
1930	TEST_POST_CLEAN=
1931	ifeq ($(COVERAGE),1)
1932	TEST_POST_CLEAN=$(MAKE) clean_cov
1933	TEST_MAKE_FLAGS+=-j1
1934	endif
1935
1936
1937	%.test: %.dummy
1938	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
1939	( \
1940	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
1941	"UNITDIR=$(@D)" \
1942	"UNITLIBNAME=$(@F:.test=)" \
1943	"COVERAGE=$(COVERAGE)" \
1944	"cflags=$(cflags)" \
1945	"ARB_PID=$(ARB_PID)_$(@F)" \
1946	runtest; \
1947	$(TEST_POST_CLEAN) \
1948	) >$(TEST_LOG_DIR)/$(@F).log 2>&1; echo "- $(@F)")
1949
1950
1951	test_base: $(UNIT_TESTER_LIB:.a=.dummy)
1952
1953	clean_cov:
1954	find . \( -name ".gcda" -o -name ".gcov" -o -name "*.cov" \) -exec rm {} \;
1955
1956	clean_cov_all: clean_cov
1957	find . \( -name "*.gcno" \) -exec rm {} \;
1958
1959	run_tests: test_base clean_cov
1960	$(MAKE) "ARB_PID=UT_$$$$" run_tests_faked_arbpid
1961
1962	run_tests_faked_arbpid:
1963	+@$(TEST_RUN_SUITE) init
1964	@echo "fake[1]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
1965	$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(TESTED_UNITS)
1966	@echo "fake[1]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
1967	+@$(TEST_RUN_SUITE) cleanup
1968	$(MAKE) clean_cov
1969
1970	ut:
1971	ifeq ($(UNIT_TESTS),1)
1972	@echo $(MAKE) run_tests
1973	@$(MAKE) run_tests
1974	else
1975	@echo "Not compiled with unit tests"
1976	endif
1977
1978
1979	aut:
1980	+@$(TEST_RUN_SUITE) unskip
1981	$(MAKE) ut
1982
1983	# --------------------------------------------------------------------------------
1984
1985	TIMELOG=$(ARBHOME)/arb_time.log
1986	TIMEARGS=--append --output=$(TIMELOG) --format=" %E(%S+%U) %P [%C]"
1987	TIMECMD=/usr/bin/time $(TIMEARGS)
1988
1989	time_one:
1990	ifeq ($(ONE_TIMED_TARGET),)
1991	@echo "Error: You have to pass ONE_TIMED_TARGET to $@"
1992	false
1993	else
1994	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET)"
1995	@$(TIMECMD) $(MAKE) $(ONE_TIMED_TARGET)
1996	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET) [done]"
1997	endif
1998
1999	timed_target:
2000	ifeq ($(TIMED_TARGET),)
2001	@echo "Error: You have to pass TIMED_TARGET to $@"
2002	false
2003	else
2004	@echo "Build time:" > $(TIMELOG)
2005	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2006	@cat $(TIMELOG)
2007	@rm $(TIMELOG)
2008	endif
2009
2010	timed_target_tested:
2011	ifeq ($(TIMED_TARGET),)
2012	@echo "Error: You have to pass TIMED_TARGET to $@"
2013	false
2014	else
2015	@echo "Build time:" > $(TIMELOG)
2016	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2017	$(MAKE) "ONE_TIMED_TARGET=ut" time_one
2018	@cat $(TIMELOG)
2019	@rm $(TIMELOG)
2020	endif
2021
2022	clean_timed_target:
2023	ifeq ($(TIMED_TARGET),)
2024	@echo "Error: You have to pass TIMED_TARGET to $@"
2025	false
2026	else
2027	@echo "Build time:" > $(TIMELOG)
2028	$(MAKE) "ONE_TIMED_TARGET=clean" time_one
2029	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2030	@cat $(TIMELOG)
2031	@rm $(TIMELOG)
2032	endif
2033
2034	# --------------------------------------------------------------------------------
2035
2036	build: arb
2037	$(MAKE) binlink preplib
2038	ifeq ("$(DEVELOPER)","SAVETEST")
2039	$(MAKE) save_test
2040	endif
2041
2042	all:
2043	@echo "Build time" > $(TIMELOG)
2044	@echo "$(SEP) $(MAKE) build"
2045	@$(TIMECMD) $(MAKE) build
2046	@echo $(SEP)
2047	@echo "made 'all' with success."
2048	@echo "to start arb enter 'arb'"
2049	ifeq ($(UNIT_TESTS),1)
2050	@echo $(MAKE) run_tests
2051	@$(TIMECMD) $(MAKE) run_tests
2052	endif
2053	@echo "$(SEP) $(MAKE) build [done]"
2054	@cat $(TIMELOG)
2055	@rm $(TIMELOG)
2056
2057

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