Context Navigation

Makefile

Revision 8737, 57.4 KB (checked in by westram, 9 days ago)
RegExpr::match returns NULL if didMatch returns false few simple tests for regexpr (as place to tdd complicated regular expressions)
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`

Line
1	# =============================================================== #
2	# #
3	# File : Makefile #
4	# #
5	# Institute of Microbiology (Technical University Munich) #
6	# http://www.arb-home.de/ #
7	# #
8	# =============================================================== #
9
10	# -----------------------------------------------------
11	# The ARB Makefile is aware of the following defines:
12	#
13	# 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	ifdef DARWIN
50	# GCC,GPP and CPPreal now set in the Portfile
51	else
52	GCC:=$(CC)
53	GPP:=$(CXX)
54	CPPreal:=cpp
55
56	# to use clang-static-analyzer , call make like this:
57	# setenv CLANG_STATIC_CHECKER 1 ; scan-build make -j5 build
58	ifeq ($(CLANG_STATIC_CHECKER),1)
59	CCC_ANALYZER_CPLUSPLUS=1
60	endif
61	endif
62
63
64	# ---------------------- compiler version detection
65
66	# supported compiler versions:
67
68	ALLOWED_GCC_4xx_VERSIONS=\
69	4.2.1 \
70	4.3 4.3.1 4.3.2 4.3.3 4.3.4 \
71	4.4 4.4.1 4.4.3 4.4.5 \
72	4.5.2 \
73	4.6 4.6.1
74
75	ALLOWED_GCC_VERSIONS=$(ALLOWED_GCC_4xx_VERSIONS)
76
77	GCC_VERSION_FOUND=$(shell $(GCC) -dumpversion)
78	GCC_VERSION_ALLOWED=$(strip $(subst ___,,$(foreach version,$(ALLOWED_GCC_VERSIONS),$(findstring ___$(version)___,___$(GCC_VERSION_FOUND)___))))
79
80	#---------------------- split gcc version
81
82	SPLITTED_VERSION:=$(subst ., ,$(GCC_VERSION_FOUND))
83
84	USE_GCC_MAJOR:=$(word 1,$(SPLITTED_VERSION))
85	USE_GCC_MINOR:=$(word 2,$(SPLITTED_VERSION))
86	USE_GCC_PATCHLEVEL:=$(word 3,$(SPLITTED_VERSION))
87
88	USE_GCC_452_OR_HIGHER:=
89	ifeq ($(USE_GCC_MAJOR),4)
90	ifeq ($(USE_GCC_MINOR),5)
91	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),23456789)','')
92	USE_GCC_452_OR_HIGHER:=yes
93	endif
94	else
95	ifneq ('$(findstring $(USE_GCC_MINOR),6789)','')
96	USE_GCC_452_OR_HIGHER:=yes
97	endif
98	endif
99	else
100	USE_GCC_452_OR_HIGHER:=yes
101	endif
102
103	#---------------------- define special directories for non standard builds
104
105	ifdef DARWIN
106	OSX_FW:=/System/Library/Frameworks
107	OSX_FW_OPENGL:=$(OSX_FW)/OpenGL.framework/Versions/A/Libraries
108	OSX_FW_GLUT:=$(OSX_FW)/GLUT.framework/Versions/A/Libraries
109	OSX_FW_IMAGEIO:=$(OSX_FW)/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources
110	endif
111
112	#----------------------
113
114	ifdef DARWIN
115	LINK_STATIC=1# link static
116	else
117	LINK_STATIC=0# link dynamically
118	endif
119
120	shared_cflags :=# flags for shared lib compilation
121	lflags :=# linker flags
122	extended_warnings :=# warning flags for C and C++-compiler
123	extended_cpp_warnings :=# warning flags for C++-compiler only
124
125
126	ifeq ($(DEBUG),0)
127	dflags := -DNDEBUG# defines
128	ifdef DARWIN
129	cflags := -O3# compiler flags (C and C++)
130	else
131	cflags := -O4# compiler flags (C and C++)
132	lflags += -O99# linker flags
133	endif
134	endif
135
136	ifeq ($(DEBUG),1)
137	dflags := -DDEBUG
138
139	gdb_common := -g -g3 -ggdb -ggdb3
140
141	cflags := -O0 $(gdb_common) # (using dwarf - cant debug inlines here, incredible slow on showing variable content)
142	# cflags := -O0 $(gdb_common) -gstabs+ # using stabs+ (enable this for bigger debug session: debugs inlines, quick var inspect, BUT valgrind stops working :/)
143	# cflags := -O0 $(gdb_common) -gstabs # using stabs (same here IIRC)
144	# cflags := -O2 $(gdb_common) # use this for callgrind (force inlining)
145	ifndef DARWIN
146	lflags += -g
147	endif
148
149	# control how much you get spammed
150	POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl
151	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --original# dont modify compiler output
152	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --hide-Noncopyable-advices
153	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --show-useless-Weff++
154	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --no-warnings
155	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --only-first-error
156	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --no-warnings --only-first-error
157
158	# Enable extra warnings
159	extended_warnings :=
160	extended_cpp_warnings :=
161
162	# C and C++
163	extended_warnings += -Wwrite-strings -Wunused -Wno-aggregate-return -Wshadow
164
165	# C++ only
166	extended_cpp_warnings += -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute
167	extended_cpp_warnings += -Wctor-dtor-privacy# < gcc 3
168	# extended_cpp_warnings += -Wfloat-equal# gcc 3.0
169
170	# ------- above only warnings available in 3.0
171
172	extended_cpp_warnings += -Weffc++# gcc 3.0.1
173	extended_cpp_warnings += -Wmissing-noreturn# gcc 3.0.2
174	# extended_cpp_warnings += -Wold-style-cast# gcc 3.0.4 (warn about 28405 old-style casts)
175	extended_cpp_warnings += -Winit-self# gcc 3.4.0
176	extended_cpp_warnings += -Wstrict-aliasing# gcc 3.4
177	extended_cpp_warnings += -Wextra# gcc 3.4.0
178	ifeq ('$(USE_GCC_452_OR_HIGHER)','yes')
179	extended_cpp_warnings += -Wlogical-op# gcc 4.5.2
180	endif
181
182	ifeq ($(DEBUG_GRAPHICS),1)
183	dflags += -DDEBUG_GRAPHICS
184	endif
185	endif
186
187	#---------------------- developer
188
189	ifneq ($(DEVELOPER),ANY) # ANY=default setting (skip all developer specific code)
190	ifdef dflags
191	dflags += -DDEVEL_$(DEVELOPER)# activate developer/release specific code
192	endif
193	endif
194
195	ifndef SHOWTODO
196	ifeq ($(DEVELOPER),RALF)
197	SHOWTODO:=1
198	else
199	SHOWTODO:=0
200	endif
201	endif
202	ifeq ($(SHOWTODO),1)
203	dflags += -DWARN_TODO# activate "TODO" warnings
204	endif
205
206	#---------------------- 32 or 64 bit
207
208	ifndef ARB_64
209	ARB_64=0#default to 32bit
210	endif
211	ifndef BUILDHOST_64
212	BUILDHOST_64:=$(ARB_64)# assume build host is same as version (see config.makefile)
213	endif
214
215	cross_cflags:=
216	cross_lflags:=
217
218	ifeq ($(ARB_64),1)
219	dflags += -DARB_64 #-fPIC
220	lflags +=
221	shared_cflags += -fPIC
222
223	ifeq ($(BUILDHOST_64),1)
224	# build 64-bit ARB version on 64-bit host
225	CROSS_LIB:=# empty = autodetect below
226	ifdef DARWIN
227	cross_cflags += -arch x86_64
228	cross_lflags += -arch x86_64
229	endif
230	else
231	# build 64-bit ARB version on 32-bit host
232	CROSS_LIB:=/lib64
233	cross_cflags += -m64
234	cross_lflags += -m64 -m elf_x86_64
235	endif
236	else
237	ifeq ($(BUILDHOST_64),1)
238	# build 32-bit ARB version on 64-bit host
239	CROSS_LIB:=# empty = autodetect below
240	cross_cflags += -m32
241	cross_lflags += -m32 -m elf_i386
242	else
243	# build 32-bit ARB version on 32-bit host
244	CROSS_LIB:=/lib
245	endif
246	endif
247
248	cflags += $(cross_cflags)
249	lflags += $(cross_lflags)
250
251	ifeq ('$(CROSS_LIB)','')
252	# autodetect libdir
253	ifeq ($(ARB_64),1)
254	CROSS_LIB:=$(shell (test -d /lib64 && echo lib64) \|\| echo lib)
255	else
256	CROSS_LIB:=$(shell (test -d /lib32 && echo lib32) \|\| echo lib)
257	endif
258	endif
259
260	#---------------------- unit tests
261
262	ifndef UNIT_TESTS
263	UNIT_TESTS=0#default is "no tests"
264	endif
265	ifeq ($(UNIT_TESTS),1)
266	dflags += -DUNIT_TESTS
267	UNIT_TESTER_LIB=UNIT_TESTER/UNIT_TESTER.a
268	else
269	UNIT_TESTER_LIB=
270	endif
271
272	#---------------------- use gcov
273
274	ifndef COVERAGE
275	COVERAGE=0#default is "no"
276	endif
277	ifneq ($(COVERAGE),0)
278	GCOVFLAGS=-ftest-coverage -fprofile-arcs
279	cflags += $(GCOVFLAGS)
280	EXECLIBS=-lgcov
281	else
282	GCOVFLAGS=
283	EXECLIBS=
284	endif
285
286	#---------------------- other flags
287
288	dflags += -D$(MACH) # define machine
289
290	ifdef DARWIN
291	shared_cflags += -fno-common
292	else
293	dflags += $(shell getconf LFS_CFLAGS)
294	endif
295
296	cflags += -pipe
297	cflags += -fmessage-length=0# don't wrap compiler output
298	cflags += -fshow-column# show columns
299	cflags += -funit-at-a-time
300	cflags += -fPIC
301	cflags += -fno-common# link all global data into one namespace
302	cflags += -fstrict-aliasing# gcc 3.4
303	#cflags += -save-temps# uncomment to see preprocessor output
304
305	#---------------------- X11 location
306
307	ifdef DARWIN
308	XHOME:=$(PREFIX)
309	else
310	XHOME:=/usr/X11R6
311	endif
312
313	XINCLUDES:=-I$(XHOME)/include
314	ifdef DARWIN
315	XINCLUDES += -I$(OSX_FW)/GLUT.framework/Headers -I$(OSX_FW)/OpenGL.framework/Headers -I$(OSX_SDK)/usr/include/krb5
316
317	XLIBS := -L$(XHOME)/lib -lXm -lpng -lz -lXt -lX11 -lXext -lXp -lXmu -lXi
318	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGL.dylib:$(OSX_FW_OPENGL)/libGL.dylib
319	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGLU.dylib:$(OSX_FW_OPENGL)/libGLU.dylib
320	else
321	XLIBS:=-L$(XHOME)/$(CROSS_LIB) -lXm -lXpm -lXt -lXext -lX11
322	endif
323
324	#---------------------- open GL
325
326	ifeq ($(OPENGL),1)
327	cflags += -DARB_OPENGL # activate OPENGL code
328	GL := gl # this is the name of the OPENGL base target
329	GL_LIB_SYS := -lGL -lGLU
330	GL_LIB_ARB := -L$(ARBHOME)/GL/glAW -lglAW
331
332	ifdef DEBIAN
333	GL_LIB_SYS += -lpthread
334	endif
335
336	GL_PNGLIBS_ARB := -L$(ARBHOME)/GL/glpng -lglpng_arb
337	GL_PNGLIBS_SYS := -lpng
338
339	GLEWLIB := -lGLEW -lGLw
340	ifdef DARWIN
341	GLUTLIB := -glut
342	else
343	GLUTLIB := -lglut
344	endif
345
346	GL_LIBS_SYS := $(GL_LIB_SYS) $(GL_PNGLIBS_SYS) $(GLEWLIB) $(GLUTLIB)
347	GL_LIBS_ARB := $(GL_LIB_ARB) $(GL_PNGLIBS_ARB)
348
349	RNA3D_LIB := RNA3D/RNA3D.a
350
351	else
352
353	GL_LIBS_ARB:=# no opengl -> no libs
354	GL_LIBS_SYS:=# no opengl -> no libs
355	GL:=# don't build ARB openGL libs
356
357	RNA3D_LIB :=
358
359	endif
360
361
362
363	GL_LIBS:=$(GL_LIBS_ARB) $(GL_LIBS_SYS)
364
365	#---------------------- tiff lib:
366
367	TIFFLIBS := -ltiff
368
369	#---------------------- basic libs:
370
371	SYSLIBS:=
372
373	ifdef DARWIN
374	SYSLIBS += -lstdc++
375	else
376	SYSLIBS += -lm
377	endif
378
379	#---------------------- include symbols?
380
381	ifeq ($(TRACESYM),1)
382	ifdef DARWIN
383	cdynamic =
384	ldynamic =
385	else
386	cdynamic = -rdynamic -Wl,--export-dynamic
387	ldynamic = --export-dynamic
388	endif
389	endif
390
391	#---------------------- system dependent commands
392
393	ifdef DARWIN
394	TIME:=gtime
395	else
396	TIME:=/usr/bin/time
397	endif
398
399	# -------------------------------------------------------------------------
400	# Don't put any machine/version/etc conditionals below!
401	# (instead define variables above)
402	# -------------------------------------------------------------------------
403
404	cflags += -W -Wall $(dflags) $(extended_warnings) $(cdynamic)
405
406	cppflags := $(extended_cpp_warnings)
407
408	ifeq ($(DEVELOPER),RALF)
409	HAVE_GNUPP0X=`SOURCE_TOOLS/requireVersion.pl 4.3 $(GCC_VERSION_FOUND)`
410	ifeq ($(HAVE_GNUPP0X),1)
411	# ensure compatibility with upcoming C++ standard
412	cppflags += -std=gnu++0x
413	endif
414	endif
415
416	# compiler settings:
417
418	ACC := $(GCC)# compile C
419	CPP := $(GPP) $(cppflags)# compile C++
420	ACCLIB := $(ACC) $(shared_cflags)# compile C (shared libs)
421	CPPLIB := $(CPP) $(shared_cflags)# compile C++ (shared libs)
422
423	# preprocessor
424	ifdef DARWIN
425	PP := $(GCC) -E -x c-header
426	else
427	PP := $(CPPreal)
428	endif
429
430	LINK_STATIC_LIB := ld $(lflags) $(ldynamic) -r -o# link static lib
431	LINK_EXECUTABLE := $(GPP) $(lflags) $(cdynamic) -o# link executable (c++)
432
433	ifeq ($(LINK_STATIC),1)
434	SHARED_LIB_SUFFIX = a# static lib suffix
435	LINK_SHARED_LIB := $(LINK_STATIC_LIB)
436	else
437	SHARED_LIB_SUFFIX = so# shared lib suffix
438	LINK_SHARED_LIB := $(GPP) $(lflags) $(cdynamic) -shared $(GCOVFLAGS) -o# link shared lib
439	endif
440
441	# other used tools
442
443
444	ifdef DARWIN
445	XMKMF := $(PREFIX)/bin/xmkmf
446	else
447	XMKMF := /usr/bin/X11/xmkmf
448	endif
449
450	MAKEDEPEND_PLAIN = makedepend
451
452	MAKEDEPEND = $(FORCEMASK);$(MAKEDEPEND_PLAIN)
453
454	#SEP:=--------------------------------------------------------------------------------
455	SEP=[`date +%M:%S.%N`] ------------------------------------------------
456	# to analyse timings run
457	# make -j9 clean; make -j9 all \| grep '^\[' \| sort
458	# make -j9 "TIMED_TARGET=perl" clean_timed_target \| grep '^\[' \| sort
459
460
461
462	# delete variables unused below
463
464	lflags:=
465
466	# -------------------------
467	# Main arb targets:
468	# -------------------------
469
470	first_target:
471	$(MAKE) checks
472	@echo $(SEP)
473	@echo 'Main targets:'
474	@echo ''
475	@echo ' all - Compile ARB + TOOLs + and copy shared libs + link foreign software'
476	@echo ' (That is most likely the target you want)'
477	@echo ''
478	@echo ' clean - remove generated files ("SUBDIR/SUBDIR.clean" to clean only SUBDIR)'
479	@echo ' rebuild - clean + all'
480	@echo ' relink - remove all binaries and relink them from objects'
481	@echo ''
482	@echo 'Some often used sub targets (make all makes them all):'
483	@echo ''
484	@echo ' arb - Just compile ARB (but none of the integrated tools)'
485	@echo ' menus - create GDEHELP/ARB_GDEmenus from GDEHELP/ARB_GDEmenus.source'
486	@echo ' perl - Compile the PERL XSUBS into lib/ARB.so and create links in lib to perl'
487	@echo ' binlink - Create all links in the bin directory'
488	@echo ''
489	@echo 'Development targets:'
490	@echo ''
491	@echo ' depends - create or update dependencies ("SUBDIR/SUBDIR.depends" to update only SUBDIR)'
492	@echo ' proto - create or update prototypes ("SUBDIR/SUBDIR.proto" to update only SUBDIR)'
493	@echo ' tags - create tags for xemacs'
494	@echo ' show - show available shortcuts (AKA subtargets)'
495	@echo ' up - shortcut for depends+proto+tags'
496	ifeq ($(UNIT_TESTS),1)
497	@echo ' ut - only run tests'
498	endif
499	@echo ' modified - rebuild files modified in svn checkout (does touch)'
500	@echo ' touch - touch files modified in svn checkout'
501	@echo ''
502	@echo 'Internal maintenance:'
503	@echo ''
504	@echo ' rel_minor - build a release (increases minor version number)'
505	@echo ' rel_major - build a release (increases MAJOR version number)'
506	@echo ' tarfile - make rebuild and create arb version tarfile ("tarfile_quick" to skip rebuild)'
507	@echo ' save - save all basic ARB sources into arbsrc_DATE ("savetest" to check filelist)'
508	@echo ' patch - save svn diff to patchfile'
509	@echo ' source_doc - create doxygen documentation'
510	@echo ' relocated - rebuild partly (use when you have relocated ARBHOME)'
511	@echo ' check_res - check ressource usage'
512	@echo ' dep_graph - Build dependency graphs'
513	@echo ' clean_cov - Clean coverage results'
514	@echo ''
515	@echo $(SEP)
516	@echo ''
517
518
519	# auto-generate config.makefile:
520
521	CONFIG_MAKEFILE_FOUND=$(wildcard config.makefile)
522
523	config.makefile : config.makefile.template
524	@echo --------------------------------------------------------------------------------
525	ifeq ($(strip $(CONFIG_MAKEFILE_FOUND)),)
526	@cp $< $@
527	@echo '$(ARBHOME)/$@:1: has been generated.'
528	@echo 'Please edit $@ to configure your system!'
529	@echo --------------------------------------------------------------------------------
530	@false
531	else
532	@echo '$(ARBHOME)/$<:1: is more recent than'
533	@echo '$(ARBHOME)/$@:1:'
534	@ls -al config.makefile*
535	@echo --------------------------------------------------------------------------------
536	@echo "Updating $@ (if this fails, check manually)"
537	SOURCE_TOOLS/update_config_makefile.pl
538	@echo "Sucessfully updated $@"
539	@echo --------------------------------------------------------------------------------
540	@ls -al config.makefile*
541	@echo --------------------------------------------------------------------------------
542	@echo "Diff to your old config.makefile:"
543	@echo --------------------------------------------------------------------------------
544	-diff $@.bak $@
545	@echo --------------------------------------------------------------------------------
546	endif
547
548	# check if everything is configured correctly
549
550	check_DEVELOPER:
551	ifndef DEVELOPER
552	@echo 'config.makefile:1: DEVELOPER not defined'
553	@false
554	endif
555
556	check_DEBUG:
557	ifndef dflags
558	@echo 'config.makefile:1: DEBUG has to be defined. Valid values are 0 and 1'
559	@false
560	endif
561
562	check_ARB_64:
563	ifndef ARB_64
564	@echo 'config.makefile:1: ARB_64 has to be defined. Valid values are 0 and 1'
565	@false
566	endif
567
568	# ---------------------------------------- check gcc version
569
570	check_same_GCC_VERSION:
571	$(ARBHOME)/SOURCE_TOOLS/check_same_gcc_version.pl $(GCC_VERSION_ALLOWED)
572
573	check_GCC_VERSION:
574	@echo 'GCC version check:'
575	@echo " - Your version is '$(GCC_VERSION_FOUND)'"
576	ifeq ('$(GCC_VERSION_ALLOWED)', '')
577	@echo ' - This version is not in the list of supported gcc-versions:'
578	@$(foreach version,$(ALLOWED_GCC_VERSIONS),echo ' * $(version)';)
579	@echo ' - You may either ..'
580	@echo ' - add your version to ALLOWED_GCC_VERSIONS in the Makefile and try it out or'
581	@echo ' - switch to one of the allowed versions (see arb_README_gcc.txt for installing'
582	@echo ' a different version of gcc)'
583	@echo ''
584	@false
585	else
586	@echo " - Supported gcc version '$(GCC_VERSION_ALLOWED)' detected - fine!"
587	@echo ''
588	$(MAKE) check_same_GCC_VERSION
589
590	endif
591
592	GCC_WITH_VTABLE_AFTER_CLASS=#occurred only with no longer supported $(ALLOWED_GCC_295_VERSIONS)
593	HAVE_GCC_WITH_VTABLE_AFTER_CLASS=$(strip $(foreach version,$(GCC_WITH_VTABLE_AFTER_CLASS),$(findstring $(version),$(GCC_VERSION_ALLOWED))))
594
595	# depending on the version of gcc the location of the vtable pointer differs.
596	ifeq ('$(HAVE_GCC_WITH_VTABLE_AFTER_CLASS)', '')
597	VTABLE_INFRONTOF_CLASS=1
598	else
599	VTABLE_INFRONTOF_CLASS=0
600	endif
601
602	#---------------------- check ARBHOME
603
604	# use arb_INSTALL.txt to determine whether ARBHOME points to correct directory
605	ARB_INSTALL_FOUND=$(wildcard $(ARBHOME)/arb_INSTALL.txt)
606
607	check_ARBHOME:
608	ifeq ($(strip $(ARB_INSTALL_FOUND)),)
609	@echo ------------------------------------------------------------
610	@echo "ARBHOME is set to '$(ARBHOME)'"
611	@echo "The environment variable ARBHOME has to point to the top arb source directory."
612	@echo "If you use bash enter:"
613	@echo " export ARBHOME='`pwd`'"
614	@echo ------------------------------------------------------------
615	@false
616	endif
617
618	ARB_PATH_SET=$(findstring $(ARBHOME)/bin,$(PATH))
619
620	check_PATH: check_ARBHOME
621	ifeq ($(strip $(ARB_PATH_SET)),)
622	@echo ------------------------------------------------------------
623	@echo "The environment variable PATH has to contain $(ARBHOME)/bin"
624	@echo "If you use bash enter:"
625	@echo ' export PATH=$$ARBHOME/bin:$$PATH'
626	@echo ------------------------------------------------------------
627	@false
628	endif
629
630	check_TOOLS:
631	@util/arb_check_build_env.pl \
632	"$(ACC)" \
633	"$(CPP)" \
634	"$(GPP)" \
635	"$(PP)" \
636	"$(ACCLIB)" \
637	"$(CPPLIB)" \
638	"$(XMKMF)" \
639	"$(MAKEDEPEND_PLAIN)" \
640	"$(LINK_SHARED_LIB)" \
641	"$(LINK_SHARED_LIB)" \
642
643
644	check_ENVIRONMENT : check_PATH check_TOOLS
645
646	check_tabs: check_setup
647	ifeq ($(DEBUG),1)
648	@SOURCE_TOOLS/tabBrake.pl
649	endif
650
651	force_tab_check:
652	@touch -t 198001010000 SOURCE_TOOLS/stamp.tabBrake
653	@$(MAKE) check_tabs
654
655
656	# ---------------------
657
658	check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION
659	@echo Your setup seems to be ok.
660
661	checks: check_setup check_tabs
662	@rm -f SOURCE_TOOLS/postcompile.sav
663
664
665	# end test section ------------------------------
666
667	CORE_LIB=-lCORE
668	ARBDB_LIB=-lARBDB $(CORE_LIB)
669	LIBS = $(ARBDB_LIB) $(SYSLIBS)
670
671	GUI_LIBS_PREFIX:=
672	ifdef DARWIN
673	# this seem to be added at wrong place, since opengl is only needed to link EDIT4
674	GUI_LIBS_PREFIX:=-framework GLUT -framework OpenGL
675	endif
676
677	GUI_LIBS = $(GUI_LIBS_PREFIX) $(LIBS) -lWINDOW -lAWT $(XLIBS)
678	LIBPATH = -L$(ARBHOME)/lib
679
680	DEST_LIB = lib
681	DEST_BIN = bin
682
683	AINCLUDES := -I. -I$(ARBHOME)/INCLUDE $(XINCLUDES)
684	CPPINCLUDES := -I. -I$(ARBHOME)/INCLUDE $(XINCLUDES)
685	MAKEDEPENDFLAGS := -- $(cflags) -- -DARB_OPENGL -DUNIT_TESTS -D__cplusplus -I. -Y$(ARBHOME)/INCLUDE
686
687	ifeq ($(VTABLE_INFRONTOF_CLASS),1)
688	# Some code in ARB depends on the location of the vtable pointer
689	# (it does a cast from class AP_tree to struct GBT_TREE). In order to
690	# work around that hack properly, we define FAKE_VTAB_PTR
691	# if the vtable is located at the beginning of class.
692	# We are really sorry for that hack.
693	cflags:=$(cflags) -DFAKE_VTAB_PTR=char
694	endif
695
696	# -------------------------------
697	# old PTSERVER or PTPAN?
698
699	ifeq ($(PTPAN),1)
700	# PTPAN only libs
701	ARCHS_PT_SERVER = \
702	ptpan/PROBE.a
703	else
704	ifeq ($(PTPAN),2)
705	# special mode to compile both servers (developers only!)
706	ARCHS_PT_SERVER = \
707	ptpan/PROBE.a \
708	PROBE/PROBE.a
709	ARCHS_PT_SERVER_LINK = PROBE/PROBE.a# default to old ptserver
710	else
711	# PT-server only libs
712	ARCHS_PT_SERVER = \
713	PROBE/PROBE.a
714	endif
715	endif
716
717	ifndef ARCHS_PT_SERVER_LINK
718	ARCHS_PT_SERVER_LINK = $(ARCHS_PT_SERVER)
719	endif
720
721	# ---------------------------------------
722	# wrap main()
723
724	use_ARB_main=$(ARBHOME)/SOURCE_TOOLS/arb_main_cpp.o
725	use_ARB_main_C=$(ARBHOME)/SOURCE_TOOLS/arb_main_c.o
726
727	arbmainwrapper:
728	$(MAKE) -C SOURCE_TOOLS -r "cflags = $(cflags)" mainwrapper
729
730	# ---------------------------------------
731	# List of standard top level directories
732	#
733	# sub-makefiles have to define the targets
734	# - 'depends' and
735	# - 'clean'
736	#
737	# when adding new libs here, also add a dependency vs 'links' or 'links_non_perl' below
738
739	ARCHS = \
740	$(ARCHS_PT_SERVER) \
741	AISC/AISC.a \
742	AISC_MKPTPS/AISC_MKPTPS.a \
743	ARBDB/libARBDB.a \
744	CORE/libCORE.a \
745	ARB_GDE/ARB_GDE.a \
746	AWT/libAWT.a \
747	AWTC/AWTC.a \
748	AWTI/AWTI.a \
749	CONSENSUS_TREE/CONSENSUS_TREE.a \
750	CONVERTALN/CONVERTALN.a \
751	DBSERVER/DBSERVER.a \
752	DIST/DIST.a \
753	EDIT4/EDIT4.a \
754	EISPACK/EISPACK.a \
755	GDE/GDE.a \
756	GENOM/GENOM.a \
757	GENOM_IMPORT/GENOM_IMPORT.a \
758	GL/GL.a \
759	ISLAND_HOPPING/ISLAND_HOPPING.a \
760	MERGE/MERGE.a \
761	MULTI_PROBE/MULTI_PROBE.a \
762	NALIGNER/NALIGNER.a \
763	NAMES/NAMES.a \
764	NAMES_COM/server.a \
765	NTREE/NTREE.a \
766	PARSIMONY/PARSIMONY.a \
767	PERLTOOLS/PERLTOOLS.a \
768	PGT/PGT.a \
769	PHYLO/PHYLO.a \
770	PRIMER_DESIGN/PRIMER_DESIGN.a \
771	PROBE_COM/server.a \
772	PROBE_DESIGN/PROBE_DESIGN.a \
773	PROBE_SET/PROBE_SET.a \
774	READSEQ/READSEQ.a \
775	RNA3D/RNA3D.a \
776	RNACMA/RNACMA.a \
777	SECEDIT/SECEDIT.a \
778	SEQ_QUALITY/SEQ_QUALITY.a \
779	SERVERCNTRL/SERVERCNTRL.a \
780	SL/SL.a \
781	STAT/STAT.a \
782	TOOLS/TOOLS.a \
783	TREEGEN/TREEGEN.a \
784	UNIT_TESTER/UNIT_TESTER.a \
785	WETC/WETC.a \
786	WINDOW/libWINDOW.a \
787	XML/XML.a \
788
789	# -----------------------
790	# library packets
791
792	ARCHS_CLIENT_PROBE = PROBE_COM/client.a
793	ARCHS_CLIENT_NAMES = NAMES_COM/client.a
794	ARCHS_MAKEBIN = AISC_MKPTPS/AISC_MKPTPS.a AISC/AISC.a
795
796	# communication libs need aisc and aisc_mkpts:
797
798	AISC/AISC.dummy: proto_tools
799
800	comtools: AISC/AISC.dummy
801
802	ARCHS_SEQUENCE = \
803	SL/SEQUENCE/SEQUENCE.a \
804	SL/ALIVIEW/ALIVIEW.a \
805	SL/PRONUC/PRONUC.a \
806
807	ARCHS_TREE = \
808	$(ARCHS_SEQUENCE) \
809	SL/FILTER/FILTER.a \
810	SL/ARB_TREE/ARB_TREE.a \
811
812	# parsimony tree (used by NTREE, PARSIMONY, STAT(->EDIT4), DIST(obsolete!))
813	ARCHS_AP_TREE = \
814	$(ARCHS_TREE) \
815	SL/AP_TREE/AP_TREE.a \
816
817	# --------------------------------------------------------------------------------
818	# dependencies for linking shared libs
819
820	link_core: core
821	link_db: db link_core
822	link_aw: aw link_db
823	link_awt: awt link_aw
824
825	#***************************************************************************************
826	# Individual Programs Section
827	#***************************************************************************************
828
829	#********************************* arb_ntree ************************************
830	NTREE = bin/arb_ntree
831	ARCHS_NTREE = \
832	NTREE/NTREE.a \
833	$(ARCHS_AP_TREE) \
834	ARB_GDE/ARB_GDE.a \
835	AWTC/AWTC.a \
836	AWTI/AWTI.a \
837	CONSENSUS_TREE/CONSENSUS_TREE.a \
838	GENOM/GENOM.a \
839	GENOM_IMPORT/GENOM_IMPORT.a \
840	MERGE/MERGE.a \
841	MULTI_PROBE/MULTI_PROBE.a \
842	PRIMER_DESIGN/PRIMER_DESIGN.a \
843	PROBE_DESIGN/PROBE_DESIGN.a \
844	SEQ_QUALITY/SEQ_QUALITY.a \
845	SERVERCNTRL/SERVERCNTRL.a \
846	SL/AW_NAME/AW_NAME.a \
847	SL/DB_UI/DB_UI.a \
848	SL/DB_SCANNER/DB_SCANNER.a \
849	SL/DB_QUERY/DB_QUERY.a \
850	SL/SEQIO/SEQIO.a \
851	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
852	SL/HELIX/HELIX.a \
853	SL/REGEXPR/REGEXPR.a \
854	SL/REFENTRIES/REFENTRIES.a \
855	SL/NDS/NDS.a \
856	SL/ITEMS/ITEMS.a \
857	SL/LOCATION/LOCATION.a \
858	SL/TRANSLATE/TRANSLATE.a \
859	SL/TREEDISP/TREEDISP.a \
860	SL/TREE_ADMIN/TREE_ADMIN.a \
861	SL/TREE_READ/TREE_READ.a \
862	SL/TREE_WRITE/TREE_WRITE.a \
863	STAT/STAT.a \
864	XML/XML.a \
865
866	$(NTREE): $(ARCHS_NTREE:.a=.dummy) link_awt
867	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NTREE) $(GUI_LIBS) \|\| ( \
868	echo "$(SEP) Link $@"; \
869	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS)" ; \
870	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS) && \
871	echo "$(SEP) Link $@ [done]"; \
872	)
873
874	#********************************* arb_edit4 ************************************
875	EDIT4 = bin/arb_edit4
876
877	ARCHS_EDIT4 := \
878	EDIT4/EDIT4.a \
879	$(ARCHS_AP_TREE) \
880	ARB_GDE/ARB_GDE.a \
881	AWTC/AWTC.a \
882	ISLAND_HOPPING/ISLAND_HOPPING.a \
883	SECEDIT/SECEDIT.a \
884	SERVERCNTRL/SERVERCNTRL.a \
885	SL/AW_HELIX/AW_HELIX.a \
886	SL/AW_NAME/AW_NAME.a \
887	SL/FAST_ALIGNER/FAST_ALIGNER.a \
888	SL/ITEMS/ITEMS.a \
889	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
890	SL/HELIX/HELIX.a \
891	SL/TRANSLATE/TRANSLATE.a \
892	STAT/STAT.a \
893	XML/XML.a \
894
895	ifeq ($(OPENGL),1)
896	ARCHS_EDIT4 += RNA3D/RNA3D.a
897	endif
898
899	LIBS_EDIT4 := $(GL_LIBS)
900
901	$(EDIT4): $(ARCHS_EDIT4:.a=.dummy) link_awt
902	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_EDIT4) $(GUI_LIBS) \|\| ( \
903	echo "$(SEP) Link $@"; \
904	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4) $(EXECLIBS)" ; \
905	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4) $(EXECLIBS) && \
906	echo "$(SEP) Link $@ [done]"; \
907	)
908
909	#********************************* arb_rnacma ************************************
910	RNACMA = bin/arb_rnacma
911	ARCHS_RNACMA = \
912	RNACMA/RNACMA.a \
913
914	$(RNACMA) : $(ARCHS_RNACMA:.a=.dummy) link_db
915	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_RNACMA) \|\| ( \
916	echo "$(SEP) Link $@"; \
917	echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_RNACMA) $(LIBS) $(EXECLIBS)"; \
918	$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_RNACMA) $(LIBS) $(EXECLIBS) && \
919	echo "$(SEP) Link $@ [done]"; \
920	)
921
922	#********************************* arb_pgt ************************************
923
924	PGT = bin/arb_pgt
925	ARCHS_PGT = \
926	PGT/PGT.a \
927
928	PGT_SYS_LIBS=$(XLIBS) $(TIFFLIBS) $(LIBS)
929
930	$(PGT) : $(ARCHS_PGT:.a=.dummy) link_db
931	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PGT) \|\| ( \
932	echo "$(SEP) Link $@"; \
933	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PGT) $(PGT_SYS_LIBS) $(EXECLIBS) "; \
934	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PGT) $(PGT_SYS_LIBS) $(EXECLIBS) && \
935	echo "$(SEP) Link $@ [done]"; \
936	)
937
938
939	#********************************* arb_wetc ************************************
940	WETC = bin/arb_wetc
941	ARCHS_WETC = \
942	WETC/WETC.a \
943	SL/HELIX/HELIX.a \
944	SL/FILTER/FILTER.a \
945	XML/XML.a \
946
947	$(WETC): $(ARCHS_WETC:.a=.dummy) link_awt
948	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_WETC) $(GUI_LIBS) \|\| ( \
949	echo "$(SEP) Link $@"; \
950	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC) $(GUI_LIBS) $(EXECLIBS)" ; \
951	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC) $(GUI_LIBS) $(EXECLIBS) && \
952	echo "$(SEP) Link $@ [done]"; \
953	)
954
955	#********************************* arb_dist ************************************
956	DIST = bin/arb_dist
957	ARCHS_DIST = \
958	$(ARCHS_AP_TREE) \
959	CONSENSUS_TREE/CONSENSUS_TREE.a \
960	DIST/DIST.a \
961	EISPACK/EISPACK.a \
962	SERVERCNTRL/SERVERCNTRL.a \
963	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
964	SL/HELIX/HELIX.a \
965	SL/MATRIX/MATRIX.a \
966	SL/NDS/NDS.a \
967	SL/ITEMS/ITEMS.a \
968	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.a \
969	XML/XML.a \
970
971	$(DIST): $(ARCHS_DIST:.a=.dummy) link_awt
972	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_DIST) $(GUI_LIBS) \|\| ( \
973	echo "$(SEP) Link $@"; \
974	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS)" ; \
975	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS) && \
976	echo "$(SEP) Link $@ [done]"; \
977	)
978
979	#********************************* arb_pars ************************************
980	PARSIMONY = bin/arb_pars
981	ARCHS_PARSIMONY = \
982	$(ARCHS_AP_TREE) \
983	PARSIMONY/PARSIMONY.a \
984	SERVERCNTRL/SERVERCNTRL.a \
985	SL/AW_NAME/AW_NAME.a \
986	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
987	SL/HELIX/HELIX.a \
988	SL/NDS/NDS.a \
989	SL/ITEMS/ITEMS.a \
990	SL/TRANSLATE/TRANSLATE.a \
991	SL/TREEDISP/TREEDISP.a \
992	XML/XML.a \
993
994	$(PARSIMONY): $(ARCHS_PARSIMONY:.a=.dummy) link_awt
995	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PARSIMONY) $(GUI_LIBS) \|\| ( \
996	echo "$(SEP) Link $@"; \
997	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(EXECLIBS)" ; \
998	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(EXECLIBS) && \
999	echo "$(SEP) Link $@ [done]"; \
1000	)
1001
1002	#********************************* arb_convert_aln ************************************
1003	CONVERT_ALN = bin/arb_convert_aln
1004	ARCHS_CONVERT_ALN = \
1005	CONVERTALN/CONVERTALN.a \
1006
1007	$(CONVERT_ALN) : $(ARCHS_CONVERT_ALN:.a=.dummy) link_db
1008	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_CONVERT_ALN) \|\| ( \
1009	echo "$(SEP) Link $@"; \
1010	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN) $(LIBS) $(ARBDB_LIB) $(EXECLIBS)"; \
1011	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN) $(LIBS) $(ARBDB_LIB) $(EXECLIBS) && \
1012	echo "$(SEP) Link $@ [done]"; \
1013	)
1014
1015	#********************************* arb_treegen ************************************
1016
1017	TREEGEN = bin/arb_treegen
1018	ARCHS_TREEGEN = \
1019	TREEGEN/TREEGEN.a \
1020
1021	$(TREEGEN) : $(ARCHS_TREEGEN:.a=.dummy)
1022	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_TREEGEN) \|\| ( \
1023	echo "$(SEP) Link $@"; \
1024	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN) $(EXECLIBS)" ; \
1025	$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN) $(EXECLIBS) && \
1026	echo "$(SEP) Link $@ [done]"; \
1027	)
1028
1029	#********************************* arb_naligner ************************************
1030	NALIGNER = bin/arb_naligner
1031	ARCHS_NALIGNER = \
1032	NALIGNER/NALIGNER.a \
1033	SERVERCNTRL/SERVERCNTRL.a \
1034	SL/HELIX/HELIX.a \
1035
1036	$(NALIGNER): $(ARCHS_NALIGNER:.a=.dummy) link_db
1037	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NALIGNER) \|\| ( \
1038	echo "$(SEP) Link $@"; \
1039	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(LIBS) $(EXECLIBS)" ; \
1040	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(LIBS) $(EXECLIBS) && \
1041	echo "$(SEP) Link $@ [done]"; \
1042	)
1043
1044	#********************************* arb_phylo ************************************
1045	PHYLO = bin/arb_phylo
1046	ARCHS_PHYLO = \
1047	PHYLO/PHYLO.a \
1048	SL/HELIX/HELIX.a \
1049	SL/FILTER/FILTER.a \
1050	SL/MATRIX/MATRIX.a \
1051	XML/XML.a \
1052
1053	$(PHYLO): $(ARCHS_PHYLO:.a=.dummy) link_awt
1054	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PHYLO) $(GUI_LIBS) \|\| ( \
1055	echo "$(SEP) Link $@"; \
1056	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO) $(GUI_LIBS) $(EXECLIBS)" ; \
1057	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO) $(GUI_LIBS) $(EXECLIBS) && \
1058	echo "$(SEP) Link $@ [done]"; \
1059	)
1060
1061	#***************************************************************************************
1062	# SERVER SECTION
1063	#***************************************************************************************
1064
1065	#********************************* arb_db_server ************************************
1066	DBSERVER = bin/arb_db_server
1067	ARCHS_DBSERVER = \
1068	DBSERVER/DBSERVER.a \
1069	SERVERCNTRL/SERVERCNTRL.a \
1070
1071	$(DBSERVER): $(ARCHS_DBSERVER:.a=.dummy) link_db
1072	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_DBSERVER) $(ARBDB_LIB) \|\| ( \
1073	echo "$(SEP) Link $@"; \
1074	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER) $(ARBDB_LIB) PROBE_COM/client.a $(SYSLIBS) $(EXECLIBS)" ; \
1075	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER) $(ARBDB_LIB) PROBE_COM/client.a $(SYSLIBS) $(EXECLIBS) && \
1076	echo "$(SEP) Link $@ [done]"; \
1077	)
1078
1079	#********************************* arb_pt_server ************************************
1080	PROBE = bin/arb_pt_server
1081	ARCHS_PROBE_COMMON = \
1082	SERVERCNTRL/SERVERCNTRL.a \
1083	SL/HELIX/HELIX.a \
1084	SL/PTCLEAN/PTCLEAN.a \
1085
1086	ARCHS_PROBE_LINK = \
1087	$(ARCHS_PROBE_COMMON) \
1088	$(ARCHS_PT_SERVER_LINK) \
1089
1090	ARCHS_PROBE_DEPEND = \
1091	$(ARCHS_PROBE_COMMON) \
1092	$(ARCHS_PT_SERVER) \
1093
1094	$(PROBE): $(ARCHS_PROBE_DEPEND:.a=.dummy) link_db
1095	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) config.makefile \|\| ( \
1096	echo "$(SEP) Link $@"; \
1097	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) PROBE_COM/server.a $(SYSLIBS) $(EXECLIBS)" ; \
1098	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) PROBE_COM/server.a $(SYSLIBS) $(EXECLIBS) && \
1099	echo "$(SEP) Link $@ [done]"; \
1100	)
1101
1102	#********************************* arb_name_server ************************************
1103	NAMES = bin/arb_name_server
1104	ARCHS_NAMES = \
1105	NAMES/NAMES.a \
1106	SERVERCNTRL/SERVERCNTRL.a \
1107
1108	$(NAMES): $(ARCHS_NAMES:.a=.dummy) link_db
1109	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) \|\| ( \
1110	echo "$(SEP) Link $@"; \
1111	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS) $(EXECLIBS)" ; \
1112	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS) $(EXECLIBS) && \
1113	echo "$(SEP) Link $@ [done]"; \
1114	)
1115
1116	#********************************* SHARED LIBRARIES SECTION ************************************
1117
1118	prepare_libdir: addlibs
1119
1120	addlibs:
1121	(perl $(ARBHOME)/SOURCE_TOOLS/provide_libs.pl \
1122	"arbhome=$(ARBHOME)" \
1123	"opengl=$(OPENGL)" \
1124	"link_static=$(LINK_STATIC)" \
1125	)
1126
1127	#***************************************************************************************
1128	# Recursive calls to sub-makefiles
1129	#***************************************************************************************
1130
1131	include SOURCE_TOOLS/export2sub
1132
1133	%.depends:
1134	@cp -p $(@D)/Makefile $(@D)/Makefile.old # save old Makefile
1135	@$(MAKE) -C $(@D) -r \
1136	"AUTODEPENDS=1" \
1137	"MAIN=nothing" \
1138	"cflags=noCflagsHere_use_MAKEDEPENDFLAGS" \
1139	depends;
1140	@grep "^# DO NOT DELETE" $(@D)/Makefile >/dev/null
1141	@cat $(@D)/Makefile \
1142	\| SOURCE_TOOLS/fix_depends.pl \
1143	>$(@D)/Makefile.2
1144	@mv $(@D)/Makefile.old $(@D)/Makefile # restore old Makefile
1145	@$(ARBHOME)/SOURCE_TOOLS/mv_if_diff $(@D)/Makefile.2 $(@D)/Makefile # update Makefile if changed
1146
1147	%.proto:
1148	@$(MAKE) -C $(@D) \
1149	"AUTODEPENDS=0" \
1150	"MAIN=nothing" \
1151	"cflags=noCflags" \
1152	proto
1153
1154	%.clean:
1155	@$(MAKE) -C $(@D) \
1156	"AUTODEPENDS=0" \
1157	"MAIN=nothing" \
1158	"cflags=noCflags" \
1159	clean
1160
1161
1162	# stop wrong targets
1163	target_is_missing_lib_prefix:
1164	@echo "Error: Denied to build shared library target with missing 'lib'-prefix"
1165	false
1166
1167	ARBDB/ARBDB.dummy: target_is_missing_lib_prefix
1168	CORE/CORE.dummy: target_is_missing_lib_prefix
1169	AWT/AWT.dummy: target_is_missing_lib_prefix
1170	WINDOW/WINDOW.dummy: target_is_missing_lib_prefix
1171
1172	# rule to generate main target (normally a library):
1173	%.dummy:
1174	@( export ID=$$$$; LANG=C; \
1175	(( \
1176	echo "$(SEP) Make $(@D)"; \
1177	$(MAKE) -C $(@D) -r \
1178	"AUTODEPENDS=1" \
1179	"MAIN = $(@F:.dummy=.a)" \
1180	"cflags = $(cflags) -DIN_ARB_$(subst /,_,$(@D))" && \
1181	echo "$(SEP) Make $(@D) [done]"; \
1182	) >$(@D).$$ID.log 2>&1 && (cat $(@D).$$ID.log;rm $(@D).$$ID.log)) \|\| (cat $(@D).$$ID.log;rm $(@D).$$ID.log;false))
1183
1184	# Additional dependencies for subtargets:
1185
1186	PROBE_COM/PROBE_COM.dummy : comtools
1187	NAMES_COM/NAMES_COM.dummy : comtools
1188
1189	com: PROBE_COM/PROBE_COM.dummy NAMES_COM/NAMES_COM.dummy
1190
1191	PROBE_COM/server.dummy:
1192	@echo Unwanted request to make target $<
1193	false
1194
1195	PROBE_COM/client.dummy:
1196	@echo Unwanted request to make target $<
1197	false
1198
1199	NAMES_COM/server.dummy:
1200	@echo Unwanted request to make target $<
1201	false
1202
1203	NAMES_COM/client.dummy:
1204	@echo Unwanted request to make target $<
1205	false
1206
1207
1208	ARBDB/libARBDB.dummy: links
1209	CORE/libCORE.dummy: links
1210
1211	PERLTOOLS/PERLTOOLS.dummy: core db
1212
1213	# all subdirs perl not depends on go here:
1214	AWT/libAWT.dummy: links_non_perl
1215	AWTI/AWTI.dummy: links_non_perl
1216	CONSENSUS_TREE/CONSENSUS_TREE.dummy: links_non_perl
1217	CONVERTALN/CONVERTALN.dummy: links_non_perl
1218	DBSERVER/DBSERVER.dummy: links_non_perl
1219	DIST/DIST.dummy: links_non_perl
1220	EDIT4/EDIT4.dummy: links_non_perl templ com
1221	EISPACK/EISPACK.dummy: links_non_perl
1222	GDE/GDE.dummy: links_non_perl
1223	GENOM/GENOM.dummy: links_non_perl
1224	GENOM_IMPORT/GENOM_IMPORT.dummy: links_non_perl
1225	ISLAND_HOPPING/ISLAND_HOPPING.dummy: links_non_perl
1226	MERGE/MERGE.dummy: links_non_perl
1227	NTREE/NTREE.dummy: links_non_perl templ
1228	PARSIMONY/PARSIMONY.dummy: links_non_perl
1229	PGT/PGT.dummy: links_non_perl
1230	PHYLO/PHYLO.dummy: links_non_perl
1231	PRIMER_DESIGN/PRIMER_DESIGN.dummy: links_non_perl
1232	PROBE_SET/PROBE_SET.dummy: links_non_perl link_db
1233	READSEQ/READSEQ.dummy: links_non_perl
1234	RNACMA/RNACMA.dummy: links_non_perl header_libs
1235	SECEDIT/SECEDIT.dummy: links_non_perl
1236	SEQ_QUALITY/SEQ_QUALITY.dummy: links_non_perl
1237	SERVERCNTRL/SERVERCNTRL.dummy: links_non_perl com
1238	SL/ALIVIEW/ALIVIEW.dummy: links_non_perl
1239	SL/AP_TREE/AP_TREE.dummy: links_non_perl
1240	SL/ARB_TREE/ARB_TREE.dummy: links_non_perl
1241	SL/AW_HELIX/AW_HELIX.dummy: links_non_perl
1242	SL/DB_QUERY/DB_QUERY.dummy: links_non_perl
1243	SL/DB_SCANNER/DB_SCANNER.dummy: links_non_perl
1244	SL/DB_UI/DB_UI.dummy: links_non_perl
1245	SL/FAST_ALIGNER/FAST_ALIGNER.dummy: links_non_perl
1246	SL/FILTER/FILTER.dummy: links_non_perl
1247	SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy: links_non_perl
1248	SL/HELIX/HELIX.dummy: links_non_perl
1249	SL/ITEMS/ITEMS.dummy: links_non_perl
1250	SL/LOCATION/LOCATION.dummy: links_non_perl
1251	SL/MATRIX/MATRIX.dummy: links_non_perl
1252	SL/NDS/NDS.dummy: links_non_perl
1253	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.dummy: links_non_perl
1254	SL/PRONUC/PRONUC.dummy: links_non_perl
1255	SL/PTCLEAN/PTCLEAN.dummy: links_non_perl link_db
1256	SL/REFENTRIES/REFENTRIES.dummy: links_non_perl
1257	SL/REGEXPR/REGEXPR.dummy: links_non_perl
1258	SL/SEQIO/SEQIO.dummy: links_non_perl
1259	SL/SEQUENCE/SEQUENCE.dummy: links_non_perl
1260	SL/TRANSLATE/TRANSLATE.dummy: links_non_perl
1261	SL/TREE_ADMIN/TREE_ADMIN.dummy: links_non_perl
1262	SL/TREE_READ/TREE_READ.dummy: links_non_perl
1263	SL/TREE_WRITE/TREE_WRITE.dummy: links_non_perl
1264	SL/TREEDISP/TREEDISP.dummy: links_non_perl
1265	STAT/STAT.dummy: links_non_perl
1266	TREEGEN/TREEGEN.dummy: links_non_perl
1267	WETC/WETC.dummy: links_non_perl
1268	WINDOW/libWINDOW.dummy: links_non_perl
1269	XML/XML.dummy: links_non_perl
1270
1271	ifeq ($(OPENGL),1)
1272	GL/glAW/glAW.dummy: links_non_perl
1273	GL/glpng/glpng.dummy: links_non_perl
1274	GL/GL.dummy: GL/glAW/glAW.dummy GL/glpng/glpng.dummy
1275	RNA3D/RNA3D.dummy: links_non_perl gl
1276	endif
1277
1278	UNIT_TESTER/UNIT_TESTER.dummy: link_db \
1279	SERVERCNTRL/SERVERCNTRL.dummy \
1280
1281	TOOLS/TOOLS.dummy : links_non_perl link_db \
1282	SERVERCNTRL/SERVERCNTRL.dummy \
1283	SL/TREE_WRITE/TREE_WRITE.dummy \
1284	SL/TREE_READ/TREE_READ.dummy \
1285	CONSENSUS_TREE/CONSENSUS_TREE.dummy \
1286	XML/XML.dummy \
1287
1288	AWTC/AWTC.dummy : com
1289
1290	NAMES/NAMES.dummy : com
1291	SL/AW_NAME/AW_NAME.dummy : com
1292
1293	PROBE/PROBE.dummy : com
1294	ptpan/PROBE.dummy : com
1295	MULTI_PROBE/MULTI_PROBE.dummy : com
1296	PROBE_DESIGN/PROBE_DESIGN.dummy : com
1297	NALIGNER/NALIGNER.dummy : com
1298
1299	ARB_GDE/ARB_GDE.dummy : proto_tools
1300
1301	#***************************************************************************************
1302	# Short aliases to make targets
1303	#***************************************************************************************
1304
1305	show:
1306	@echo $(SEP)
1307	@echo 'Aliases for often needed targets:'
1308	@echo ''
1309	@echo ' executables:'
1310	@echo ''
1311	@echo ' nt arb_ntree'
1312	@echo ' e4 arb_edit4 (includes secedit)'
1313	@echo ' di arb_dist'
1314	@echo ' ph arb_phylo'
1315	@echo ' pa arb_parsimony'
1316	@echo ' tg arb_treegen'
1317	@echo ' ds arb_dbserver'
1318	@echo ' pt arb_pt_server'
1319	@echo ' na arb_name_server'
1320	@echo ''
1321	@echo ' libraries:'
1322	@echo ''
1323	@echo ' com communication libraries'
1324	@echo ' db ARB database'
1325	@echo ' aw GUI lib'
1326	@echo ' awt GUI toolkit'
1327	@echo ' awtc general purpose library'
1328	@echo ' awti import/export library'
1329	@echo ' mp multi probe library'
1330	@echo ' ge genome library'
1331	@echo ' pd probe design lib'
1332	@echo ' prd primer design lib'
1333	@echo ''
1334	@echo ' other targets:'
1335	@echo ''
1336	@echo ' help recompile help files'
1337	@echo ' tools make small tools used by arb'
1338	@echo ''
1339	@echo ' foreign targets:'
1340	@echo ''
1341	@echo ' gde GDE'
1342	@echo ' agde ARB_GDE'
1343	@echo ''
1344	@echo 'for other targets inspect $(ARBHOME)/Makefile'
1345	@echo ''
1346	@echo $(SEP)
1347
1348	source_doc:
1349	@echo "Remove some links (doxygen crashes otherwise):"
1350	find . $ -name "AISC" -o -name "C" -o -name "GDEHELP" $ -type l -exec rm {} \;
1351	doxygen
1352	$(MAKE) forcelinks
1353
1354	dep_graph:
1355	@echo "Building some dependency graphs"
1356	SOURCE_TOOLS/dependency_graphs.pl
1357
1358	help: HELP_SOURCE/HELP_SOURCE.dummy
1359
1360	# @@@ when backtracing code is in libCORE, link vs ARBDB is no longer needed
1361	HELP_SOURCE/HELP_SOURCE.dummy: link_db xml menus
1362
1363	db: ARBDB/libARBDB.dummy
1364	core: CORE/libCORE.dummy
1365	aw: WINDOW/libWINDOW.dummy
1366	awt: AWT/libAWT.dummy
1367	awtc: AWTC/AWTC.dummy
1368	awti: AWTI/AWTI.dummy
1369
1370	mp: MULTI_PROBE/MULTI_PROBE.dummy
1371	mg: MERGE/MERGE.dummy
1372	ge: GENOM/GENOM.dummy
1373	prd: PRIMER_DESIGN/PRIMER_DESIGN.dummy
1374
1375	nt: menus $(NTREE)
1376
1377	nal: $(NALIGNER)
1378
1379	di: $(DIST)
1380	ph: $(PHYLO)
1381	pa: $(PARSIMONY)
1382	tg: $(TREEGEN)
1383
1384	ifeq ($(OPENGL),1)
1385	3d: RNA3D/RNA3D.dummy
1386	gl: GL/GL.dummy
1387	else
1388	noopengl:
1389	@echo "invalid target for OPENGL=0"
1390	3d: noopengl
1391	gl: noopengl
1392	endif
1393
1394	SL/SL.dummy: com
1395
1396	ds: $(DBSERVER)
1397	pt: $(PROBE)
1398	pst: PROBE_SET/PROBE_SET.dummy
1399	pd: PROBE_DESIGN/PROBE_DESIGN.dummy
1400	na: $(NAMES)
1401	sq: SEQ_QUALITY/SEQ_QUALITY.dummy
1402	cma: $(RNACMA)
1403
1404	sec: SECEDIT/SECEDIT.dummy
1405
1406	e4: $(EDIT4) readseq menus
1407
1408	gi: GENOM_IMPORT/GENOM_IMPORT.dummy
1409	wetc: $(WETC)
1410
1411	pgt: $(PGT)
1412	xml: XML/XML.dummy
1413	xmlin: XML_IMPORT/XML_IMPORT.dummy# broken
1414	templ: TEMPLATES/TEMPLATES.dummy
1415	stat: STAT/STAT.dummy $(NTREE) $(EDIT4)
1416	fa: SL/FAST_ALIGNER/FAST_ALIGNER.dummy
1417
1418	#********************************************************************************
1419
1420	up_by_remake: depends proto libdepends
1421
1422	up: up_by_remake tags valgrind_update
1423
1424	#********************************************************************************
1425
1426	touch:
1427	SOURCE_TOOLS/touch_modified.pl
1428
1429	modified: touch
1430	$(MAKE) all
1431
1432	#********************************************************************************
1433
1434	libdepends:
1435	$(MAKE) -C "SOURCE_TOOLS" libdepends
1436
1437	#********************************************************************************
1438
1439	depends: templ comtools
1440	@echo "$(SEP) Partially build com interface"
1441	-rm PROBE_COM/.depends
1442	-rm NAMES_COM/.depends
1443	-rm PERL2ARB/.depends
1444	$(MAKE) PROBE_COM/PROBE_COM.depends
1445	$(MAKE) NAMES_COM/NAMES_COM.depends
1446	@echo $(SEP) Updating dependencies
1447	$(MAKE) $(ARCHS:.a=.depends) \
1448	HELP_SOURCE/HELP_SOURCE.depends \
1449
1450	depend: depends
1451
1452	AISC_MKPTPS/AISC_MKPTPS.dummy: links
1453
1454	proto_tools: AISC_MKPTPS/AISC_MKPTPS.dummy
1455
1456	proto: proto_tools
1457	@echo $(SEP) Updating prototypes
1458	$(MAKE) \
1459	ARBDB/ARBDB.proto \
1460	ARB_GDE/ARB_GDE.proto \
1461	CORE/CORE.proto \
1462	CONVERTALN/CONVERTALN.proto \
1463	NTREE/NTREE.proto \
1464	$(ARCHS_PT_SERVER:.a=.proto) \
1465	SERVERCNTRL/SERVERCNTRL.proto \
1466	SL/SL.proto \
1467
1468	#********************************************************************************
1469
1470	valgrind_update: links
1471	@echo $(SEP) Updating for valgrind
1472	$(MAKE) -C SOURCE_TOOLS valgrind_update
1473
1474	#********************************************************************************
1475
1476	TAGFILE=TAGS
1477	TAGFILE_TMP=TAGS.tmp
1478
1479	TAG_SOURCE_HEADERS=TAGS.headers
1480	TAG_SOURCE_CODE=TAGS.codefiles
1481
1482	TAG_SOURCE_LISTS=$(TAG_SOURCE_HEADERS) $(TAG_SOURCE_CODE)
1483
1484	ETAGS=ctags -e -f $(TAGFILE_TMP) --sort=no --if0=no --extra=q
1485	ETAGS_TYPES=--C-kinds=cgnsut --C++-kinds=cgnsut
1486	ETAGS_FUN =--C-kinds=fm --C++-kinds=fm
1487	ETAGS_REST =--C-kinds=dev --C++-kinds=dev
1488
1489	$(TAG_SOURCE_HEADERS): links
1490	# find . $ -name '.[ch]xx' -o -name ".[ch]" $ -type f \| grep -v -i perl5 > $@
1491	# workaround a bug in ctags 5.8:
1492	find . $ -name '.hxx' -o -name ".h" $ -type f \| grep -v -i perl5 \| sed -e 's/^.\///g' > $@
1493
1494	$(TAG_SOURCE_CODE): links
1495	# find . $ -name '.[ch]xx' -o -name ".[ch]" $ -type f \| grep -v -i perl5 > $@
1496	# workaround a bug in ctags 5.8:
1497	find . $ -name '.cxx' -o -name ".c" $ -type f \| grep -v -i perl5 \| sed -e 's/^.\///g' > $@
1498
1499	tags: $(TAG_SOURCE_LISTS)
1500	$(ETAGS) $(ETAGS_TYPES) -L $(TAG_SOURCE_HEADERS)
1501	$(ETAGS) -a $(ETAGS_FUN) -L $(TAG_SOURCE_HEADERS)
1502	$(ETAGS) -a $(ETAGS_REST) -L $(TAG_SOURCE_HEADERS)
1503	$(ETAGS) -a $(ETAGS_TYPES) -L $(TAG_SOURCE_CODE)
1504	$(ETAGS) -a $(ETAGS_FUN) -L $(TAG_SOURCE_CODE)
1505	$(ETAGS) -a $(ETAGS_REST) -L $(TAG_SOURCE_CODE)
1506	mv_if_diff $(TAGFILE_TMP) $(TAGFILE)
1507	rm $(TAG_SOURCE_LISTS)
1508
1509	#********************************************************************************
1510
1511	LINKSTAMP=SOURCE_TOOLS/stamp.generate_all_links
1512
1513	links: checks $(LINKSTAMP) arbmainwrapper
1514	links_no_checks: $(LINKSTAMP) arbmainwrapper
1515
1516	forcelinks:
1517	-rm $(LINKSTAMP)
1518	$(MAKE) links
1519
1520	$(LINKSTAMP): SOURCE_TOOLS/generate_all_links.sh
1521	+SOURCE_TOOLS/generate_all_links.sh
1522	touch $(LINKSTAMP)
1523
1524	clean_links:
1525	# avoid to delete linked pts, nas or arb_tcp.dat:
1526	find . -path './lib' -prune -o -type l -exec rm {} \;
1527	@rm -f $(LINKSTAMP) lib/inputMasks/format.readme
1528
1529	redo_links: clean_links
1530	$(MAKE) links_no_checks
1531
1532	#********************************************************************************
1533
1534	header_libs:
1535	$(MAKE) -C HEADERLIBS all
1536
1537	#********************************************************************************
1538
1539	gde: GDE/GDE.dummy
1540	GDE: gde
1541	agde: ARB_GDE/ARB_GDE.dummy
1542
1543	tools: TOOLS/TOOLS.dummy
1544
1545	convert: $(CONVERT_ALN)
1546	readseq: READSEQ/READSEQ.dummy
1547
1548	#***************************************************************************************
1549	# Some user commands
1550	#***************************************************************************************
1551
1552	menus: binlink links
1553	@(( \
1554	echo "$(SEP) Make GDEHELP"; \
1555	$(MAKE) -C GDEHELP -r "PP=$(PP)" all && \
1556	echo "$(SEP) Make GDEHELP [done]"; \
1557	) > GDEHELP.log 2>&1 && (cat GDEHELP.log;rm GDEHELP.log)) \|\| (cat GDEHELP.log;rm GDEHELP.log;false)
1558
1559	ifeq ($(DEBUG),1)
1560	BIN_TARGET=develall
1561	else
1562	BIN_TARGET=all
1563	endif
1564
1565
1566	binlink:
1567	$(MAKE) -C bin $(BIN_TARGET)
1568
1569	preplib:
1570	(cd lib;$(MAKE) all)
1571
1572	# --------------------------------------------------------------------------------
1573	# This section is quite tricky:
1574	#
1575	# make 'perl' is a BIG target, so when it has to be made, it has to be started
1576	# as early as possible to reduce overall compile time. Since 'make' does not
1577	# provide any priotities, i force it to build all 'perl'-prerequisites early, by
1578	# adding artificial dependencies to these prerequisites
1579	#
1580	# That behavior is likely to be system-dependent.
1581	# My goal was only to make it work on my current development system,
1582	# where this saves about 20% of overall build time.
1583
1584	ifeq ($(WITHPERL),1)
1585	links_non_perl: PERLTOOLS/PERLTOOLS.dummy
1586	perltools: links_non_perl
1587	perl: realperl
1588	else
1589	links_non_perl: links
1590	perl:
1591	$(MAKE) "WITHPERL=1" perl
1592	endif
1593
1594	# ---------------------------------------- perl
1595
1596	ifeq ($(ARB_64),$(BUILDHOST_64))
1597	TEST_PERL_SCRIPTS=$(MAKE) -C PERL_SCRIPTS/test test
1598	else
1599	TEST_PERL_SCRIPTS=echo "skipping perl script compilation (when cross-compiling)"
1600	endif
1601
1602	realperl: perltools
1603	(( \
1604	echo "$(SEP) Make PERL2ARB" ; \
1605	$(TIME) $(MAKE) -C PERL2ARB -r -f Makefile.main \
1606	"AUTODEPENDS=1" \
1607	"dflags=$(dflags)" \
1608	"cross_cflags=$(cross_cflags) $(dflags)" \
1609	"cross_lflags=$(cross_lflags)" \
1610	all && \
1611	$(TEST_PERL_SCRIPTS) && \
1612	echo "$(SEP) Make PERL2ARB [done]" ; \
1613	) > PERL2ARB.log 2>&1 && (cat PERL2ARB.log;rm PERL2ARB.log)) \|\| (cat PERL2ARB.log;rm PERL2ARB.log;false)
1614
1615	perl_clean:
1616	@$(MAKE) -C PERL2ARB -r -f Makefile.main \
1617	"AUTODEPENDS=0" \
1618	clean
1619
1620	PERL2ARB/PERL2ARB.clean:
1621	$(MAKE) perl_clean
1622
1623
1624	# ----------------------------------------
1625
1626	CLOC=cloc-1.08.pl
1627	CLOCFLAGS=--no3 --quiet --progress-rate=0
1628	CLOCARB=--exclude-dir=GDE .
1629	CLOCEXT=GDE
1630	CLOCCODE=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.code.def
1631	CLOCREST=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.rest.def
1632	CLOCFILT=tail --lines=+4
1633
1634	cloc:
1635	@echo 'Arb code:'
1636	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCARB) \| $(CLOCFILT)
1637	@echo 'Arb rest:'
1638	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCARB) \| $(CLOCFILT)
1639	@echo 'External code:'
1640	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCEXT) \| $(CLOCFILT)
1641	@echo 'External rest:'
1642	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCEXT) \| $(CLOCFILT)
1643
1644	# ---------------------------------------- check ressources
1645
1646	check_res:
1647	$(ARBHOME)/SOURCE_TOOLS/check_ressources.pl
1648
1649	# ---------------------------------------- cleaning
1650
1651	rmbak:
1652	@echo "Cleanup:"
1653	@find . \( -name '*%' \
1654	-o -name '*.bak' \
1655	-o -name '*~' \) \
1656	-o -name 'core' \
1657	-exec rm -v {} \;
1658
1659	bin_reinit:
1660	$(MAKE) bin/bin.clean
1661	$(MAKE) -C "bin" all
1662
1663	clean_directories:
1664	-rm -rf \
1665	$(ARBHOME)/PROBE_SET/bin \
1666	$(ARBHOME)/INCLUDE \
1667
1668	libclean:
1669	-find $(ARBHOME) -type f $ -name '*.a' ! -type l $ -exec rm -f {} \;
1670
1671	objclean:
1672	-find $(ARBHOME) -type f $ -name '*.o' ! -type l $ -exec rm -f {} \;
1673
1674	# bin.clean and HELP_SOURCE.clean interfere
1675	clean3:
1676	$(MAKE) bin/bin.clean
1677	$(MAKE) HELP_SOURCE/HELP_SOURCE.clean
1678
1679	clean2: $(ARCHS:.a=.clean) \
1680	clean3 \
1681	rmbak \
1682	libclean \
1683	objclean \
1684	lib/lib.clean \
1685	GDEHELP/GDEHELP.clean \
1686	HEADERLIBS/HEADERLIBS.clean \
1687	SOURCE_TOOLS/SOURCE_TOOLS.clean \
1688	UNIT_TESTER/UNIT_TESTER.clean \
1689	TEMPLATES/TEMPLATES.clean \
1690	perl_clean \
1691	clean_directories \
1692
1693	rm -f *.last_gcc config.makefile.bak
1694
1695	# links are needed for cleanup
1696	clean: redo_links
1697	$(MAKE) clean2
1698	$(MAKE) clean_cov_all clean_links
1699
1700	# 'relocated' is about 50% faster than 'rebuild'
1701	reloc_clean: links
1702	@echo "---------------------------------------- Relocation cleanup"
1703	$(MAKE) \
1704	perl_clean \
1705	GDEHELP/GDEHELP.clean \
1706	HELP_SOURCE/genhelp/genhelp.clean \
1707	bin/bin.clean \
1708	libclean \
1709	objclean
1710
1711	relocated: links
1712	$(MAKE) reloc_clean
1713	@echo "---------------------------------------- and remake"
1714	$(MAKE) build
1715
1716	# -----------------------------------
1717	# some stress tests:
1718
1719	rebuild4ever: rebuild
1720	$(MAKE) rebuild4ever
1721
1722	build4ever: build
1723	$(MAKE) build4ever
1724
1725	clean4ever: clean
1726	$(MAKE) clean4ever
1727
1728	test4ever: ut
1729	$(MAKE) test4ever
1730
1731	perl4ever: clean
1732	$(MAKE) links
1733	$(MAKE) perl
1734	$(MAKE) perl4ever
1735
1736
1737	# -----------------------------------
1738
1739	rebuild: clean
1740	$(MAKE) all
1741
1742	relink: bin/bin.clean libclean
1743	$(MAKE) build
1744
1745	tarfile: rebuild
1746	$(MAKE) prepare_libdir
1747	util/arb_compress
1748
1749	tarfile_quick: build
1750	$(MAKE) prepare_libdir
1751	util/arb_compress
1752
1753	save: sourcetarfile
1754
1755	patch:
1756	SOURCE_TOOLS/arb_create_patch.sh arbPatch
1757
1758	# test early whether save will work
1759	savetest:
1760	@util/arb_srclst.pl >/dev/null
1761
1762	testsave: savetest
1763
1764	sourcetarfile: rmbak
1765	util/arb_save
1766
1767	save2: rmbak
1768	util/arb_save ignore
1769
1770	save_test: rmbak
1771	@echo "Testing source list.."
1772	@util/arb_srclst.pl > /dev/null
1773
1774	save_test_no_error:
1775	@-$(MAKE) save_test
1776
1777	rel_minor:
1778	touch SOURCE_TOOLS/inc_minor.stamp
1779	$(MAKE) do_release
1780
1781	rel_major:
1782	touch SOURCE_TOOLS/inc_major.stamp
1783	$(MAKE) do_release
1784
1785	do_release:
1786	@echo Building release
1787	@echo PATH=$(PATH)
1788	@echo ARBHOME=$(ARBHOME)
1789	-rm arb.tgz arbsrc.tgz
1790	$(MAKE) testsave
1791	$(MAKE) templ # auto upgrades version early
1792	$(MAKE) tarfile sourcetarfile
1793
1794	release_quick:
1795	-rm arb.tgz arbsrc.tgz
1796	$(MAKE) tarfile_quick sourcetarfile
1797
1798	# --------------------------------------------------------------------------------
1799
1800	MAKE_IF_COMMITTED=$(MAKE) -C SOURCE_TOOLS -f Makefile.commitbuild
1801
1802	build_CTARGET:
1803	+$(MAKE_IF_COMMITTED) "CTARGET=$(CTARGET)" build_CTARGET
1804
1805	reset_committed_build:
1806	+$(MAKE_IF_COMMITTED) reset
1807
1808	# --------------------------------------------------------------------------------
1809
1810	arbapplications: nt pa e4 wetc pt na nal di ph ds pgt wetc cma
1811
1812	arb_external: convert tools gde readseq tg pst xmlin
1813
1814	arb_no_perl: arbapplications help arb_external
1815
1816	arb:
1817	$(MAKE) "WITHPERL=1" perl arb_no_perl
1818
1819	# --------------------------------------------------------------------------------
1820	# special targets for SOURCE_TOOLS/remake_after_change.pl
1821
1822	rac_arb_dist: di
1823	rac_arb_edit4: e4
1824	rac_arb_ntree: nt
1825	rac_arb_pars: pa
1826	rac_arb_phylo: ph
1827	rac_arb_wetc: wetc
1828	rac_arb_naligner: nal
1829	rac_arb_pt_server: pt
1830	rac_arb_db_server: ds
1831	rac_arb_name_server: na
1832	rac_arb_pgt: pgt
1833	rac_arb_convert_aln: convert
1834	rac_arb_treegen: tg
1835	rac_arb_rnacma: cma
1836
1837	# --------------------------------------------------------------------------------
1838	# unit testing
1839	# @@@ work in progress
1840	#
1841	# goal is to automatically test all libraries/executables using TESTED_UNITS_AUTO
1842	#
1843	# currently not all test executables link w/o error
1844	# (see UNITS_WORKING, UNITS_UNTESTABLE_ATM and UNITS_NEED_FIX)
1845
1846	# define RNA3D/RNA3D.test
1847	RNA3D_TEST := $(subst .a,.test,$(RNA3D_LIB))
1848
1849	TESTED_UNITS_AUTO = $(ARCHS:.a=.test)
1850
1851	UNITS_WORKING = \
1852	$(RNA3D_TEST) \
1853	ARB_GDE/ARB_GDE.test \
1854	AWTI/AWTI.test \
1855	DIST/DIST.test \
1856	EISPACK/EISPACK.test \
1857	GENOM/GENOM.test \
1858	GENOM_IMPORT/GENOM_IMPORT.test \
1859	GL/glAW/libglAW.test \
1860	GL/glpng/libglpng_arb.test \
1861	ISLAND_HOPPING/ISLAND_HOPPING.test \
1862	NALIGNER/NALIGNER.test \
1863	NAMES/NAMES.test \
1864	PARSIMONY/PARSIMONY.test \
1865	PGT/PGT.test \
1866	PHYLO/PHYLO.test \
1867	PRIMER_DESIGN/PRIMER_DESIGN.test \
1868	PROBE_DESIGN/PROBE_DESIGN.test \
1869	SECEDIT/SECEDIT.test \
1870	SEQ_QUALITY/SEQ_QUALITY.test \
1871	SERVERCNTRL/SERVERCNTRL.test \
1872	SL/ALIVIEW/ALIVIEW.test \
1873	SL/AP_TREE/AP_TREE.test \
1874	SL/ARB_TREE/ARB_TREE.test \
1875	SL/AW_HELIX/AW_HELIX.test \
1876	SL/AW_NAME/AW_NAME.test \
1877	SL/DB_SCANNER/DB_SCANNER.test \
1878	SL/GUI_ALIVIEW/GUI_ALIVIEW.test \
1879	SL/HELIX/HELIX.test \
1880	SL/ITEMS/ITEMS.test \
1881	SL/LOCATION/LOCATION.test \
1882	SL/MATRIX/MATRIX.test \
1883	SL/NDS/NDS.test \
1884	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.test \
1885	SL/REFENTRIES/REFENTRIES.test \
1886	SL/SEQUENCE/SEQUENCE.test \
1887	SL/TRANSLATE/TRANSLATE.test \
1888	SL/TREE_ADMIN/TREE_ADMIN.test \
1889	SL/TREE_READ/TREE_READ.test \
1890	SL/TREE_WRITE/TREE_WRITE.test \
1891	STAT/STAT.test \
1892	TREEGEN/TREEGEN.test \
1893	WETC/WETC.test \
1894	XML/XML.test \
1895
1896	# untestable units
1897
1898	UNITS_NEED_FIX = \
1899	ptpan/PROBE.test \
1900
1901	UNITS_UNTESTABLE_ATM = \
1902	PROBE_SET/PROBE_SET.test \
1903	XML_IMPORT/XML_IMPORT.test \
1904
1905	# for the moment, put all units containing tests into UNITS_TESTED or UNITS_TESTED_FIRST
1906
1907	UNITS_TESTED_FIRST = \
1908	SL/REGEXPR/REGEXPR.test \
1909	SL/FILTER/FILTER.test \
1910	ARBDB/libARBDB.test \
1911	CONSENSUS_TREE/CONSENSUS_TREE.test \
1912	TOOLS/arb_consensus_tree.test \
1913	TOOLS/arb_test.test \
1914	TOOLS/arb_probe.test \
1915	AWTC/AWTC.test \
1916
1917	UNITS_TESTED = \
1918	DBSERVER/DBSERVER.test \
1919	AWT/libAWT.test \
1920	CORE/libCORE.test \
1921	SL/TREEDISP/TREEDISP.test \
1922	NTREE/NTREE.test \
1923	AISC_MKPTPS/mkptypes.test \
1924	EDIT4/EDIT4.test \
1925	MERGE/MERGE.test \
1926	MULTI_PROBE/MULTI_PROBE.test \
1927	SERVERCNTRL/SERVERCNTRL.test \
1928	SL/FAST_ALIGNER/FAST_ALIGNER.test \
1929	SL/PRONUC/PRONUC.test \
1930	WINDOW/libWINDOW.test \
1931	HELP_SOURCE/arb_help2xml.test \
1932	CONVERTALN/CONVERTALN.test \
1933	SL/SEQIO/SEQIO.test \
1934	SL/PTCLEAN/PTCLEAN.test \
1935	PROBE/PROBE.test \
1936	SL/DB_QUERY/DB_QUERY.test \
1937
1938	TESTED_UNITS_MANUAL = \
1939	$(UNITS_TESTED_FIRST) \
1940	$(UNITS_TESTED) \
1941
1942	# $(UNITS_WORKING)
1943
1944	# see UNIT_TESTER/sym2testcode.pl@disableErrorOnUnitsWithoutTests
1945
1946	#TESTED_UNITS = $(TESTED_UNITS_AUTO)
1947	TESTED_UNITS = $(TESTED_UNITS_MANUAL)
1948
1949	# ----------------------------------------
1950
1951	TEST_LOG_DIR = UNIT_TESTER/logs
1952	TEST_RUN_SUITE=$(MAKE) $(NODIR) -C UNIT_TESTER -f Makefile.suite -r
1953	TEST_MAKE_FLAGS=
1954	TEST_POST_CLEAN=
1955	ifeq ($(COVERAGE),1)
1956	TEST_POST_CLEAN=$(MAKE) clean_cov
1957	TEST_MAKE_FLAGS+=-j1
1958	endif
1959
1960
1961	%.test: %.dummy
1962	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
1963	( \
1964	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
1965	"UNITDIR=$(@D)" \
1966	"UNITLIBNAME=$(@F:.test=)" \
1967	"COVERAGE=$(COVERAGE)" \
1968	"cflags=$(cflags)" \
1969	"ARB_PID=$(ARB_PID)_$(@F)" \
1970	runtest; \
1971	$(TEST_POST_CLEAN) \
1972	) >$(TEST_LOG_DIR)/$(@F).log 2>&1; echo "- $(@F)")
1973
1974
1975	test_base: $(UNIT_TESTER_LIB:.a=.dummy)
1976
1977	clean_cov:
1978	find . $ -name ".gcda" -o -name ".gcov" -o -name "*.cov" $ -exec rm {} \;
1979
1980	clean_cov_all: clean_cov
1981	find . $ -name "*.gcno" $ -exec rm {} \;
1982
1983	run_tests: test_base clean_cov
1984	$(MAKE) "ARB_PID=UT_$$$$" run_tests_faked_arbpid
1985
1986	run_tests_faked_arbpid:
1987	+@$(TEST_RUN_SUITE) init
1988	@echo "fake[1]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
1989	$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(TESTED_UNITS)
1990	@echo "fake[1]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
1991	+@$(TEST_RUN_SUITE) cleanup
1992	@$(MAKE) clean_cov >/dev/null
1993
1994	ut:
1995	ifeq ($(UNIT_TESTS),1)
1996	@echo $(MAKE) run_tests
1997	@$(MAKE) run_tests
1998	else
1999	@echo "Not compiled with unit tests"
2000	endif
2001
2002
2003	aut:
2004	+@$(TEST_RUN_SUITE) unskip
2005	$(MAKE) ut
2006
2007	# --------------------------------------------------------------------------------
2008
2009	TIMELOG=$(ARBHOME)/arb_time.log
2010	TIMEARGS=--append --output=$(TIMELOG) --format=" %E(%S+%U) %P [%C]"
2011	TIMECMD=$(TIME) $(TIMEARGS)
2012
2013	time_one:
2014	ifeq ($(ONE_TIMED_TARGET),)
2015	@echo "Error: You have to pass ONE_TIMED_TARGET to $@"
2016	false
2017	else
2018	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET)"
2019	@$(TIMECMD) $(MAKE) $(ONE_TIMED_TARGET)
2020	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET) [done]"
2021	endif
2022
2023	timed_target:
2024	ifeq ($(TIMED_TARGET),)
2025	@echo "Error: You have to pass TIMED_TARGET to $@"
2026	false
2027	else
2028	@echo "Build time:" > $(TIMELOG)
2029	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2030	@cat $(TIMELOG)
2031	@rm $(TIMELOG)
2032	endif
2033
2034	timed_target_tested:
2035	ifeq ($(TIMED_TARGET),)
2036	@echo "Error: You have to pass TIMED_TARGET to $@"
2037	false
2038	else
2039	@echo "Build time:" > $(TIMELOG)
2040	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2041	$(MAKE) "ONE_TIMED_TARGET=ut" time_one
2042	@cat $(TIMELOG)
2043	@rm $(TIMELOG)
2044	endif
2045
2046	clean_timed_target:
2047	ifeq ($(TIMED_TARGET),)
2048	@echo "Error: You have to pass TIMED_TARGET to $@"
2049	false
2050	else
2051	@echo "Build time:" > $(TIMELOG)
2052	$(MAKE) "ONE_TIMED_TARGET=clean" time_one
2053	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2054	@cat $(TIMELOG)
2055	@rm $(TIMELOG)
2056	endif
2057
2058	# --------------------------------------------------------------------------------
2059
2060	build: arb
2061	$(MAKE) binlink preplib
2062
2063	all:
2064	@echo "Build time" > $(TIMELOG)
2065	@echo "$(SEP) $(MAKE) build"
2066	@$(TIMECMD) $(MAKE) build
2067	@echo $(SEP)
2068	@echo "made 'all' with success."
2069	@echo "to start arb enter 'arb'"
2070	ifeq ($(UNIT_TESTS),1)
2071	@echo $(MAKE) run_tests
2072	@$(TIMECMD) $(MAKE) run_tests
2073	endif
2074	@echo "$(SEP) $(MAKE) build [done]"
2075	@$(MAKE) save_test_no_error >/dev/null # just show hints
2076	@cat $(TIMELOG)
2077	@rm $(TIMELOG)
2078

Note: See TracBrowser for help on using the browser.

Context Navigation

root/trunk/Makefile

Download in other formats: