1 | # =============================================================== # |
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2 | # # |
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3 | # File : Makefile # |
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4 | # Time-stamp: <Tue Jul/08/2008 12:39 MET Coder@ReallySoft.de> # |
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5 | # # |
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6 | # Institute of Microbiology (Technical University Munich) # |
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7 | # http://www.arb-home.de/ # |
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8 | # # |
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9 | # =============================================================== # |
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10 | |
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11 | # ----------------------------------------------------- |
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12 | # The ARB Makefile is aware of the following defines: |
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13 | # |
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14 | # BUILDHOST_64=0/1 1=>compile on 64 bit platform (defaults to ARB_64) |
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15 | # DEVELOPER=name special compilation (values: ANY,RELEASE,your name) |
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16 | # OPENGL=0/1 whether OPENGL is available |
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17 | # |
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18 | # ----------------------------------------------------- |
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19 | # ARB Makefile and ARB source code are aware of the following defines: |
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20 | # |
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21 | # $(MACH) name of the machine (LINUX,SUN4,SUN5,HP,SGI or DIGITAL; see config.makefile) |
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22 | # DEBUG compiles the DEBUG sections |
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23 | # DEBUG_GRAPHICS all X-graphics are flushed immediately (for debugging) |
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24 | # ARB_64=0/1 1=>compile 64 bit version |
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25 | # |
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26 | # ----------------------------------------------------- |
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27 | # The ARB source code is aware of the following defines: |
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28 | # |
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29 | # HAVE_BOOL should be true if compiler supports the type 'bool' |
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30 | # NO_REGEXPR for machines w/o regular expression library |
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31 | # NDEBUG doesnt compile the DEBUG sections |
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32 | # DEVEL_$(DEVELOPER) developer-dependent flag (enables you to have private sections in code) |
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33 | # DEVELOPER='ANY' (default setting) will be ignored |
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34 | # configurable in config.makefile |
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35 | # |
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36 | # ----------------------------------------------------- |
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37 | # Read configuration |
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38 | include config.makefile |
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39 | |
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40 | FORCEMASK = umask 002 |
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41 | |
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42 | # ---------------------- [unconditionally used options] |
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43 | |
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44 | GCC:=gcc |
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45 | GPP:=g++ -fmessage-length=0 |
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46 | CPPreal:=cpp |
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47 | |
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48 | ifdef DARWIN |
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49 | GCC:=gcc2 |
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50 | GPP:=g++2 |
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51 | endif |
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52 | |
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53 | # ---------------------- compiler version detection |
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54 | |
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55 | # supported compiler versions: |
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56 | |
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57 | ALLOWED_GCC_3xx_VERSIONS=3.2 3.3.1 3.3.3 3.3.4 3.3.5 3.3.6 3.4.0 3.4.2 3.4.3 |
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58 | ALLOWED_GCC_4xx_VERSIONS=4.0.0 4.0.2 4.0.3 4.1.1 4.1.2 4.1.3 4.2.0 4.2.1 4.2.3 4.3.1 |
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59 | ALLOWED_GCC_VERSIONS=$(ALLOWED_GCC_3xx_VERSIONS) $(ALLOWED_GCC_4xx_VERSIONS) |
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60 | |
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61 | GCC_VERSION_FOUND=$(shell $(GCC) -dumpversion) |
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62 | GCC_VERSION_ALLOWED=$(strip $(subst ___,,$(foreach version,$(ALLOWED_GCC_VERSIONS),$(findstring ___$(version)___,___$(GCC_VERSION_FOUND)___)))) |
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63 | |
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64 | USING_GCC_3XX=$(strip $(foreach version,$(ALLOWED_GCC_3xx_VERSIONS),$(findstring $(version),$(GCC_VERSION_ALLOWED)))) |
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65 | USING_GCC_4XX=$(strip $(foreach version,$(ALLOWED_GCC_4xx_VERSIONS),$(findstring $(version),$(GCC_VERSION_ALLOWED)))) |
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66 | |
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67 | #---------------------- |
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68 | |
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69 | shared_cflags :=# flags for shared lib compilation |
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70 | |
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71 | ifeq ($(DEBUG),0) |
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72 | dflags := -DNDEBUG# defines |
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73 | cflags := -O4# compiler flags (C and C++) |
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74 | lflags := -O99 --strip-all# linker flags |
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75 | endif |
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76 | |
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77 | ifeq ($(DEBUG),1) |
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78 | dflags := -DDEBUG |
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79 | cflags := -O0 -g -g3 -ggdb -ggdb3 |
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80 | lflags := -g |
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81 | |
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82 | POST_COMPILE := 2>&1 | $(ARBHOME)/SOURCE_TOOLS/postcompile.pl |
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83 | |
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84 | # Enable several warnings |
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85 | extended_warnings := -Wwrite-strings -Wunused -Wno-aggregate-return -Wshadow |
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86 | extended_cpp_warnings := -Wnon-virtual-dtor -Wreorder -Wpointer-arith |
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87 | ifneq ('$(USING_GCC_3XX)','') |
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88 | extended_cpp_warnings += -Wdisabled-optimization -Wmissing-format-attribute |
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89 | extended_cpp_warnings += -Wmissing-noreturn # -Wfloat-equal |
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90 | endif |
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91 | ifneq ('$(USING_GCC_4XX)','') |
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92 | # extended_cpp_warnings += -Wwhatever |
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93 | endif |
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94 | |
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95 | ifeq ($(DEBUG_GRAPHICS),1) |
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96 | dflags += -DDEBUG_GRAPHICS |
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97 | endif |
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98 | endif |
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99 | |
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100 | #---------------------- developer |
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101 | |
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102 | ifneq ($(DEVELOPER),ANY) # ANY=default setting (skip all developer specific code) |
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103 | ifdef dflags |
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104 | dflags += -DDEVEL_$(DEVELOPER)# activate developer/release specific code |
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105 | endif |
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106 | endif |
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107 | |
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108 | #---------------------- 32 or 64 bit |
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109 | |
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110 | ifndef ARB_64 |
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111 | ARB_64=0#default to 32bit |
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112 | endif |
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113 | ifndef BUILDHOST_64 |
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114 | BUILDHOST_64:=$(ARB_64)# assume build host is same as version (see config.makefile) |
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115 | endif |
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116 | |
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117 | ifeq ($(ARB_64),1) |
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118 | dflags += -DARB_64 #-fPIC |
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119 | lflags += |
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120 | shared_cflags += -fPIC |
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121 | |
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122 | ifeq ($(BUILDHOST_64),1) |
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123 | # build 64-bit ARB version on 64-bit host |
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124 | CROSS_LIB:=# empty = autodetect below |
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125 | else |
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126 | # build 64-bit ARB version on 32-bit host |
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127 | CROSS_LIB:=/lib64 |
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128 | cflags += -m64 |
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129 | lflags += -m64 -m elf_x86_64 |
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130 | endif |
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131 | else |
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132 | ifeq ($(BUILDHOST_64),1) |
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133 | # build 32-bit ARB version on 64-bit host |
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134 | CROSS_LIB:=# empty = autodetect below |
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135 | cflags += -m32 |
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136 | lflags += -m32 -m elf_i386 |
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137 | else |
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138 | # build 32-bit ARB version on 32-bit host |
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139 | CROSS_LIB:=/lib |
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140 | endif |
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141 | endif |
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142 | |
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143 | ifeq ('$(CROSS_LIB)','') |
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144 | # autodetect libdir |
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145 | ifeq ($(ARB_64),1) |
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146 | CROSS_LIB:=`(test -d /lib64 && echo lib64) || echo lib` |
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147 | else |
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148 | CROSS_LIB:=`(test -d /lib32 && echo lib32) || echo lib` |
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149 | endif |
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150 | endif |
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151 | |
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152 | #---------------------- other flags |
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153 | |
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154 | dflags += -D$(MACH) # define machine |
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155 | dflags += -DHAVE_BOOL # all have bool [@@@ TODO: remove dependent code from ARB source] |
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156 | dflags += -DNO_REGEXPR # for machines w/o regular expression library |
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157 | |
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158 | ifdef DARWIN |
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159 | cflags += -no-cpp-precomp |
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160 | shared_cflags += -fno-common |
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161 | dflags += |
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162 | lflags += $(LDFLAGS) -force_flat_namespace -Wl,-stack_size -Wl,10000000 -Wl,-stack_addr -Wl,c0000000 |
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163 | endif |
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164 | |
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165 | cflags += -pipe |
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166 | |
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167 | #---------------------- X11 location |
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168 | |
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169 | X11R6=1# we use X11R6 |
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170 | |
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171 | ifeq ($(X11R6),1) |
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172 | XHOME:=/usr/X11R6 |
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173 | XINCLUDES:=-I$(XHOME)/include |
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174 | else |
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175 | XHOME:=/usr/X11 |
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176 | XINCLUDES:=-I$(XHOME)/include -I$(XHOME)/include/Xm |
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177 | endif |
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178 | |
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179 | XLIBS:=-L$(XHOME)/$(CROSS_LIB) -lXm -lXpm -lXp -lXt -lXext -lX11 |
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180 | |
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181 | #---------------------- open GL |
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182 | |
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183 | ifeq ($(OPENGL),1) |
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184 | cflags += -DARB_OPENGL # activate OPENGL code |
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185 | endif |
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186 | |
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187 | ifeq ($(OPENGL),1) |
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188 | GL:=gl # this is the name of the OPENGL base target |
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189 | ifdef DEBIAN |
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190 | GL_LIB:=-lGL -lpthread |
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191 | else |
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192 | GL_LIB:=-lGL |
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193 | endif |
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194 | GL_PNGLIBS:= -L$(ARBHOME)/GL/glpng -lglpng_arb -lpng |
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195 | GLLIBS:=-lGLEW -lGLw -lglut $(GL_PNGLIBS) |
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196 | endif |
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197 | |
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198 | XLIBS += $(GL_LIB) |
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199 | |
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200 | #---------------------- basic libs: |
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201 | |
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202 | SYSLIBS := -lm |
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203 | ifdef DARWIN |
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204 | SYSLIBS += -lstdc++ |
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205 | endif |
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206 | |
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207 | ifdef SEER |
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208 | SEERLIB = SEER/SEER.a # @@@ not compiled for very long time. Dunno what SEER is.. |
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209 | else |
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210 | SEERLIB = |
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211 | endif |
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212 | |
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213 | # ------------------------------------------------------------------------- |
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214 | # Don't put any machine/version/etc conditionals below! |
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215 | # (instead define variables above) |
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216 | # ------------------------------------------------------------------------- |
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217 | |
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218 | cflags += -W -Wall $(dflags) $(extended_warnings) |
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219 | cppflags := $(extended_cpp_warnings) |
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220 | |
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221 | # compiler settings: |
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222 | |
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223 | ACC := $(GCC)# compile C |
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224 | CPP := $(GPP) $(cppflags)# compile C++ |
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225 | ACCLIB := $(ACC) $(shared_cflags)# compile C (shared libs) |
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226 | CCPLIB := $(CPP) $(shared_cflags)# compile C++ (shared libs) |
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227 | |
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228 | PP := $(CPPreal)# preprocessor |
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229 | |
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230 | SHARED_LIB_SUFFIX = so# shared lib suffix (can be set to 'a' to link statically) |
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231 | |
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232 | LINK_STATIC_LIB := ld $(lflags) -r -o# link static lib |
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233 | LINK_SHARED_LIB := $(GPP) $(lflags) -shared -o# link shared lib |
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234 | LINK_EXECUTABLE := $(GPP) $(lflags) -o# link executable (c++) |
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235 | |
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236 | # other used tools |
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237 | |
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238 | CTAGS := etags |
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239 | XMKMF := /usr/bin/X11/xmkmf |
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240 | MAKEDEPEND = $(FORCEMASK);makedepend |
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241 | |
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242 | SEP=-------------------------------------------------------------------------------- |
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243 | |
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244 | # delete variables unused below |
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245 | |
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246 | lflags:= |
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247 | |
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248 | # ------------------------- |
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249 | # Main arb targets: |
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250 | # ------------------------- |
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251 | |
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252 | first_target: |
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253 | $(MAKE) checks |
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254 | @echo $(SEP) |
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255 | @echo 'Main targets:' |
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256 | @echo '' |
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257 | @echo ' all - Compile ARB + TOOLs + and copy shared libs + link foreign software' |
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258 | @echo ' (That is most likely the target you want)' |
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259 | @echo '' |
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260 | @echo ' clean - remove generated files ("SUBDIR/SUBDIR.clean" to clean only SUBDIR)' |
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261 | @echo ' rebuild - clean + all' |
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262 | @echo ' relink - remove all binaries and relink them from objects' |
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263 | @echo '' |
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264 | @echo 'Some often used sub targets (make all makes them all):' |
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265 | @echo '' |
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266 | @echo ' arb - Just compile ARB (but none of the integrated tools)' |
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267 | @echo ' menus - create GDEHELP/ARB_GDEmenus from GDEHELP/ARB_GDEmenus.source' |
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268 | @echo ' perl - Compile the PERL XSUBS into lib/ARB.so and create links in lib to perl' |
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269 | @echo ' binlink - Create all links in the bin directory' |
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270 | @echo '' |
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271 | @echo 'Development targets:' |
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272 | @echo '' |
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273 | @echo ' depends - create or update dependencies ("SUBDIR/SUBDIR.depends" to update only SUBDIR)' |
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274 | @echo ' proto - create or update prototypes ("SUBDIR/SUBDIR.proto" to update only SUBDIR)' |
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275 | @echo ' tags - create tags for xemacs' |
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276 | @echo ' rmbak - remove all "*%" and cores' |
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277 | @echo ' show - show available shortcuts (AKA subtargets)' |
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278 | @echo ' up - shortcut for depends+proto+tags' |
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279 | @echo '' |
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280 | @echo 'Internal maintainance:' |
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281 | @echo '' |
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282 | @echo ' release - make tarfile + make save ("release_quick" to skip rebuild)' |
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283 | @echo ' tarfile - make rebuild and create arb version tarfile ("tarfile_quick" to skip rebuild)' |
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284 | # @echo ' tarale - compress emacs and ale lisp files int arb_ale.tar.gz' |
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285 | @echo ' save - save all basic ARB sources into arbsrc_DATE' |
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286 | # @echo ' savedepot - save all extended ARB source (DEPOT2 subdir) into arbdepot_DATE.cpio.gz' |
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287 | @echo ' rtc_patch - create LIBLINK/libRTC8M.so (SOLARIS ONLY)' |
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288 | @echo ' source_doc - create doxygen documentation' |
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289 | @echo '' |
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290 | @echo $(SEP) |
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291 | @echo '' |
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292 | |
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293 | |
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294 | # auto-generate config.makefile: |
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295 | |
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296 | CONFIG_MAKEFILE_FOUND=$(wildcard config.makefile) |
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297 | |
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298 | config.makefile : config.makefile.template |
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299 | @echo -------------------------------------------------------------------------------- |
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300 | ifeq ($(strip $(CONFIG_MAKEFILE_FOUND)),) |
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301 | @cp $< $@ |
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302 | @echo '$@:1: has been generated.' |
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303 | @echo 'Please edit $@ to configure your system!' |
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304 | @echo '(not needed for linux systems - simply type "make all")' |
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305 | else |
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306 | @echo '$<:1: is more recent than' |
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307 | @echo '$@:1:' |
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308 | @ls -al config.makefile* |
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309 | @echo "you may either:" |
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310 | @echo "- ignore it and touch $@" |
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311 | @echo "- merge difference between $@ and $< (recommended)" |
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312 | @echo "- remove $@, run make again and edit the freshly generated $@" |
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313 | endif |
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314 | @echo -------------------------------------------------------------------------------- |
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315 | @false |
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316 | |
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317 | # check if everything is configured correctly |
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318 | |
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319 | check_DEVELOPER: |
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320 | ifndef DEVELOPER |
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321 | @echo 'config.makefile:1: DEVELOPER not defined' |
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322 | @false |
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323 | endif |
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324 | |
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325 | check_DEBUG: |
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326 | ifndef dflags |
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327 | @echo 'config.makefile:1: DEBUG has to be defined. Valid values are 0 and 1' |
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328 | @false |
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329 | endif |
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330 | |
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331 | check_ARB_64: |
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332 | ifndef ARB_64 |
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333 | @echo 'config.makefile:1: ARB_64 has to be defined. Valid values are 0 and 1' |
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334 | @false |
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335 | endif |
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336 | |
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337 | # ---------------------------------------- check gcc version |
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338 | |
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339 | check_same_GCC_VERSION: |
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340 | $(ARBHOME)/SOURCE_TOOLS/check_same_gcc_version.pl $(GCC_VERSION_ALLOWED) |
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341 | |
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342 | check_GCC_VERSION: |
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343 | @echo 'GCC version check:' |
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344 | @echo " - Your version is '$(GCC_VERSION_FOUND)'" |
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345 | ifeq ('$(GCC_VERSION_ALLOWED)', '') |
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346 | @echo ' - This version is not in the list of supported gcc-versions:' |
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347 | @$(foreach version,$(ALLOWED_GCC_VERSIONS),echo ' * $(version)';) |
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348 | @echo ' - You may either ..' |
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349 | @echo ' - add your version to ALLOWED_GCC_VERSIONS in the Makefile and try it out or' |
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350 | @echo ' - switch to one of the allowed versions (see arb_README_gcc.txt for installing' |
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351 | @echo ' a different version of gcc)' |
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352 | @echo '' |
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353 | @/bin/false |
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354 | else |
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355 | @echo " - Supported gcc version '$(GCC_VERSION_ALLOWED)' detected - fine!" |
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356 | @echo '' |
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357 | $(MAKE) check_same_GCC_VERSION |
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358 | |
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359 | endif |
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360 | |
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361 | GCC_WITH_VTABLE_AFTER_CLASS=$(ALLOWED_GCC_295_VERSIONS) |
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362 | HAVE_GCC_WITH_VTABLE_AFTER_CLASS=$(strip $(foreach version,$(GCC_WITH_VTABLE_AFTER_CLASS),$(findstring $(version),$(GCC_VERSION_ALLOWED)))) |
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363 | |
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364 | # depending on the version of gcc the location of the vtable pointer differs. |
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365 | ifeq ('$(HAVE_GCC_WITH_VTABLE_AFTER_CLASS)', '') |
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366 | VTABLE_INFRONTOF_CLASS=1 |
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367 | else |
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368 | VTABLE_INFRONTOF_CLASS=0 |
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369 | endif |
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370 | |
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371 | #---------------------- check ARBHOME |
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372 | |
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373 | # use arb_INSTALL.txt to determine whether ARBHOME points to correct directory |
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374 | ARB_INSTALL_FOUND=$(wildcard $(ARBHOME)/arb_INSTALL.txt) |
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375 | |
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376 | check_ARBHOME: |
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377 | ifeq ($(strip $(ARB_INSTALL_FOUND)),) |
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378 | @echo ------------------------------------------------------------ |
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379 | @echo "ARBHOME is set to '$(ARBHOME)'" |
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380 | @echo "The environment variable ARBHOME has to point to the top arb source directory." |
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381 | @echo "If you use bash enter:" |
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382 | @echo " export ARBHOME='`pwd`'" |
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383 | @echo ------------------------------------------------------------ |
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384 | @false |
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385 | endif |
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386 | |
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387 | ARB_PATH_SET=$(findstring $(ARBHOME)/bin,$(PATH)) |
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388 | |
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389 | check_PATH: check_ARBHOME |
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390 | ifeq ($(strip $(ARB_PATH_SET)),) |
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391 | @echo ------------------------------------------------------------ |
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392 | @echo "The environment variable PATH has to contain $(ARBHOME)/bin" |
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393 | @echo "If you use bash enter:" |
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394 | @echo ' export PATH=$$ARBHOME/bin:$$PATH' |
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395 | @echo ------------------------------------------------------------ |
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396 | @false |
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397 | endif |
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398 | |
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399 | check_ENVIRONMENT : check_PATH |
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400 | |
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401 | check_tabs: check_setup |
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402 | ifeq ($(DEBUG),1) |
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403 | @SOURCE_TOOLS/tabBrake.pl |
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404 | endif |
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405 | |
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406 | force_tab_check: |
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407 | touch -t 198001010000 SOURCE_TOOLS/tabBrake.stamp |
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408 | $(MAKE) check_tabs |
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409 | |
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410 | |
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411 | # --------------------- |
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412 | |
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413 | check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION |
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414 | @echo Your setup seems to be ok. |
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415 | |
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416 | checks: check_setup check_tabs |
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417 | |
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418 | |
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419 | # end test section ------------------------------ |
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420 | |
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421 | ARBDB_LIB=-lARBDB |
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422 | ARBDBPP_LIB=-lARBDBPP |
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423 | |
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424 | LIBS = $(ARBDB_LIB) $(SYSLIBS) |
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425 | GUI_LIBS = $(LIBS) -lAW -lAWT $(RTC) $(XLIBS) |
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426 | |
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427 | LIBPATH = -L$(ARBHOME)/LIBLINK |
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428 | |
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429 | DEST_LIB = lib |
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430 | DEST_BIN = bin |
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431 | |
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432 | AINCLUDES = -I. -I$(ARBHOME)/INCLUDE $(XINCLUDES) |
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433 | CPPINCLUDES = -I. -I$(ARBHOME)/INCLUDE $(XINCLUDES) |
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434 | MAKEDEPENDFLAGS = -- $(cflags) -DARB_OPENGL -I. -Y$(ARBHOME)/INCLUDE -- |
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435 | |
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436 | ifeq ($(VTABLE_INFRONTOF_CLASS),1) |
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437 | # Some code in ARB depends on the location of the vtable pointer |
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438 | # (it does a cast from class AP_tree to struct GBT_TREE). In order to |
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439 | # work around that hack properly, we define FAKE_VTAB_PTR |
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440 | # if the vtable is located at the beginning of class. |
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441 | # We are really sorry for that hack. |
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442 | cflags:=$(cflags) -DFAKE_VTAB_PTR=char |
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443 | endif |
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444 | |
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445 | #***** List of all Directories |
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446 | |
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447 | # ALEIO/ALEIO.a \ |
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448 | |
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449 | ARCHS = \ |
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450 | AISC/dummy.a \ |
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451 | AISC_MKPTPS/dummy.a \ |
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452 | ALIV3/ALIV3.a \ |
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453 | ARBDB/libARBDB.a \ |
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454 | ARBDB2/libARBDB.a \ |
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455 | ARBDBPP/libARBDBPP.a \ |
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456 | ARBDBS/libARBDB.a \ |
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457 | ARBDB_COMPRESS/ARBDB_COMPRESS.a \ |
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458 | ARB_GDE/ARB_GDE.a \ |
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459 | AWDEMO/AWDEMO.a \ |
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460 | AWT/libAWT.a \ |
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461 | AWTC/AWTC.a \ |
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462 | AWTI/AWTI.a \ |
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463 | CAT/CAT.a \ |
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464 | CONSENSUS_TREE/CONSENSUS_TREE.a \ |
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465 | CONVERTALN/CONVERTALN.a \ |
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466 | DBSERVER/DBSERVER.a \ |
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467 | DIST/DIST.a \ |
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468 | EDIT/EDIT.a \ |
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469 | EDIT4/EDIT4.a \ |
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470 | EISPACK/EISPACK.a \ |
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471 | GDE/GDE.a \ |
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472 | GENOM/GENOM.a \ |
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473 | GENOM_IMPORT/GENOM_IMPORT.a \ |
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474 | GL/GL.a \ |
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475 | ISLAND_HOPPING/ISLAND_HOPPING.a \ |
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476 | MERGE/MERGE.a \ |
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477 | MULTI_PROBE/MULTI_PROBE.a \ |
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478 | NALIGNER/NALIGNER.a \ |
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479 | NAMES/NAMES.a \ |
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480 | NAMES_COM/server.a \ |
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481 | NTREE/NTREE.a \ |
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482 | PARSIMONY/PARSIMONY.a \ |
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483 | PGT/PGT.a \ |
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484 | PHYLO/PHYLO.a \ |
---|
485 | PRIMER_DESIGN/PRIMER_DESIGN.a \ |
---|
486 | PROBE/PROBE.a \ |
---|
487 | PROBE_COM/server.a \ |
---|
488 | PROBE_DESIGN/PROBE_DESIGN.a \ |
---|
489 | PROBE_SERVER/PROBE_SERVER.a \ |
---|
490 | PROBE_SET/PROBE_SET.a \ |
---|
491 | READSEQ/READSEQ.a \ |
---|
492 | RNA3D/RNA3D.a \ |
---|
493 | SECEDIT/SECEDIT.a \ |
---|
494 | SEER/SEER.a \ |
---|
495 | SEQ_QUALITY/SEQ_QUALITY.a \ |
---|
496 | SERVERCNTRL/SERVERCNTRL.a \ |
---|
497 | SL/SL.a \ |
---|
498 | STAT/STAT.a \ |
---|
499 | TEST/TEST.a \ |
---|
500 | TOOLS/TOOLS.a \ |
---|
501 | TREEGEN/TREEGEN.a \ |
---|
502 | TRS/TRS.a \ |
---|
503 | WETC/WETC.a \ |
---|
504 | WINDOW/libAW.a \ |
---|
505 | XML/XML.a \ |
---|
506 | |
---|
507 | #ARCHS_CLIENTACC = PROBE_COM/client.a |
---|
508 | #ARCHS_CLIENTCPP = NAMES_COM/client.a |
---|
509 | ARCHS_CLIENT_PROBE = PROBE_COM/client.a |
---|
510 | ARCHS_CLIENT_NAMES = NAMES_COM/client.a |
---|
511 | #ARCHS_CLIENT = $(ARCHS_CLIENT_NAMES) |
---|
512 | ARCHS_MAKEBIN = AISC_MKPTPS/dummy.a AISC/dummy.a |
---|
513 | |
---|
514 | ARCHS_COMMUNICATION = NAMES_COM/server.a \ |
---|
515 | PROBE_COM/server.a |
---|
516 | |
---|
517 | # communication libs need aisc and aisc_mkpts: |
---|
518 | $(ARCHS_COMMUNICATION:.a=.dummy) : $(ARCHS_MAKEBIN:.a=.dummy) |
---|
519 | |
---|
520 | #*************************************************************************************** |
---|
521 | # Individual Programs Section |
---|
522 | #*************************************************************************************** |
---|
523 | |
---|
524 | #*********************************** arb_ntree ************************************** |
---|
525 | NTREE = bin/arb_ntree |
---|
526 | ARCHS_NTREE = \ |
---|
527 | $(ARCHS_CLIENT_PROBE) \ |
---|
528 | $(SEERLIB) \ |
---|
529 | ARB_GDE/ARB_GDE.a \ |
---|
530 | AWTC/AWTC.a \ |
---|
531 | AWTI/AWTI.a \ |
---|
532 | CAT/CAT.a \ |
---|
533 | GENOM/GENOM.a \ |
---|
534 | GENOM_IMPORT/GENOM_IMPORT.a \ |
---|
535 | ISLAND_HOPPING/ISLAND_HOPPING.a \ |
---|
536 | MERGE/MERGE.a \ |
---|
537 | MULTI_PROBE/MULTI_PROBE.a \ |
---|
538 | NTREE/NTREE.a \ |
---|
539 | PRIMER_DESIGN/PRIMER_DESIGN.a \ |
---|
540 | PROBE_DESIGN/PROBE_DESIGN.a \ |
---|
541 | SEQ_QUALITY/SEQ_QUALITY.a \ |
---|
542 | SERVERCNTRL/SERVERCNTRL.a \ |
---|
543 | SL/AW_NAME/AW_NAME.a \ |
---|
544 | SL/HELIX/HELIX.a \ |
---|
545 | SL/DB_SCANNER/DB_SCANNER.a \ |
---|
546 | SL/FILE_BUFFER/FILE_BUFFER.a \ |
---|
547 | STAT/STAT.a \ |
---|
548 | XML/XML.a \ |
---|
549 | |
---|
550 | $(NTREE): $(ARCHS_NTREE:.a=.dummy) NAMES_COM/server.dummy shared_libs |
---|
551 | @SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NTREE) $(GUI_LIBS) || ( \ |
---|
552 | echo Link $@ ; \ |
---|
553 | echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_NTREE) $(GUI_LIBS)" ; \ |
---|
554 | $(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_NTREE) $(GUI_LIBS) \ |
---|
555 | ) |
---|
556 | |
---|
557 | #*********************************** arb_rna3d ************************************** |
---|
558 | RNA3D = bin/arb_rna3d |
---|
559 | ARCHS_RNA3D = \ |
---|
560 | RNA3D/RNA3D.a \ |
---|
561 | |
---|
562 | $(RNA3D): $(ARCHS_RNA3D:.a=.dummy) shared_libs |
---|
563 | @echo $@ currently does not work as standalone application |
---|
564 | false |
---|
565 | |
---|
566 | #*********************************** arb_edit ************************************** |
---|
567 | EDIT = bin/arb_edit |
---|
568 | ARCHS_EDIT = \ |
---|
569 | NAMES_COM/client.a \ |
---|
570 | SERVERCNTRL/SERVERCNTRL.a \ |
---|
571 | EDIT/EDIT.a \ |
---|
572 | ARB_GDE/ARB_GDE.a \ |
---|
573 | STAT/STAT.a \ |
---|
574 | XML/XML.a \ |
---|
575 | SL/HELIX/HELIX.a \ |
---|
576 | SL/AW_HELIX/AW_HELIX.a \ |
---|
577 | SL/AW_NAME/AW_NAME.a \ |
---|
578 | |
---|
579 | $(EDIT): $(ARCHS_EDIT:.a=.dummy) shared_libs |
---|
580 | @SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_EDIT) $(GUI_LIBS) || ( \ |
---|
581 | echo Link $@ ; \ |
---|
582 | echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_EDIT) -lARBDBPP $(GUI_LIBS)" ; \ |
---|
583 | $(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_EDIT) -lARBDBPP $(GUI_LIBS) ; \ |
---|
584 | ) |
---|
585 | |
---|
586 | #*********************************** arb_edit4 ************************************** |
---|
587 | EDIT4 = bin/arb_edit4 |
---|
588 | |
---|
589 | ARCHS_EDIT4 := \ |
---|
590 | NAMES_COM/client.a \ |
---|
591 | AWTC/AWTC.a \ |
---|
592 | EDIT4/EDIT4.a \ |
---|
593 | SECEDIT/SECEDIT.a \ |
---|
594 | SERVERCNTRL/SERVERCNTRL.a \ |
---|
595 | STAT/STAT.a \ |
---|
596 | ARB_GDE/ARB_GDE.a \ |
---|
597 | ISLAND_HOPPING/ISLAND_HOPPING.a \ |
---|
598 | SL/HELIX/HELIX.a \ |
---|
599 | SL/AW_HELIX/AW_HELIX.a \ |
---|
600 | SL/AW_NAME/AW_NAME.a \ |
---|
601 | SL/FILE_BUFFER/FILE_BUFFER.a \ |
---|
602 | XML/XML.a \ |
---|
603 | |
---|
604 | ifeq ($(OPENGL),1) |
---|
605 | ARCHS_EDIT4 += RNA3D/RNA3D.a |
---|
606 | endif |
---|
607 | LIBS_EDIT4 := $(GLLIBS) |
---|
608 | |
---|
609 | $(EDIT4): $(ARCHS_EDIT4:.a=.dummy) shared_libs |
---|
610 | @SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_EDIT4) $(GUI_LIBS) || ( \ |
---|
611 | echo Link $@ ; \ |
---|
612 | echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_EDIT4) $(GUI_LIBS) $(LIBS_EDIT4)" ; \ |
---|
613 | $(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_EDIT4) $(GUI_LIBS) $(LIBS_EDIT4) \ |
---|
614 | ) |
---|
615 | |
---|
616 | #*********************************** arb_pgt ************************************** |
---|
617 | |
---|
618 | PGT = bin/arb_pgt |
---|
619 | ARCHS_PGT = \ |
---|
620 | PGT/PGT.a \ |
---|
621 | |
---|
622 | PGT_SYS_LIBS=$(XLIBS) -ltiff $(LIBS) |
---|
623 | |
---|
624 | $(PGT) : $(ARCHS_PGT:.a=.dummy) shared_libs |
---|
625 | @SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PGT) || ( \ |
---|
626 | echo Link $@ ; \ |
---|
627 | echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_PGT) $(PGT_SYS_LIBS)"; \ |
---|
628 | $(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_PGT) $(PGT_SYS_LIBS); \ |
---|
629 | ) |
---|
630 | |
---|
631 | |
---|
632 | #*********************************** arb_wetc ************************************** |
---|
633 | WETC = bin/arb_wetc |
---|
634 | ARCHS_WETC = \ |
---|
635 | WETC/WETC.a \ |
---|
636 | SL/HELIX/HELIX.a \ |
---|
637 | XML/XML.a \ |
---|
638 | |
---|
639 | $(WETC): $(ARCHS_WETC:.a=.dummy) shared_libs |
---|
640 | @SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_WETC) $(GUI_LIBS) || ( \ |
---|
641 | echo Link $@ ; \ |
---|
642 | echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_WETC) $(GUI_LIBS)" ; \ |
---|
643 | $(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_WETC) $(GUI_LIBS) ; \ |
---|
644 | ) |
---|
645 | |
---|
646 | #*********************************** arb_dist ************************************** |
---|
647 | DIST = bin/arb_dist |
---|
648 | ARCHS_DIST = \ |
---|
649 | $(ARCHS_CLIENT_PROBE) \ |
---|
650 | DIST/DIST.a \ |
---|
651 | SERVERCNTRL/SERVERCNTRL.a \ |
---|
652 | CONSENSUS_TREE/CONSENSUS_TREE.a \ |
---|
653 | EISPACK/EISPACK.a \ |
---|
654 | SL/HELIX/HELIX.a \ |
---|
655 | XML/XML.a \ |
---|
656 | |
---|
657 | $(DIST): $(ARCHS_DIST:.a=.dummy) shared_libs |
---|
658 | @SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_DIST) $(GUI_LIBS) || ( \ |
---|
659 | echo Link $@ ; \ |
---|
660 | echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_DIST) $(GUI_LIBS)" ; \ |
---|
661 | $(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_DIST) $(GUI_LIBS) ; \ |
---|
662 | ) |
---|
663 | |
---|
664 | #*********************************** arb_pars ************************************** |
---|
665 | PARSIMONY = bin/arb_pars |
---|
666 | ARCHS_PARSIMONY = \ |
---|
667 | NAMES_COM/client.a \ |
---|
668 | SERVERCNTRL/SERVERCNTRL.a \ |
---|
669 | PARSIMONY/PARSIMONY.a \ |
---|
670 | SL/HELIX/HELIX.a \ |
---|
671 | SL/AW_NAME/AW_NAME.a \ |
---|
672 | XML/XML.a \ |
---|
673 | |
---|
674 | $(PARSIMONY): $(ARCHS_PARSIMONY:.a=.dummy) shared_libs |
---|
675 | @SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PARSIMONY) $(GUI_LIBS) || ( \ |
---|
676 | echo Link $@ ; \ |
---|
677 | echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_PARSIMONY) $(GUI_LIBS)" ; \ |
---|
678 | $(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_PARSIMONY) $(GUI_LIBS) ; \ |
---|
679 | ) |
---|
680 | |
---|
681 | #*********************************** arb_treegen ************************************** |
---|
682 | TREEGEN = bin/arb_treegen |
---|
683 | ARCHS_TREEGEN = \ |
---|
684 | TREEGEN/TREEGEN.a \ |
---|
685 | |
---|
686 | $(TREEGEN) : $(ARCHS_TREEGEN:.a=.dummy) |
---|
687 | @SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_TREEGEN) || ( \ |
---|
688 | echo Link $@ ; \ |
---|
689 | echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_TREEGEN)" ; \ |
---|
690 | $(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_TREEGEN) ; \ |
---|
691 | ) |
---|
692 | |
---|
693 | #*********************************** arb_naligner ************************************** |
---|
694 | NALIGNER = bin/arb_naligner |
---|
695 | ARCHS_NALIGNER = \ |
---|
696 | $(ARCHS_CLIENT_PROBE) \ |
---|
697 | NALIGNER/NALIGNER.a \ |
---|
698 | SERVERCNTRL/SERVERCNTRL.a \ |
---|
699 | SL/HELIX/HELIX.a \ |
---|
700 | |
---|
701 | $(NALIGNER): $(ARCHS_NALIGNER:.a=.dummy) shared_libs |
---|
702 | @SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NALIGNER) || ( \ |
---|
703 | echo Link $@ ; \ |
---|
704 | echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_NALIGNER) $(LIBS)" ; \ |
---|
705 | $(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_NALIGNER) $(LIBS) \ |
---|
706 | ) |
---|
707 | |
---|
708 | #*********************************** arb_secedit ************************************** |
---|
709 | SECEDIT = bin/arb_secedit |
---|
710 | ARCHS_SECEDIT = \ |
---|
711 | SECEDIT/SECEDIT.a \ |
---|
712 | XML/XML.a \ |
---|
713 | |
---|
714 | $(SECEDIT): $(ARCHS_SECEDIT:.a=.dummy) shared_libs |
---|
715 | @echo $@ currently does not work as standalone application |
---|
716 | false |
---|
717 | |
---|
718 | |
---|
719 | #*********************************** arb_phylo ************************************** |
---|
720 | PHYLO = bin/arb_phylo |
---|
721 | ARCHS_PHYLO = \ |
---|
722 | PHYLO/PHYLO.a \ |
---|
723 | SL/HELIX/HELIX.a \ |
---|
724 | XML/XML.a \ |
---|
725 | |
---|
726 | $(PHYLO): $(ARCHS_PHYLO:.a=.dummy) shared_libs |
---|
727 | @SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PHYLO) $(GUI_LIBS) || ( \ |
---|
728 | echo Link $@ ; \ |
---|
729 | echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_PHYLO) $(GUI_LIBS)" ; \ |
---|
730 | $(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_PHYLO) $(GUI_LIBS) ; \ |
---|
731 | ) |
---|
732 | |
---|
733 | #*************************************************************************************** |
---|
734 | # SERVER SECTION |
---|
735 | #*************************************************************************************** |
---|
736 | |
---|
737 | #*********************************** arb_db_server ************************************** |
---|
738 | DBSERVER = bin/arb_db_server |
---|
739 | ARCHS_DBSERVER = \ |
---|
740 | DBSERVER/DBSERVER.a \ |
---|
741 | SERVERCNTRL/SERVERCNTRL.a \ |
---|
742 | |
---|
743 | $(DBSERVER): $(ARCHS_DBSERVER:.a=.dummy) shared_libs |
---|
744 | @SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_DBSERVER) $(ARBDB_LIB) || ( \ |
---|
745 | echo Link $@ ; \ |
---|
746 | echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_DBSERVER) $(ARBDB_LIB) $(SYSLIBS)" ; \ |
---|
747 | $(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_DBSERVER) $(ARBDB_LIB) $(SYSLIBS) ; \ |
---|
748 | ) |
---|
749 | |
---|
750 | #*********************************** arb_pt_server ************************************** |
---|
751 | PROBE = bin/arb_pt_server |
---|
752 | ARCHS_PROBE = \ |
---|
753 | PROBE_COM/server.a \ |
---|
754 | PROBE/PROBE.a \ |
---|
755 | SERVERCNTRL/SERVERCNTRL.a \ |
---|
756 | SL/HELIX/HELIX.a \ |
---|
757 | |
---|
758 | $(PROBE): $(ARCHS_PROBE:.a=.dummy) shared_libs |
---|
759 | @SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PROBE) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) || ( \ |
---|
760 | echo Link $@ ; \ |
---|
761 | echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_PROBE) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS)" ; \ |
---|
762 | $(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_PROBE) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS) ; \ |
---|
763 | ) |
---|
764 | |
---|
765 | #*********************************** arb_name_server ************************************** |
---|
766 | NAMES = bin/arb_name_server |
---|
767 | ARCHS_NAMES = \ |
---|
768 | NAMES_COM/server.a \ |
---|
769 | NAMES/NAMES.a \ |
---|
770 | SERVERCNTRL/SERVERCNTRL.a \ |
---|
771 | |
---|
772 | $(NAMES): $(ARCHS_NAMES:.a=.dummy) shared_libs |
---|
773 | @SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) || ( \ |
---|
774 | echo Link $@ ; \ |
---|
775 | echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) $(SYSLIBS)" ; \ |
---|
776 | $(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) $(SYSLIBS) ; \ |
---|
777 | ) |
---|
778 | |
---|
779 | #*********************************** TEST SECTION ************************************** |
---|
780 | AWDEMO = tb/awdemo |
---|
781 | ARCHS_AWDEMO = \ |
---|
782 | AWDEMO/AWDEMO.a \ |
---|
783 | |
---|
784 | $(AWDEMO): $(ARCHS_AWDEMO:.a=.dummy) shared_libs |
---|
785 | @echo $(SEP) Link $@ |
---|
786 | $(LINK_EXECUTABLE) $@ $(ARCHS_AWDEMO) $(LIBS) |
---|
787 | |
---|
788 | TEST = tb/dbtest |
---|
789 | ARCHS_TEST = \ |
---|
790 | TEST/TEST.a \ |
---|
791 | XML/XML.a \ |
---|
792 | |
---|
793 | $(TEST): $(ARCHS_TEST:.a=.dummy) shared_libs |
---|
794 | @echo $(SEP) Link $@ |
---|
795 | $(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_TEST) -lAWT $(LIBS) |
---|
796 | |
---|
797 | ALIV3 = bin/aliv3 |
---|
798 | ARCHS_ALIV3 = \ |
---|
799 | ALIV3/ALIV3.a \ |
---|
800 | SL/HELIX/HELIX.a \ |
---|
801 | |
---|
802 | $(ALIV3): $(ARCHS_ALIV3:.a=.dummy) shared_libs |
---|
803 | @echo $(SEP) Link $@ |
---|
804 | $(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_ALIV3) $(ARBDB_LIB) $(SYSLIBS) $(CCPLIBS) |
---|
805 | |
---|
806 | |
---|
807 | ACORR = tb/acorr |
---|
808 | ARCHS_ACORR = \ |
---|
809 | DIST/DIST.a \ |
---|
810 | SERVERCNTRL/SERVERCNTRL.a \ |
---|
811 | FINDCORRASC/FINDCORRASC.a \ |
---|
812 | FINDCORRMATH/FINDCORRMATH.a \ |
---|
813 | FINDCORRWIN/FINDCORRWIN.a \ |
---|
814 | XML/XML.a \ |
---|
815 | |
---|
816 | $(ACORR): $(ARCHS_ACORR:.a=.dummy) shared_libs |
---|
817 | @echo $(SEP) Link $@ |
---|
818 | $(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_ACORR) -lAWT $(ARBDBPP_LIB) $(LIBS) |
---|
819 | |
---|
820 | |
---|
821 | ARBDB_COMPRESS = tb/arbdb_compress |
---|
822 | ARCHS_ARBDB_COMPRESS = \ |
---|
823 | ARBDB_COMPRESS/ARBDB_COMPRESS.a \ |
---|
824 | |
---|
825 | $(ARBDB_COMPRESS): $(ARCHS_ARBDB_COMPRESS:.a=.dummy) shared_libs |
---|
826 | @echo $(SEP) Link $@ |
---|
827 | $(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_ARBDB_COMPRESS) $(ARBDB_LIB) |
---|
828 | |
---|
829 | #*********************************** OTHER EXECUTABLES ******************************************** |
---|
830 | |
---|
831 | |
---|
832 | #*********************************** SHARED LIBRARIES SECTION ************************************** |
---|
833 | |
---|
834 | shared_libs: dball aw awt |
---|
835 | @echo -------------------- Updating shared libraries |
---|
836 | $(MAKE) libs |
---|
837 | |
---|
838 | libs: lib/libARBDB.$(SHARED_LIB_SUFFIX) \ |
---|
839 | lib/libARBDBPP.$(SHARED_LIB_SUFFIX) \ |
---|
840 | lib/libARBDO.$(SHARED_LIB_SUFFIX) \ |
---|
841 | lib/libAW.$(SHARED_LIB_SUFFIX) \ |
---|
842 | lib/libAWT.$(SHARED_LIB_SUFFIX) |
---|
843 | |
---|
844 | lib/lib%.$(SHARED_LIB_SUFFIX): LIBLINK/lib%.$(SHARED_LIB_SUFFIX) |
---|
845 | cp $< $@ |
---|
846 | |
---|
847 | # lib/$(MOTIF_LIBNAME): $(MOTIF_LIBPATH) |
---|
848 | # cp $< $@ |
---|
849 | |
---|
850 | #*************************************************************************************** |
---|
851 | # Rekursiv calls to submakefiles |
---|
852 | #*************************************************************************************** |
---|
853 | |
---|
854 | %.depends: |
---|
855 | @cp -p $(@D)/Makefile $(@D)/Makefile.old # save old Makefile |
---|
856 | @$(MAKE) -C $(@D) -r \ |
---|
857 | "AUTODEPENDS=1" \ |
---|
858 | "LD_LIBRARY_PATH = ${LD_LIBRARY_PATH}" \ |
---|
859 | "MAKEDEPENDFLAGS = $(MAKEDEPENDFLAGS)" \ |
---|
860 | "MAKEDEPEND=$(MAKEDEPEND)" \ |
---|
861 | "ARBHOME=$(ARBHOME)" \ |
---|
862 | depends; |
---|
863 | @grep "^# DO NOT DELETE" $(@D)/Makefile >/dev/null |
---|
864 | @cat $(@D)/Makefile \ |
---|
865 | | SOURCE_TOOLS/fix_depends.pl \ |
---|
866 | >$(@D)/Makefile.2 |
---|
867 | @mv $(@D)/Makefile.old $(@D)/Makefile # restore old Makefile |
---|
868 | @$(ARBHOME)/SOURCE_TOOLS/mv_if_diff $(@D)/Makefile.2 $(@D)/Makefile # update Makefile if changed |
---|
869 | |
---|
870 | %.proto: |
---|
871 | @$(MAKE) -C $(@D) \ |
---|
872 | "AUTODEPENDS=0" \ |
---|
873 | proto |
---|
874 | |
---|
875 | %.clean: |
---|
876 | @$(MAKE) -C $(@D) \ |
---|
877 | "AUTODEPENDS=0" \ |
---|
878 | "MACH=$(MACH)" \ |
---|
879 | "OPENGL=$(OPENGL)" \ |
---|
880 | clean |
---|
881 | |
---|
882 | # rule to generate main target (normally a library): |
---|
883 | %.dummy: |
---|
884 | @( export ID=$$$$; \ |
---|
885 | (( \ |
---|
886 | echo "$(SEP) Make everything in $(@D)"; \ |
---|
887 | $(MAKE) -C $(@D) -r \ |
---|
888 | "ACC = $(ACC)" \ |
---|
889 | "ACCLIB = $(ACCLIB)" \ |
---|
890 | "AINCLUDES = $(AINCLUDES)" \ |
---|
891 | "ARBHOME = $(ARBHOME)" \ |
---|
892 | "ARLIB = $(ARLIB)" \ |
---|
893 | "AUTODEPENDS=1" \ |
---|
894 | "CCPLIB = $(CCPLIB)" \ |
---|
895 | "CCPLIBS = $(CCPLIBS)" \ |
---|
896 | "CPP = $(CPP)" \ |
---|
897 | "CPPINCLUDES = $(CPPINCLUDES)" \ |
---|
898 | "DEBUG=$(DEBUG)" \ |
---|
899 | "LD_LIBRARY_PATH = $(LD_LIBRARY_PATH)" \ |
---|
900 | "LIBPATH = $(LIBPATH)" \ |
---|
901 | "LINK_EXECUTABLE = $(LINK_EXECUTABLE)" \ |
---|
902 | "LINK_STATIC_LIB = $(LINK_STATIC_LIB)" \ |
---|
903 | "LINK_SHARED_LIB = $(LINK_SHARED_LIB)" \ |
---|
904 | "MAIN = $(@F:.dummy=.a)" \ |
---|
905 | "OPENGL = $(OPENGL)" \ |
---|
906 | "POST_COMPILE = $(POST_COMPILE)" \ |
---|
907 | "SHARED_LIB_SUFFIX = $(SHARED_LIB_SUFFIX)" \ |
---|
908 | "STATIC = $(STATIC)"\ |
---|
909 | "SYSLIBS = $(SYSLIBS)" \ |
---|
910 | "XHOME = $(XHOME)" \ |
---|
911 | "XLIBS = $(XLIBS)" \ |
---|
912 | "cflags = $(cflags) -DIN_ARB_$(subst /,_,$(@D))" \ |
---|
913 | ) >$(@D).$$ID.log 2>&1 && (cat $(@D).$$ID.log;rm $(@D).$$ID.log)) || (cat $(@D).$$ID.log;rm $(@D).$$ID.log;false)) |
---|
914 | |
---|
915 | # Additional dependencies for subtargets: |
---|
916 | |
---|
917 | comtools: $(ARCHS_MAKEBIN:.a=.dummy) |
---|
918 | |
---|
919 | PROBE_COM/PROBE_COM.dummy : comtools |
---|
920 | PROBE_COM/server.dummy : comtools |
---|
921 | PROBE_COM/client.dummy : comtools |
---|
922 | |
---|
923 | NAMES_COM/NAMES_COM.dummy : comtools |
---|
924 | NAMES_COM/server.dummy : comtools |
---|
925 | NAMES_COM/client.dummy : comtools |
---|
926 | |
---|
927 | com_probe: PROBE_COM/PROBE_COM.dummy |
---|
928 | com_names: NAMES_COM/NAMES_COM.dummy |
---|
929 | |
---|
930 | TOOLS/TOOLS.dummy : shared_libs SERVERCNTRL/SERVERCNTRL.dummy CAT/CAT.dummy com_probe |
---|
931 | |
---|
932 | AWTC/AWTC.dummy : com_names com_probe |
---|
933 | |
---|
934 | NAMES/NAMES.dummy : com_names |
---|
935 | SL/AW_NAME/AW_NAME.dummy : com_names |
---|
936 | |
---|
937 | PROBE/PROBE.dummy : com_probe |
---|
938 | MULTI_PROBE/MULTI_PROBE.dummy : com_probe |
---|
939 | PROBE_DESIGN/PROBE_DESIGN.dummy : com_probe |
---|
940 | NALIGNER/NALIGNER.dummy : com_probe |
---|
941 | |
---|
942 | ARB_GDE/ARB_GDE.dummy : proto_tools |
---|
943 | |
---|
944 | |
---|
945 | #*************************************************************************************** |
---|
946 | # Short aliases to make targets |
---|
947 | #*************************************************************************************** |
---|
948 | |
---|
949 | show: |
---|
950 | @echo $(SEP) |
---|
951 | @echo 'Aliases for often needed targets:' |
---|
952 | @echo '' |
---|
953 | @echo ' executables:' |
---|
954 | @echo '' |
---|
955 | @echo ' nt arb_ntree' |
---|
956 | @echo ' e4 arb_edit4 (includes secedit)' |
---|
957 | @echo ' di arb_dist' |
---|
958 | @echo ' ph arb_phylo' |
---|
959 | @echo ' pa arb_parsimony' |
---|
960 | @echo ' tg arb_treegen' |
---|
961 | @echo ' ds arb_dbserver' |
---|
962 | @echo ' pt arb_pt_server' |
---|
963 | @echo ' na arb_name_server' |
---|
964 | @echo '' |
---|
965 | @echo ' libraries:' |
---|
966 | @echo '' |
---|
967 | @echo ' com communication libraries' |
---|
968 | @echo ' dball ARB database (all versions: db dbs and db2)' |
---|
969 | @echo ' aw GUI lib' |
---|
970 | @echo ' awt GUI toolkit' |
---|
971 | @echo ' awtc general purpose library' |
---|
972 | @echo ' awti import/export library' |
---|
973 | @echo ' mp multi probe library' |
---|
974 | @echo ' ge genome library' |
---|
975 | @echo ' pd probe design lib' |
---|
976 | @echo ' prd primer design lib' |
---|
977 | @echo ' ih island hopper' |
---|
978 | @echo '' |
---|
979 | @echo ' other targets:' |
---|
980 | @echo '' |
---|
981 | @echo ' help recompile help files' |
---|
982 | @echo ' test test arbdb (needs fix)' |
---|
983 | @echo ' demo GUI demo (needs fix)' |
---|
984 | @echo ' tools make small tools used by arb' |
---|
985 | @echo '' |
---|
986 | @echo ' optional targets (not build by make all)' |
---|
987 | @echo '' |
---|
988 | @echo ' ps ARB probe server' |
---|
989 | @echo ' pc ARB probe client (you need java)' |
---|
990 | @echo '' |
---|
991 | @echo ' foreign targets:' |
---|
992 | @echo '' |
---|
993 | @echo ' gde GDE' |
---|
994 | @echo ' agde ARB_GDE' |
---|
995 | @echo '' |
---|
996 | @echo 'for other targets inspect $(ARBHOME)/Makefile' |
---|
997 | @echo '' |
---|
998 | @echo $(SEP) |
---|
999 | |
---|
1000 | source_doc: |
---|
1001 | doxygen |
---|
1002 | |
---|
1003 | mbin: $(ARCHS_MAKEBIN:.a=.dummy) |
---|
1004 | |
---|
1005 | com: $(ARCHS_COMMUNICATION:.a=.dummy) |
---|
1006 | |
---|
1007 | help: HELP_SOURCE/HELP_SOURCE.dummy |
---|
1008 | |
---|
1009 | HELP_SOURCE/HELP_SOURCE.dummy: xml menus# need to create some files in GDE-subtree first |
---|
1010 | |
---|
1011 | dball: db dbs db2 dp |
---|
1012 | db: ARBDB/libARBDB.dummy |
---|
1013 | dbs: ARBDBS/libARBDB.dummy |
---|
1014 | db2: ARBDB2/libARBDB.dummy |
---|
1015 | dp: ARBDBPP/libARBDBPP.dummy |
---|
1016 | aw: WINDOW/libAW.dummy |
---|
1017 | awt: AWT/libAWT.dummy |
---|
1018 | awtc: AWTC/AWTC.dummy |
---|
1019 | awti: AWTI/AWTI.dummy |
---|
1020 | |
---|
1021 | ih: ISLAND_HOPPING/ISLAND_HOPPING.dummy |
---|
1022 | |
---|
1023 | mp: MULTI_PROBE/MULTI_PROBE.dummy |
---|
1024 | mg: MERGE/MERGE.dummy |
---|
1025 | ge: GENOM/GENOM.dummy |
---|
1026 | prd: PRIMER_DESIGN/PRIMER_DESIGN.dummy |
---|
1027 | |
---|
1028 | nt: menus $(NTREE) |
---|
1029 | ed: $(EDIT) |
---|
1030 | |
---|
1031 | al: $(ALIGNER) |
---|
1032 | nal: $(NALIGNER) |
---|
1033 | a3: $(ALIV3) |
---|
1034 | |
---|
1035 | di: $(DIST) |
---|
1036 | ph: $(PHYLO) |
---|
1037 | pa: $(PARSIMONY) |
---|
1038 | tg: $(TREEGEN) |
---|
1039 | |
---|
1040 | 3d: RNA3D/RNA3D.dummy |
---|
1041 | gl: GL/GL.dummy |
---|
1042 | sl: NAMES_COM/NAMES_COM.dummy |
---|
1043 | $(MAKE) SL/SL.dummy |
---|
1044 | |
---|
1045 | ds: $(DBSERVER) |
---|
1046 | pt: $(PROBE) |
---|
1047 | ps: PROBE_SERVER/PROBE_SERVER.dummy |
---|
1048 | pc: PROBE_WEB/PROBE_WEB.dummy |
---|
1049 | pst: PROBE_SET/PROBE_SET.dummy |
---|
1050 | pd: PROBE_DESIGN/PROBE_DESIGN.dummy |
---|
1051 | na: $(NAMES) |
---|
1052 | |
---|
1053 | ac: $(ARBDB_COMPRESS) # unused? does not compile |
---|
1054 | |
---|
1055 | test: $(TEST) |
---|
1056 | demo: $(AWDEMO) |
---|
1057 | |
---|
1058 | sec: SECEDIT/SECEDIT.dummy |
---|
1059 | |
---|
1060 | e4: $(EDIT4) |
---|
1061 | gi: GENOM_IMPORT/GENOM_IMPORT.dummy |
---|
1062 | we: $(WETC) |
---|
1063 | eb: $(EDITDB) |
---|
1064 | |
---|
1065 | pgt: $(PGT) |
---|
1066 | xml: XML/XML.dummy |
---|
1067 | templ: TEMPLATES/TEMPLATES.dummy |
---|
1068 | |
---|
1069 | #******************************************************************************** |
---|
1070 | |
---|
1071 | up: depends proto tags valgrind_update |
---|
1072 | |
---|
1073 | #******************************************************************************** |
---|
1074 | |
---|
1075 | depends: $(ARCHS:.a=.depends) \ |
---|
1076 | HELP_SOURCE/HELP_SOURCE.depends \ |
---|
1077 | |
---|
1078 | proto_tools: AISC_MKPTPS/AISC_MKPTPS.dummy |
---|
1079 | |
---|
1080 | proto: proto_tools TOOLS/TOOLS.dummy |
---|
1081 | $(MAKE) \ |
---|
1082 | AISC/AISC.proto \ |
---|
1083 | ARBDB/ARBDB.proto \ |
---|
1084 | ARB_GDE/ARB_GDE.proto \ |
---|
1085 | CONVERTALN/CONVERTALN.proto \ |
---|
1086 | NTREE/NTREE.proto \ |
---|
1087 | PROBE/PROBE.proto \ |
---|
1088 | SERVERCNTRL/SERVERCNTRL.proto \ |
---|
1089 | TRS/TRS.proto \ |
---|
1090 | AISC_COM/AISC_COM.proto \ |
---|
1091 | GDE/GDE.proto \ |
---|
1092 | |
---|
1093 | #******************************************************************************** |
---|
1094 | |
---|
1095 | valgrind_update: |
---|
1096 | $(MAKE) -C SOURCE_TOOLS valgrind_update |
---|
1097 | |
---|
1098 | #******************************************************************************** |
---|
1099 | |
---|
1100 | TAGFILE=TAGS |
---|
1101 | TAGFILE_TMP=TAGS.tmp |
---|
1102 | |
---|
1103 | tags: tags_$(MACH) |
---|
1104 | mv $(TAGFILE_TMP) $(TAGFILE) |
---|
1105 | |
---|
1106 | tags_LINUX: tags2 |
---|
1107 | tags_SUN5: tags1 |
---|
1108 | |
---|
1109 | tags1: |
---|
1110 | # first search class definitions |
---|
1111 | $(CTAGS) -f $(TAGFILE_TMP) --language=none "--regex=/^[ \t]*class[ \t]+\([^ \t]+\)/" `find . -name '*.[ch]xx' -type f` |
---|
1112 | $(CTAGS) -f $(TAGFILE_TMP) --append --language=none "--regex=/\([^ \t]+\)::/" `find . -name '*.[ch]xx' -type f` |
---|
1113 | # then append normal tags (headers first) |
---|
1114 | $(CTAGS) -f $(TAGFILE_TMP) --append --members ARBDB/*.h `find . -name '*.[h]xx' -type f` |
---|
1115 | $(CTAGS) -f $(TAGFILE_TMP) --append ARBDB/*.c `find . -name '*.[c]xx' -type f` |
---|
1116 | |
---|
1117 | # if the above tag creation does not work -> try tags2: |
---|
1118 | tags2: |
---|
1119 | ctags -f $(TAGFILE_TMP) -e --c-types=cdt --sort=no `find . \( -name '*.[ch]xx' -o -name "*.[ch]" \) -type f | grep -v -i perl5` |
---|
1120 | ctags -f $(TAGFILE_TMP) -a -e --c-types=f-tvx --sort=no `find . \( -name '*.[ch]xx' -o -name "*.[ch]" \) -type f | grep -v -i perl5` |
---|
1121 | |
---|
1122 | #******************************************************************************** |
---|
1123 | |
---|
1124 | links: SOURCE_TOOLS/generate_all_links.stamp |
---|
1125 | |
---|
1126 | SOURCE_TOOLS/generate_all_links.stamp: SOURCE_TOOLS/generate_all_links.sh |
---|
1127 | SOURCE_TOOLS/generate_all_links.sh |
---|
1128 | touch SOURCE_TOOLS/generate_all_links.stamp |
---|
1129 | |
---|
1130 | gde: GDE/GDE.dummy |
---|
1131 | GDE: gde |
---|
1132 | agde: ARB_GDE/ARB_GDE.dummy |
---|
1133 | tools: TOOLS/TOOLS.dummy |
---|
1134 | trs: TRS/TRS.dummy |
---|
1135 | convert: SL/FILE_BUFFER/FILE_BUFFER.dummy |
---|
1136 | $(MAKE) CONVERTALN/CONVERTALN.dummy |
---|
1137 | |
---|
1138 | readseq: READSEQ/READSEQ.dummy |
---|
1139 | |
---|
1140 | #*************************************************************************************** |
---|
1141 | # Some user commands |
---|
1142 | #*************************************************************************************** |
---|
1143 | rtc_patch: |
---|
1144 | rtc_patch_area -so LIBLINK/libRTC8M.so |
---|
1145 | |
---|
1146 | menus: binlink |
---|
1147 | @(( \ |
---|
1148 | echo $(SEP) Make everything in GDEHELP; \ |
---|
1149 | $(MAKE) -C GDEHELP -r "PP=$(PP)" all \ |
---|
1150 | ) > GDEHELP.log 2>&1 && (cat GDEHELP.log;rm GDEHELP.log)) || (cat GDEHELP.log;rm GDEHELP.log;false) |
---|
1151 | |
---|
1152 | ifeq ($(DEBUG),1) |
---|
1153 | BIN_TARGET=develall |
---|
1154 | else |
---|
1155 | BIN_TARGET=all |
---|
1156 | endif |
---|
1157 | |
---|
1158 | |
---|
1159 | binlink: |
---|
1160 | $(MAKE) -C bin $(BIN_TARGET) |
---|
1161 | |
---|
1162 | bin/arb_%: DEPOT2/% |
---|
1163 | cp $< $@ |
---|
1164 | bin/%: DEPOT2/% |
---|
1165 | cp $< $@ |
---|
1166 | |
---|
1167 | |
---|
1168 | preplib: |
---|
1169 | (cd lib;$(MAKE) all) |
---|
1170 | |
---|
1171 | # ---------------------------------------- perl |
---|
1172 | |
---|
1173 | perl: tools |
---|
1174 | @echo $(SEP) Make everything in PERL2ARB |
---|
1175 | @$(MAKE) -C PERL2ARB -r -f Makefile.main \ |
---|
1176 | "AUTODEPENDS=1" \ |
---|
1177 | "MACH=$(MACH)" \ |
---|
1178 | "dflags=$(dflags)" \ |
---|
1179 | "ARBHOME=$(ARBHOME)" \ |
---|
1180 | "DEBUG=$(DEBUG)" \ |
---|
1181 | "MAKEDEPEND=$(MAKEDEPEND)" \ |
---|
1182 | "MAKEDEPENDFLAGS=$(MAKEDEPENDFLAGS)" \ |
---|
1183 | all |
---|
1184 | |
---|
1185 | perl_clean: |
---|
1186 | @$(MAKE) -C PERL2ARB -r -f Makefile.main \ |
---|
1187 | "AUTODEPENDS=0" \ |
---|
1188 | "MACH=$(MACH)" \ |
---|
1189 | clean |
---|
1190 | |
---|
1191 | # ---------------------------------------- |
---|
1192 | |
---|
1193 | wc: |
---|
1194 | wc `find . -type f \( -name '*.[ch]' -o -name '*.[ch]xx' \) -print` |
---|
1195 | |
---|
1196 | # ---------------------------------------- cleaning |
---|
1197 | |
---|
1198 | rmbak: |
---|
1199 | find . \( -name '*%' -o -name '*.bak' -o -name 'core' \ |
---|
1200 | -o -name 'infile' -o -name treefile -o -name outfile \ |
---|
1201 | -o -name 'gde*_?' -o -name '*~' \) \ |
---|
1202 | -print -exec rm {} \; |
---|
1203 | |
---|
1204 | bclean: |
---|
1205 | @echo Cleaning bin directory |
---|
1206 | find bin -type l -exec rm {} \; |
---|
1207 | find bin -type f \! \( -name ".cvsignore" -o -name "Makefile" -o -path "bin/CVS*" \) -exec rm {} \; |
---|
1208 | cd bin;make all |
---|
1209 | |
---|
1210 | libclean: |
---|
1211 | rm -f `find . -type f \( -name '*.a' ! -type l \) -print` |
---|
1212 | |
---|
1213 | clean2: $(ARCHS:.a=.clean) \ |
---|
1214 | GDEHELP/GDEHELP.clean \ |
---|
1215 | HELP_SOURCE/HELP_SOURCE.clean \ |
---|
1216 | SOURCE_TOOLS/SOURCE_TOOLS.clean \ |
---|
1217 | bin/bin.clean \ |
---|
1218 | perl_clean |
---|
1219 | rm -f *.last_gcc |
---|
1220 | |
---|
1221 | # links are needed for cleanup |
---|
1222 | clean: links |
---|
1223 | $(MAKE) clean2 |
---|
1224 | |
---|
1225 | # ----------------------------------- |
---|
1226 | |
---|
1227 | rebuild: clean |
---|
1228 | $(MAKE) all |
---|
1229 | |
---|
1230 | relink: bclean libclean |
---|
1231 | $(MAKE) all |
---|
1232 | |
---|
1233 | savedepot: rmbak |
---|
1234 | util/arb_save_depot |
---|
1235 | |
---|
1236 | tarfile: rebuild |
---|
1237 | util/arb_compress |
---|
1238 | |
---|
1239 | tarfile_quick: all |
---|
1240 | util/arb_compress |
---|
1241 | |
---|
1242 | save: sourcetarfile |
---|
1243 | |
---|
1244 | # test early whether save will work |
---|
1245 | testsave: |
---|
1246 | @util/arb_srclst.pl >/dev/null |
---|
1247 | |
---|
1248 | sourcetarfile: rmbak |
---|
1249 | util/arb_save |
---|
1250 | |
---|
1251 | save2: rmbak |
---|
1252 | util/arb_save ignore |
---|
1253 | |
---|
1254 | release: |
---|
1255 | @echo Making release |
---|
1256 | @echo PATH=$(PATH) |
---|
1257 | @echo ARBHOME=$(ARBHOME) |
---|
1258 | -rm arb.tgz arbsrc.tgz |
---|
1259 | $(MAKE) testsave |
---|
1260 | $(MAKE) tarfile sourcetarfile |
---|
1261 | |
---|
1262 | release_quick: |
---|
1263 | -rm arb.tgz arbsrc.tgz |
---|
1264 | $(MAKE) tarfile_quick sourcetarfile |
---|
1265 | |
---|
1266 | # -------------------------------------------------------------------------------- |
---|
1267 | |
---|
1268 | # basic arb libraries |
---|
1269 | arbbasic: links preplib |
---|
1270 | $(MAKE) arbbasic2 |
---|
1271 | |
---|
1272 | arbbasic2: templ mbin com ${MAKE_RTC} sl $(GL) |
---|
1273 | |
---|
1274 | # shared arb libraries |
---|
1275 | arbshared: dball aw dp awt |
---|
1276 | |
---|
1277 | # needed arb applications |
---|
1278 | arbapplications: nt pa ed e4 we pt na al nal di ph ds trs pgt |
---|
1279 | |
---|
1280 | # optionally things (no real harm for ARB if any of them fails): |
---|
1281 | arbxtras: tg ps pc pst a3 |
---|
1282 | |
---|
1283 | tryxtras: |
---|
1284 | @echo $(SEP) |
---|
1285 | @( $(MAKE) arbxtras || ( \ |
---|
1286 | echo $(SEP) ;\ |
---|
1287 | echo "One of the optional tools failed to build (see error somewhere above)" ;\ |
---|
1288 | echo "ARB will work nevertheless!" ) ) |
---|
1289 | |
---|
1290 | arb: arbbasic |
---|
1291 | $(MAKE) arbshared arbapplications help |
---|
1292 | |
---|
1293 | all: checks |
---|
1294 | $(MAKE) links |
---|
1295 | $(MAKE) com |
---|
1296 | $(MAKE) arb |
---|
1297 | $(MAKE) libs |
---|
1298 | $(MAKE) convert tools gde readseq |
---|
1299 | $(MAKE) binlink |
---|
1300 | $(MAKE) perl |
---|
1301 | -$(MAKE) tryxtras |
---|
1302 | @echo $(SEP) |
---|
1303 | @echo "made 'all' with success." |
---|
1304 | @echo "to start arb enter 'arb'" |
---|
1305 | |
---|
1306 | # DO NOT DELETE |
---|