1 | |
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2 | Welcome to the 'ARB' Sequence Database Tools |
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3 | |
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4 | |
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5 | System Requirements |
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6 | ------------------- |
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7 | |
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8 | |
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9 | ARB is currently developed on Linux PCs only. |
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10 | |
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11 | Compiling ARB using the gcc compiler (versions 2.95.3, 3.x and 4.x series) |
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12 | as well works on Mac OSX and Sun OS - but we do not publish or support |
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13 | these versions. |
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14 | |
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15 | |
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16 | Hardware Requirements (Linux): |
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17 | |
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18 | Good We use |
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19 | Real memory : 1 Gb 4 Gb |
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20 | Free discspace : 1 Gb more |
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21 | Computer speed : 2 GHz Cpu 2 GHz Dual Cpu |
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22 | |
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23 | |
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24 | Note : Memory is more important than a fast processor! |
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25 | |
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26 | |
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27 | Files needed to install ARB |
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28 | --------------------------- |
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29 | |
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30 | File |
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31 | |
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32 | 'arb_install.sh' // install script |
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33 | 'arb.*.tgz' // ARB program |
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34 | |
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35 | |
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36 | Available ARB versions: |
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37 | |
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38 | 'arb.32.*.tgz' // 32 bit versions |
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39 | 'arb.64.*.tgz' // 64 bit versions |
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40 | |
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41 | 'arb.*.SuSE*.tgz // SuSE version |
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42 | 'arb.*.Ubuntu*.tgz // Ubuntu version (recommended) |
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43 | |
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44 | 'arb.*.OPENGL.tgz' // OPENGL version (contains RNA3D, a 3D-molecule-viewer) |
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45 | |
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46 | |
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47 | Choose a 32-bit-version, if your system is 32-bit, |
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48 | choose a 64-bit-version, if your system is 64-bit. |
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49 | |
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50 | Normally one of the Ubuntu versions should work for you, only |
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51 | use one of the SuSE versions, if the Ubuntu version has problems |
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52 | (e.g. does not display group names in ARB_EDIT4). |
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53 | |
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54 | |
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55 | Install/Update ARB |
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56 | ------------------ |
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57 | |
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58 | ARB consists of more than 1200 files which are installed into a single |
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59 | directory. Creating this directory, copying all data into it, and setting |
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60 | the permissions correctly is done by the installation script |
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61 | |
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62 | 'arb_install.sh' |
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63 | |
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64 | Goto the directory, where the files |
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65 | |
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66 | 'arb_install.sh' // install script |
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67 | 'arb_README.txt' // this file |
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68 | 'arb.*.tgz' // ARB binaries |
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69 | |
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70 | are located and type |
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71 | |
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72 | '/bin/sh arb_install.sh' |
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73 | |
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74 | Answer all questions asked by the script. |
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75 | |
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76 | Notes:- The script will ask about a pt_server directory. This is a |
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77 | directory where arb will store big index files. |
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78 | You should enter a different path as you do not want to |
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79 | recreate those files after an ARB update. |
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80 | - Normally pressing enter will be a good choice. |
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81 | - You can rerun the script many times, it can be used to |
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82 | change an existing installation. |
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83 | |
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84 | Change your .cshrc/.profile files: |
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85 | |
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86 | Set the environment variable ARBHOME |
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87 | to the ARB installation directory |
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88 | Append $ARBHOME/bin to your PATH |
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89 | |
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90 | reread it, (logout+login ) |
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91 | |
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92 | goto a directory with a demo database 'eg demo.arb' |
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93 | and start 'ARB' with |
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94 | |
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95 | 'arb' |
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96 | |
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97 | |
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98 | Additional information |
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99 | ---------------------- |
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100 | |
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101 | * See arb_INSTALL.txt for additional software needed and/or useful |
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102 | together with ARB. |
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103 | |
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104 | |
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105 | PT_server |
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106 | --------- |
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107 | |
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108 | To Install 'ARB' you have to know that some modules use a so |
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109 | called 'pt_server' (prefix tree server). |
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110 | |
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111 | ARB needs a writeable directory to store the pt_server files. |
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112 | Those files are needed for fast database search |
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113 | (by probe_design, probe_match and the automatic aligner) |
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114 | and need a lot of disc space (up to several 100 mega bytes, |
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115 | e.g. 4000 16S RNA sequences require about 40 MB). |
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116 | This files are not created now. They can be build by any user via |
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117 | <ARB_NTREE/Probes/PT_SERVER admin/Build server> |
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118 | You may define a special directory as the pt_server files location. |
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119 | This prevents any loss of data installing a new version of |
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120 | ARB. |
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121 | To minimize the use of ressources in a workstation cluster |
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122 | only one pt_server for each database is started on a user defined |
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123 | host. The first user starts the pt_server, and all other users |
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124 | can connect to it. |
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125 | |
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126 | |
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127 | What you should know: Swap |
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128 | -------------------------- |
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129 | |
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130 | Arb needs a lot of virtual memory |
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131 | (about 50 Mbyte for 5000 Sequences, Length = 3000). |
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132 | You can find out about installed swap space by typing: |
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133 | |
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134 | Linux 'top' |
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135 | SunOS 1.x: 'pstat -s' |
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136 | System V / SGI 'swap -s' |
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137 | OSF 'swapon -sv' |
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138 | |
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139 | Call your system administrator or local guru to increase your |
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140 | swap. (If you don't have such a nice person, try to read the |
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141 | man pages: 'man -k swap') |
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142 | |
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143 | |
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144 | The Database |
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145 | ------------ |
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146 | |
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147 | In the current release a small dataset (demo.arb) is provided. |
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148 | This database contains a selection of artificial and real-life |
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149 | sequences. |
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150 | |
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151 | The intention of providing this small dataset first is to give |
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152 | you the opportunity to get familiar with the program and to |
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153 | test the performance of your computer system as well as the |
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154 | stability of ARB on your system. |
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155 | |
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156 | |
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157 | Bugs |
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158 | ---- |
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159 | |
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160 | ARB is running properly and stably on our systems. However, it |
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161 | may be that there are bugs never detected by us or never |
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162 | appearing on our systems. Please don't hesitate to inform us |
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163 | about any bugs. A detailed description of the steps performed |
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164 | before the problem was evident and of the number and types of |
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165 | modules running at the same time would be extremely helpful to |
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166 | our computer scientists. |
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167 | |
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168 | Please report bugs into our bug tracker at |
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169 | http://bugs.arb-home.de/ |
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170 | |
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171 | |
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172 | Support |
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173 | ------- |
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174 | |
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175 | Please send any comments, bug reports or questions to |
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176 | |
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177 | arb@arb-home.de |
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178 | |
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179 | |
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180 | Copyright Notice |
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181 | ---------------- |
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182 | |
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183 | Please see the file |
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184 | |
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185 | arb_LICENSE.txt |
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186 | |
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187 | in the ARB installation directory. |
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188 | |
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189 | |
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190 | Disclaimer |
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191 | ---------- |
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192 | |
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193 | THE AUTHORS OF ARB GIVE NO WARRANTIES, EXPRESSED OR IMPLIED |
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194 | FOR THE SOFTWARE AND DOCUMENTATION PROVIDED, INCLUDING, BUT |
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195 | NOT LIMITED TO WARRANTY OF MERCHANTABILITY AND WARRANTY OF |
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196 | FITNESS FOR A PARTICULAR PURPOSE. |
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197 | |
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198 | |
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199 | Have fun! |
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200 | |
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201 | |
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