Mercurial > repos > mvdbeek > package_r_3_2_2

annotate tool_dependencies.xml @ 7:883acf7a3ddb draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit d8c9384565aa9b4beaeb04348d41cb4c95547b92-dirty
author mvdbeek
date Fri, 09 Oct 2015 06:36:45 -0400
parents f79ac4050af2
children
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a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
mvdbeek
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1 <?xml version="1.0"?>
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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2 <tool_dependency>
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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3 <package name="R" version="3.2.2">
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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4 <install version="1.0">
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5 <actions_group>
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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6 <!--
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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7 <actions architecture="x86_64" os="linux">
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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8 <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.2.1-Linux-x86_64.tar.gz</action>
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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9 <action type="move_directory_files">
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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10 <source_directory>.</source_directory>
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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11 <destination_directory>$INSTALL_DIR</destination_directory>
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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12 </action>
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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13 <action type="set_environment">
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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14 <environment_variable action="set_to" name="TCL_LIBRARY">$INSTALL_DIR/lib/libtcl8.4.so</environment_variable>
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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15 <environment_variable action="set_to" name="TK_LIBRARY">$INSTALL_DIR/lib/libtk8.4.so</environment_variable>
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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16 </action>
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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17 </actions>
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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18 -->
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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19 <actions>
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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20 <action type="download_by_url">http://cran.rstudio.com/src/base/R-3/R-3.2.2.tar.gz</action>
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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21 <package name="atlas" version="3.10.2">
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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22 <repository changeset_revision="86b7c19454fa" name="package_atlas_3_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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23 </package>
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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24 <package name="readline" version="6.3">
5
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25 <repository changeset_revision="caf1e20aac98" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
0
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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26 </package>
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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27 <package name="libpng" version="1.6.7">
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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28 <repository changeset_revision="ac6ef08bf0e6" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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29 </package>
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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30 <package name="pixman" version="0.32.6">
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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31 <repository changeset_revision="2db67636b074" name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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32 </package>
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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33 <package name="freetype" version="2.5.2">
7
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34 <repository changeset_revision="d39e2eb401ec" name="package_freetype_2_5_2" owner="mvdbeek" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
0
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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35 </package>
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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36 <package name="ncurses" version="6.0">
5
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37 <repository changeset_revision="7fae9c4b2d10" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
0
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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38 </package>
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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39 <package name="fontconfig" version="2.11.1">
7
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40 <repository changeset_revision="922099dd5efa" name="package_fontconfig_2_11_1" owner="mvdbeek" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
0
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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41 </package>
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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42 <action type="set_environment_for_install">
5
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43 <repository changeset_revision="caf1e20aac98" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
0
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44 <package name="readline" version="6.3" />
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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45 </repository>
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46 <repository changeset_revision="ac6ef08bf0e6" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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47 <package name="libpng" version="1.6.7" />
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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48 </repository>
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49 <repository changeset_revision="2db67636b074" name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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50 <package name="pixman" version="0.32.6" />
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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51 </repository>
7
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52 <repository changeset_revision="d39e2eb401ec" name="package_freetype_2_5_2" owner="mvdbeek" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
0
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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53 <package name="freetype" version="2.5.2" />
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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54 </repository>
5
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55 <repository changeset_revision="7fae9c4b2d10" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
0
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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56 <package name="ncurses" version="6.0" />
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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57 </repository>
7
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58 <repository changeset_revision="922099dd5efa" name="package_fontconfig_2_11_1" owner="mvdbeek" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
0
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59 <package name="fontconfig" version="2.11.1" />
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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60 </repository>
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61 </action>
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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62 <action type="shell_command">
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63 export LDFLAGS="-L$LIBPNG_LIB_PATH -L$NCURSES_LIB_PATH -L$READLINE_LIB_PATH" &amp;&amp;
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64 export LDFLAGS="$LDFLAGS -Wl,-rpath,$NCURSES_LIB_PATH" &amp;&amp;
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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65 export LDFLAGS="$LDFLAGS -Wl,-rpath,$READLINE_LIB_PATH" &amp;&amp;
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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66 export LDFLAGS="$LDFLAGS -Wl,-rpath,$PIXMAN_LIB_PATH" &amp;&amp;
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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67 export LDFLAGS="$LDFLAGS -Wl,-rpath,$LIBPNG_LIB_PATH" &amp;&amp;
a8d93b065b4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_2 commit b07fb0cfe8300ce810ba76417deeda88680e828f-dirty
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68 export LDFLAGS="$LDFLAGS -Wl,-rpath,$FREETYPE_LIB_PATH" &amp;&amp;
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69 export LDFLAGS="$LDFLAGS -Wl,-rpath,$FONTCONFIG_ROOT_PATH" &amp;&amp;
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70 export CFLAGS="-I$PNG_INCLUDES -I$C_INCLUDE_PATH -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH -I$LIBPNG_INCLUDE_PATH -I$FONTCONFIG_ROOT_PATH" &amp;&amp;
2
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71 export CXXFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH -I$LIBPNG_INCLUDE_PATH -I$FONTCONFIG_ROOT_PATH" &amp;&amp;
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72 export CPPFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH -I$LIBPNG_INCLUDE_PATH -I$FONTCONFIG_ROOT_PATH" &amp;&amp;
0
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73 ./configure --with-tcltk \
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74 --with-blas \
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75 --with-lapack \
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76 --with-readline \
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77 --with-libpng \
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78 --without-x \
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79 --enable-R-shlib \
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80 --disable-R-framework \
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81 --libdir=$INSTALL_DIR/lib \
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82 --prefix=$INSTALL_DIR
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83 </action>
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84 <action type="make_install" />
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85 <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action>
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86 <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action>
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87 </actions>
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88 <action type="set_environment">
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89 <environment_variable action="set_to" name="R_DOC_DIR">$INSTALL_DIR/lib/R/doc</environment_variable>
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90 <environment_variable action="set_to" name="R_HOME_DIR">$INSTALL_DIR/lib/R</environment_variable>
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91 <environment_variable action="set_to" name="R_INCLUDE_DIR">$INSTALL_DIR/lib/R/include</environment_variable>
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92 <environment_variable action="set_to" name="R_SHARE_DIR">$INSTALL_DIR/lib/R/share</environment_variable>
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93 <environment_variable action="set_to" name="R_ROOT_DIR">$INSTALL_DIR</environment_variable>
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94 <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
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95 <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable>
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96 <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
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97 <environment_variable action="prepend_to" name="PKG_CONFIG_DIR">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>
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98 <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>
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99 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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100 </action>
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101 </actions_group>
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102 </install>
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103 <readme>
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104 The precompiled versions of this package were built 2015-07-27.
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105 R is a free software environment for statistical computing and graphics.
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106 NOTE: See custom compilation options above.
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107 </readme>
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108 </package>
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109 </tool_dependency>