Mercurial > repos > iuc > package_r_3_2_0

annotate tool_dependencies.xml @ 5:d973c8e9b29e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2-dirty
author iuc
date Sun, 26 Jul 2015 16:02:05 -0400
parents be3f2a89a9fc
children 11baf5863be2
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0
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
iuc
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1 <?xml version="1.0"?>
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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2 <tool_dependency>
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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3 <package name="R" version="3.2.0">
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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4 <install version="1.0">
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5 <actions_group>
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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6 <actions architecture="x86_64" os="linux">
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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7 <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.2.0-Linux-x86_64.tar.gz</action>
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
iuc
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8 <action type="move_directory_files">
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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9 <source_directory>.</source_directory>
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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10 <destination_directory>$INSTALL_DIR</destination_directory>
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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11 </action>
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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12 <action type="set_environment">
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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13 <environment_variable action="set_to" name="TCL_LIBRARY">$INSTALL_DIR/lib/libtcl8.4.so</environment_variable>
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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14 <environment_variable action="set_to" name="TK_LIBRARY">$INSTALL_DIR/lib/libtk8.4.so</environment_variable>
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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15 </action>
5
d973c8e9b29e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2-dirty
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16 <action type="shell_command"><![CDATA[
d973c8e9b29e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2-dirty
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17 command -v gfortran || return 0
d973c8e9b29e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2-dirty
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18 BUNDLED_LGF_CANON=$INSTALL_DIR/lib/libgfortran.so.3.0.0 &&
d973c8e9b29e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2-dirty
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19 BUNDLED_LGF_VERS=`objdump -p $BUNDLED_LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1` &&
d973c8e9b29e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2-dirty
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20 echo 'program test; end program test' > test.f90 &&
d973c8e9b29e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2-dirty
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21 gfortran -o test test.f90 &&
d973c8e9b29e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2-dirty
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22 LGF=`ldd test | grep libgfortran | awk '{print $3}'` &&
d973c8e9b29e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2-dirty
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23 LGF_CANON=`readlink -f $LGF` &&
d973c8e9b29e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2-dirty
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24 LGF_VERS=`objdump -p $LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1` &&
d973c8e9b29e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2-dirty
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25 if [ $LGF_VERS -gt $BUNDLED_LGF_VERS ]; then
d973c8e9b29e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2-dirty
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26 cp -p $BUNDLED_LGF_CANON ${BUNDLED_LGF_CANON}.bundled &&
d973c8e9b29e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2-dirty
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27 cp -p $LGF_CANON $BUNDLED_LGF_CANON
d973c8e9b29e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2-dirty
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28 fi
d973c8e9b29e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2-dirty
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29 ]]></action>
0
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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30 </actions>
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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31 <actions architecture="x86_64" os="darwin">
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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32 <action type="download_by_url">https://cran.rstudio.com/src/base/R-3/R-3.2.0.tar.gz</action>
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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33
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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34 <package name="readline" version="6.2">
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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35 <repository name="package_readline_6_2" owner="iuc" prior_installation_required="True" />
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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36 </package>
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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37 <package name="libpng" version="1.6.7">
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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38 <repository name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" />
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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39 </package>
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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40 <package name="cairo" version="1.12.14">
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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41 <repository name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" />
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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42 </package>
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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43 <package name="pixman" version="0.32.4">
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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44 <repository name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" />
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45 </package>
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46 <package name="freetype" version="2.5.2">
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47 <repository name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" />
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48 </package>
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49 <package name="ncurses" version="5.9">
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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50 <repository name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" />
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51 </package>
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52
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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53 <action type="set_environment_for_install">
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54 <repository name="package_readline_6_2" owner="iuc" prior_installation_required="True" >
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55 <package name="readline" version="6.2" />
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56 </repository>
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57 <repository name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" >
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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58 <package name="libpng" version="1.6.7" />
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59 </repository>
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60 <repository name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" >
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61 <package name="cairo" version="1.12.14" />
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62 </repository>
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63 <repository name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" >
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64 <package name="pixman" version="0.32.4" />
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65 </repository>
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66 <repository name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" >
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67 <package name="freetype" version="2.5.2" />
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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68 </repository>
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69 <repository name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" >
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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70 <package name="ncurses" version="5.9" />
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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71 </repository>
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72 </action>
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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73 <action type="shell_command"><![CDATA[
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74 export LDFLAGS="-L$PNG_LIBS -L$NCURSES_LIB_PATH -L$READLINE_LIB_PATH" &&
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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75 export LDFLAGS="$LDFLAGS -Wl,-rpath,$NCURSES_LIB_PATH" &&
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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76 export LDFLAGS="$LDFLAGS -Wl,-rpath,$READLINE_LIB_PATH" &&
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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77 export LDFLAGS="$LDFLAGS -Wl,-rpath,$PIXMAN_LIB_PATH" &&
b689e15fa6fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit ec34b8cb4b41c0aa114475c262100409236d2bf2
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78 export LDFLAGS="$LDFLAGS -Wl,-rpath,$PNG_LIB_PATH" &&
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79 export LDFLAGS="$LDFLAGS -Wl,-rpath,$FREETYPE_LIB_PATH" &&
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80 export CFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH" &&
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81 export CXXFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH" &&
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82 export CPPFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH" &&
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83 ./configure --with-tcltk \
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84 --with-blas \
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85 --with-lapack \
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86 --with-readline \
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87 --with-cairo \
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88 --with-libpng \
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89 --without-x \
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90 --enable-R-shlib \
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91 --disable-R-framework \
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92 --libdir=$INSTALL_DIR/lib \
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93 --prefix=$INSTALL_DIR
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94 ]]></action>
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95 <action type="make_install" />
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96 <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action>
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97 <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action>
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98 </actions>
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99 <action type="set_environment">
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100 <environment_variable action="set_to" name="R_DOC_DIR">$INSTALL_DIR/lib/R/doc</environment_variable>
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101 <environment_variable action="set_to" name="R_HOME_DIR">$INSTALL_DIR/lib/R</environment_variable>
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102 <environment_variable action="set_to" name="R_INCLUDE_DIR">$INSTALL_DIR/lib/R/include</environment_variable>
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103 <environment_variable action="set_to" name="R_SHARE_DIR">$INSTALL_DIR/lib/R/share</environment_variable>
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104 <environment_variable action="set_to" name="R_ROOT_DIR">$INSTALL_DIR</environment_variable>
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105 <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
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106 <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable>
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107 <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
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108 <environment_variable action="set_to" name="PKG_CONFIG_DIR">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>
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109 <environment_variable action="set_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>
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110 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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111 </action>
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112 </actions_group>
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113 </install>
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114 <readme>
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115 R is a free software environment for statistical computing and graphics.
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116 NOTE: See custom compilation options above.
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117 </readme>
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118 </package>
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119 </tool_dependency>