Mercurial > repos > iuc > package_r_3_1_2

annotate tool_dependencies.xml @ 3:68077fb03d75 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_2 commit bd736b6361ba659a1251dd1a1a05f7e3b633bdf5
author iuc
date Tue, 22 Dec 2015 19:34:39 -0500
parents 41f43a2064ba
children 73cd1d529330
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="R" version="3.1.2">
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4 <install version="1.0">
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5 <actions_group>
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6 <actions architecture="x86_64" os="linux">
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7 <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.1.2-Linux-x84_64.tgz</action>
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8 <action type="move_directory_files">
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9 <source_directory>.</source_directory>
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10 <destination_directory>$INSTALL_DIR</destination_directory>
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11 </action>
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12 <action type="set_environment">
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13 <environment_variable action="set_to" name="TCL_LIBRARY">$INSTALL_DIR/lib/libtcl8.4.so</environment_variable>
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14 <environment_variable action="set_to" name="TK_LIBRARY">$INSTALL_DIR/lib/libtk8.4.so</environment_variable>
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15 </action>
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16 </actions>
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17 <actions architecture="x86_64" os="darwin">
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18 <action type="download_by_url">http://cran.rstudio.com/src/base/R-3/R-3.1.2.tar.gz</action>
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19 <package name="readline" version="6.2">
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20 <repository changeset_revision="618c94461551" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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21 </package>
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22 <package name="libpng" version="1.6.7">
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23 <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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24 </package>
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25 <package name="cairo" version="1.12.14">
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26 <repository changeset_revision="8f011e7388e1" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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27 </package>
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28 <package name="pixman" version="0.32.4">
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29 <repository changeset_revision="bcf53d429118" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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30 </package>
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31 <package name="freetype" version="2.5.2">
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32 <repository changeset_revision="34ebf47e4941" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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33 </package>
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34 <package name="ncurses" version="5.9">
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35 <repository changeset_revision="d14cd2be7d8d" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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36 </package>
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37 <action type="set_environment_for_install">
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38 <repository changeset_revision="618c94461551" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
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39 <package name="readline" version="6.2" />
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40 </repository>
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41 <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
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42 <package name="libpng" version="1.6.7" />
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43 </repository>
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44 <repository changeset_revision="8f011e7388e1" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
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45 <package name="cairo" version="1.12.14" />
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46 </repository>
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47 <repository changeset_revision="bcf53d429118" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
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48 <package name="pixman" version="0.32.4" />
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49 </repository>
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50 <repository changeset_revision="34ebf47e4941" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
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51 <package name="freetype" version="2.5.2" />
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52 </repository>
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53 <repository changeset_revision="d14cd2be7d8d" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
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54 <package name="ncurses" version="5.9" />
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55 </repository>
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56 </action>
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57 <action type="shell_command">
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58 export LDFLAGS="-L$PNG_LIBS -L$NCURSES_LIB_PATH -L$READLINE_LIB_PATH" &amp;&amp;
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59 export LDFLAGS="$LDFLAGS -Wl,-rpath,$NCURSES_LIB_PATH" &amp;&amp;
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60 export LDFLAGS="$LDFLAGS -Wl,-rpath,$READLINE_LIB_PATH" &amp;&amp;
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61 export LDFLAGS="$LDFLAGS -Wl,-rpath,$PIXMAN_LIB_PATH" &amp;&amp;
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62 export LDFLAGS="$LDFLAGS -Wl,-rpath,$PNG_LIB_PATH" &amp;&amp;
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63 export LDFLAGS="$LDFLAGS -Wl,-rpath,$FREETYPE_LIB_PATH" &amp;&amp;
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64 export CFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH" &amp;&amp;
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65 export CXXFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH" &amp;&amp;
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66 export CPPFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH" &amp;&amp;
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67 ./configure --with-tcltk \
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68 --with-blas \
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69 --with-lapack \
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70 --with-readline \
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71 --with-cairo \
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72 --with-libpng \
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73 --without-x \
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74 --enable-R-shlib \
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75 --disable-R-framework \
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76 --libdir=$INSTALL_DIR/lib \
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77 --prefix=$INSTALL_DIR
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78 </action>
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79 <action type="make_install" />
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80 <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action>
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81 <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action>
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82 </actions>
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83 <action type="set_environment">
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84 <environment_variable action="set_to" name="R_DOC_DIR">$INSTALL_DIR/lib/R/doc</environment_variable>
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85 <environment_variable action="set_to" name="R_HOME_DIR">$INSTALL_DIR/lib/R</environment_variable>
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86 <environment_variable action="set_to" name="R_INCLUDE_DIR">$INSTALL_DIR/lib/R/include</environment_variable>
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87 <environment_variable action="set_to" name="R_SHARE_DIR">$INSTALL_DIR/lib/R/share</environment_variable>
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88 <environment_variable action="set_to" name="R_ROOT_DIR">$INSTALL_DIR</environment_variable>
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89 <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
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90 <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable>
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91 <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
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92 <environment_variable action="set_to" name="PKG_CONFIG_DIR">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>
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93 <environment_variable action="set_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>
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94 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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95 </action>
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96 </actions_group>
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97 </install>
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98 <readme>
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99 The precompiled versions of this package were built 2014-12-21.
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100 R is a free software environment for statistical computing and graphics.
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101 NOTE: See custom compilation options above.
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102 </readme>
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103 </package>
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104 </tool_dependency>