Mercurial > repos > iuc > package_r_3_2_1

annotate tool_dependencies.xml @ 4:e36e1db5e729 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit c5b99dd9482d52035bbfec5ac717f60ef968e989-dirty
author iuc
date Sat, 10 Oct 2015 08:20:29 -0400
parents 798497c71146
children 9bf8af8b27e8
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3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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1 <?xml version="1.0"?>
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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2 <tool_dependency>
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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3 <package name="R" version="3.2.1">
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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4 <install version="1.0">
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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5 <actions_group>
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
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6 <actions architecture="x86_64" os="linux">
1
bbbf393f5300 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 14be1b424bf939451dd8c4706b14a7cac6941165
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7 <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.2.1-Linux-x86_64.tar.gz</action>
0
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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8 <action type="move_directory_files">
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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9 <source_directory>.</source_directory>
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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10 <destination_directory>$INSTALL_DIR</destination_directory>
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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11 </action>
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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12 <action type="set_environment">
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
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13 <environment_variable action="set_to" name="TCL_LIBRARY">$INSTALL_DIR/lib/libtcl8.4.so</environment_variable>
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
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14 <environment_variable action="set_to" name="TK_LIBRARY">$INSTALL_DIR/lib/libtk8.4.so</environment_variable>
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
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15 </action>
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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16 </actions>
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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17 <actions>
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
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18 <action type="download_by_url">http://cran.rstudio.com/src/base/R-3/R-3.2.1.tar.gz</action>
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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19 <package name="atlas" version="3.10.2">
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
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20 <repository changeset_revision="86b7c19454fa" name="package_atlas_3_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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21 </package>
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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22 <package name="readline" version="6.3">
3
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23 <repository changeset_revision="caf1e20aac98" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
0
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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24 </package>
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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25 <package name="libpng" version="1.6.7">
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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26 <repository changeset_revision="ac6ef08bf0e6" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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27 </package>
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
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28 <package name="cairo" version="1.12.14">
4
e36e1db5e729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit c5b99dd9482d52035bbfec5ac717f60ef968e989-dirty
iuc
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29 <repository changeset_revision="8181dc284f85" name="package_cairo_1_12_14" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
0
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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30 </package>
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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31 <package name="pixman" version="0.32.6">
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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32 <repository changeset_revision="2db67636b074" name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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33 </package>
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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34 <package name="freetype" version="2.5.2">
4
e36e1db5e729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit c5b99dd9482d52035bbfec5ac717f60ef968e989-dirty
iuc
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35 <repository changeset_revision="2460955a5704" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
0
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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36 </package>
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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37 <package name="ncurses" version="6.0">
3
798497c71146 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
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38 <repository changeset_revision="7fae9c4b2d10" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
0
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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39 </package>
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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40 <package name="fontconfig" version="2.11.1">
4
e36e1db5e729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit c5b99dd9482d52035bbfec5ac717f60ef968e989-dirty
iuc
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41 <repository changeset_revision="204a8c713d82" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
0
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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42 </package>
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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43 <action type="set_environment_for_install">
3
798497c71146 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
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44 <repository changeset_revision="caf1e20aac98" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
0
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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45 <package name="readline" version="6.3" />
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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46 </repository>
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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47 <repository changeset_revision="ac6ef08bf0e6" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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48 <package name="libpng" version="1.6.7" />
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
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49 </repository>
4
e36e1db5e729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit c5b99dd9482d52035bbfec5ac717f60ef968e989-dirty
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50 <repository changeset_revision="8181dc284f85" name="package_cairo_1_12_14" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
0
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
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51 <package name="cairo" version="1.12.14" />
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
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52 </repository>
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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53 <repository changeset_revision="2db67636b074" name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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54 <package name="pixman" version="0.32.6" />
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
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55 </repository>
4
e36e1db5e729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit c5b99dd9482d52035bbfec5ac717f60ef968e989-dirty
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56 <repository changeset_revision="2460955a5704" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
0
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
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57 <package name="freetype" version="2.5.2" />
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
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58 </repository>
3
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59 <repository changeset_revision="7fae9c4b2d10" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
0
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
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60 <package name="ncurses" version="6.0" />
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
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61 </repository>
4
e36e1db5e729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit c5b99dd9482d52035bbfec5ac717f60ef968e989-dirty
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62 <repository changeset_revision="204a8c713d82" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
0
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
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63 <package name="fontconfig" version="2.11.1" />
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
iuc
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64 </repository>
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
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65 </action>
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
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66 <action type="shell_command">
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
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67 export LDFLAGS="-L$LIBPNG_LIB_PATH -L$PNG_LIBS -L$NCURSES_LIB_PATH -L$READLINE_LIB_PATH" &amp;&amp;
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
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68 export LDFLAGS="$LDFLAGS -Wl,-rpath,$NCURSES_LIB_PATH" &amp;&amp;
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
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69 export LDFLAGS="$LDFLAGS -Wl,-rpath,$READLINE_LIB_PATH" &amp;&amp;
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
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70 export LDFLAGS="$LDFLAGS -Wl,-rpath,$PIXMAN_LIB_PATH" &amp;&amp;
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
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71 export LDFLAGS="$LDFLAGS -Wl,-rpath,$LIBPNG_LIB_PATH" &amp;&amp;
3d28600fc82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1cd98503d73171f005e88d60a8e3d7d319fc914d
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72 export LDFLAGS="$LDFLAGS -Wl,-rpath,$FREETYPE_LIB_PATH" &amp;&amp;
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73 export LDFLAGS="$LDFLAGS -Wl,-rpath,$FONTCONFIG_LIB_PATH" &amp;&amp;
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74 export LDFLAGS="$LDFLAGS -Wl,-rpath,$CAIRO_LIB_PATH" &amp;&amp;
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75 export CFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH -I$LIBPNG_INCLUDE_PATH -I$FONTCONFIG_INCLUDE_PATH -I$CAIRO_INCLUDE_PATH" &amp;&amp;
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76 export CXXFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH -I$LIBPNG_INCLUDE_PATH -I$FONTCONFIG_INCLUDE_PATH -I$CAIRO_INCLUDE_PATH" &amp;&amp;
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77 export CPPFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH -I$LIBPNG_INCLUDE_PATH -I$FONTCONFIG_INCLUDE_PATH -I$CAIRO_INCLUDE_PATH" &amp;&amp;
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78 ./configure --with-tcltk \
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79 --with-blas \
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80 --with-lapack \
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81 --with-readline \
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82 --with-cairo \
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83 --with-libpng \
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84 --without-x \
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85 --enable-R-shlib \
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86 --disable-R-framework \
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87 --libdir=$INSTALL_DIR/lib \
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88 --prefix=$INSTALL_DIR
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89 </action>
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90 <action type="make_install" />
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91 <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action>
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92 <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action>
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93 </actions>
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94 <action type="set_environment">
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95 <environment_variable action="set_to" name="R_DOC_DIR">$INSTALL_DIR/lib/R/doc</environment_variable>
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96 <environment_variable action="set_to" name="R_HOME_DIR">$INSTALL_DIR/lib/R</environment_variable>
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97 <environment_variable action="set_to" name="R_INCLUDE_DIR">$INSTALL_DIR/lib/R/include</environment_variable>
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98 <environment_variable action="set_to" name="R_SHARE_DIR">$INSTALL_DIR/lib/R/share</environment_variable>
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99 <environment_variable action="set_to" name="R_ROOT_DIR">$INSTALL_DIR</environment_variable>
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100 <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
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101 <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable>
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102 <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
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103 <environment_variable action="prepend_to" name="PKG_CONFIG_DIR">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>
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104 <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>
0
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105 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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106 </action>
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107 </actions_group>
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108 </install>
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109 <readme>
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110 The precompiled versions of this package were built 2015-07-27.
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111 R is a free software environment for statistical computing and graphics.
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112 NOTE: See custom compilation options above.
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113 </readme>
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114 </package>
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115 </tool_dependency>