Mercurial > repos > iuc > package_r_3_1_0

annotate tool_dependencies.xml @ 0:39c1607cec88 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
author iuc
date Tue, 19 May 2015 15:01:08 -0400
parents
children 50d55f57638e
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0
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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diff changeset
2 <tool_dependency>
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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3 <package name="R" version="3.1.0">
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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4 <install version="1.0">
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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diff changeset
5 <actions_group>
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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diff changeset
6 <actions architecture="x86_64" os="darwin">
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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7 <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/R/R-3.1.0-Darwin-x86_64.tgz</action>
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
8 <action type="move_directory_files">
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
9 <source_directory>.</source_directory>
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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10 <destination_directory>$INSTALL_DIR</destination_directory>
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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diff changeset
11 </action>
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
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12 <action type="shell_command">sh $INSTALL_DIR/darwin_post_install.sh $INSTALL_DIR</action>
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
13 </actions>
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
14 <actions architecture="x86_64" os="linux">
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
15 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/R/R-3.1.0-Linux-x86_64.tgz</action>
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
16 <action type="move_directory_files">
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
17 <source_directory>.</source_directory>
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
18 <destination_directory>$INSTALL_DIR</destination_directory>
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
19 </action>
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
20 <action type="set_environment">
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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21 <environment_variable action="set_to" name="TCL_LIBRARY">$INSTALL_DIR/lib/libtcl8.4.so</environment_variable>
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
22 <environment_variable action="set_to" name="TK_LIBRARY">$INSTALL_DIR/lib/libtk8.4.so</environment_variable>
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
23 </action>
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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24 </actions>
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
25 <actions>
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
26 <package name="readline" version="6.2">
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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27 <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
28 </package>
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
29 <package name="libpng" version="1.6.7">
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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30 <repository changeset_revision="db14a391648d" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
31 </package>
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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32 <package name="cairo" version="1.12.14">
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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33 <repository changeset_revision="b39299b4b6e1" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
34 </package>
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
35 <package name="pixman" version="0.32.4">
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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36 <repository changeset_revision="3d44a209a6b9" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
37 </package>
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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38 <package name="freetype" version="2.5.2">
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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39 <repository changeset_revision="58782940c411" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
40 </package>
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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41 <action type="download_by_url">http://cran.rstudio.com/src/base/R-3/R-3.1.0.tar.gz</action>
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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42 <action type="set_environment_for_install">
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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43 <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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44 <package name="readline" version="6.2" />
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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45 </repository>
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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46 <repository changeset_revision="db14a391648d" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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47 <package name="libpng" version="1.6.7" />
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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48 </repository>
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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49 <repository changeset_revision="b39299b4b6e1" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
50 <package name="cairo" version="1.12.14" />
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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51 </repository>
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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52 <repository changeset_revision="3d44a209a6b9" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
53 <package name="pixman" version="0.32.4" />
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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54 </repository>
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
55 <repository changeset_revision="58782940c411" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
diff changeset
56 <package name="freetype" version="2.5.2" />
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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57 </repository>
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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58 </action>
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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59 <action type="shell_command">
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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60 export LDFLAGS="-L$PNG_LIBS -L$READLINE_LIB_PATH" &amp;&amp;
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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61 export LDFLAGS="$LDFLAGS -Wl,-rpath,$READLINE_LIB_PATH" &amp;&amp;
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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62 export LDFLAGS="$LDFLAGS -Wl,-rpath,$PIXMAN_LIB_PATH" &amp;&amp;
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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63 export LDFLAGS="$LDFLAGS -Wl,-rpath,$PNG_LIB_PATH" &amp;&amp;
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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64 export LDFLAGS="$LDFLAGS -Wl,-rpath,$FREETYPE_LIB_PATH" &amp;&amp;
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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65 export CFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" &amp;&amp;
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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66 export CXXFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" &amp;&amp;
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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67 export CPPFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" &amp;&amp;
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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68 ./configure --with-tcltk \
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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69 --with-blas \
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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70 --with-lapack \
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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71 --with-readline \
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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72 --with-cairo \
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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73 --with-libpng \
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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74 --without-x \
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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75 --enable-R-shlib \
39c1607cec88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
iuc
parents:
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76 --disable-R-framework \
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77 --libdir=$INSTALL_DIR/lib \
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78 --prefix=$INSTALL_DIR
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79 </action>
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80 <action type="make_install" />
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81 <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action>
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82 <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action>
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83 </actions>
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84 <action type="set_environment">
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85 <environment_variable action="set_to" name="R_DOC_DIR">$INSTALL_DIR/lib/R/doc</environment_variable>
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86 <environment_variable action="set_to" name="R_HOME_DIR">$INSTALL_DIR/lib/R</environment_variable>
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87 <environment_variable action="set_to" name="R_INCLUDE_DIR">$INSTALL_DIR/lib/R/include</environment_variable>
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88 <environment_variable action="set_to" name="R_SHARE_DIR">$INSTALL_DIR/lib/R/share</environment_variable>
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89 <environment_variable action="set_to" name="R_ROOT_DIR">$INSTALL_DIR</environment_variable>
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90 <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
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91 <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable>
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92 <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
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93 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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94 </action>
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95 </actions_group>
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96 </install>
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97 <readme>
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98 The precompiled versions of this package were built 2014-07-21.
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99 R is a free software environment for statistical computing and graphics.
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100 NOTE: See custom compilation options above.
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101 </readme>
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102 </package>
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103 </tool_dependency>