Mercurial > repos > iuc > package_r_3_1_1
diff tool_dependencies.xml @ 3:e2fb38782bf5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_1 commit 630c0f1ac3419322998d92a1653f260c664283ab
| author | iuc |
|---|---|
| date | Mon, 04 Jan 2016 05:40:06 -0500 |
| parents | 9688b7af58d0 |
| children | a3a99aa3ce01 |
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--- a/tool_dependencies.xml Tue Dec 22 19:34:32 2015 -0500 +++ b/tool_dependencies.xml Mon Jan 04 05:40:06 2016 -0500 @@ -1,71 +1,50 @@ <?xml version="1.0"?> <tool_dependency> + <package name="readline" version="6.2"> + <repository changeset_revision="1007a3015bdb" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="libpng" version="1.6.7"> + <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="cairo" version="1.12.14"> + <repository changeset_revision="8f011e7388e1" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="pixman" version="0.32.4"> + <repository changeset_revision="bcf53d429118" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="freetype" version="2.5.2"> + <repository changeset_revision="34ebf47e4941" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="ncurses" version="5.9"> + <repository changeset_revision="47ad4d7ba9fe" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> <package name="R" version="3.1.1"> <install version="1.0"> - <actions_group> - <actions architecture="x86_64" os="linux"> - <action type="download_by_url">http://cran.rstudio.com/src/base/R-3/R-3.1.1.tar.gz</action> - <package name="readline" version="6.2"> - <repository changeset_revision="618c94461551" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="libpng" version="1.6.7"> - <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="cairo" version="1.12.14"> - <repository changeset_revision="8f011e7388e1" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="pixman" version="0.32.4"> - <repository changeset_revision="bcf53d429118" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="freetype" version="2.5.2"> - <repository changeset_revision="34ebf47e4941" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <action type="set_environment"> - <environment_variable action="set_to" name="TCL_LIBRARY">$INSTALL_DIR/lib/libtcl8.4.so</environment_variable> - <environment_variable action="set_to" name="TK_LIBRARY">$INSTALL_DIR/lib/libtk8.4.so</environment_variable> - </action> - <action type="set_environment_for_install"> - <repository changeset_revision="618c94461551" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="readline" version="6.2" /> - </repository> - <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="libpng" version="1.6.7" /> - </repository> - <repository changeset_revision="8f011e7388e1" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="cairo" version="1.12.14" /> - </repository> - <repository changeset_revision="bcf53d429118" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="pixman" version="0.32.4" /> - </repository> - <repository changeset_revision="34ebf47e4941" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="freetype" version="2.5.2" /> - </repository> - </action> - <action type="shell_command"> - export LDFLAGS="-L$PNG_LIBS -L$READLINE_LIB_PATH" && - export LDFLAGS="$LDFLAGS -Wl,-rpath,$READLINE_LIB_PATH" && - export LDFLAGS="$LDFLAGS -Wl,-rpath,$PIXMAN_LIB_PATH" && - export LDFLAGS="$LDFLAGS -Wl,-rpath,$PNG_LIB_PATH" && - export LDFLAGS="$LDFLAGS -Wl,-rpath,$FREETYPE_LIB_PATH" && - export CFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" && - export CXXFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" && - export CPPFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" && - ./configure --with-tcltk \ - --with-blas \ - --with-lapack \ - --with-readline \ - --with-cairo \ - --with-libpng \ - --without-x \ - --enable-R-shlib \ - --disable-R-framework \ - --libdir=$INSTALL_DIR/lib \ - --prefix=$INSTALL_DIR - </action> - <action type="make_install" /> - <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action> - <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action> - </actions> + <actions> + <action type="download_by_url">http://cran.rstudio.com/src/base/R-3/R-3.1.1.tar.gz</action> + <action type="set_environment_for_install"> + <repository changeset_revision="1007a3015bdb" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="readline" version="6.2" /> + </repository> + <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="libpng" version="1.6.7" /> + </repository> + <repository changeset_revision="8f011e7388e1" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="cairo" version="1.12.14" /> + </repository> + <repository changeset_revision="bcf53d429118" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="pixman" version="0.32.4" /> + </repository> + <repository changeset_revision="34ebf47e4941" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="freetype" version="2.5.2" /> + </repository> + <repository changeset_revision="47ad4d7ba9fe" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="ncurses" version="5.9" /> + </repository> + </action> + <action type="autoconf">--with-tcltk --with-blas --with-lapack --with-readline --with-cairo --with-libpng --without-x --without-aqua --enable-R-shlib --disable-R-framework --libdir=$INSTALL_DIR/lib</action> + <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action> + <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action> <action type="set_environment"> <environment_variable action="set_to" name="R_DOC_DIR">$INSTALL_DIR/lib/R/doc</environment_variable> <environment_variable action="set_to" name="R_HOME_DIR">$INSTALL_DIR/lib/R</environment_variable> @@ -77,13 +56,13 @@ <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable> <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> </action> - </actions_group> + </actions> </install> <readme> - Using Rstudio cran which seems to be properly versioned. - darwin needs work - I have no mac access... - R is a free software environment for statistical computing and graphics. - NOTE: See custom compilation options above. + Using Rstudio cran which seems to be properly versioned. + darwin needs work - I have no mac access... + R is a free software environment for statistical computing and graphics. + NOTE: See custom compilation options above. </readme> </package> </tool_dependency>