Mercurial > repos > brenninc > brenninc_r_sept32105
changeset 1:82d4f7a6feb0 draft
Uploaded
| author | brenninc |
|---|---|
| date | Fri, 04 Sep 2015 08:26:15 -0400 |
| parents | a75708b0e142 |
| children | f0ec34556396 |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 33 insertions(+), 99 deletions(-) [+] |
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--- a/tool_dependencies.xml Thu Sep 03 09:46:13 2015 -0400 +++ b/tool_dependencies.xml Fri Sep 04 08:26:15 2015 -0400 @@ -1,117 +1,51 @@ <?xml version="1.0"?> <tool_dependency> - <package name="brenninc_R" version="3.2.1"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://cran.rstudio.com/src/base/R-3/R-3.2.1.tar.gz</action> - <package name="atlas" version="3.10.2"> - <repository changeset_revision="86b7c19454fa" name="package_atlas_3_10" owner="iuc" prior_installation_required="True" - toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="readline" version="6.3"> - <repository changeset_revision="40f8ebe365e9" name="package_readline_6_3" owner="iuc" prior_installation_required="True" - toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="libpng" version="1.6.7"> - <repository changeset_revision="ac6ef08bf0e6" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" - toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="cairo" version="1.12.14"> - <repository changeset_revision="5c25a57405a9" name="package_cairo_1_12_14" owner="iuc" prior_installation_required="True" - toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="pixman" version="0.32.6"> - <repository changeset_revision="2db67636b074" name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" - toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="freetype" version="2.5.2"> - <repository changeset_revision="8999860ddf69" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" - toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="ncurses" version="6.0"> - <repository changeset_revision="9331b44bf167" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" - toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="fontconfig" version="2.11.1"> - <repository changeset_revision="1db671dd3e91" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" - toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> + <package name="pixman" version="0.32.4"> + <repository changeset_revision="873f53f1abcd" name="package_pixman_0_32_4" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="libpng" version="1.6.7"> + <repository changeset_revision="ac6ef08bf0e6" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="freetype" version="2.5.2"> + <repository changeset_revision="8999860ddf69" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="cairo" version="1.12.14"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://depot.galaxyproject.org/package/source/cairo/cairo-1.12.14.tar.bz2</action> <action type="set_environment_for_install"> - <repository changeset_revision="40f8ebe365e9" name="package_readline_6_3" owner="iuc" prior_installation_required="True" - toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="readline" version="6.3" /> - </repository> - <repository changeset_revision="ac6ef08bf0e6" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" - toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="libpng" version="1.6.7" /> - </repository> - <repository changeset_revision="5c25a57405a9" name="package_cairo_1_12_14" owner="iuc" prior_installation_required="True" - toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="cairo" version="1.12.14" /> + <repository changeset_revision="873f53f1abcd" name="package_pixman_0_32_4" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="pixman" version="0.32.4" /> </repository> - <repository changeset_revision="2db67636b074" name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" - toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="pixman" version="0.32.6" /> - </repository> - <repository changeset_revision="8999860ddf69" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" - toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="freetype" version="2.5.2" /> + <repository changeset_revision="ac6ef08bf0e6" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="libpng" version="1.6.7" /> </repository> - <repository changeset_revision="9331b44bf167" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" - toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="ncurses" version="6.0" /> - </repository> - <repository changeset_revision="1db671dd3e91" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" - toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="fontconfig" version="2.11.1" /> + <repository changeset_revision="8999860ddf69" name="package_freetype_2_5_2" owner="iuc" 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$LIBPNG_LIB_PATH -L$PNG_LIBS -L$NCURSES_LIB_PATH -L$READLINE_LIB_PATH" && - export LDFLAGS="$LDFLAGS -Wl,-rpath,$NCURSES_LIB_PATH" && - export LDFLAGS="$LDFLAGS -Wl,-rpath,$READLINE_LIB_PATH" && - export LDFLAGS="$LDFLAGS -Wl,-rpath,$PIXMAN_LIB_PATH" && - export LDFLAGS="$LDFLAGS -Wl,-rpath,$LIBPNG_LIB_PATH" && - export LDFLAGS="$LDFLAGS -Wl,-rpath,$FREETYPE_LIB_PATH" && - export LDFLAGS="$LDFLAGS -Wl,-rpath,$FONTCONFIG_LIB_PATH" && - export LDFLAGS="$LDFLAGS -Wl,-rpath,$CAIRO_LIB_PATH" && - 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" && - 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" && - 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" && - ./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 + export LDFLAGS="-Wl,-rpath,$PIXMAN_LIB_PATH -Wl,-rpath,$LIBPNG_ROOT/lib -Wl,-rpath,$FREETYPE_LIB_PATH" && \ + ./configure --prefix=$INSTALL_DIR \ + --with-x=no \ + --enable-ft=yes \ + --enable-xcb-shm=no \ + --enable-xlib-xcb=no \ + --enable-xcb=no \ + --enable-xlib-xrender=no </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> + <!-- Create an empty cairo-xlib.h file, because R's configure script explicitly includes it even if X is disabled. --> + <action type="shell_command">touch $INSTALL_DIR/include/cairo/cairo-xlib.h</action> <action type="set_environment"> - <environment_variable action="set_to" name="R_DOC_DIR">$INSTALL_DIR/lib/R/doc</environment_variable> - <environment_variable action="set_to" name="R_HOME_DIR">$INSTALL_DIR/lib/R</environment_variable> - <environment_variable action="set_to" name="R_INCLUDE_DIR">$INSTALL_DIR/lib/R/include</environment_variable> - <environment_variable action="set_to" name="R_SHARE_DIR">$INSTALL_DIR/lib/R/share</environment_variable> - <environment_variable action="set_to" name="R_ROOT_DIR">$INSTALL_DIR</environment_variable> - <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable> - <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable> - <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable> - <environment_variable action="set_to" name="PKG_CONFIG_DIR">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable> - <environment_variable action="set_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="prepend_to" name="CAIRO_LIB_PATH">$INSTALL_DIR/lib</environment_variable> + <environment_variable action="prepend_to" name="CAIRO_INCLUDE_PATH">$INSTALL_DIR/include</environment_variable> + <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig</environment_variable> </action> </actions> </install> <readme> - The precompiled versions of this package were built 2015-07-27. - R is a free software environment for statistical computing and graphics. - NOTE: See custom compilation options above. </readme> </package> </tool_dependency>