Mercurial > repos > iuc > package_r_3_2_0
diff tool_dependencies.xml @ 6:11baf5863be2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_0 commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
| author | iuc |
|---|---|
| date | Fri, 09 Oct 2015 05:17:45 -0400 |
| parents | d973c8e9b29e |
| children | 88ca0346da36 |
line wrap: on
line diff
--- a/tool_dependencies.xml Sun Jul 26 16:02:05 2015 -0400 +++ b/tool_dependencies.xml Fri Oct 09 05:17:45 2015 -0400 @@ -4,7 +4,7 @@ <install version="1.0"> <actions_group> <actions architecture="x86_64" os="linux"> - <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.2.0-Linux-x86_64.tar.gz</action> + <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.2.0-Linux-x84_64.tgz</action> <action type="move_directory_files"> <source_directory>.</source_directory> <destination_directory>$INSTALL_DIR</destination_directory> @@ -13,73 +13,57 @@ <environment_variable action="set_to" name="TCL_LIBRARY">$INSTALL_DIR/lib/libtcl8.4.so</environment_variable> <environment_variable action="set_to" name="TK_LIBRARY">$INSTALL_DIR/lib/libtk8.4.so</environment_variable> </action> - <action type="shell_command"><![CDATA[ - command -v gfortran || return 0 - BUNDLED_LGF_CANON=$INSTALL_DIR/lib/libgfortran.so.3.0.0 && - BUNDLED_LGF_VERS=`objdump -p $BUNDLED_LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1` && - echo 'program test; end program test' > test.f90 && - gfortran -o test test.f90 && - LGF=`ldd test | grep libgfortran | awk '{print $3}'` && - LGF_CANON=`readlink -f $LGF` && - LGF_VERS=`objdump -p $LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1` && - if [ $LGF_VERS -gt $BUNDLED_LGF_VERS ]; then - cp -p $BUNDLED_LGF_CANON ${BUNDLED_LGF_CANON}.bundled && - cp -p $LGF_CANON $BUNDLED_LGF_CANON - fi - ]]></action> </actions> - <actions architecture="x86_64" os="darwin"> - <action type="download_by_url">https://cran.rstudio.com/src/base/R-3/R-3.2.0.tar.gz</action> - + <actions> + <action type="download_by_url">http://cran.rstudio.com/src/base/R-3/R-3.2.0.tar.gz</action> <package name="readline" version="6.2"> - <repository name="package_readline_6_2" owner="iuc" prior_installation_required="True" /> + <repository changeset_revision="93fad0d5cab9" 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 name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" /> + <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 name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" /> + <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 name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" /> + <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 name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" /> + <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 name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" /> + <repository changeset_revision="387c0609c0b7" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> - <action type="set_environment_for_install"> - <repository name="package_readline_6_2" owner="iuc" prior_installation_required="True" > + <repository changeset_revision="93fad0d5cab9" 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 name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" > + <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 name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" > + <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 name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" > + <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 name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" > + <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 name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" > + <repository changeset_revision="387c0609c0b7" 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="shell_command"><![CDATA[ - export LDFLAGS="-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="$LDFLAGS -Wl,-rpath,$PNG_LIB_PATH" && - export LDFLAGS="$LDFLAGS -Wl,-rpath,$FREETYPE_LIB_PATH" && - export CFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH" && - export CXXFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH" && - export CPPFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH" && + <action type="shell_command"> + export LDFLAGS="-L$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="$LDFLAGS -Wl,-rpath,$PNG_LIB_PATH" && + export LDFLAGS="$LDFLAGS -Wl,-rpath,$FREETYPE_LIB_PATH" && + export CFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH" && + export CXXFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH" && + export CPPFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH" && ./configure --with-tcltk \ --with-blas \ --with-lapack \ @@ -91,7 +75,7 @@ --disable-R-framework \ --libdir=$INSTALL_DIR/lib \ --prefix=$INSTALL_DIR - ]]></action> + </action> <action type="make_install" /> <action type="shell_command">sed -i.bak -e 's;$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> @@ -112,6 +96,7 @@ </actions_group> </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>