Mercurial > repos > brenninc > test_r_cairo_oct1_2015
changeset 2:304b62d6e6cf draft
Uploaded
| author | brenninc |
|---|---|
| date | Thu, 01 Oct 2015 09:08:19 -0400 |
| parents | 110f8e93a946 |
| children | e5e60b114550 |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 94 insertions(+), 66 deletions(-) [+] |
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--- a/tool_dependencies.xml Thu Oct 01 05:42:34 2015 -0400 +++ b/tool_dependencies.xml Thu Oct 01 09:08:19 2015 -0400 @@ -1,74 +1,102 @@ <?xml version="1.0"?> <tool_dependency> - <package name="R" version="3.1.2"> - <repository toolshed="https://testtoolshed.g2.bx.psu.edu/" name="brenninc_r_sept32105" owner="brenninc" changeset_revision="3ab867976871" prior_installation_required="True" /> - </package> - <package name="R_extend_level_one" version="0.0.1"> + <package name="R" version="3.2.1"> <install version="1.0"> <actions> - <action type="setup_r_environment"> - <repository changeset_revision="3ab867976871" name="brenninc_r_sept32105" owner="brenninc" toolshed="https://testtoolshed.g2.bx.psu.edu/"> - <package name="R" version="3.1.2" /> - <!-- includes base, boot, - class, cluster, codetools, compiler, - datasets, - foreign, - graphics, grDevices, grid, - KernSmooth, - lattice, - MASS, Matrix, methods, mgcv, - nlme, nnet, - parallel, - rpart, - spatial, splines, stats, stats4, survival, - tcltk, tools, - utils--> - - </repository> - <!--No dependencies Not on https://bioarchive.galaxyproject.org --> - <package>https://cran.r-project.org/src/contrib/acepack_1.3-3.3.tar.gz</package> - <package>https://cran.r-project.org/src/contrib/colorspace_1.2-6.tar.gz</package> - <!-- Imports graphics - Suggests: KernSmooth, MASS, kernlab, mvtnorm, vcd, dichromat, tcltk--> - <package>https://cran.r-project.org/src/contrib/digest_0.6.8.tar.gz</package> - <package>https://cran.r-project.org/src/contrib/dichromat_2.0-0.tar.gz</package> - <!-- Depends stats --> - <package>https://cran.r-project.org/src/contrib/Formula_1.2-1.tar.gz</package> - <!-- Depends stats --> - <package>https://cran.r-project.org/src/contrib/gtable_0.1.2.tar.gz</package> - <!-- Depends grid - Suggests: testthat, plyr--> - <package>https://cran.r-project.org/src/contrib/labeling_0.3.tar.gz</package> - <package>https://cran.r-project.org/src/contrib/magrittr_1.5.tar.gz</package> - <!-- Suggests: testthat, knitr --> - <package>https://cran.r-project.org/src/contrib/proto_0.3-10.tar.gz</package> - <!-- Suggests: graph, Rgraphviz --> - <package>https://cran.r-project.org/src/contrib/Rcpp_0.12.0.tar.gz</package> - <!-- Imports: methods, utils - Suggests: RUnit, inline, rbenchmark, highlight, pkgKitten (≥ 0.1.2) --> - <package>https://cran.r-project.org/src/contrib/RColorBrewer_1.1-2.tar.gz</package> - <package>https://cran.r-project.org/src/contrib/rjson_0.2.15.tar.gz</package> - <package>https://cran.r-project.org/src/contrib/snow_0.3-13.tar.gz</package> - <!-- Depends: R (≥ 2.12.1), utils - Suggests: Rmpi, rpvm, rlecuyer, rsprng, nws --> - <package>https://cran.r-project.org/src/contrib/SparseM_1.7.tar.gz</package> - <!-- Depends: R (≥ 2.15), methods - Imports: graphics, stats, utils --> - <package>https://cran.r-project.org/src/contrib/stringi_0.5-5.tar.gz</package> - <!-- Depends: R (≥ 2.13.1) - Imports: tools, utils, stats --> - <package>https://cran.r-project.org/src/contrib/XML_3.98-1.3.tar.gz</package> - <!-- Depends: R (≥ 2.13.0), methods, utils - Suggests: bitops, RCurl --> - <package>https://cran.r-project.org/src/contrib/xtable_1.7-4.tar.gz</package> - <package>https://cran.r-project.org/src/contrib/stringr_1.0.0.tar.gz</package> - <!-- Depends: R (≥ 2.14) - Imports: stringi (≥ 0.4.1), magrittr - Suggests: testthat, knitr --> - </action> + <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="1.14.2"> + <repository changeset_revision="9fe5875b0ede" name="package_cairo_1_14_2" 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="55f81025bcb0" 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="e1df54930f90" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <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="9fe5875b0ede" name="package_cairo_1_14_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="cairo" version="1.14.2" /> + </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="55f81025bcb0" 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> + <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="e1df54930f90" 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> + </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 + </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' $INSTALL_DIR/lib/R/bin/R</action> + <action type="set_environment"> + <environment_variable action="set_to" name="R_DOC_DIR">$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> + </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> - -