Mercurial > repos > brenninc > brenninc_r_sept32105
changeset 6:02588f939252 draft
Uploaded
| author | brenninc |
|---|---|
| date | Tue, 06 Oct 2015 11:48:37 -0400 |
| parents | 4395fcf5d40c |
| children | f930f6e4c537 |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 77 insertions(+), 50 deletions(-) [+] |
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--- a/tool_dependencies.xml Fri Oct 02 06:28:54 2015 -0400 +++ b/tool_dependencies.xml Tue Oct 06 11:48:37 2015 -0400 @@ -1,9 +1,5 @@ <?xml version="1.0"?> <tool_dependency> - <package name="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> @@ -28,7 +24,19 @@ <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> + <package name="libmxl2" version="2.9.1"> + <repository changeset_revision="df7589f53a88" name="package_libxml2_2_9_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="R" version="3.2.1"> + <repository toolshed="https://testtoolshed.g2.bx.psu.edu/" name="brenninc_r_sept32105" owner="brenninc" changeset_revision="4395fcf5d40c" prior_installation_required="True" /> + </package> + <package name="R_cairo" version="0.0.3"> + <install version="1.0"> + <actions> <action type="set_environment_for_install"> + <repository changeset_revision="86b7c19454fa" name="package_atlas_3_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" > + <package name="atlas" version="3.10.2"/> + </repository> <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> @@ -50,53 +58,72 @@ <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">$INSTALL_DIR/lib/R/library</environment_variable> - <environment_variable action="prepend_to" name="PKG_CONFIG_DIR">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable> - <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - </action> + <repository changeset_revision="df7589f53a88" name="package_libxml2_2_9_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" > + <package name="libmxl2" version="2.9.1"/> + </repository> + </action> + <action type="setup_r_environment"> + <repository toolshed="https://testtoolshed.g2.bx.psu.edu/" name="brenninc_r_sept32105" owner="brenninc" changeset_revision="4395fcf5d40c" prior_installation_required="True" > + <package name="R" version="3.2.1" /> + <!-- 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> + <package>https://cran.r-project.org/src/contrib/acepack_1.3-3.3.tar.gz</package> + <package>https://cran.r-project.org/src/contrib/Cairo_1.5-9.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/Archive/Rcpp/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/stringr_1.0.0.tar.gz</package> + <!-- Depends: R (≥ 2.14) + Imports: stringi (≥ 0.4.1), magrittr + Suggests: testthat, knitr --> + <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> + </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> + +