Mercurial > repos > brenninc > test_r_cairo_oct1_2015
comparison tool_dependencies.xml @ 3:e5e60b114550 draft
Uploaded
| author | brenninc |
|---|---|
| date | Thu, 01 Oct 2015 09:10:31 -0400 |
| parents | 304b62d6e6cf |
| children | 07c908f7dd21 |
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| 2:304b62d6e6cf | 3:e5e60b114550 |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | 2 <tool_dependency> |
| 3 <package name="R" version="3.2.1"> | 3 <package name="R" version="3.1.2"> |
| 4 <repository toolshed="https://testtoolshed.g2.bx.psu.edu/" name="brenninc_r_sept32105" owner="brenninc" changeset_revision="1d7f08f14e93" prior_installation_required="True" /> | |
| 5 </package> | |
| 6 <package name="R_extend_level_one" version="0.0.1"> | |
| 4 <install version="1.0"> | 7 <install version="1.0"> |
| 5 <actions> | 8 <actions> |
| 6 <action type="download_by_url">http://cran.rstudio.com/src/base/R-3/R-3.2.1.tar.gz</action> | 9 <action type="setup_r_environment"> |
| 7 <package name="atlas" version="3.10.2"> | 10 <repository changeset_revision="1d7f08f14e93" name="brenninc_r_sept32105" owner="brenninc" toolshed="https://testtoolshed.g2.bx.psu.edu/"> |
| 8 <repository changeset_revision="86b7c19454fa" name="package_atlas_3_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> | 11 <package name="R" version="3.1.2" /> |
| 9 </package> | 12 <!-- includes base, boot, |
| 10 <package name="readline" version="6.3"> | 13 class, cluster, codetools, compiler, |
| 11 <repository changeset_revision="40f8ebe365e9" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> | 14 datasets, |
| 12 </package> | 15 foreign, |
| 13 <package name="libpng" version="1.6.7"> | 16 graphics, grDevices, grid, |
| 14 <repository changeset_revision="ac6ef08bf0e6" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> | 17 KernSmooth, |
| 15 </package> | 18 lattice, |
| 16 <package name="cairo" version="1.14.2"> | 19 MASS, Matrix, methods, mgcv, |
| 17 <repository changeset_revision="9fe5875b0ede" name="package_cairo_1_14_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> | 20 nlme, nnet, |
| 18 </package> | 21 parallel, |
| 19 <package name="pixman" version="0.32.6"> | 22 rpart, |
| 20 <repository changeset_revision="2db67636b074" name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> | 23 spatial, splines, stats, stats4, survival, |
| 21 </package> | 24 tcltk, tools, |
| 22 <package name="freetype" version="2.5.2"> | 25 utils--> |
| 23 <repository changeset_revision="55f81025bcb0" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> | 26 |
| 24 </package> | 27 </repository> |
| 25 <package name="ncurses" version="6.0"> | 28 <!--No dependencies Not on https://bioarchive.galaxyproject.org --> |
| 26 <repository changeset_revision="9331b44bf167" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> | 29 <package>https://cran.r-project.org/src/contrib/acepack_1.3-3.3.tar.gz</package> |
| 27 </package> | 30 <package>https://cran.r-project.org/src/contrib/colorspace_1.2-6.tar.gz</package> |
| 28 <package name="fontconfig" version="2.11.1"> | 31 <!-- Imports graphics |
| 29 <repository changeset_revision="e1df54930f90" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> | 32 Suggests: KernSmooth, MASS, kernlab, mvtnorm, vcd, dichromat, tcltk--> |
| 30 </package> | 33 <package>https://cran.r-project.org/src/contrib/digest_0.6.8.tar.gz</package> |
| 31 <action type="set_environment_for_install"> | 34 <package>https://cran.r-project.org/src/contrib/dichromat_2.0-0.tar.gz</package> |
| 32 <repository changeset_revision="40f8ebe365e9" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> | 35 <!-- Depends stats --> |
| 33 <package name="readline" version="6.3" /> | 36 <package>https://cran.r-project.org/src/contrib/Formula_1.2-1.tar.gz</package> |
| 34 </repository> | 37 <!-- Depends stats --> |
| 35 <repository changeset_revision="ac6ef08bf0e6" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> | 38 <package>https://cran.r-project.org/src/contrib/gtable_0.1.2.tar.gz</package> |
| 36 <package name="libpng" version="1.6.7" /> | 39 <!-- Depends grid |
| 37 </repository> | 40 Suggests: testthat, plyr--> |
| 38 <repository changeset_revision="9fe5875b0ede" name="package_cairo_1_14_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> | 41 <package>https://cran.r-project.org/src/contrib/labeling_0.3.tar.gz</package> |
| 39 <package name="cairo" version="1.14.2" /> | 42 <package>https://cran.r-project.org/src/contrib/magrittr_1.5.tar.gz</package> |
| 40 </repository> | 43 <!-- Suggests: testthat, knitr --> |
| 41 <repository changeset_revision="2db67636b074" name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> | 44 <package>https://cran.r-project.org/src/contrib/proto_0.3-10.tar.gz</package> |
| 42 <package name="pixman" version="0.32.6" /> | 45 <!-- Suggests: graph, Rgraphviz --> |
| 43 </repository> | 46 <package>https://cran.r-project.org/src/contrib/Rcpp_0.12.0.tar.gz</package> |
| 44 <repository changeset_revision="55f81025bcb0" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> | 47 <!-- Imports: methods, utils |
| 45 <package name="freetype" version="2.5.2" /> | 48 Suggests: RUnit, inline, rbenchmark, highlight, pkgKitten (≥ 0.1.2) --> |
| 46 </repository> | 49 <package>https://cran.r-project.org/src/contrib/RColorBrewer_1.1-2.tar.gz</package> |
| 47 <repository changeset_revision="9331b44bf167" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> | 50 <package>https://cran.r-project.org/src/contrib/rjson_0.2.15.tar.gz</package> |
| 48 <package name="ncurses" version="6.0" /> | 51 <package>https://cran.r-project.org/src/contrib/snow_0.3-13.tar.gz</package> |
| 49 </repository> | 52 <!-- Depends: R (≥ 2.12.1), utils |
| 50 <repository changeset_revision="e1df54930f90" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> | 53 Suggests: Rmpi, rpvm, rlecuyer, rsprng, nws --> |
| 51 <package name="fontconfig" version="2.11.1" /> | 54 <package>https://cran.r-project.org/src/contrib/SparseM_1.7.tar.gz</package> |
| 52 </repository> | 55 <!-- Depends: R (≥ 2.15), methods |
| 53 </action> | 56 Imports: graphics, stats, utils --> |
| 54 <action type="shell_command"> | 57 <package>https://cran.r-project.org/src/contrib/stringi_0.5-5.tar.gz</package> |
| 55 export LDFLAGS="-L$LIBPNG_LIB_PATH -L$PNG_LIBS -L$NCURSES_LIB_PATH -L$READLINE_LIB_PATH" && | 58 <!-- Depends: R (≥ 2.13.1) |
| 56 export LDFLAGS="$LDFLAGS -Wl,-rpath,$NCURSES_LIB_PATH" && | 59 Imports: tools, utils, stats --> |
| 57 export LDFLAGS="$LDFLAGS -Wl,-rpath,$READLINE_LIB_PATH" && | 60 <package>https://cran.r-project.org/src/contrib/XML_3.98-1.3.tar.gz</package> |
| 58 export LDFLAGS="$LDFLAGS -Wl,-rpath,$PIXMAN_LIB_PATH" && | 61 <!-- Depends: R (≥ 2.13.0), methods, utils |
| 59 export LDFLAGS="$LDFLAGS -Wl,-rpath,$LIBPNG_LIB_PATH" && | 62 Suggests: bitops, RCurl --> |
| 60 export LDFLAGS="$LDFLAGS -Wl,-rpath,$FREETYPE_LIB_PATH" && | 63 <package>https://cran.r-project.org/src/contrib/xtable_1.7-4.tar.gz</package> |
| 61 export LDFLAGS="$LDFLAGS -Wl,-rpath,$FONTCONFIG_LIB_PATH" && | 64 <package>https://cran.r-project.org/src/contrib/stringr_1.0.0.tar.gz</package> |
| 62 export LDFLAGS="$LDFLAGS -Wl,-rpath,$CAIRO_LIB_PATH" && | 65 <!-- Depends: R (≥ 2.14) |
| 63 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" && | 66 Imports: stringi (≥ 0.4.1), magrittr |
| 64 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" && | 67 Suggests: testthat, knitr --> |
| 65 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" && | 68 </action> |
| 66 ./configure --with-tcltk \ | |
| 67 --with-blas \ | |
| 68 --with-lapack \ | |
| 69 --with-readline \ | |
| 70 --with-cairo \ | |
| 71 --with-libpng \ | |
| 72 --without-x \ | |
| 73 --enable-R-shlib \ | |
| 74 --disable-R-framework \ | |
| 75 --libdir=$INSTALL_DIR/lib \ | |
| 76 --prefix=$INSTALL_DIR | |
| 77 </action> | |
| 78 <action type="make_install" /> | |
| 79 <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action> | |
| 80 <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action> | |
| 81 <action type="set_environment"> | |
| 82 <environment_variable action="set_to" name="R_DOC_DIR">$INSTALL_DIR/lib/R/doc</environment_variable> | |
| 83 <environment_variable action="set_to" name="R_HOME_DIR">$INSTALL_DIR/lib/R</environment_variable> | |
| 84 <environment_variable action="set_to" name="R_INCLUDE_DIR">$INSTALL_DIR/lib/R/include</environment_variable> | |
| 85 <environment_variable action="set_to" name="R_SHARE_DIR">$INSTALL_DIR/lib/R/share</environment_variable> | |
| 86 <environment_variable action="set_to" name="R_ROOT_DIR">$INSTALL_DIR</environment_variable> | |
| 87 <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable> | |
| 88 <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable> | |
| 89 <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable> | |
| 90 <environment_variable action="set_to" name="PKG_CONFIG_DIR">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable> | |
| 91 <environment_variable action="set_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable> | |
| 92 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> | |
| 93 </action> | |
| 94 </actions> | 69 </actions> |
| 95 </install> | 70 </install> |
| 96 <readme> | |
| 97 The precompiled versions of this package were built 2015-07-27. | |
| 98 R is a free software environment for statistical computing and graphics. | |
| 99 NOTE: See custom compilation options above. | |
| 100 </readme> | |
| 101 </package> | 71 </package> |
| 102 </tool_dependency> | 72 </tool_dependency> |
| 73 | |
| 74 |