Mercurial > repos > pieterlukasse > prims_metabolomics_r_dependencies
changeset 2:16ad47f8751f
adding lib png and other options
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Fri, 07 Nov 2014 12:04:54 +0100 |
| parents | e6171a39dd04 |
| children | a0b2e0545d72 |
| files | INSTALL.r tool_dependencies.xml |
| diffstat | 2 files changed, 54 insertions(+), 2 deletions(-) [+] |
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--- a/INSTALL.r Thu Nov 06 16:05:24 2014 +0100 +++ b/INSTALL.r Fri Nov 07 12:04:54 2014 +0100 @@ -4,7 +4,7 @@ source("http://bioconductor.org/biocLite.R") biocLite() -# upgrage? Some packages are "old" and can be upgraded with: biocLite("BiocUpgrade") +# upgrade? Some packages are "old" and can be upgraded with: biocLite("BiocUpgrade") # install metaMS and multtest for differential analysis tool (from xcms)
--- a/tool_dependencies.xml Thu Nov 06 16:05:24 2014 +0100 +++ b/tool_dependencies.xml Fri Nov 07 12:04:54 2014 +0100 @@ -7,13 +7,65 @@ <install version="1.0"> <actions_group> <actions> + <package name="readline" version="6.2"> + <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="libpng" version="1.6.7"> + <repository changeset_revision="db14a391648d" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="cairo" version="1.12.14"> + <repository changeset_revision="b39299b4b6e1" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="pixman" version="0.32.4"> + <repository changeset_revision="3d44a209a6b9" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="freetype" version="2.5.2"> + <repository changeset_revision="58782940c411" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <action type="download_by_url">http://cran.rstudio.com/src/base/R-3/R-3.0.3.tar.gz</action> + <action type="set_environment_for_install"> + <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu"> + <package name="readline" version="6.2" /> + </repository> + <repository changeset_revision="db14a391648d" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu"> + <package name="libpng" version="1.6.7" /> + </repository> + <repository changeset_revision="b39299b4b6e1" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu"> + <package name="cairo" version="1.12.14" /> + </repository> + <repository changeset_revision="3d44a209a6b9" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu"> + <package name="pixman" version="0.32.4" /> + </repository> + <repository changeset_revision="58782940c411" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu"> + <package name="freetype" version="2.5.2" /> + </repository> + </action> <action type="download_by_url">http://cran.r-project.org/src/base/R-3/R-3.1.1.tar.gz</action> <action type="move_directory_files"> <source_directory>.</source_directory> <destination_directory>$INSTALL_DIR</destination_directory> </action> <action type="shell_command"> - cd $INSTALL_DIR; $INSTALL_DIR/configure --libdir=$INSTALL_DIR/lib --prefix=$INSTALL_DIR + cd $INSTALL_DIR; + export LDFLAGS="-L$PNG_LIBS -L$READLINE_LIB_PATH" && + export LDFLAGS="$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$READLINE_INCLUDE_PATH" && + export CXXFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" && + export CPPFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" && + $INSTALL_DIR/configure --with-tcltk \ + --with-blas \ + --with-lapack \ + --with-readline \ + --with-cairo \ + --with-libpng \ + --without-x \ + --enable-R-shlib \ + --disable-R-framework \ + --libdir=$INSTALL_DIR/lib \ + --prefix=$INSTALL_DIR </action> <action type="shell_command">make -C $INSTALL_DIR</action> </actions>