Mercurial > repos > iuc > package_r_3_2_1

changeset 2:2ce7fd67f394 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 6eaf4336ff90294e503dedf930ccbe31f8b4efe9
author iuc
date Thu, 03 Dec 2015 07:23:45 -0500
parents fae49a02a848
children d0bf97420fb5
files tool_dependencies.xml
diffstat 1 files changed, 26 insertions(+), 32 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Wed Nov 04 09:57:52 2015 -0500
+++ b/tool_dependencies.xml	Thu Dec 03 07:23:45 2015 -0500
@@ -9,6 +9,23 @@
                         <source_directory>.</source_directory>
                         <destination_directory>$INSTALL_DIR</destination_directory>
                     </action>
+                    <action type="shell_command">
+                        command -v gfortran || return 0
+                        BUNDLED_LGF_CANON=$INSTALL_DIR/lib/libgfortran.so.3.0.0 &amp;&amp;
+                        BUNDLED_LGF_FQSO=$INSTALL_DIR/lib/libgfortran.so.3 &amp;&amp;
+                        BUNDLED_LGF_VERS=`objdump -p $BUNDLED_LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1` &amp;&amp;
+                        echo 'program test; end program test' &gt; test.f90 &amp;&amp;
+                        gfortran -o test test.f90 &amp;&amp;
+                        LGF=`ldd test | grep libgfortran | awk '{print $3}'` &amp;&amp;
+                        LGF_CANON=`readlink -f $LGF` &amp;&amp;
+                        LGF_VERS=`objdump -p $LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1` &amp;&amp;
+                        if [ $LGF_VERS -gt $BUNDLED_LGF_VERS ]; then
+                            cp -p $BUNDLED_LGF_CANON ${BUNDLED_LGF_CANON}.bundled &amp;&amp;
+                            cp -p $BUNDLED_LGF_FQSO ${BUNDLED_LGF_FQSO}.bundled &amp;&amp;
+                            cp -p $LGF_CANON $BUNDLED_LGF_CANON &amp;&amp;
+                            cp -p $LGF_CANON $BUNDLED_LGF_FQSO
+                        fi
+                    </action>
                     <action type="set_environment">
                         <environment_variable action="set_to" name="TCL_LIBRARY">$INSTALL_DIR/lib/libtcl8.4.so</environment_variable>
                         <environment_variable action="set_to" name="TK_LIBRARY">$INSTALL_DIR/lib/libtk8.4.so</environment_variable>
@@ -26,19 +43,19 @@
                         <repository changeset_revision="05df724aefbb" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
                     </package>
                     <package name="cairo" version="1.12.14">
-                        <repository changeset_revision="8294add5c76e" name="package_cairo_1_12_14" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+                        <repository changeset_revision="3d4edf152b1b" name="package_cairo_1_12_14" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
                     </package>
                     <package name="pixman" version="0.32.6">
-                        <repository changeset_revision="b67e27ea8bd3" name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+                        <repository changeset_revision="06f701aa92e2" name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
                     </package>
                     <package name="freetype" version="2.5.2">
-                        <repository changeset_revision="ee307f3ce5dc" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+                        <repository changeset_revision="3b09e7916896" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
                     </package>
                     <package name="ncurses" version="6.0">
                         <repository changeset_revision="c921f7ce9ca7" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
                     </package>
                     <package name="fontconfig" version="2.11.1">
-                        <repository changeset_revision="b20e4c53891e" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+                        <repository changeset_revision="2ce32675340e" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
                     </package>
                     <action type="set_environment_for_install">
                         <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
@@ -47,46 +64,23 @@
                         <repository changeset_revision="05df724aefbb" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                             <package name="libpng" version="1.6.7" />
                         </repository>
-                        <repository changeset_revision="8294add5c76e" name="package_cairo_1_12_14" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <repository changeset_revision="3d4edf152b1b" name="package_cairo_1_12_14" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                             <package name="cairo" version="1.12.14" />
                         </repository>
-                        <repository changeset_revision="b67e27ea8bd3" name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <repository changeset_revision="06f701aa92e2" name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                             <package name="pixman" version="0.32.6" />
                         </repository>
-                        <repository changeset_revision="ee307f3ce5dc" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <repository changeset_revision="3b09e7916896" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                             <package name="freetype" version="2.5.2" />
                         </repository>
                         <repository changeset_revision="c921f7ce9ca7" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                             <package name="ncurses" version="6.0" />
                         </repository>
-                        <repository changeset_revision="b20e4c53891e" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <repository changeset_revision="2ce32675340e" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.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$READLINE_LIB_PATH" &amp;&amp;
-                        export LDFLAGS="$LDFLAGS -Wl,-rpath,$NCURSES_LIB_PATH" &amp;&amp; 
-                        export LDFLAGS="$LDFLAGS -Wl,-rpath,$READLINE_LIB_PATH" &amp;&amp;
-                        export LDFLAGS="$LDFLAGS -Wl,-rpath,$PIXMAN_LIB_PATH" &amp;&amp;
-                        export LDFLAGS="$LDFLAGS -Wl,-rpath,$LIBPNG_LIB_PATH" &amp;&amp;
-                        export LDFLAGS="$LDFLAGS -Wl,-rpath,$FREETYPE_LIB_PATH" &amp;&amp;
-                        export LDFLAGS="$LDFLAGS -Wl,-rpath,$FONTCONFIG_LIB_PATH" &amp;&amp;
-                        export LDFLAGS="$LDFLAGS -Wl,-rpath,$CAIRO_LIB_PATH" &amp;&amp;
-                        export CFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH -I$LIBPNG_INCLUDE_PATH -I$FONTCONFIG_INCLUDE_PATH -I$CAIRO_INCLUDE_PATH" &amp;&amp;
-                        export CXXFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH -I$LIBPNG_INCLUDE_PATH -I$FONTCONFIG_INCLUDE_PATH -I$CAIRO_INCLUDE_PATH" &amp;&amp;
-                        export CPPFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH -I$LIBPNG_INCLUDE_PATH -I$FONTCONFIG_INCLUDE_PATH -I$CAIRO_INCLUDE_PATH" &amp;&amp;
-                        ./configure --with-tcltk \
-                                    --with-blas \
-                                    --with-lapack \
-                                    --with-readline \
-                                    --with-cairo \
-                                    --with-libpng \
-                                    --without-x \
-                                    --enable-R-shlib \
-                                    --disable-R-framework \
-                                    --libdir=$INSTALL_DIR/lib \
-                                    --prefix=$INSTALL_DIR 
-                    </action>
+                    <action type="autoconf">--with-tcltk --with-blas --with-lapack --with-readline --with-cairo --with-libpng --without-x --enable-R-shlib --disable-R-framework --libdir=$INSTALL_DIR/lib</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>