| Previous changeset 1:fae49a02a848 (2015-11-04) Next changeset 3:d0bf97420fb5 (2015-12-04) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 6eaf4336ff90294e503dedf930ccbe31f8b4efe9 |
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modified:
tool_dependencies.xml |
| b |
| diff -r fae49a02a848 -r 2ce7fd67f394 tool_dependencies.xml --- a/tool_dependencies.xml Wed Nov 04 09:57:52 2015 -0500 +++ b/tool_dependencies.xml Thu Dec 03 07:23:45 2015 -0500 |
| [ |
| b'@@ -9,6 +9,23 @@\n <source_directory>.</source_directory>\n <destination_directory>$INSTALL_DIR</destination_directory>\n </action>\n+ <action type="shell_command">\n+ command -v gfortran || return 0\n+ BUNDLED_LGF_CANON=$INSTALL_DIR/lib/libgfortran.so.3.0.0 &&\n+ BUNDLED_LGF_FQSO=$INSTALL_DIR/lib/libgfortran.so.3 &&\n+ BUNDLED_LGF_VERS=`objdump -p $BUNDLED_LGF_CANON | grep GFORTRAN_1 | sed -r \'s/.*GFORTRAN_1\\.([0-9])+/\\1/\' | sort -n | tail -1` &&\n+ echo \'program test; end program test\' > test.f90 &&\n+ gfortran -o test test.f90 &&\n+ LGF=`ldd test | grep libgfortran | awk \'{print $3}\'` &&\n+ LGF_CANON=`readlink -f $LGF` &&\n+ LGF_VERS=`objdump -p $LGF_CANON | grep GFORTRAN_1 | sed -r \'s/.*GFORTRAN_1\\.([0-9])+/\\1/\' | sort -n | tail -1` &&\n+ if [ $LGF_VERS -gt $BUNDLED_LGF_VERS ]; then\n+ cp -p $BUNDLED_LGF_CANON ${BUNDLED_LGF_CANON}.bundled &&\n+ cp -p $BUNDLED_LGF_FQSO ${BUNDLED_LGF_FQSO}.bundled &&\n+ cp -p $LGF_CANON $BUNDLED_LGF_CANON &&\n+ cp -p $LGF_CANON $BUNDLED_LGF_FQSO\n+ fi\n+ </action>\n <action type="set_environment">\n <environment_variable action="set_to" name="TCL_LIBRARY">$INSTALL_DIR/lib/libtcl8.4.so</environment_variable>\n <environment_variable action="set_to" name="TK_LIBRARY">$INSTALL_DIR/lib/libtk8.4.so</environment_variable>\n@@ -26,19 +43,19 @@\n <repository changeset_revision="05df724aefbb" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />\n </package>\n <package name="cairo" version="1.12.14">\n- <repository changeset_revision="8294add5c76e" name="package_cairo_1_12_14" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />\n+ <repository changeset_revision="3d4edf152b1b" name="package_cairo_1_12_14" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />\n </package>\n <package name="pixman" version="0.32.6">\n- <repository changeset_revision="b67e27ea8bd3" name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />\n+ <repository changeset_revision="06f701aa92e2" name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />\n </package>\n <package name="freetype" version="2.5.2">\n- <repository changeset_revision="ee307f3ce5dc" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />\n+ <repository changeset_revision="3b09e7916896" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />\n </package>\n <package name="ncurses" version="6.0">\n <repository changeset_revision="c921f7ce9ca7" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />\n </package>\n <package name="fontconfig" version="2.11.1">\n- <repository changeset_revision="b20e4c53891e" name="package_fontconfig_2'..b'.bx.psu.edu">\n <package name="pixman" version="0.32.6" />\n </repository>\n- <repository changeset_revision="ee307f3ce5dc" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">\n+ <repository changeset_revision="3b09e7916896" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">\n <package name="freetype" version="2.5.2" />\n </repository>\n <repository changeset_revision="c921f7ce9ca7" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">\n <package name="ncurses" version="6.0" />\n </repository>\n- <repository changeset_revision="b20e4c53891e" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">\n+ <repository changeset_revision="2ce32675340e" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">\n <package name="fontconfig" version="2.11.1" />\n </repository>\n </action>\n- <action type="shell_command">\n- export LDFLAGS="-L$LIBPNG_LIB_PATH -L$PNG_LIBS -L$NCURSES_LIB_PATH -L$READLINE_LIB_PATH" &&\n- export LDFLAGS="$LDFLAGS -Wl,-rpath,$NCURSES_LIB_PATH" && \n- export LDFLAGS="$LDFLAGS -Wl,-rpath,$READLINE_LIB_PATH" &&\n- export LDFLAGS="$LDFLAGS -Wl,-rpath,$PIXMAN_LIB_PATH" &&\n- export LDFLAGS="$LDFLAGS -Wl,-rpath,$LIBPNG_LIB_PATH" &&\n- export LDFLAGS="$LDFLAGS -Wl,-rpath,$FREETYPE_LIB_PATH" &&\n- export LDFLAGS="$LDFLAGS -Wl,-rpath,$FONTCONFIG_LIB_PATH" &&\n- export LDFLAGS="$LDFLAGS -Wl,-rpath,$CAIRO_LIB_PATH" &&\n- export CFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH -I$LIBPNG_INCLUDE_PATH -I$FONTCONFIG_INCLUDE_PATH -I$CAIRO_INCLUDE_PATH" &&\n- export CXXFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH -I$LIBPNG_INCLUDE_PATH -I$FONTCONFIG_INCLUDE_PATH -I$CAIRO_INCLUDE_PATH" &&\n- export CPPFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH -I$LIBPNG_INCLUDE_PATH -I$FONTCONFIG_INCLUDE_PATH -I$CAIRO_INCLUDE_PATH" &&\n- ./configure --with-tcltk \\\n- --with-blas \\\n- --with-lapack \\\n- --with-readline \\\n- --with-cairo \\\n- --with-libpng \\\n- --without-x \\\n- --enable-R-shlib \\\n- --disable-R-framework \\\n- --libdir=$INSTALL_DIR/lib \\\n- --prefix=$INSTALL_DIR \n- </action>\n+ <action type="autoconf">--with-tcltk --with-blas --with-lapack --with-readline --with-cairo --with-libpng --without-x --enable-R-shlib --disable-R-framework --libdir=$INSTALL_DIR/lib</action>\n <action type="make_install" />\n <action type="shell_command">sed -i.bak -e \'s;$INSTALL_DIR;\\${R_ROOT_DIR};g\' $INSTALL_DIR/bin/R</action>\n <action type="shell_command">sed -i.bak -e \'s;$INSTALL_DIR;\\${R_ROOT_DIR};g\' $INSTALL_DIR/lib/R/bin/R</action>\n' |