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Created April 17, 2012 18:14
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EBImage build failure with clang
Raw
gistfile1.txt
> source("http://bioconductor.org/biocLite.R")
BiocInstaller version 1.4.3, ?biocLite for help
> biocLite("EBImage")
BioC_mirror: http://bioconductor.org
Using R version 2.15, BiocInstaller version 1.4.3.
Installing package(s) 'EBImage'
trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/EBImage_3.12.0.tar.gz'
Content type 'application/x-gzip' length 4738660 bytes (4.5 Mb)
opened URL
==================================================
downloaded 4.5 Mb
* installing *source* package ‘EBImage’ ...
checking for Magick-config... yes
* found ImageMagick version 6.7.5 Q16
* found ImageMagick includes in -I/usr/local/Cellar/imagemagick/6.7.5-7/include/ImageMagick
checking for pkg-config... yes
* compiling with GTK+ support
-----------------------------------------------------
configure: creating ./config.status
config.status: creating src/Makevars
** libs
/usr/bin/clang -I/usr/local/Cellar/r/2.15.0/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/readline/6.2.2/include -I/usr/X11/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT -I/usr/local/Cellar/gtk+/2.24.10/include/gtk-2.0 -I/usr/local/Cellar/gtk+/2.24.10/lib/gtk-2.0/include -I/usr/local/Cellar/atk/2.2.0/include/atk-1.0 -I/usr/local/Cellar/gdk-pixbuf/2.24.1/include/gdk-pixbuf-2.0 -I/usr/local/Cellar/pango/1.28.4/include/pango-1.0 -I/usr/local/Cellar/glib/2.30.3/include/glib-2.0 -I/usr/local/Cellar/glib/2.30.3/lib/glib-2.0/include -I/usr/local/Cellar/gettext/0.18.1.1/include -I/usr/local/Cellar/glib/2.30.3/include -I/usr/local/Cellar/pixman/0.24.4/include/pixman-1 -I/usr/X11/include/cairo -I/usr/X11/include -I/usr/X11/include/freetype2 -I/usr/X11/include/libpng15 -Wall -I/usr/local/Cellar/imagemagick/6.7.5-7/include/ImageMagick -I/usr/local/Cellar/imagemagick/6.7.5-7/include/ImageMagick -fPIC -Os -w -pipe -march=native -Qunused-arguments -c EBImage.c -o EBImage.o
/usr/bin/clang -I/usr/local/Cellar/r/2.15.0/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/readline/6.2.2/include -I/usr/X11/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT -I/usr/local/Cellar/gtk+/2.24.10/include/gtk-2.0 -I/usr/local/Cellar/gtk+/2.24.10/lib/gtk-2.0/include -I/usr/local/Cellar/atk/2.2.0/include/atk-1.0 -I/usr/local/Cellar/gdk-pixbuf/2.24.1/include/gdk-pixbuf-2.0 -I/usr/local/Cellar/pango/1.28.4/include/pango-1.0 -I/usr/local/Cellar/glib/2.30.3/include/glib-2.0 -I/usr/local/Cellar/glib/2.30.3/lib/glib-2.0/include -I/usr/local/Cellar/gettext/0.18.1.1/include -I/usr/local/Cellar/glib/2.30.3/include -I/usr/local/Cellar/pixman/0.24.4/include/pixman-1 -I/usr/X11/include/cairo -I/usr/X11/include -I/usr/X11/include/freetype2 -I/usr/X11/include/libpng15 -Wall -I/usr/local/Cellar/imagemagick/6.7.5-7/include/ImageMagick -I/usr/local/Cellar/imagemagick/6.7.5-7/include/ImageMagick -fPIC -Os -w -pipe -march=native -Qunused-arguments -c conversions.c -o conversions.o
/usr/bin/clang -I/usr/local/Cellar/r/2.15.0/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/readline/6.2.2/include -I/usr/X11/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT -I/usr/local/Cellar/gtk+/2.24.10/include/gtk-2.0 -I/usr/local/Cellar/gtk+/2.24.10/lib/gtk-2.0/include -I/usr/local/Cellar/atk/2.2.0/include/atk-1.0 -I/usr/local/Cellar/gdk-pixbuf/2.24.1/include/gdk-pixbuf-2.0 -I/usr/local/Cellar/pango/1.28.4/include/pango-1.0 -I/usr/local/Cellar/glib/2.30.3/include/glib-2.0 -I/usr/local/Cellar/glib/2.30.3/lib/glib-2.0/include -I/usr/local/Cellar/gettext/0.18.1.1/include -I/usr/local/Cellar/glib/2.30.3/include -I/usr/local/Cellar/pixman/0.24.4/include/pixman-1 -I/usr/X11/include/cairo -I/usr/X11/include -I/usr/X11/include/freetype2 -I/usr/X11/include/libpng15 -Wall -I/usr/local/Cellar/imagemagick/6.7.5-7/include/ImageMagick -I/usr/local/Cellar/imagemagick/6.7.5-7/include/ImageMagick -fPIC -Os -w -pipe -march=native -Qunused-arguments -c display.c -o display.o
/usr/bin/clang -I/usr/local/Cellar/r/2.15.0/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/readline/6.2.2/include -I/usr/X11/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT -I/usr/local/Cellar/gtk+/2.24.10/include/gtk-2.0 -I/usr/local/Cellar/gtk+/2.24.10/lib/gtk-2.0/include -I/usr/local/Cellar/atk/2.2.0/include/atk-1.0 -I/usr/local/Cellar/gdk-pixbuf/2.24.1/include/gdk-pixbuf-2.0 -I/usr/local/Cellar/pango/1.28.4/include/pango-1.0 -I/usr/local/Cellar/glib/2.30.3/include/glib-2.0 -I/usr/local/Cellar/glib/2.30.3/lib/glib-2.0/include -I/usr/local/Cellar/gettext/0.18.1.1/include -I/usr/local/Cellar/glib/2.30.3/include -I/usr/local/Cellar/pixman/0.24.4/include/pixman-1 -I/usr/X11/include/cairo -I/usr/X11/include -I/usr/X11/include/freetype2 -I/usr/X11/include/libpng15 -Wall -I/usr/local/Cellar/imagemagick/6.7.5-7/include/ImageMagick -I/usr/local/Cellar/imagemagick/6.7.5-7/include/ImageMagick -fPIC -Os -w -pipe -march=native -Qunused-arguments -c distmap.c -o distmap.o
/usr/bin/clang -I/usr/local/Cellar/r/2.15.0/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/readline/6.2.2/include -I/usr/X11/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT -I/usr/local/Cellar/gtk+/2.24.10/include/gtk-2.0 -I/usr/local/Cellar/gtk+/2.24.10/lib/gtk-2.0/include -I/usr/local/Cellar/atk/2.2.0/include/atk-1.0 -I/usr/local/Cellar/gdk-pixbuf/2.24.1/include/gdk-pixbuf-2.0 -I/usr/local/Cellar/pango/1.28.4/include/pango-1.0 -I/usr/local/Cellar/glib/2.30.3/include/glib-2.0 -I/usr/local/Cellar/glib/2.30.3/lib/glib-2.0/include -I/usr/local/Cellar/gettext/0.18.1.1/include -I/usr/local/Cellar/glib/2.30.3/include -I/usr/local/Cellar/pixman/0.24.4/include/pixman-1 -I/usr/X11/include/cairo -I/usr/X11/include -I/usr/X11/include/freetype2 -I/usr/X11/include/libpng15 -Wall -I/usr/local/Cellar/imagemagick/6.7.5-7/include/ImageMagick -I/usr/local/Cellar/imagemagick/6.7.5-7/include/ImageMagick -fPIC -Os -w -pipe -march=native -Qunused-arguments -c drawable.c -o drawable.o
/usr/bin/clang -I/usr/local/Cellar/r/2.15.0/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/readline/6.2.2/include -I/usr/X11/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT -I/usr/local/Cellar/gtk+/2.24.10/include/gtk-2.0 -I/usr/local/Cellar/gtk+/2.24.10/lib/gtk-2.0/include -I/usr/local/Cellar/atk/2.2.0/include/atk-1.0 -I/usr/local/Cellar/gdk-pixbuf/2.24.1/include/gdk-pixbuf-2.0 -I/usr/local/Cellar/pango/1.28.4/include/pango-1.0 -I/usr/local/Cellar/glib/2.30.3/include/glib-2.0 -I/usr/local/Cellar/glib/2.30.3/lib/glib-2.0/include -I/usr/local/Cellar/gettext/0.18.1.1/include -I/usr/local/Cellar/glib/2.30.3/include -I/usr/local/Cellar/pixman/0.24.4/include/pixman-1 -I/usr/X11/include/cairo -I/usr/X11/include -I/usr/X11/include/freetype2 -I/usr/X11/include/libpng15 -Wall -I/usr/local/Cellar/imagemagick/6.7.5-7/include/ImageMagick -I/usr/local/Cellar/imagemagick/6.7.5-7/include/ImageMagick -fPIC -Os -w -pipe -march=native -Qunused-arguments -c features_haralick.c -o features_haralick.o
/usr/bin/clang -I/usr/local/Cellar/r/2.15.0/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/readline/6.2.2/include -I/usr/X11/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT -I/usr/local/Cellar/gtk+/2.24.10/include/gtk-2.0 -I/usr/local/Cellar/gtk+/2.24.10/lib/gtk-2.0/include -I/usr/local/Cellar/atk/2.2.0/include/atk-1.0 -I/usr/local/Cellar/gdk-pixbuf/2.24.1/include/gdk-pixbuf-2.0 -I/usr/local/Cellar/pango/1.28.4/include/pango-1.0 -I/usr/local/Cellar/glib/2.30.3/include/glib-2.0 -I/usr/local/Cellar/glib/2.30.3/lib/glib-2.0/include -I/usr/local/Cellar/gettext/0.18.1.1/include -I/usr/local/Cellar/glib/2.30.3/include -I/usr/local/Cellar/pixman/0.24.4/include/pixman-1 -I/usr/X11/include/cairo -I/usr/X11/include -I/usr/X11/include/freetype2 -I/usr/X11/include/libpng15 -Wall -I/usr/local/Cellar/imagemagick/6.7.5-7/include/ImageMagick -I/usr/local/Cellar/imagemagick/6.7.5-7/include/ImageMagick -fPIC -Os -w -pipe -march=native -Qunused-arguments -c features_hull.c -o features_hull.o
/usr/bin/clang -I/usr/local/Cellar/r/2.15.0/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/readline/6.2.2/include -I/usr/X11/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT -I/usr/local/Cellar/gtk+/2.24.10/include/gtk-2.0 -I/usr/local/Cellar/gtk+/2.24.10/lib/gtk-2.0/include -I/usr/local/Cellar/atk/2.2.0/include/atk-1.0 -I/usr/local/Cellar/gdk-pixbuf/2.24.1/include/gdk-pixbuf-2.0 -I/usr/local/Cellar/pango/1.28.4/include/pango-1.0 -I/usr/local/Cellar/glib/2.30.3/include/glib-2.0 -I/usr/local/Cellar/glib/2.30.3/lib/glib-2.0/include -I/usr/local/Cellar/gettext/0.18.1.1/include -I/usr/local/Cellar/glib/2.30.3/include -I/usr/local/Cellar/pixman/0.24.4/include/pixman-1 -I/usr/X11/include/cairo -I/usr/X11/include -I/usr/X11/include/freetype2 -I/usr/X11/include/libpng15 -Wall -I/usr/local/Cellar/imagemagick/6.7.5-7/include/ImageMagick -I/usr/local/Cellar/imagemagick/6.7.5-7/include/ImageMagick -fPIC -Os -w -pipe -march=native -Qunused-arguments -c features_moments.c -o features_moments.o
/usr/bin/clang -I/usr/local/Cellar/r/2.15.0/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/readline/6.2.2/include -I/usr/X11/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT -I/usr/local/Cellar/gtk+/2.24.10/include/gtk-2.0 -I/usr/local/Cellar/gtk+/2.24.10/lib/gtk-2.0/include -I/usr/local/Cellar/atk/2.2.0/include/atk-1.0 -I/usr/local/Cellar/gdk-pixbuf/2.24.1/include/gdk-pixbuf-2.0 -I/usr/local/Cellar/pango/1.28.4/include/pango-1.0 -I/usr/local/Cellar/glib/2.30.3/include/glib-2.0 -I/usr/local/Cellar/glib/2.30.3/lib/glib-2.0/include -I/usr/local/Cellar/gettext/0.18.1.1/include -I/usr/local/Cellar/glib/2.30.3/include -I/usr/local/Cellar/pixman/0.24.4/include/pixman-1 -I/usr/X11/include/cairo -I/usr/X11/include -I/usr/X11/include/freetype2 -I/usr/X11/include/libpng15 -Wall -I/usr/local/Cellar/imagemagick/6.7.5-7/include/ImageMagick -I/usr/local/Cellar/imagemagick/6.7.5-7/include/ImageMagick -fPIC -Os -w -pipe -march=native -Qunused-arguments -c features_zernike.c -o features_zernike.o
/usr/bin/clang -I/usr/local/Cellar/r/2.15.0/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/readline/6.2.2/include -I/usr/X11/include -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT -I/usr/local/Cellar/gtk+/2.24.10/include/gtk-2.0 -I/usr/local/Cellar/gtk+/2.24.10/lib/gtk-2.0/include -I/usr/local/Cellar/atk/2.2.0/include/atk-1.0 -I/usr/local/Cellar/gdk-pixbuf/2.24.1/include/gdk-pixbuf-2.0 -I/usr/local/Cellar/pango/1.28.4/include/pango-1.0 -I/usr/local/Cellar/glib/2.30.3/include/glib-2.0 -I/usr/local/Cellar/glib/2.30.3/lib/glib-2.0/include -I/usr/local/Cellar/gettext/0.18.1.1/include -I/usr/local/Cellar/glib/2.30.3/include -I/usr/local/Cellar/pixman/0.24.4/include/pixman-1 -I/usr/X11/include/cairo -I/usr/X11/include -I/usr/X11/include/freetype2 -I/usr/X11/include/libpng15 -Wall -I/usr/local/Cellar/imagemagick/6.7.5-7/include/ImageMagick -I/usr/local/Cellar/imagemagick/6.7.5-7/include/ImageMagick -fPIC -Os -w -pipe -march=native -Qunused-arguments -c filters_magick.c -o filters_magick.o
/usr/bin/clang++ -I/usr/local/Cellar/r/2.15.0/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/readline/6.2.2/include -I/usr/X11/include -Wall -I/usr/local/Cellar/imagemagick/6.7.5-7/include/ImageMagick -I/usr/local/Cellar/imagemagick/6.7.5-7/include/ImageMagick -fPIC -Os -w -pipe -march=native -Qunused-arguments -c floodFill.cpp -o floodFill.o
floodFill.cpp:174:57: error: redefinition of default argument
_floodFill(T *m, XYPoint size, XYPoint xy, T rc, double tol=1e-3) {
^ ~~~~
floodFill.cpp:21:68: note: previous definition is here
template <class T> void _floodFill(T*, XYPoint, XYPoint, T, double tol=1e-3);
^ ~~~~
1 error generated.
make: *** [floodFill.o] Error 1
ERROR: compilation failed for package ‘EBImage’
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