[BioC] EBImage install: wsObjects() problem
colin davenport
colindaven at gmail.com
Thu Jul 31 14:27:39 CEST 2008
Dear EBImage users
I have a strange issues with the EBImage packet. Apparently it
installs fine (see below), and
most functions are found and work very nicely. However I cannot access the very
important
wsObjects() or wsPaint() functions.
Has anyone experienced similar problems?
What are the dependencies for these functions ?
I am using R 2.7.1 CRAN on an Ubuntu 8.04 system.
I used these instructions to install R and bioconductor
http://hocuspokus.net/2008/05/07/installing-r-bioconductor-on-ubuntu-804/
One thing .. the bioconductor flagged up errors with the following packages
affy
annaffy
affyPLM
Thanks for your help !
Colin
*******
> biocLite("EBImage")
Running biocinstall version 2.2.10 with R version 2.7.1
Your version of R requires version 2.2 of BioConductor.
Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
argument 'lib' is missing: using '/usr/local/lib/R/site-library'
trying URL 'http://bioconductor.org/packages/2.2/bioc/src/contrib/EBImage_2.4.0.tar.gz'
Content type 'application/x-gzip' length 1180830 bytes (1.1 Mb)
opened URL
==================================================
downloaded 1.1 Mb
* Installing *source* package 'EBImage' ...
checking for Magick-config... yes
* found ImageMagick version 6.3.7 Q16
* found ImageMagick includes in -I/usr/include
checking for pkg-config... yes
* compiling with GTK+ support
-----------------------------------------------------
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/usr/share/R/include -DUSE_GTK -DGLIB_GETTEXT
-I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include
-I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0
-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include
-I/usr/include/freetype2 -I/usr/include/libpng12
-I/usr/include/pixman-1 -Wall -I/usr/include -I/usr/include -fpic
-g -O2 -c colors.c -o colors.o
gcc -std=gnu99 -I/usr/share/R/include -DUSE_GTK -DGLIB_GETTEXT
-I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include
-I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0
-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include
-I/usr/include/freetype2 -I/usr/include/libpng12
-I/usr/include/pixman-1 -Wall -I/usr/include -I/usr/include -fpic
-g -O2 -c conversions.c -o conversions.o
gcc -std=gnu99 -I/usr/share/R/include -DUSE_GTK -DGLIB_GETTEXT
-I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include
-I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0
-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include
-I/usr/include/freetype2 -I/usr/include/libpng12
-I/usr/include/pixman-1 -Wall -I/usr/include -I/usr/include -fpic
-g -O2 -c display.c -o display.o
gcc -std=gnu99 -I/usr/share/R/include -DUSE_GTK -DGLIB_GETTEXT
-I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include
-I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0
-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include
-I/usr/include/freetype2 -I/usr/include/libpng12
-I/usr/include/pixman-1 -Wall -I/usr/include -I/usr/include -fpic
-g -O2 -c drawable.c -o drawable.o
gcc -std=gnu99 -I/usr/share/R/include -DUSE_GTK -DGLIB_GETTEXT
-I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include
-I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0
-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include
-I/usr/include/freetype2 -I/usr/include/libpng12
-I/usr/include/pixman-1 -Wall -I/usr/include -I/usr/include -fpic
-g -O2 -c EBImage.c -o EBImage.o
gcc -std=gnu99 -I/usr/share/R/include -DUSE_GTK -DGLIB_GETTEXT
-I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include
-I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0
-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include
-I/usr/include/freetype2 -I/usr/include/libpng12
-I/usr/include/pixman-1 -Wall -I/usr/include -I/usr/include -fpic
-g -O2 -c features_haralick.c -o features_haralick.o
gcc -std=gnu99 -I/usr/share/R/include -DUSE_GTK -DGLIB_GETTEXT
-I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include
-I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0
-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include
-I/usr/include/freetype2 -I/usr/include/libpng12
-I/usr/include/pixman-1 -Wall -I/usr/include -I/usr/include -fpic
-g -O2 -c features_hull.c -o features_hull.o
gcc -std=gnu99 -I/usr/share/R/include -DUSE_GTK -DGLIB_GETTEXT
-I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include
-I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0
-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include
-I/usr/include/freetype2 -I/usr/include/libpng12
-I/usr/include/pixman-1 -Wall -I/usr/include -I/usr/include -fpic
-g -O2 -c features_moments.c -o features_moments.o
gcc -std=gnu99 -I/usr/share/R/include -DUSE_GTK -DGLIB_GETTEXT
-I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include
-I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0
-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include
-I/usr/include/freetype2 -I/usr/include/libpng12
-I/usr/include/pixman-1 -Wall -I/usr/include -I/usr/include -fpic
-g -O2 -c features_zernike.c -o features_zernike.o
gcc -std=gnu99 -I/usr/share/R/include -DUSE_GTK -DGLIB_GETTEXT
-I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include
-I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0
-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include
-I/usr/include/freetype2 -I/usr/include/libpng12
-I/usr/include/pixman-1 -Wall -I/usr/include -I/usr/include -fpic
-g -O2 -c filters_distmap.c -o filters_distmap.o
g++ -I/usr/share/R/include -Wall -I/usr/include -I/usr/include
-fpic -g -O2 -c filters_floodfill.cpp -o filters_floodfill.o
gcc -std=gnu99 -I/usr/share/R/include -DUSE_GTK -DGLIB_GETTEXT
-I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include
-I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0
-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include
-I/usr/include/freetype2 -I/usr/include/libpng12
-I/usr/include/pixman-1 -Wall -I/usr/include -I/usr/include -fpic
-g -O2 -c filters_magick.c -o filters_magick.o
gcc -std=gnu99 -I/usr/share/R/include -DUSE_GTK -DGLIB_GETTEXT
-I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include
-I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0
-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include
-I/usr/include/freetype2 -I/usr/include/libpng12
-I/usr/include/pixman-1 -Wall -I/usr/include -I/usr/include -fpic
-g -O2 -c filters_morph.c -o filters_morph.o
gcc -std=gnu99 -I/usr/share/R/include -DUSE_GTK -DGLIB_GETTEXT
-I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include
-I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0
-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include
-I/usr/include/freetype2 -I/usr/include/libpng12
-I/usr/include/pixman-1 -Wall -I/usr/include -I/usr/include -fpic
-g -O2 -c filters_normalize.c -o filters_normalize.o
g++ -I/usr/share/R/include -Wall -I/usr/include -I/usr/include
-fpic -g -O2 -c filters_propagate.cpp -o filters_propagate.o
gcc -std=gnu99 -I/usr/share/R/include -DUSE_GTK -DGLIB_GETTEXT
-I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include
-I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0
-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include
-I/usr/include/freetype2 -I/usr/include/libpng12
-I/usr/include/pixman-1 -Wall -I/usr/include -I/usr/include -fpic
-g -O2 -c filters_thresh.c -o filters_thresh.o
g++ -I/usr/share/R/include -Wall -I/usr/include -I/usr/include
-fpic -g -O2 -c filters_watershed.cpp -o filters_watershed.o
gcc -std=gnu99 -I/usr/share/R/include -DUSE_GTK -DGLIB_GETTEXT
-I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include
-I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0
-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include
-I/usr/include/freetype2 -I/usr/include/libpng12
-I/usr/include/pixman-1 -Wall -I/usr/include -I/usr/include -fpic
-g -O2 -c frameDist.c -o frameDist.o
frameDist.c:27: warning: C99 inline functions are not supported; using GNU89
frameDist.c:27: warning: to disable this warning use -fgnu89-inline or
the gnu_inline function attribute
frameDist.c:119: warning: C99 inline functions are not supported; using GNU89
frameDist.c:130: warning: C99 inline functions are not supported; using GNU89
frameDist.c:169: warning: C99 inline functions are not supported; using GNU89
gcc -std=gnu99 -I/usr/share/R/include -DUSE_GTK -DGLIB_GETTEXT
-I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include
-I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0
-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include
-I/usr/include/freetype2 -I/usr/include/libpng12
-I/usr/include/pixman-1 -Wall -I/usr/include -I/usr/include -fpic
-g -O2 -c io.c -o io.o
gcc -std=gnu99 -I/usr/share/R/include -DUSE_GTK -DGLIB_GETTEXT
-I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include
-I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0
-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include
-I/usr/include/freetype2 -I/usr/include/libpng12
-I/usr/include/pixman-1 -Wall -I/usr/include -I/usr/include -fpic
-g -O2 -c objects.c -o objects.o
gcc -std=gnu99 -I/usr/share/R/include -DUSE_GTK -DGLIB_GETTEXT
-I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include
-I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0
-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include
-I/usr/include/freetype2 -I/usr/include/libpng12
-I/usr/include/pixman-1 -Wall -I/usr/include -I/usr/include -fpic
-g -O2 -c tools.c -o tools.o
g++ -shared -o EBImage.so colors.o conversions.o display.o drawable.o
EBImage.o features_haralick.o features_hull.o features_moments.o
features_zernike.o filters_distmap.o filters_floodfill.o
filters_magick.o filters_morph.o filters_normalize.o
filters_propagate.o filters_thresh.o filters_watershed.o frameDist.o
io.o objects.o tools.o -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0
-lgdk_pixbuf-2.0 -lm -lpangocairo-1.0 -lpango-1.0 -lcairo
-lgobject-2.0 -lgmodule-2.0 -ldl -lglib-2.0 -L/usr/lib
-Wl,-Bsymbolic-functions -L/usr/lib/X11 -lfreetype -lz -L/usr/lib
-lWand -lMagick -lWand -L/usr/lib/R/lib -lR
** R
** data
** inst
** preparing package for lazy loading
** help
>>> Building/Updating help pages for package 'EBImage'
Formats: text html latex example
EBImage-deprecated text html latex
EBImage-package text html latex
Image.generic.methods text html latex
channel text html latex example
class.Image text html latex example
class.IndexedImage text html latex example
constructors text html latex example
denoising text html latex example
display text html latex example
distmap text html latex example
drawable text html latex example
enhancing text html latex
features-edge text html latex example
features-haralick text html latex example
features-hull text html latex example
features-moments text html latex example
features-zernike text html latex example
filter2 text html latex
floodfill text html latex example
frameDist text html latex
getFeatures text html latex example
input-output text html latex example
internals text html latex
matchObjects text html latex
morphology text html latex example
normalize text html latex example
paintObjects text html latex example
propagate text html latex example
rmObjects text html latex example
segmenting text html latex
stackObjects text html latex example
thresholding text html latex example
tile text html latex example
transformations text html latex
watershed text html latex example
** building package indices ...
* DONE (EBImage)
The downloaded packages are in
/tmp/RtmpkUYqhJ/downloaded_packages
> library(EBImage)
Attaching package: 'EBImage'
The following object(s) are masked from package:Biobase :
channel,
combine
> thresh
standardGeneric for "thresh" defined from package "EBImage"
function (x, ...)
standardGeneric("thresh")
<environment: 0x85c9810>
Methods may be defined for arguments: x
Use showMethods("thresh") for currently available ones.
>
> wsObjects()
Error: could not find function "wsObjects"
>
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