EBImage install: wsObjects() problem
2
0
Entering edit mode
@colin-davenport-2957
Last seen 7.7 years ago
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/EBIm age_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" >
EBImage EBImage • 1.0k views
ADD COMMENT
0
Entering edit mode
@martin-morgan-1513
Last seen 6 days ago
United States
Hi Colin -- "colin davenport" <colindaven at="" gmail.com=""> writes: > Dear EBImage users >[SNIP] > I used these instructions to install R and bioconductor > http://hocuspokus.net/2008/05/07/installing-r-bioconductor-on- ubuntu-804/ >From a quick parse of this file it looks like the expectation is that R and its packages are installed as root. This sounds like a bad idea, or at least it seems like you'd like to install packages into a user-defined directory, e.g., using an environment variable R_LIBS, as discussed in the "R Installation and Administration" page http://cran.fhcrc.org/doc/manuals/R-admin.html > One thing .. the bioconductor flagged up errors with the following packages > affy > annaffy > affyPLM You've installed on top of a previous installation, and so need to update.packages. See the instructions on http://bioconductor.org/download i.e., in a new R session > source("http://bioconductor.org/biocLite.R") > update.packages(repos=biocinstallRepos(), ask=FALSE) Martin > 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/EB Image_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" >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793
ADD COMMENT
0
Entering edit mode
Oleg Sklyar ▴ 260
@oleg-sklyar-1882
Last seen 7.7 years ago
Dear Colin, you have probably updated from a *very* old version: the functions have been renamed long ago (just about 2 years I guess) and more functionality added to them. See watershed, getObjects etc as well as paintObjects Best, Oleg colin davenport wrote: > 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/EB Image_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" > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Dr Oleg Sklyar * EBI-EMBL, Cambridge CB10 1SD, UK * +44-1223-494466
ADD COMMENT

Login before adding your answer.

Traffic: 249 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6