[BioC] EBImage install: wsObjects() problem
Martin Morgan
mtmorgan at fhcrc.org
Thu Jul 31 22:47:27 CEST 2008
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/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"
>>
>
> _______________________________________________
> 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
More information about the Bioconductor
mailing list