Package: EBImage

Version: 1.2.2

Command: /loc/biocbuild/1.8d/R/bin/R CMD check EBImage_1.2.2.tar.gz

RetCode: 1

Time: 74.8 seconds

Status: ERROR

CheckDir: EBImage.Rcheck

Warnings: NA

* checking for working latex ... OK
* using log directory '/loc/biocbuild/1.8d/Rpacks/EBImage.Rcheck'
* using Version 2.3.1 (2006-06-01)
* checking for file 'EBImage/DESCRIPTION' ... OK
* this is package 'EBImage' version '1.2.2'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'EBImage' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for syntax errors ... OK
* checking R files for library.dynam ... OK
* checking S3 generic/method consistency ... WARNING

See section 'Generic functions and methods' of the 'Writing R Extensions'
manual.
* checking replacement functions ... WARNING

In R, the argument of a replacement function which corresponds to the right
hand side must be named 'value'.
* checking foreign function calls ... WARNING

See section 'System and foreign language interfaces' of the 'Writing R
Extensions' manual.
* checking Rd files ... OK
* checking for missing documentation entries ... WARNING

All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... WARNING



* checking Rd \usage sections ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* checking for portable compilation flags in Makevars ... OK
* creating EBImage-Ex.R ... OK
* checking examples ... ERROR
Running examples in EBImage-Ex.R failed.
The error most likely occurred in:

> ### * algorithms2D.objectCount
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: objectCount
> ### Title: Counts Objects in an Image or a Stack of Images
> ### Aliases: objectCount
> ### Keywords: dplot manip array
> 
> ### ** Examples
> 
>     im = read.image("http://www.ebi.ac.uk/~osklyar/projects/EBImage/examples/segmented.tif")
>     # get the distance map
>     dm = distMap(im)
Error in .notImageError(x) : argument must be of class 'Image2D' or 'Image3D'
Execution halted

* Installing *source* package 'EBImage' ...
checking for Magick++-config... yes
ImageMagick version 6.2.8 found
checking for Magick++-config... yes
ImageMagick++ includes located in -I/usr/local/include
R found in: /loc/biocbuild/1.8d/R
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/R/include  -I/usr/local/include  -I/usr/local/include -D_REENTRANT -pthreads -fPIC  -g -O2 -c algorithms2D.cpp -o algorithms2D.o
g++ -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/R/include  -I/usr/local/include  -I/usr/local/include -D_REENTRANT -pthreads -fPIC  -g -O2 -c common.cpp -o common.o
g++ -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/R/include  -I/usr/local/include  -I/usr/local/include -D_REENTRANT -pthreads -fPIC  -g -O2 -c conversions.cpp -o conversions.o
g++ -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/R/include  -I/usr/local/include  -I/usr/local/include -D_REENTRANT -pthreads -fPIC  -g -O2 -c display.cpp -o display.o
g++ -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/R/include  -I/usr/local/include  -I/usr/local/include -D_REENTRANT -pthreads -fPIC  -g -O2 -c filters2D.cpp -o filters2D.o
g++ -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/R/include  -I/usr/local/include  -I/usr/local/include -D_REENTRANT -pthreads -fPIC  -g -O2 -c filters2D_magick.cpp -o filters2D_magick.o
g++ -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/R/include  -I/usr/local/include  -I/usr/local/include -D_REENTRANT -pthreads -fPIC  -g -O2 -c io.cpp -o io.o
g++ -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/R/include  -I/usr/local/include  -I/usr/local/include -D_REENTRANT -pthreads -fPIC  -g -O2 -c libmain.cpp -o libmain.o
g++ -G -L/usr/local/lib -o EBImage.so algorithms2D.o common.o conversions.o display.o filters2D.o filters2D_magick.o io.o libmain.o -L/usr/local/lib -L/usr/openwin/lib -R/usr/openwin/lib -L/usr/local/lib -R/usr/local/lib -lfreetype -lz -L/usr/local/lib -lMagick++ -lMagick -lfreetype -ljpeg -lXext -lSM -lICE -lX11 -lsocket -lnsl -lXt -lbz2 -lz -lpthread -lm -lpthread -lWand -lMagick  
** R
** inst
** save image
** help
 >>> Building/Updating help pages for package 'EBImage'
     Formats: text html latex example 
  algorithms2D.objectCount          text    html    latex   example
  class.Image2D                     text    html    latex   example
  class.Image3D                     text    html    latex   example
  filters2D.distMap                 text    html    latex   example
  filters2D.magick-colors           text    html    latex   example
  filters2D.magick-enhance          text    html    latex   example
  filters2D.magick-segment          text    html    latex   example
  filters2D.magick-transform        text    html    latex   example
  filters2D.magick                  text    html    latex   example
  filters2D.thresh                  text    html    latex   example
  image.io                          text    html    latex   example
  internals                         text    html    latex
** building package indices ...
* DONE (EBImage)