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Package 80/294HostnameOS / ArchBUILDCHECKBUILD BIN
EBImage 2.6.0
Gregoire Pau
Bioconductor Changelog
Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/EBImage
Last Changed Rev: 34811 / Revision: 38965
Last Changed Date: 2008-10-21 15:32:58 -0700 (Tue, 21 Oct 2008)
wilson2 Linux (openSUSE 11.1) / x86_64  OK [ WARNINGS ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
pelham Mac OS X Leopard (10.5.6) / i386  OK  OK  OK 
Package: EBImage
Version: 2.6.0
Command: /home/biocbuild/bbs-2.3-bioc/R/bin/R CMD check --no-vignettes EBImage_2.6.0.tar.gz
StartedAt: 2009-04-18 15:19:26 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 15:20:24 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 58.5 seconds
RetCode: 0
Status: WARNINGS
CheckDir: EBImage.Rcheck
Warnings: 6

Command output

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.3-bioc/meat/EBImage.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: UTF-8
* checking for file 'EBImage/DESCRIPTION' ... OK
* this is package 'EBImage' version '2.6.0'
* checking package name space information ... OK
* 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 non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... WARNING
Xlib:  extension "RANDR" missing on display ":4363.0".
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... WARNING
Xlib:  extension "RANDR" missing on display ":4363.0".
See section 'Generic functions and methods' of the 'Writing R Extensions'
manual.
* checking replacement functions ... WARNING
Xlib:  extension "RANDR" missing on display ":4363.0".
In R, the argument of a replacement function which corresponds to the right
hand side must be named 'value'.
* checking foreign function calls ... WARNING
Xlib:  extension "RANDR" missing on display ":4363.0".
See the chapter 'System and foreign language interfaces' of the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
Xlib:  extension "RANDR" missing on display ":4363.0".
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Xlib:  extension "RANDR" missing on display ":4363.0".
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... WARNING
Xlib:  extension "RANDR" missing on display ":4363.0".
Xlib:  extension "RANDR" missing on display ":4363.0".
Xlib:  extension "RANDR" missing on display ":4363.0".
* checking Rd \usage sections ... NOTE
Xlib:  extension "RANDR" missing on display ":4363.0".
The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating EBImage-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating EBImage-manual.tex ... OK
* checking EBImage-manual.tex using pdflatex ... OK

WARNING: There were 6 warnings, see
  /loc/home/biocbuild/bbs-2.3-bioc/meat/EBImage.Rcheck/00check.log
for details

EBImage.Rcheck/00install.out:

* Installing *source* package 'EBImage' ...
checking for Magick-config... yes
* found ImageMagick version 6.4.3 Q16 
* found ImageMagick includes in -I/usr/include/ImageMagick
checking for pkg-config... yes
* compiling with GTK+ support
-----------------------------------------------------
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include   -DUSE_GTK -DGLIB_GETTEXT -I/usr/include/gtk-2.0 -I/usr/lib64/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/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12   -Wall -I/usr/include/ImageMagick -fopenmp -I/usr/include/ImageMagick  -fpic  -g -O2 -Wall -c colors.c -o colors.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include   -DUSE_GTK -DGLIB_GETTEXT -I/usr/include/gtk-2.0 -I/usr/lib64/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/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12   -Wall -I/usr/include/ImageMagick -fopenmp -I/usr/include/ImageMagick  -fpic  -g -O2 -Wall -c conversions.c -o conversions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include   -DUSE_GTK -DGLIB_GETTEXT -I/usr/include/gtk-2.0 -I/usr/lib64/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/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12   -Wall -I/usr/include/ImageMagick -fopenmp -I/usr/include/ImageMagick  -fpic  -g -O2 -Wall -c display.c -o display.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include   -DUSE_GTK -DGLIB_GETTEXT -I/usr/include/gtk-2.0 -I/usr/lib64/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/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12   -Wall -I/usr/include/ImageMagick -fopenmp -I/usr/include/ImageMagick  -fpic  -g -O2 -Wall -c drawable.c -o drawable.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include   -DUSE_GTK -DGLIB_GETTEXT -I/usr/include/gtk-2.0 -I/usr/lib64/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/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12   -Wall -I/usr/include/ImageMagick -fopenmp -I/usr/include/ImageMagick  -fpic  -g -O2 -Wall -c EBImage.c -o EBImage.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include   -DUSE_GTK -DGLIB_GETTEXT -I/usr/include/gtk-2.0 -I/usr/lib64/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/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12   -Wall -I/usr/include/ImageMagick -fopenmp -I/usr/include/ImageMagick  -fpic  -g -O2 -Wall -c features_haralick.c -o features_haralick.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include   -DUSE_GTK -DGLIB_GETTEXT -I/usr/include/gtk-2.0 -I/usr/lib64/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/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12   -Wall -I/usr/include/ImageMagick -fopenmp -I/usr/include/ImageMagick  -fpic  -g -O2 -Wall -c features_hull.c -o features_hull.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include   -DUSE_GTK -DGLIB_GETTEXT -I/usr/include/gtk-2.0 -I/usr/lib64/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/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12   -Wall -I/usr/include/ImageMagick -fopenmp -I/usr/include/ImageMagick  -fpic  -g -O2 -Wall -c features_moments.c -o features_moments.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include   -DUSE_GTK -DGLIB_GETTEXT -I/usr/include/gtk-2.0 -I/usr/lib64/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/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12   -Wall -I/usr/include/ImageMagick -fopenmp -I/usr/include/ImageMagick  -fpic  -g -O2 -Wall -c features_zernike.c -o features_zernike.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include   -DUSE_GTK -DGLIB_GETTEXT -I/usr/include/gtk-2.0 -I/usr/lib64/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/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12   -Wall -I/usr/include/ImageMagick -fopenmp -I/usr/include/ImageMagick  -fpic  -g -O2 -Wall -c filters_distmap.c -o filters_distmap.o
g++ -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include   -Wall -I/usr/include/ImageMagick -fopenmp -I/usr/include/ImageMagick  -fpic  -g -O2 -Wall -c filters_floodfill.cpp -o filters_floodfill.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include   -DUSE_GTK -DGLIB_GETTEXT -I/usr/include/gtk-2.0 -I/usr/lib64/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/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12   -Wall -I/usr/include/ImageMagick -fopenmp -I/usr/include/ImageMagick  -fpic  -g -O2 -Wall -c filters_magick.c -o filters_magick.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include   -DUSE_GTK -DGLIB_GETTEXT -I/usr/include/gtk-2.0 -I/usr/lib64/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/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12   -Wall -I/usr/include/ImageMagick -fopenmp -I/usr/include/ImageMagick  -fpic  -g -O2 -Wall -c filters_morph.c -o filters_morph.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include   -DUSE_GTK -DGLIB_GETTEXT -I/usr/include/gtk-2.0 -I/usr/lib64/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/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12   -Wall -I/usr/include/ImageMagick -fopenmp -I/usr/include/ImageMagick  -fpic  -g -O2 -Wall -c filters_normalize.c -o filters_normalize.o
g++ -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include   -Wall -I/usr/include/ImageMagick -fopenmp -I/usr/include/ImageMagick  -fpic  -g -O2 -Wall -c filters_propagate.cpp -o filters_propagate.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include   -DUSE_GTK -DGLIB_GETTEXT -I/usr/include/gtk-2.0 -I/usr/lib64/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/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12   -Wall -I/usr/include/ImageMagick -fopenmp -I/usr/include/ImageMagick  -fpic  -g -O2 -Wall -c filters_thresh.c -o filters_thresh.o
g++ -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include   -Wall -I/usr/include/ImageMagick -fopenmp -I/usr/include/ImageMagick  -fpic  -g -O2 -Wall -c filters_watershed.cpp -o filters_watershed.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include   -DUSE_GTK -DGLIB_GETTEXT -I/usr/include/gtk-2.0 -I/usr/lib64/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/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12   -Wall -I/usr/include/ImageMagick -fopenmp -I/usr/include/ImageMagick  -fpic  -g -O2 -Wall -c frameDist.c -o frameDist.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include   -DUSE_GTK -DGLIB_GETTEXT -I/usr/include/gtk-2.0 -I/usr/lib64/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/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12   -Wall -I/usr/include/ImageMagick -fopenmp -I/usr/include/ImageMagick  -fpic  -g -O2 -Wall -c io.c -o io.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include   -DUSE_GTK -DGLIB_GETTEXT -I/usr/include/gtk-2.0 -I/usr/lib64/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/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12   -Wall -I/usr/include/ImageMagick -fopenmp -I/usr/include/ImageMagick  -fpic  -g -O2 -Wall -c objects.c -o objects.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include   -DUSE_GTK -DGLIB_GETTEXT -I/usr/include/gtk-2.0 -I/usr/lib64/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/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12   -Wall -I/usr/include/ImageMagick -fopenmp -I/usr/include/ImageMagick  -fpic  -g -O2 -Wall -c tools.c -o tools.o
g++ -shared -L/usr/local/lib64 -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 -lgio-2.0 -lpangoft2-1.0 -lgdk_pixbuf-2.0 -lpangocairo-1.0 -lcairo -lpango-1.0 -lfreetype -lz -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lglib-2.0   -L/usr/lib64 -L/usr/lib64 -lfreetype -lz -L/usr/lib64 -lMagickCore -L/usr/lib64 -lMagickWand -lMagickCore     -L/home/biocbuild/bbs-2.3-bioc/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)