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| IMPORTANT NOTE: R was configured with --enable-strict-barrier on lamb1 |
| Package 66/247 | Hostname | OS | Arch | BUILD | CHECK | BUILD BIN |
EBImage2.1.20Oleg SklyarLast Changed Date: 2007-08-24 17:16:24 -0700 Last Changed Rev: 26639 | lamb1 | Linux (SUSE 10.1) | x86_64 | OK | OK | |
| wellington | Linux (SUSE 9.2) | i686 | ERROR | skipped | ||
| liverpool | Windows Server 2003 R2 (32-bit) | x64 | OK | WARNINGS | OK | |
| pitt | Mac OS X (10.4.10) | i386 | OK | [ ERROR ] | OK |
| Package: EBImage |
| Version: 2.1.20 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check EBImage_2.1.20.tar.gz |
| RetCode: 1 |
| Time: 50.2 seconds |
| Status: ERROR |
| CheckDir: EBImage.Rcheck |
| Warnings: NA |
* checking for working latex ... OK
* using log directory '/Users/biocbuild/bbs-2.1-bioc/meat/EBImage.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-08-10 r42465)
* checking for file 'EBImage/DESCRIPTION' ... OK
* this is package 'EBImage' version '2.1.20'
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... 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 $BLAS_LIBS ... OK
* creating EBImage-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'EBImage-Ex.R' failed.
The error most likely occurred in:
> ### * drawable
>
> flush(stderr()); flush(stdout())
magick/string.c:774: failed assertion `string != (char *) NULL'
>
> ### Name: drawtext
> ### Title: Drawing primitives on images
> ### Aliases: drawtext drawfont
> ### Keywords: file
>
> ### ** Examples
>
> ## Dear Mac users. This example is currently excluded from MacOS builds as it
> ## fails in ImageMagick string assertion. Although I tried to find the reason for
> ## the problem, I do not have a test environment (MacOS). Please test it and
> ## report what goes wrong here and at which stage. Thank you. Oleg
>
> if ( length(grep("apple", Sys.getenv("R_PROFILE"))) == 0 ) {
+ ## load images
+ f <- paste( system.file(package="EBImage"), "images/Gene1_G.tif", sep="/" )
+ ii = normalize(read.image(f), separate=TRUE)
+ ## segment
+ mask = thresh(ii, 25, 25, 0.02)
+ mk3 = morphKern(3)
+ mk5 = morphKern(5)
+ mask = dilate(erode(closing(mask, mk5), mk3), mk5)
+ ## index objects in images and remove bad ones
+ io = watershed( distmap(mask), 1.5, 1)
+ ft = hull.features(io)
+ mf = moments(io, ii) ## need these for intensity and size
+ for ( i in seq_along(ft) ) ft[[i]] = cbind(ft[[i]], mf[[i]])
+ io = rmObjects(io, lapply(ft, function(x)
+ which(x[,"h.s"] < 150 | x[,"int"] < 50 | 0.3 * x[,"h.p"] < x[,"h.edge"] )
+ ))
+ ## get centres of objects (list, for ii is a stack of 4)
+ xy <- lapply(ft, function(x) x[,1:2])
+ # create labels for objects (list, for ii is a stack of 4)
+ labels <- lapply(xy, function(x) as.character(1:nrow(x)))
+ ## set font properties: semi bold
+ f <- drawfont()
+ f$weight=600
+ ## draw annotations, recycle 2 colours between 4 images
+ annot <- drawtext(channel(ii,"rgb"), xy, labels, font=f, col=c("#F0B769","#ACEE3F"))
+ if (interactive()) display(annot)
+ }
EBImage.Rcheck/00install.out:
* Installing *source* package 'EBImage' ...
checking for Magick-config... yes
* found ImageMagick version 6.3.3
* found ImageMagick includes in -I/usr/local/include
checking for pkg-config... no
checking for pkgconfig... (cached) no
* pkg-config/pkgconfig not found: compiling without GTK+ support
-----------------------------------------------------
configure: creating ./config.status
config.status: creating src/Makevars
** libs
** arch - i386
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -Wall -g -O2 -Wall -W -D_THREAD_SAFE -I/usr/local/include -fPIC -g -O2 -Wall -std=gnu99 -march=nocona -c EBImage.c -o EBImage.o
EBImage.c: In function 'R_unload_EBImage':
EBImage.c:137: warning: unused parameter 'winDll'
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -Wall -g -O2 -Wall -W -D_THREAD_SAFE -I/usr/local/include -fPIC -g -O2 -Wall -std=gnu99 -march=nocona -c colors.c -o colors.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -Wall -g -O2 -Wall -W -D_THREAD_SAFE -I/usr/local/include -fPIC -g -O2 -Wall -std=gnu99 -march=nocona -c conversions.c -o conversions.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -Wall -g -O2 -Wall -W -D_THREAD_SAFE -I/usr/local/include -fPIC -g -O2 -Wall -std=gnu99 -march=nocona -c display.c -o display.o
display.c: In function 'lib_display':
display.c:42: warning: unused parameter 'nogtk'
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -Wall -g -O2 -Wall -W -D_THREAD_SAFE -I/usr/local/include -fPIC -g -O2 -Wall -std=gnu99 -march=nocona -c drawable.c -o drawable.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -Wall -g -O2 -Wall -W -D_THREAD_SAFE -I/usr/local/include -fPIC -g -O2 -Wall -std=gnu99 -march=nocona -c features_haralick.c -o features_haralick.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -Wall -g -O2 -Wall -W -D_THREAD_SAFE -I/usr/local/include -fPIC -g -O2 -Wall -std=gnu99 -march=nocona -c features_hull.c -o features_hull.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -Wall -g -O2 -Wall -W -D_THREAD_SAFE -I/usr/local/include -fPIC -g -O2 -Wall -std=gnu99 -march=nocona -c features_moments.c -o features_moments.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -Wall -g -O2 -Wall -W -D_THREAD_SAFE -I/usr/local/include -fPIC -g -O2 -Wall -std=gnu99 -march=nocona -c features_zernike.c -o features_zernike.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -Wall -g -O2 -Wall -W -D_THREAD_SAFE -I/usr/local/include -fPIC -g -O2 -Wall -std=gnu99 -march=nocona -c filters_distmap.c -o filters_distmap.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -Wall -g -O2 -Wall -W -D_THREAD_SAFE -I/usr/local/include -fPIC -g -O2 -Wall -std=gnu99 -march=nocona -c filters_magick.c -o filters_magick.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -Wall -g -O2 -Wall -W -D_THREAD_SAFE -I/usr/local/include -fPIC -g -O2 -Wall -std=gnu99 -march=nocona -c filters_morph.c -o filters_morph.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -Wall -g -O2 -Wall -W -D_THREAD_SAFE -I/usr/local/include -fPIC -g -O2 -Wall -std=gnu99 -march=nocona -c filters_normalize.c -o filters_normalize.o
g++-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -Wall -g -O2 -Wall -W -D_THREAD_SAFE -I/usr/local/include -fPIC -g -O2 -Wall -march=nocona -c filters_propagate.cpp -o filters_propagate.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -Wall -g -O2 -Wall -W -D_THREAD_SAFE -I/usr/local/include -fPIC -g -O2 -Wall -std=gnu99 -march=nocona -c filters_thresh.c -o filters_thresh.o
g++-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -Wall -g -O2 -Wall -W -D_THREAD_SAFE -I/usr/local/include -fPIC -g -O2 -Wall -march=nocona -c filters_watershed.cpp -o filters_watershed.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -Wall -g -O2 -Wall -W -D_THREAD_SAFE -I/usr/local/include -fPIC -g -O2 -Wall -std=gnu99 -march=nocona -c io.c -o io.o
io.c: In function 'lib_chooseImages':
io.c:85: warning: unused parameter 'mode'
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -Wall -g -O2 -Wall -W -D_THREAD_SAFE -I/usr/local/include -fPIC -g -O2 -Wall -std=gnu99 -march=nocona -c objects.c -o objects.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -Wall -g -O2 -Wall -W -D_THREAD_SAFE -I/usr/local/include -fPIC -g -O2 -Wall -std=gnu99 -march=nocona -c tools.c -o tools.o
g++-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o EBImage.so EBImage.o colors.o conversions.o display.o drawable.o features_haralick.o features_hull.o features_moments.o features_zernike.o filters_distmap.o filters_magick.o filters_morph.o filters_normalize.o filters_propagate.o filters_thresh.o filters_watershed.o io.o objects.o tools.o -L/usr/local/lib -L/usr/X11R6/lib -L/usr/local/lib -lfreetype -lz -Wl,-framework,CoreServices,-framework,ApplicationServices -lMagick -ltiff -lfreetype -ljpeg -lXext -lSM -lICE -lX11 -lXt -lbz2 -lz -lpthread -lm -lpthread -lWand -lMagick -lWand -F/Library/Frameworks/R.framework/.. -framework R
** R
** inst
** preparing package for lazy loading
** help
>>> Building/Updating help pages for package 'EBImage'
Formats: text html latex example
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
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
features-hull text html latex
features-moments text html latex example
features-zernike text html latex
getFeatures text html latex
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
segmenting text html latex
stackObjects text html latex
thresholding text html latex example
tile text html latex
transformations text html latex
watershed text html latex example
** building package indices ...
* DONE (EBImage)