EBImage 4.11.7
Andrzej Oleś
| Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/EBImage | | Last Changed Rev: 106668 / Revision: 107696 | | Last Changed Date: 2015-07-22 11:01:29 -0700 (Wed, 22 Jul 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EBImage_4.11.7.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/EBImage.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EBImage/DESCRIPTION’ ... OK
* this is package ‘EBImage’ version ‘4.11.7’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘EBImage’ can be installed ... [8s/8s] OK
* checking installed package size ... NOTE
installed size is 7.6Mb
sub-directories of 1Mb or more:
doc 5.4Mb
images 1.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [45s/49s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
EBImage 7.597 1.819 11.207
stackObjects 5.203 1.672 6.947
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test.R’ [3s/3s]
Comparing ‘test.Rout’ to ‘test.Rout.save’ ...329,334c329,334
< checking 'dilateGrayscale' ... OK (hash=2144831)
< checking 'openingGrayscale' ... OK (hash=2027341)
< checking 'closingGrayscale' ... OK (hash=2028876)
< checking 'whiteTopHatGrayscale' ... OK (hash=4244.465)
< checking 'blackTopHatGrayscale' ... OK (hash=-6489.398)
< checking 'selfcomplementaryTopHatGrayscale' ... OK (hash=11314.64)
---
> checking 'dilateGrayscale' ... OK (hash=2131265)
> checking 'openingGrayscale' ... OK (hash=2011378)
> checking 'closingGrayscale' ... OK (hash=2020192)
> checking 'whiteTopHatGrayscale' ... OK (hash=24772.23)
> checking 'blackTopHatGrayscale' ... OK (hash=-15958.24)
> checking 'selfcomplementaryTopHatGrayscale' ... OK (hash=8814.088)
464,470c464,470
< checking 'erodeGrayscale' ... OK (hash=2185462)
< checking 'dilateGrayscale' ... OK (hash=2525741)
< checking 'openingGrayscale' ... OK (hash=2365914)
< checking 'closingGrayscale' ... OK (hash=2328339)
< checking 'whiteTopHatGrayscale' ... OK (hash=-11634.23)
< checking 'blackTopHatGrayscale' ... OK (hash=-26369.65)
< checking 'selfcomplementaryTopHatGrayscale' ... OK (hash=-37575.43)
---
> checking 'erodeGrayscale' ... OK (hash=2165546)
> checking 'dilateGrayscale' ... OK (hash=2490913)
> checking 'openingGrayscale' ... OK (hash=2332450)
> checking 'closingGrayscale' ... OK (hash=2304995)
> checking 'whiteTopHatGrayscale' ... OK (hash=22258.68)
> checking 'blackTopHatGrayscale' ... OK (hash=-49714.21)
> checking 'selfcomplementaryTopHatGrayscale' ... OK (hash=-27455.43)
[3s/3s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.2-bioc/meat/EBImage.Rcheck/00check.log’
for details.
* installing *source* package ‘EBImage’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c EBImage.c -o EBImage.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c distmap.c -o distmap.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c drawCircle.c -o drawCircle.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c floodFill.cpp -o floodFill.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c greyscale_morphology.c -o greyscale_morphology.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c haralick.c -o haralick.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c medianFilter.c -o medianFilter.o
medianFilter.c:463:45: warning: unused variable 'j' [-Wunused-variable]
int nprotect = 0, x, y, z, r, memsize, i, j, imagesize, framesize;
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c morphology.c -o morphology.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c nativeRaster.c -o nativeRaster.o
nativeRaster.c:14:11: warning: unused variable 'in' [-Wunused-variable]
double *in;
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c normalize.c -o normalize.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c objects.c -o objects.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c ocontour.c -o ocontour.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c propagate.cpp -o propagate.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c spatial.c -o spatial.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c thresh.c -o thresh.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c tile.c -o tile.o
tile.c:21:29: warning: unused variable 'ifg' [-Wunused-variable]
int nprotect, nx, ny, nz, ifg, ibg, nxr, nyr, * iim, i, j, index, x, y;
^
tile.c:21:34: warning: unused variable 'ibg' [-Wunused-variable]
int nprotect, nx, ny, nz, ifg, ibg, nxr, nyr, * iim, i, j, index, x, y;
^
tile.c:142:37: warning: unused variable 'id' [-Wunused-variable]
void *src, *tgt; double *dd; int *id;
^
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c tools.c -o tools.o
tools.c:119:20: warning: unused variable 'colorMode' [-Wunused-variable]
int width,height,colorMode,nbChannels;
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c watershed.cpp -o watershed.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o EBImage.so EBImage.o distmap.o drawCircle.o floodFill.o greyscale_morphology.o haralick.o medianFilter.o morphology.o nativeRaster.o normalize.o objects.o ocontour.o propagate.o spatial.o thresh.o tile.o tools.o watershed.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/EBImage.Rcheck/EBImage/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (EBImage)