BioC 3.0: CHECK report for EBImage on perceval

Package: EBImage

Version: 4.8.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch EBImage_4.8.3.tar.gz

StartedAt: 2015-04-10 01:02:52 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 01:05:23 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 151.1 seconds

RetCode: 0

Status:  OK

CheckDir: EBImage.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch EBImage_4.8.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/EBImage.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EBImage/DESCRIPTION’ ... OK
* this is package ‘EBImage’ version ‘4.8.3’
* 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/12s] OK
* checking installed package size ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [80s/86s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
EBImage      13.859  2.992  18.577
stackObjects  9.016  2.942  12.042
display       6.987  2.188   9.279
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test.R’ [6s/6s]
  Comparing ‘test.Rout’ to ‘test.Rout.save’ ...202,205c202,205
< checking 'erodeGreyScale' ... OK (hash=1915548)
< checking 'dilateGreyScale' ... OK (hash=2144831)
< checking 'whiteTopHatGreyScale' ... OK (hash=11729.92)
< checking 'selfcomplementaryTopHatGreyScale' ... OK (hash=-2898.296)
---
> checking 'erodeGreyScale' ... OK (hash=1910799)
> checking 'dilateGreyScale' ... OK (hash=2131265)
> checking 'whiteTopHatGreyScale' ... OK (hash=24772.23)
> checking 'selfcomplementaryTopHatGreyScale' ... OK (hash=8814.088)
254,257c254,257
< checking 'erodeGreyScale' ... OK (hash=2210109)
< checking 'dilateGreyScale' ... OK (hash=2525741)
< checking 'whiteTopHatGreyScale' ... OK (hash=-11297.79)
< checking 'selfcomplementaryTopHatGreyScale' ... OK (hash=-43774.66)
---
> checking 'erodeGreyScale' ... OK (hash=2165546)
> checking 'dilateGreyScale' ... OK (hash=2490913)
> checking 'whiteTopHatGreyScale' ... OK (hash=22258.68)
> checking 'selfcomplementaryTopHatGreyScale' ... OK (hash=-27455.43)
 [6s/6s] 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

* installing *source* package ‘EBImage’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c EBImage.c -o EBImage.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c distmap.c -o distmap.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c drawCircle.c -o drawCircle.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c floodFill.cpp -o floodFill.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c greyscale_morphology.c -o greyscale_morphology.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c haralick.c -o haralick.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c medianFilter.c -o medianFilter.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c morphology.c -o morphology.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c normalize.c -o normalize.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c objects.c -o objects.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ocontour.c -o ocontour.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c propagate.cpp -o propagate.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c spatial.c -o spatial.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c thresh.c -o thresh.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c tile.c -o tile.o
tile.c: In function ‘tile’:
tile.c:21: warning: unused variable ‘ibg’
tile.c:21: warning: unused variable ‘ifg’
tile.c: In function ‘untile’:
tile.c:142: warning: unused variable ‘id’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c tools.c -o tools.o
tools.c: In function ‘getColorStrides’:
tools.c:119: warning: unused variable ‘colorMode’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c watershed.cpp -o watershed.o
llvm-g++-4.2 -arch x86_64 -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 -L/usr/local/lib -o EBImage.so EBImage.o distmap.o drawCircle.o floodFill.o greyscale_morphology.o haralick.o medianFilter.o morphology.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-3.0-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)

name	user	system	elapsed
EBImage	13.859	2.992	18.577
Image	0.657	0.313	1.023
bwlabel	1.998	0.581	2.626
channel	1.304	0.815	2.505
colorLabels	0.151	0.055	0.212
combine	1.556	1.089	2.693
computeFeatures	1.393	0.531	1.944
display	6.987	2.188	9.279
distmap	0.183	0.090	0.301
drawCircle	0.080	0.047	0.149
equalize	2.598	1.369	4.014
fillHull	0.569	0.144	0.733
filter2	2.726	0.466	3.237
floodFill	0.424	0.159	0.602
gblur	0.848	0.137	1.005
io	1.579	0.520	3.620
localCurvature	1.966	0.920	2.911
medianFilter	2.426	0.537	2.980
morphology	0.243	0.067	0.363
normalize	0.043	0.060	0.123
ocontour	0.031	0.009	0.053
otsu	0.359	0.096	0.473
paintObjects	3.549	0.691	4.362
propagate	1.659	0.273	1.957
rmObjects	0.099	0.054	0.171
spatial	1.261	0.265	1.970
stackObjects	9.016	2.942	12.042
thresh	0.356	0.133	0.542
tile	1.053	0.917	2.054
transpose	0.651	0.240	0.956
watershed	0.157	0.033	0.236