BioC 2.12: CHECK report for EBImage on george2

Package: EBImage

Version: 4.2.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings EBImage_4.2.1.tar.gz

StartedAt: 2013-10-09 01:30:50 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 01:33:20 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 149.7 seconds

RetCode: 0

Status:  OK

CheckDir: EBImage.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/EBImage.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EBImage/DESCRIPTION’ ... OK
* this is package ‘EBImage’ version ‘4.2.1’
* 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 ... [9s/10s] OK
* checking installed package size ... OK
* checking package 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 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 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 line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [78s/84s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
EBImage      15.057  0.732  17.680
stackObjects 13.089  2.052  15.341
paintObjects  6.468  0.176   6.658
display       5.629  0.032   6.013
io            4.008  0.136   6.077
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test.R’ [6s/7s]
  Comparing ‘test.Rout’ to ‘test.Rout.save’ ... OK
 [7s/7s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘EBImage’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c EBImage.c -o EBImage.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c distmap.c -o distmap.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c drawCircle.c -o drawCircle.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c floodFill.cpp -o floodFill.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c greyscale_morphology.c -o greyscale_morphology.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c haralick.c -o haralick.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c medianFilter.c -o medianFilter.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c morphology.c -o morphology.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c normalize.c -o normalize.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c objects.c -o objects.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c ocontour.c -o ocontour.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c propagate.cpp -o propagate.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c spatial.c -o spatial.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c thresh.c -o thresh.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c tile.c -o tile.o
tile.c: In function ‘tile’:
tile.c:21:51: warning: variable ‘iim’ set but not used [-Wunused-but-set-variable]
tile.c:21:34: warning: variable ‘ibg’ set but not used [-Wunused-but-set-variable]
tile.c: In function ‘untile’:
tile.c:129:37: warning: unused variable ‘id’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c tools.c -o tools.o
tools.c: In function ‘validImage’:
tools.c:44:11: warning: variable ‘dp’ set but not used [-Wunused-but-set-variable]
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c watershed.cpp -o watershed.o
g++ -shared -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 -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-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	15.057	0.732	17.680
Image	0.792	0.024	0.815
bwlabel	2.376	0.044	2.480
channel	4.124	0.248	4.762
combine	0.012	0.000	0.009
computeFeatures	2.476	0.080	3.160
display	5.629	0.032	6.013
distmap	0.108	0.000	0.123
drawCircle	0.128	0.000	0.149
fillHull	0.700	0.000	0.714
filter2	2.852	0.000	2.860
floodFill	0.452	0.000	0.453
gblur	0.652	0.004	0.661
io	4.008	0.136	6.077
localCurvature	3.172	0.008	3.186
medianFilter	4.541	0.416	4.981
morphology	0.072	0.000	0.073
normalize	0.088	0.000	0.089
ocontour	0.056	0.000	0.056
paintObjects	6.468	0.176	6.658
propagate	2.268	0.040	2.449
rmObjects	0.188	0.008	0.195
spatial	0.304	0.000	0.304
stackObjects	13.089	2.052	15.341
thresh	0.488	0.032	0.518
tile	0.812	0.064	0.875
transpose	0.372	0.020	0.392
watershed	0.132	0.004	0.135