BioC 3.0: CHECK report for EBImage on zin1

Package: EBImage

Version: 4.8.3

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings EBImage_4.8.3.tar.gz

StartedAt: 2015-04-09 23:30:08 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 23:31:28 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 79.7 seconds

RetCode: 0

Status:  OK

CheckDir: EBImage.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings EBImage_4.8.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/EBImage.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘4.8.3’
* 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 ... [6s/6s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [38s/41s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
EBImage      7.872  0.316   9.667
stackObjects 5.293  1.072   6.523
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test.R’ [3s/3s]
  Comparing ‘test.Rout’ to ‘test.Rout.save’ ... OK
 [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

* installing *source* package ‘EBImage’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-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-3.0-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-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c drawCircle.c -o drawCircle.o
g++ -I/home/biocbuild/bbs-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c ocontour.c -o ocontour.o
g++ -I/home/biocbuild/bbs-3.0-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-3.0-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-3.0-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-3.0-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: unused variable ‘ibg’ [-Wunused-variable]
tile.c:21:29: warning: unused variable ‘ifg’ [-Wunused-variable]
tile.c: In function ‘untile’:
tile.c:142:37: warning: unused variable ‘id’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-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]
tools.c: In function ‘getColorStrides’:
tools.c:119:20: warning: unused variable ‘colorMode’ [-Wunused-variable]
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c watershed.cpp -o watershed.o
g++ -shared -L/home/biocbuild/bbs-3.0-bioc/R/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 -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/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	7.872	0.316	9.667
Image	0.404	0.000	0.407
bwlabel	1.088	0.032	1.128
channel	0.768	0.004	0.795
colorLabels	0.120	0.004	0.123
combine	0.752	0.008	0.769
computeFeatures	0.928	0.012	0.943
display	3.805	0.092	3.941
distmap	0.144	0.000	0.144
drawCircle	0.100	0.012	0.111
equalize	1.544	0.004	1.553
fillHull	0.372	0.004	0.404
filter2	1.396	0.020	1.420
floodFill	0.276	0.004	0.281
gblur	0.504	0.000	0.504
io	0.988	0.100	2.537
localCurvature	1.152	0.004	1.156
medianFilter	1.144	0.108	1.252
morphology	0.148	0.000	0.148
normalize	0.028	0.000	0.027
ocontour	0.056	0.004	0.059
otsu	0.240	0.000	0.239
paintObjects	2.108	0.016	2.126
propagate	1.396	0.012	1.407
rmObjects	0.052	0.000	0.053
spatial	0.772	0.000	0.777
stackObjects	5.293	1.072	6.523
thresh	0.232	0.004	0.236
tile	0.480	0.096	0.574
transpose	0.384	0.000	0.390
watershed	0.152	0.004	0.178