BioC 3.1: CHECK report for EBImage on zin2

Package: EBImage

Version: 4.10.1

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings EBImage_4.10.1.tar.gz

StartedAt: 2015-10-09 00:46:10 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 00:47:40 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 90.5 seconds

RetCode: 0

Status:  OK

CheckDir: EBImage.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings EBImage_4.10.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/EBImage.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EBImage/DESCRIPTION’ ... OK
* this is package ‘EBImage’ version ‘4.10.1’
* 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 ... [6s/11s] 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 ... [26s/41s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
EBImage      5.573  0.089  10.063
stackObjects 3.827  0.348   6.846
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’ [2s/3s]
  Comparing ‘test.Rout’ to ‘test.Rout.save’ ... OK
 [2s/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: OK

* installing *source* package ‘EBImage’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-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-3.1-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-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c drawCircle.c -o drawCircle.o
g++ -I/home/biocbuild/bbs-3.1-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-3.1-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-3.1-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-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c medianFilter.c -o medianFilter.o
medianFilter.c: In function ‘medianFilter’:
medianFilter.c:463:45: warning: unused variable ‘j’ [-Wunused-variable]
   int nprotect = 0, x, y, z, r, memsize, i, j, imagesize, framesize;
                                             ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c nativeRaster.c -o nativeRaster.o
nativeRaster.c: In function ‘nativeRaster’:
nativeRaster.c:14:11: warning: unused variable ‘in’ [-Wunused-variable]
   double *in;
           ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c objects.c -o objects.o
In file included from objects.h:5:0,
                 from objects.c:1:
objects.c: In function ‘stackObjects’:
/home/biocbuild/bbs-3.1-bioc/R/include/Rdefines.h:132:37: warning: ‘dim’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define SET_DIM(x, n)      setAttrib(x, R_DimSymbol, n)
                                     ^
objects.c:171:22: note: ‘dim’ was declared here
   SEXP res, st=NULL, dim, xys;
                      ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c ocontour.c -o ocontour.o
g++ -I/home/biocbuild/bbs-3.1-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-3.1-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-3.1-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-3.1-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]
   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: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: In function ‘untile’:
tile.c:142:37: warning: unused variable ‘id’ [-Wunused-variable]
   void *src, *tgt; double *dd; int *id;
                                     ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-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]
   double *dp;
           ^
tools.c: In function ‘getColorStrides’:
tools.c:119:20: warning: unused variable ‘colorMode’ [-Wunused-variable]
   int width,height,colorMode,nbChannels;
                    ^
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c watershed.cpp -o watershed.o
g++ -shared -L/home/biocbuild/bbs-3.1-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 nativeRaster.o normalize.o objects.o ocontour.o propagate.o spatial.o thresh.o tile.o tools.o watershed.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-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	5.573	0.089	10.063
Image	0.313	0.008	0.344
bwlabel	0.893	0.001	1.006
channel	0.554	0.000	0.694
colorLabels	0.077	0.000	0.137
combine	0.713	0.003	0.901
computeFeatures	0.669	0.004	0.788
display	2.064	0.047	3.214
distmap	0.098	0.000	0.110
drawCircle	0.027	0.000	0.026
equalize	1.078	0.000	1.657
fillHull	0.273	0.004	0.336
filter2	0.794	0.000	1.014
floodFill	0.18	0.00	0.18
gblur	0.331	0.000	0.585
io	0.596	0.007	2.524
localCurvature	0.662	0.003	0.819
medianFilter	0.884	0.039	1.388
morphology	0.105	0.000	0.105
normalize	0.018	0.000	0.017
ocontour	0.013	0.000	0.013
otsu	0.179	0.000	0.279
paintObjects	1.645	0.000	2.280
propagate	1.393	0.000	2.122
rmObjects	0.087	0.000	0.183
spatial	0.672	0.004	0.818
stackObjects	3.827	0.348	6.846
thresh	0.174	0.000	0.307
tile	0.369	0.078	0.709
transpose	0.160	0.031	0.237
watershed	0.111	0.004	0.181