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This page was generated on 2015-08-24 10:47:07 -0700 (Mon, 24 Aug 2015).
| Package 294/1071 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| EBImage 4.11.7 Andrzej Oleś
| 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 | |
| Package: EBImage |
| Version: 4.11.7 |
| Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings EBImage_4.11.7.tar.gz |
| StartedAt: 2015-08-23 23:30:18 -0700 (Sun, 23 Aug 2015) |
| EndedAt: 2015-08-23 23:31:22 -0700 (Sun, 23 Aug 2015) |
| EllapsedTime: 63.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: EBImage.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings EBImage_4.11.7.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-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 ‘4.11.7’
* 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 ... [7s/7s] OK
* checking installed package size ... NOTE
installed size is 6.6Mb
sub-directories of 1Mb or more:
doc 4.0Mb
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 ... [28s/31s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
EBImage 6.11 0.136 7.729
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test.R’ [2s/2s]
Comparing ‘test.Rout’ to ‘test.Rout.save’ ... OK
[2s/2s] 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
‘/home/biocbuild/bbs-3.2-bioc/meat/EBImage.Rcheck/00check.log’
for details.
EBImage.Rcheck/00install.out:
* installing *source* package ‘EBImage’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-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-3.2-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-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c drawCircle.c -o drawCircle.o
g++ -I/home/biocbuild/bbs-3.2-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-3.2-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-3.2-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-3.2-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-3.2-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-3.2-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-3.2-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-3.2-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-3.2-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-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c ocontour.c -o ocontour.o
g++ -I/home/biocbuild/bbs-3.2-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-3.2-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-3.2-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-3.2-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-3.2-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-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c watershed.cpp -o watershed.o
g++ -shared -L/home/biocbuild/bbs-3.2-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-3.2-bioc/R/lib -lR
installing to /home/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)
EBImage.Rcheck/EBImage-Ex.timings:
| name | user | system | elapsed | |
| EBImage | 6.110 | 0.136 | 7.729 | |
| Image | 0.324 | 0.012 | 0.337 | |
| bwlabel | 0.929 | 0.012 | 0.942 | |
| channel | 0.583 | 0.012 | 0.596 | |
| colorLabels | 0.082 | 0.004 | 0.087 | |
| combine | 0.902 | 0.004 | 0.908 | |
| computeFeatures | 0.714 | 0.000 | 0.714 | |
| display | 2.637 | 0.088 | 2.732 | |
| distmap | 0.110 | 0.004 | 0.114 | |
| drawCircle | 0.03 | 0.00 | 0.03 | |
| equalize | 1.157 | 0.004 | 1.163 | |
| fillHull | 0.313 | 0.000 | 0.313 | |
| filter2 | 0.868 | 0.000 | 0.869 | |
| floodFill | 0.184 | 0.000 | 0.191 | |
| gblur | 0.334 | 0.000 | 0.340 | |
| io | 0.694 | 0.004 | 2.126 | |
| localCurvature | 0.704 | 0.004 | 0.707 | |
| medianFilter | 0.913 | 0.012 | 0.924 | |
| morphology | 0.104 | 0.000 | 0.104 | |
| normalize | 0.018 | 0.000 | 0.018 | |
| ocontour | 0.009 | 0.004 | 0.013 | |
| otsu | 0.178 | 0.000 | 0.178 | |
| paintObjects | 1.805 | 0.015 | 1.855 | |
| propagate | 1.442 | 0.012 | 1.453 | |
| rmObjects | 0.086 | 0.000 | 0.086 | |
| spatial | 0.634 | 0.008 | 0.641 | |
| stackObjects | 3.869 | 0.268 | 4.134 | |
| thresh | 0.172 | 0.004 | 0.176 | |
| tile | 0.331 | 0.028 | 0.359 | |
| transpose | 0.172 | 0.000 | 0.172 | |
| watershed | 0.112 | 0.004 | 0.115 | |