BioC 3.2: CHECK report for EBImage on perceval

Package: EBImage

Version: 4.12.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EBImage_4.12.1.tar.gz

StartedAt: 2015-11-10 04:24:51 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 04:26:37 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 106.3 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 EBImage_4.12.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/EBImage.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘4.12.1’
* 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 ... [7s/7s] OK
* checking installed package size ... NOTE
  installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc      5.0Mb
    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 ... [51s/54s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
EBImage      7.844  2.410  11.928
stackObjects 5.389  2.346   7.736
display      3.297  1.843   5.142
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’ [6s/7s]
  Comparing ‘test.Rout’ to ‘test.Rout.save’ ...518c518
< checking 'computeFeatures' .................... PASS (97f8efe602b64bd6) 3989776
---
> checking 'computeFeatures' .................... PASS (607eae59e3423025) 3988895
600c600
< checking 'computeFeatures' .................... PASS (cf78a8f8ee93a443) 746878.2
---
> checking 'computeFeatures' .................... PASS (f17bea67c6db8efa) 746878.2
684c684
< checking 'computeFeatures' .................... PASS (94bb85e2e1c453df) 416139928
---
> checking 'computeFeatures' .................... PASS (1d847743be56e5a7) 416164140
689,690c689,690
< checking 'gblur' .............................. PASS (ec17350de55398c2) 1037581
< checking 'filter2' ............................ PASS (0ea2ee06ef12c1f4) 25640840
---
> checking 'gblur' .............................. PASS (f499c36c42da96ae) 1037581
> checking 'filter2' ............................ PASS (ae9004d59d404524) 25640840
767c767
< checking 'computeFeatures' .................... PASS (5eaf503a54600569) 749353.1
---
> checking 'computeFeatures' .................... PASS (43ed64a6574660f3) 749353.1
850c850
< checking 'computeFeatures' .................... PASS (b68f1620a082eb3d) 734993.9
---
> checking 'computeFeatures' .................... PASS (5f168ac8bf99f53d) 734993.9
 [7s/8s] 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
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/EBImage.Rcheck/00check.log’
for details.

* 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 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
morphology.c: In function ‘compute_lookup_table_for_line_dilate’:
morphology.c:59: warning: statement with no effect
morphology.c:62: warning: statement with no effect
morphology.c:65: warning: statement with no effect
morphology.c: In function ‘compute_lookup_table_for_line_erode’:
morphology.c:89: warning: statement with no effect
morphology.c:92: warning: statement with no effect
morphology.c:95: warning: statement with no effect
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 nativeRaster.c -o nativeRaster.o
nativeRaster.c: In function ‘nativeRaster’:
nativeRaster.c:38: warning: pointer targets in assignment differ in signedness
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
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
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 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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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)

name	user	system	elapsed
EBImage	7.844	2.410	11.928
Image	0.514	0.163	0.770
bwlabel	1.537	0.452	1.991
channel	0.842	0.447	1.290
colorLabels	0.112	0.048	0.161
combine	1.202	0.900	2.115
computeFeatures	0.93	0.26	1.19
display	3.297	1.843	5.142
distmap	0.156	0.024	0.181
drawCircle	0.039	0.015	0.055
equalize	1.430	0.824	2.275
fillHull	0.471	0.127	0.598
filter2	1.142	0.344	1.486
floodFill	0.281	0.054	0.335
gblur	0.476	0.078	0.555
io	1.078	0.382	3.133
localCurvature	0.908	0.309	1.219
medianFilter	1.525	0.261	1.787
morphology	0.159	0.020	0.183
normalize	0.028	0.040	0.068
ocontour	0.019	0.002	0.022
otsu	0.249	0.044	0.292
paintObjects	2.298	0.478	2.778
propagate	1.735	0.251	1.988
rmObjects	0.175	0.030	0.204
spatial	0.916	0.153	1.070
stackObjects	5.389	2.346	7.736
thresh	0.303	0.099	0.403
tile	0.561	0.561	1.124
transpose	0.272	0.228	0.499
watershed	0.145	0.016	0.162