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BioC 2.13: CHECK report for EBImage on perceval

This page was generated on 2014-04-05 09:51:50 -0700 (Sat, 05 Apr 2014).

Package 222/750HostnameOS / ArchBUILDCHECKBUILD BIN
EBImage 4.4.0
Andrzej Oles
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/EBImage
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: EBImage
Version: 4.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch EBImage_4.4.0.tar.gz
StartedAt: 2014-04-05 01:01:55 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 01:04:33 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 158.2 seconds
RetCode: 0
Status:  OK 
CheckDir: EBImage.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/EBImage.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘4.4.0’
* 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/9s] 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘parseColorMode’ ‘selectChannel’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘EBImage-introduction.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [73s/93s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
stackObjects 10.728  4.239  15.865
EBImage      10.747  3.324  16.270
display       5.682  1.635   7.684
io            2.212  1.155  17.149
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test.R’ [6s/7s]
  Comparing ‘test.Rout’ to ‘test.Rout.save’ ...254,257c254,257
< checking 'erodeGreyScale' ... OK (hash=5256840)
< checking 'dilateGreyScale' ... OK (hash=5764880)
< checking 'whiteTopHatGreyScale' ... OK (hash=136404.6)
< checking 'selfcomplementaryTopHatGreyScale' ... OK (hash=280896.1)
---
> checking 'erodeGreyScale' ... OK (hash=5123645)
> checking 'dilateGreyScale' ... OK (hash=5764578)
> checking 'whiteTopHatGreyScale' ... OK (hash=140101.3)
> checking 'selfcomplementaryTopHatGreyScale' ... OK (hash=144311.9)
 [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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/EBImage.Rcheck/00check.log’
for details.

EBImage.Rcheck/00install.out:

* 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 greyscale_morphology.c -o greyscale_morphology.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
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
tile.c: In function ‘untile’:
tile.c:129: warning: unused variable ‘id’
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/usr/local/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.13-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:

nameusersystemelapsed
EBImage10.747 3.32416.270
Image0.4220.3320.762
bwlabel1.6950.7102.476
channel2.0600.7732.870
colorLabels0.1440.1710.318
combine1.8851.1983.124
computeFeatures1.9210.7672.779
display5.6821.6357.684
distmap0.0830.0880.189
drawCircle0.0500.0580.124
fillHull0.4310.2420.698
filter21.1640.4671.655
floodFill0.1890.1660.363
gblur0.2080.1150.324
io 2.212 1.15517.149
localCurvature1.4540.8112.514
medianFilter2.6000.8123.686
morphology0.0290.0240.055
normalize0.0380.0310.071
ocontour0.0350.0250.064
paintObjects3.0701.1414.411
propagate1.4640.1491.731
rmObjects0.1010.0550.169
spatial0.2120.1720.416
stackObjects10.728 4.23915.865
thresh0.3960.2360.638
tile0.7510.8991.677
transpose0.2360.1430.413
watershed0.0830.0360.125