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BioC 3.1: CHECK report for EBImage on morelia

This page was generated on 2015-10-09 09:38:17 -0700 (Fri, 09 Oct 2015).

Package 285/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EBImage 4.10.1
Andrzej OleÅ›
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/EBImage
Last Changed Rev: 105709 / Revision: 109384
Last Changed Date: 2015-07-01 01:46:04 -0700 (Wed, 01 Jul 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: EBImage
Version: 4.10.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EBImage_4.10.1.tar.gz
StartedAt: 2015-10-09 01:29:02 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 01:30:32 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 89.9 seconds
RetCode: 0
Status:  OK 
CheckDir: EBImage.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EBImage_4.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/EBImage.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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/8s] 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 ... [41s/45s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
EBImage      6.766  1.874  10.642
stackObjects 4.624  1.613   6.247
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’ [2s/2s]
  Comparing ‘test.Rout’ to ‘test.Rout.save’ ...328,334c328,334
< checking 'erodeGrayscale' ... OK (hash=1933584)
< checking 'dilateGrayscale' ... OK (hash=2153480)
< checking 'openingGrayscale' ... OK (hash=2032872)
< checking 'closingGrayscale' ... OK (hash=2044186)
< checking 'whiteTopHatGrayscale' ... OK (hash=3278.861)
< checking 'blackTopHatGrayscale' ... OK (hash=8035.68)
< checking 'selfcomplementaryTopHatGrayscale' ... OK (hash=-3647.025)
---
> checking 'erodeGrayscale' ... OK (hash=1910799)
> checking 'dilateGrayscale' ... OK (hash=2131265)
> checking 'openingGrayscale' ... OK (hash=2011378)
> checking 'closingGrayscale' ... OK (hash=2020192)
> checking 'whiteTopHatGrayscale' ... OK (hash=24772.23)
> checking 'blackTopHatGrayscale' ... OK (hash=-15958.24)
> checking 'selfcomplementaryTopHatGrayscale' ... OK (hash=8814.088)
464,470c464,470
< checking 'erodeGrayscale' ... OK (hash=2210109)
< checking 'dilateGrayscale' ... OK (hash=2525741)
< checking 'openingGrayscale' ... OK (hash=2365578)
< checking 'closingGrayscale' ... OK (hash=2360638)
< checking 'whiteTopHatGrayscale' ... OK (hash=-11087.86)
< checking 'blackTopHatGrayscale' ... OK (hash=5929.453)
< checking 'selfcomplementaryTopHatGrayscale' ... OK (hash=-5704.68)
---
> checking 'erodeGrayscale' ... OK (hash=2165546)
> checking 'dilateGrayscale' ... OK (hash=2490913)
> checking 'openingGrayscale' ... OK (hash=2332450)
> checking 'closingGrayscale' ... OK (hash=2304995)
> checking 'whiteTopHatGrayscale' ... OK (hash=22258.68)
> checking 'blackTopHatGrayscale' ... OK (hash=-49714.21)
> checking 'selfcomplementaryTopHatGrayscale' ... OK (hash=-27455.43)
 [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

Status: OK

EBImage.Rcheck/00install.out:

* installing *source* package ‘EBImage’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c EBImage.c -o EBImage.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c distmap.c -o distmap.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c drawCircle.c -o drawCircle.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c floodFill.cpp -o floodFill.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c greyscale_morphology.c -o greyscale_morphology.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c haralick.c -o haralick.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c medianFilter.c -o medianFilter.o
medianFilter.c:463:45: warning: unused variable 'j' [-Wunused-variable]
  int nprotect = 0, x, y, z, r, memsize, i, j, imagesize, framesize;
                                            ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c morphology.c -o morphology.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c nativeRaster.c -o nativeRaster.o
nativeRaster.c:14:11: warning: unused variable 'in' [-Wunused-variable]
  double *in;
          ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c normalize.c -o normalize.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c objects.c -o objects.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c ocontour.c -o ocontour.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c propagate.cpp -o propagate.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c spatial.c -o spatial.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c thresh.c -o thresh.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c tile.c -o tile.o
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: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:142:37: warning: unused variable 'id' [-Wunused-variable]
  void *src, *tgt; double *dd; int *id;
                                    ^
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c tools.c -o tools.o
tools.c:119:20: warning: unused variable 'colorMode' [-Wunused-variable]
  int width,height,colorMode,nbChannels;
                   ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c watershed.cpp -o watershed.o
clang++ -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 -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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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)

EBImage.Rcheck/EBImage-Ex.timings:

nameusersystemelapsed
EBImage 6.766 1.87410.642
Image0.4120.1330.546
bwlabel1.1280.2471.377
channel0.6830.2780.962
colorLabels0.1070.0700.177
combine0.9020.6421.570
computeFeatures0.6690.1890.861
display2.6911.3674.065
distmap0.1070.0380.146
drawCircle0.0340.0120.046
equalize1.2100.5241.746
fillHull0.3670.1680.535
filter21.0040.2311.235
floodFill0.2260.0390.265
gblur0.3800.0470.428
io0.9070.2312.632
localCurvature0.8100.3251.139
medianFilter0.9240.1271.051
morphology0.1170.0170.136
normalize0.0240.0100.035
ocontour0.0210.0200.041
otsu0.2080.0310.239
paintObjects2.0310.3092.743
propagate1.6580.3121.976
rmObjects0.1100.0380.148
spatial0.6990.0940.794
stackObjects4.6241.6136.247
thresh0.2400.1900.431
tile0.4610.3790.842
transpose0.2730.1580.458
watershed0.1110.0130.125