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BioC 3.1: CHECK report for EBImage on moscato2

This page was generated on 2015-10-09 09:27:39 -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: rm -rf EBImage.buildbin-libdir EBImage.Rcheck && mkdir EBImage.buildbin-libdir EBImage.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=EBImage.buildbin-libdir EBImage_4.10.1.tar.gz >EBImage.Rcheck\00install.out 2>&1 && cp EBImage.Rcheck\00install.out EBImage-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=EBImage.buildbin-libdir --install="check:EBImage-install.out" --force-multiarch --no-vignettes --timings EBImage_4.10.1.tar.gz
StartedAt: 2015-10-09 01:24:47 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 01:28:11 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 204.7 seconds
RetCode: 0
Status:  OK  
CheckDir: EBImage.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf EBImage.buildbin-libdir EBImage.Rcheck && mkdir EBImage.buildbin-libdir EBImage.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=EBImage.buildbin-libdir EBImage_4.10.1.tar.gz >EBImage.Rcheck\00install.out 2>&1 && cp EBImage.Rcheck\00install.out EBImage-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=EBImage.buildbin-libdir --install="check:EBImage-install.out" --force-multiarch --no-vignettes --timings EBImage_4.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/EBImage.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'EBImage' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc      2.2Mb
    images   1.7Mb
    libs     1.3Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'E:/biocbld/bbs-3.1-bioc/meat/EBImage.buildbin-libdir/EBImage/libs/i386/EBImage.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'E:/biocbld/bbs-3.1-bioc/meat/EBImage.buildbin-libdir/EBImage/libs/x64/EBImage.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [66s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
EBImage      11.72   1.30   14.67
stackObjects  6.57   1.06    7.64
** running examples for arch 'x64' ... [54s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
EBImage      8.17   1.42   12.17
stackObjects 6.53   1.46    8.01
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test.R' [4s]
  Comparing 'test.Rout' to 'test.Rout.save' ...183c183
< checking 'medianFilter' ... OK (hash=764192.3)
---
> checking 'medianFilter' ... OK (hash=764201.8)
251c251
< checking 'medianFilter' ... OK (hash=651316.6)
---
> checking 'medianFilter' ... OK (hash=651325.7)
318c318
< checking 'medianFilter' ... OK (hash=2032099)
---
> checking 'medianFilter' ... OK (hash=2032139)
454c454
< checking 'medianFilter' ... OK (hash=2348168)
---
> checking 'medianFilter' ... OK (hash=2348208)
522c522
< checking 'medianFilter' ... OK (hash=2227445)
---
> checking 'medianFilter' ... OK (hash=2227485)
Warning message:
running command '"diff" -bw "E:\biocbld\bbs-3.1-bioc\tmpdir\RtmpSikEOF\Rdiffae74df62b65" "E:\biocbld\bbs-3.1-bioc\tmpdir\RtmpSikEOF\Rdiffbe743e281865"' had status 1 
 [4s] OK
** running tests for arch 'x64' ...
  Running 'test.R' [4s]
  Comparing 'test.Rout' to 'test.Rout.save' ...264c264
< checking 'closingGrayscale' ... OK (hash=642696.1)
---
> checking 'closingGrayscale' ... OK (hash=642689.2)
266c266
< checking 'blackTopHatGrayscale' ... OK (hash=-9353.449)
---
> checking 'blackTopHatGrayscale' ... OK (hash=-9362.273)
Warning message:
running command '"diff" -bw "E:\biocbld\bbs-3.1-bioc\tmpdir\RtmpmYirwd\Rdiffa1a404d1a5979" "E:\biocbld\bbs-3.1-bioc\tmpdir\RtmpmYirwd\Rdiffb1a4053e2401a"' had status 1 
 [5s] 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: 2 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/EBImage.Rcheck/00check.log'
for details.


EBImage.Rcheck/00install.out:


install for i386

* installing *source* package 'EBImage' ...
** libs
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c EBImage.c -o EBImage.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c distmap.c -o distmap.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c drawCircle.c -o drawCircle.o
g++ -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c floodFill.cpp -o floodFill.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c greyscale_morphology.c -o greyscale_morphology.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c haralick.c -o haralick.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c medianFilter.c -o medianFilter.o
medianFilter.c: In function 'medianFilter':
medianFilter.c:463:45: warning: unused variable 'j' [-Wunused-variable]
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c morphology.c -o morphology.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c nativeRaster.c -o nativeRaster.o
nativeRaster.c: In function 'nativeRaster':
nativeRaster.c:14:11: warning: unused variable 'in' [-Wunused-variable]
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c normalize.c -o normalize.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c objects.c -o objects.o
objects.c: In function 'stackObjects':
objects.c:239:7: warning: 'dim' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ocontour.c -o ocontour.o
g++ -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c propagate.cpp -o propagate.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c spatial.c -o spatial.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c thresh.c -o thresh.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -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]
tile.c:21:34: warning: unused variable 'ibg' [-Wunused-variable]
tile.c:21:29: warning: unused variable 'ifg' [-Wunused-variable]
tile.c: In function 'untile':
tile.c:142:37: warning: unused variable 'id' [-Wunused-variable]
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -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]
tools.c: In function 'getColorStrides':
tools.c:119:20: warning: unused variable 'colorMode' [-Wunused-variable]
g++ -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c watershed.cpp -o watershed.o
g++ -m32 -shared -s -static-libgcc -o EBImage.dll tmp.def 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 -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.1-bioc/meat/EBImage.buildbin-libdir/EBImage/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'EBImage' ...
** libs
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c EBImage.c -o EBImage.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c distmap.c -o distmap.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c drawCircle.c -o drawCircle.o
g++ -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c floodFill.cpp -o floodFill.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c greyscale_morphology.c -o greyscale_morphology.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c haralick.c -o haralick.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c medianFilter.c -o medianFilter.o
medianFilter.c: In function 'medianFilter':
medianFilter.c:463:45: warning: unused variable 'j' [-Wunused-variable]
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c morphology.c -o morphology.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c nativeRaster.c -o nativeRaster.o
nativeRaster.c: In function 'nativeRaster':
nativeRaster.c:14:11: warning: unused variable 'in' [-Wunused-variable]
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c normalize.c -o normalize.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c objects.c -o objects.o
objects.c: In function 'stackObjects':
objects.c:239:7: warning: 'dim' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ocontour.c -o ocontour.o
g++ -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c propagate.cpp -o propagate.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c spatial.c -o spatial.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c thresh.c -o thresh.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -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]
tile.c:21:34: warning: unused variable 'ibg' [-Wunused-variable]
tile.c:21:29: warning: unused variable 'ifg' [-Wunused-variable]
tile.c: In function 'untile':
tile.c:142:37: warning: unused variable 'id' [-Wunused-variable]
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -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]
tools.c: In function 'getColorStrides':
tools.c:119:20: warning: unused variable 'colorMode' [-Wunused-variable]
g++ -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c watershed.cpp -o watershed.o
g++ -m64 -shared -s -static-libgcc -o EBImage.dll tmp.def 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 -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.1-bioc/meat/EBImage.buildbin-libdir/EBImage/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'EBImage' as EBImage_4.10.1.zip
* DONE (EBImage)

EBImage.Rcheck/examples_i386/EBImage-Ex.timings:

nameusersystemelapsed
EBImage11.72 1.3014.67
Image0.640.090.73
bwlabel2.970.273.25
channel1.210.181.38
colorLabels0.140.050.19
combine1.480.442.29
computeFeatures1.590.201.80
display4.090.914.99
distmap0.200.040.25
drawCircle0.050.020.06
equalize1.960.342.31
fillHull0.670.050.72
filter21.410.121.53
floodFill0.420.030.45
gblur0.70.01.2
io1.290.162.90
localCurvature1.050.201.25
medianFilter3.930.164.09
morphology0.330.030.36
normalize0.060.000.06
ocontour0.050.000.05
otsu0.420.080.49
paintObjects3.710.474.19
propagate3.110.093.19
rmObjects0.200.050.25
spatial1.570.111.69
stackObjects6.571.067.64
thresh0.360.030.39
tile0.580.200.78
transpose0.450.050.50
watershed0.160.010.17

EBImage.Rcheck/examples_x64/EBImage-Ex.timings:

nameusersystemelapsed
EBImage 8.17 1.4212.17
Image0.500.060.57
bwlabel3.380.243.62
channel0.910.361.26
colorLabels0.110.010.13
combine1.120.521.65
computeFeatures1.010.081.09
display3.150.884.04
distmap0.140.000.14
drawCircle0.070.000.07
equalize1.960.492.45
fillHull0.550.040.59
filter21.420.111.53
floodFill0.300.040.33
gblur0.420.030.45
io1.000.152.59
localCurvature0.780.190.97
medianFilter1.150.141.31
morphology0.140.000.14
normalize0.000.020.02
ocontour0.030.000.03
otsu0.260.000.28
paintObjects2.640.182.82
propagate2.170.082.25
rmObjects0.150.030.19
spatial0.910.100.99
stackObjects6.531.468.01
thresh0.220.060.28
tile0.640.100.73
transpose0.420.060.49
watershed0.20.00.2