BioC 3.2: CHECK report for Cardinal on oaxaca

Package: Cardinal

Version: 1.2.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Cardinal_1.2.1.tar.gz

StartedAt: 2016-04-22 22:25:55 -0700 (Fri, 22 Apr 2016)

EndedAt: 2016-04-22 22:28:09 -0700 (Fri, 22 Apr 2016)

EllapsedTime: 134.4 seconds

RetCode: 0

Status:  OK

CheckDir: Cardinal.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 Cardinal_1.2.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/Cardinal.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Cardinal/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Cardinal’ version ‘1.2.1’
* 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 ‘Cardinal’ can be installed ... [13s/13s] 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 loading without being on the library search path ... 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 ... NOTE
normalize,MSImageSet : .local : <anonymous>: no visible binding for
  global variable ‘.Index’
peakAlign,MSImageSet-numeric : .local : <anonymous>: no visible binding
  for global variable ‘.Index’
peakPick,MSImageSet : .local : <anonymous>: no visible binding for
  global variable ‘.Index’
reduceBaseline,MSImageSet : .local : <anonymous>: no visible binding
  for global variable ‘.Index’
reduceDimension,MSImageSet-missing : .local : <anonymous>: no visible
  binding for global variable ‘.Index’
smoothSignal,MSImageSet : .local : <anonymous>: no visible binding for
  global variable ‘.Index’
* 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 ... [13s/13s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [23s/23s]
 [24s/24s] 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/Cardinal.Rcheck/00check.log’
for details.

* installing *source* package ‘Cardinal’ ...
** 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 dynamicAlign.c -o dynamicAlign.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 fastmap.c -o fastmap.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 localMaxima.c -o localMaxima.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 pugixml.cpp -o pugixml.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 readAnalyze.cpp -o readAnalyze.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 readImzML.cpp -o readImzML.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 smooth.c -o smooth.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 utils.cpp -o utils.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 Cardinal.so dynamicAlign.o fastmap.o localMaxima.o pugixml.o readAnalyze.o readImzML.o smooth.o spatial.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/Cardinal.Rcheck/Cardinal/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 (Cardinal)

name	user	system	elapsed
Hashmat-class	0.416	0.010	0.426
IAnnotatedDataFrame-class	0.084	0.001	0.085
ImageData-class	0.009	0.000	0.009
MIAPE-Imaging-class	0.003	0.001	0.004
MSImageData-class	0.063	0.007	0.070
MSImageProcess-class	0.002	0.000	0.001
MSImageSet-class	0.245	0.004	0.251
OPLS-methods	0.093	0.001	0.093
PCA-methods	0.081	0.001	0.081
PLS-methods	0.092	0.000	0.092
SImageData-class	0.060	0.001	0.061
SImageSet-class	0.053	0.000	0.054
colors-functions	1.169	0.002	1.170
generateImage	0.356	0.007	0.363
generateSpectrum	0.038	0.003	0.041
iSet-class	0.043	0.001	0.045
image-methods	0.609	0.011	0.654
normalize-methods	0.233	0.002	0.236
peakAlign-methods	0.515	0.002	0.517
peakFilter-methods	0.521	0.002	0.522
peakPick-methods	0.247	0.001	0.247
pixelApply-methods	0.062	0.001	0.064
pixels-methods	0.193	0.001	0.195
plot-methods	0.828	0.013	0.843
reduceBaseline-methods	0.190	0.000	0.191
reduceDimension-methods	0.241	0.001	0.242
smoothSignal-methods.R	0.208	0.001	0.210
spatialKMeans-methods	0.402	0.002	0.405
spatialShrunkenCentroids-methods	1.308	0.004	1.313
standardizeSamples-methods	0.615	0.001	0.617
topLabels-methods	0.921	0.003	0.925