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BioC 3.4: CHECK report for Cardinal on morelia

This page was generated on 2017-04-15 16:26:14 -0400 (Sat, 15 Apr 2017).

Package 163/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Cardinal 1.6.0
Kylie A. Bemis
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/Cardinal
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  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: Cardinal
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Cardinal_1.6.0.tar.gz
StartedAt: 2017-04-14 23:32:03 -0700 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:34:07 -0700 (Fri, 14 Apr 2017)
EllapsedTime: 124.1 seconds
RetCode: 0
Status:  OK 
CheckDir: Cardinal.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Cardinal_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/Cardinal.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.6.0’
* 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 ‘Cardinal’ can be installed ... 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 ... NOTE
.PCA.fit: no visible binding for global variable ‘var’
.PCA.predict: no visible binding for global variable ‘sd’
.calculateSpatialDiscriminantScores: no visible global function
  definition for ‘median’
.console: no visible global function definition for ‘flush.console’
.onAttach: no visible global function definition for ‘packageVersion’
.plot.gridsearch: no visible global function definition for ‘points’
.plot.gridsearch: no visible global function definition for ‘abline’
.plot.gridsearch: no visible global function definition for ‘legend’
.setup.layout: no visible global function definition for ‘par’
.spatialKMeans: no visible global function definition for ‘kmeans’
.spatialShrunkenCentroids.fit: no visible global function definition
  for ‘median’
.spatialShrunkenCentroids.predict: no visible global function
  definition for ‘median’
alpha.colors: no visible global function definition for ‘col2rgb’
alpha.colors: no visible global function definition for ‘rgb’
contrast.enhance.histogram: no visible global function definition for
  ‘quantile’
contrast.enhance.histogram: no visible global function definition for
  ‘tail’
contrast.enhance.suppression: no visible global function definition for
  ‘quantile’
generateSpectrum: no visible global function definition for ‘runif’
generateSpectrum: no visible global function definition for ‘rnorm’
generateSpectrum : <anonymous>: no visible global function definition
  for ‘dnorm’
gradient.colors: no visible global function definition for ‘colorRamp’
gradient.colors : <anonymous>: no visible binding for global variable
  ‘rgb’
image3d: no visible global function definition for ‘persp’
image3d: no visible global function definition for ‘points’
image3d: no visible global function definition for ‘trans3d’
intensity.colors: no visible global function definition for ‘rainbow’
intensity.colors: no visible global function definition for ‘colorRamp’
intensity.colors: no visible global function definition for ‘col2rgb’
intensity.colors : <anonymous>: no visible binding for global variable
  ‘rgb’
intensity.colors2: no visible global function definition for ‘rainbow’
interp.surface: no visible global function definition for ‘approx’
nipals.PCA: no visible binding for global variable ‘sd’
normalize.do: no visible global function definition for ‘lines’
peakAlign.do: no visible global function definition for ‘abline’
peakPick.adaptive: no visible binding for global variable ‘sd’
peakPick.adaptive: no visible global function definition for
  ‘smooth.spline’
peakPick.adaptive: no visible global function definition for ‘median’
peakPick.do: no visible global function definition for ‘lines’
peakPick.limpic: no visible binding for global variable ‘sd’
peakPick.limpic: no visible global function definition for ‘median’
peakPick.limpic: no visible global function definition for ‘quantile’
peakPick.simple: no visible binding for global variable ‘sd’
readAnalyze: no visible global function definition for ‘matter_mat’
readImzML: no visible global function definition for ‘matter_mat’
reduceBaseline.do: no visible global function definition for ‘lines’
reduceBaseline.median: no visible global function definition for
  ‘smooth.spline’
reduceDimension.do: no visible global function definition for ‘points’
reduceDimension.do: no visible global function definition for ‘lines’
risk.colors: no visible global function definition for ‘colorRamp’
risk.colors : <anonymous>: no visible binding for global variable ‘rgb’
smoothSignal.do: no visible global function definition for ‘lines’
smoothSignal.gaussian: no visible global function definition for
  ‘dnorm’
smoothSignal.ma: no visible global function definition for ‘filter’
batchProcess,MSImageSet : <anonymous>: no visible binding for global
  variable ‘.Index’
image,ResultSet: no visible global function definition for ‘rainbow’
image,ResultSet: no visible global function definition for ‘as.formula’
image,SImageSet: no visible global function definition for ‘rainbow’
image,SImageSet: no visible global function definition for ‘as.formula’
image,SImageSet: no visible global function definition for ‘legend’
image,SImageSet: no visible global function definition for ‘rgb’
initialize,MSImageProcess: no visible global function definition for
  ‘packageDescription’
normalize,MSImageSet : <anonymous>: no visible binding for global
  variable ‘.Index’
peakAlign,MSImageSet-numeric : <anonymous>: no visible binding for
  global variable ‘.Index’
peakPick,MSImageSet : <anonymous>: no visible binding for global
  variable ‘.Index’
plot,ResultSet-missing: no visible global function definition for
  ‘rainbow’
plot,ResultSet-missing: no visible global function definition for
  ‘as.formula’
plot,SImageSet-missing: no visible global function definition for
  ‘as.formula’
plot,SImageSet-missing: no visible global function definition for
  ‘abline’
plot,SImageSet-missing: no visible global function definition for
  ‘points’
plot,SImageSet-missing: no visible global function definition for
  ‘legend’
plot,SImageSet-missing: no visible global function definition for ‘rgb’
reduceBaseline,MSImageSet : <anonymous>: no visible binding for global
  variable ‘.Index’
reduceDimension,MSImageSet-missing : <anonymous>: no visible binding
  for global variable ‘.Index’
select,SImageSet: no visible global function definition for ‘locator’
show,ImageData: no visible global function definition for ‘object.size’
smoothSignal,MSImageSet : <anonymous>: no visible binding for global
  variable ‘.Index’
summary,SpatialShrunkenCentroids : <anonymous>: no visible global
  function definition for ‘pt’
summary,SpatialShrunkenCentroids : <anonymous>: no visible global
  function definition for ‘p.adjust’
summary,iSet : <anonymous>: no visible global function definition for
  ‘object.size’
summary,iSet: no visible global function definition for ‘object.size’
topLabels,ResultSet: no visible global function definition for ‘head’
Undefined global functions or variables:
  .Index abline approx as.formula col2rgb colorRamp dnorm filter
  flush.console head kmeans legend lines locator matter_mat median
  object.size p.adjust packageDescription packageVersion par persp
  points pt quantile rainbow rgb rnorm runif sd smooth.spline tail
  trans3d var
Consider adding
  importFrom("grDevices", "col2rgb", "colorRamp", "rainbow", "rgb",
             "trans3d")
  importFrom("graphics", "abline", "legend", "lines", "locator", "par",
             "persp", "points")
  importFrom("stats", "approx", "as.formula", "dnorm", "filter",
             "kmeans", "median", "p.adjust", "pt", "quantile", "rnorm",
             "runif", "sd", "smooth.spline", "var")
  importFrom("utils", "flush.console", "head", "object.size",
             "packageDescription", "packageVersion", "tail")
to your NAMESPACE file.
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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-3.4-bioc/meat/Cardinal.Rcheck/00check.log’
for details.

Cardinal.Rcheck/00install.out:

* 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-3.4-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)

Cardinal.Rcheck/Cardinal-Ex.timings:

nameusersystemelapsed
Binmat-class0.0000.0000.001
Hashmat-class0.2190.0080.226
IAnnotatedDataFrame-class0.0600.0010.061
ImageData-class0.0090.0000.009
MIAPE-Imaging-class0.0040.0010.008
MSImageData-class0.0710.0090.079
MSImageProcess-class0.0010.0000.001
MSImageSet-class0.2810.0060.288
OPLS-methods0.0780.0010.079
PCA-methods0.0560.0010.082
PLS-methods0.0680.0010.069
SImageData-class0.0580.0010.059
SImageSet-class0.0670.0010.069
batchProcess-methods0.3790.0030.381
colors-functions1.0010.0021.004
generateImage0.2640.0030.267
generateSpectrum0.0270.0030.032
iSet-class0.0620.0010.063
image-methods0.6880.0100.701
normalize-methods0.1580.0000.159
peakAlign-methods0.4060.0010.407
peakFilter-methods0.5170.0020.519
peakPick-methods0.1740.0010.174
pixelApply-methods0.0460.0000.046
pixels-methods0.1230.0010.124
plot-methods0.7740.0240.933
reduceBaseline-methods0.2140.0010.215
reduceDimension-methods0.2120.0010.213
smoothSignal-methods.R0.1440.0000.144
spatialKMeans-methods0.3140.0020.316
spatialShrunkenCentroids-methods1.1100.0091.120
standardizeSamples-methods0.4020.0010.403
topLabels-methods0.5990.0030.602