Package: Cardinal

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Cardinal_1.10.0.tar.gz

StartedAt: 2018-04-12 01:18:37 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:20:58 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 140.5 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_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/Cardinal.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.10.0’
* 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 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
.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.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’
normalize.do: no visible global function definition for ‘lines’
peakAlign.do: no visible global function definition for ‘abline’
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 global function definition for ‘median’
peakPick.limpic: no visible global function definition for ‘quantile’
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’
Undefined global functions or variables:
  .Index abline approx as.formula col2rgb colorRamp dnorm filter
  flush.console kmeans legend lines locator median object.size p.adjust
  packageDescription packageVersion par persp points pt quantile
  rainbow rgb rnorm runif smooth.spline trans3d
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", "smooth.spline")
  importFrom("utils", "flush.console", "object.size",
             "packageDescription", "packageVersion")
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-3.6-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   -fPIC  -Wall -g -O2  -c dynamicAlign.c -o dynamicAlign.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c fastmap.c -o fastmap.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c localMaxima.c -o localMaxima.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c pugixml.cpp -o pugixml.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c readAnalyze.cpp -o readAnalyze.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c readImzML.cpp -o readImzML.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c smooth.c -o smooth.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c spatial.c -o spatial.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -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-3.6-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)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(Cardinal)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: matter
Loading required package: biglm
Loading required package: DBI

Attaching package: 'matter'

The following objects are masked from 'package:base':

    apply, scale

Loading required package: ProtGenerics
Welcome to Cardinal (version 1.10.0)

    To get started, view the introductory vignettes with
    'browseVignettes("Cardinal")'.

> 
> test_check("Cardinal")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 229 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 27.291   0.502  28.109 

name	user	system	elapsed
Binmat-class	0	0	0
Hashmat-class	0.317	0.021	0.349
IAnnotatedDataFrame-class	0.120	0.005	0.127
ImageData-class	0.042	0.007	0.049
MIAPE-Imaging-class	0.004	0.001	0.005
MSImageData-class	0.254	0.010	0.267
MSImageProcess-class	0.001	0.000	0.002
MSImageSet-class	0.231	0.004	0.240
OPLS-methods	0.189	0.001	0.191
PCA-methods	0.068	0.000	0.070
PLS-methods	0.061	0.001	0.062
SImageData-class	0.094	0.002	0.096
SImageSet-class	0.073	0.001	0.075
batchProcess-methods	0.707	0.011	0.724
colors-functions	0.997	0.006	1.017
generateImage	0.344	0.006	0.358
generateSpectrum	0.038	0.001	0.039
iSet-class	0.045	0.001	0.046
image-methods	0.581	0.007	0.598
normalize-methods	0.106	0.001	0.107
peakAlign-methods	0.397	0.001	0.400
peakFilter-methods	0.393	0.001	0.396
peakPick-methods	0.136	0.000	0.137
pixelApply-methods	0.029	0.000	0.030
pixels-methods	0.083	0.001	0.084
plot-methods	0.697	0.010	0.721
reduceBaseline-methods	0.100	0.001	0.101
reduceDimension-methods	0.096	0.001	0.098
smoothSignal-methods.R	0.094	0.001	0.094
spatialKMeans-methods	0.455	0.003	0.459
spatialShrunkenCentroids-methods	1.545	0.010	1.625
standardizeSamples-methods	0.456	0.002	0.464
topLabels-methods	0.755	0.004	0.760