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BioC 3.5: CHECK report for Cardinal on toluca2

This page was generated on 2017-04-23 14:39:36 -0400 (Sun, 23 Apr 2017).

Package 172/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Cardinal 1.7.2
Kylie A. Bemis
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Cardinal
Last Changed Rev: 128177 / Revision: 129046
Last Changed Date: 2017-04-06 16:16:03 -0400 (Thu, 06 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Cardinal
Version: 1.7.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Cardinal_1.7.2.tar.gz
StartedAt: 2017-04-23 01:23:06 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 01:25:47 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 160.6 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_1.7.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Cardinal.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘1.7.2’
* 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
.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’
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’
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 median object.size
  p.adjust packageDescription packageVersion par persp points pt
  quantile rainbow rgb rnorm runif smooth.spline tail 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", "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-3.5-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-3.5-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-class0.3650.0140.379
IAnnotatedDataFrame-class0.1630.0050.169
ImageData-class0.0580.0070.065
MIAPE-Imaging-class0.0050.0010.006
MSImageData-class0.3290.0050.335
MSImageProcess-class0.0030.0010.003
MSImageSet-class0.3160.0030.319
OPLS-methods0.270.000.27
PCA-methods0.0750.0000.076
PLS-methods0.0960.0010.097
SImageData-class0.1410.0010.141
SImageSet-class0.1050.0010.106
batchProcess-methods0.8180.0030.823
colors-functions1.2540.0021.258
generateImage0.4600.0080.472
generateSpectrum0.0340.0020.036
iSet-class0.0470.0010.048
image-methods4.0960.0324.150
normalize-methods0.1150.0000.115
peakAlign-methods0.4390.0030.444
peakFilter-methods0.4410.0010.442
peakPick-methods0.1590.0010.161
pixelApply-methods0.0400.0010.041
pixels-methods0.1000.0000.102
plot-methods1.2600.0121.282
reduceBaseline-methods0.1460.0000.147
reduceDimension-methods0.1520.0010.153
smoothSignal-methods.R0.1280.0010.130
spatialKMeans-methods0.6410.0050.648
spatialShrunkenCentroids-methods1.8050.0191.825
standardizeSamples-methods0.5500.0020.552
topLabels-methods0.9550.0040.959