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This page was generated on 2023-01-02 09:00:23 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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CHECK results for ClassifyR on palomino5


To the developers/maintainers of the ClassifyR package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 330/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ClassifyR 3.3.10  (landing page)
Dario Strbenac
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/ClassifyR
git_branch: master
git_last_commit: cb13ad9
git_last_commit_date: 2022-12-12 18:58:25 -0500 (Mon, 12 Dec 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  

Summary

Package: ClassifyR
Version: 3.3.10
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ClassifyR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings ClassifyR_3.3.10.tar.gz
StartedAt: 2022-12-28 22:30:19 -0500 (Wed, 28 Dec 2022)
EndedAt: 2022-12-28 22:49:13 -0500 (Wed, 28 Dec 2022)
EllapsedTime: 1134.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ClassifyR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ClassifyR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings ClassifyR_3.3.10.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/ClassifyR.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ClassifyR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ClassifyR' version '3.3.10'
* 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 'ClassifyR' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* 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
.dmvnorm_diag: no visible global function definition for 'dnorm'
.doSelection : <anonymous> : <anonymous>: no visible global function
  definition for 'setNames'
.doSelection : <anonymous> : <anonymous>: no visible global function
  definition for 'na.omit'
.doSelection : <anonymous> : <anonymous>: no visible global function
  definition for 'median'
.doSelection : <anonymous>: no visible binding for global variable
  'trainParams'
.doSelection : <anonymous>: no visible binding for global variable
  'predictParams'
.doSelection : <anonymous>: no visible binding for global variable
  'measurementsSubset'
.doSelection : <anonymous>: no visible global function definition for
  'median'
.doSelection : <anonymous>: no visible binding for global variable
  'aResult'
.doSelection: no visible binding for global variable 'featuresLists'
.doTrain : <anonymous>: no visible global function definition for
  'median'
.filterCharacteristics: no visible global function definition for
  'na.omit'
.getFeaturesStrings : <anonymous>: no visible global function
  definition for 'first'
.getFeaturesStrings : <anonymous>: no visible global function
  definition for 'second'
.posterior_probs : <anonymous>: no visible global function definition
  for 'dmvnorm'
.samplesSplits : <anonymous>: no visible binding for global variable
  'classes'
DLDApredictInterface: no visible global function definition for
  'predict'
DMDranking : <anonymous>: no visible global function definition for
  'dist'
GLMpredictInterface: no visible global function definition for
  'predict'
GLMtrainInterface: no visible global function definition for 'glm'
GLMtrainInterface: no visible binding for global variable 'binomial'
SVMpredictInterface: no visible global function definition for
  'predict'
classifyInterface: no visible binding for global variable
  'trainingMatrix'
classifyInterface: no visible binding for global variable
  'testingMatrix'
colCoxTests: no visible global function definition for 'pnorm'
colCoxTests : <anonymous>: no visible global function definition for
  'coxph'
coxnetPredictInterface: no visible global function definition for
  'predict'
coxnetTrainInterface: no visible global function definition for
  'predict'
coxphPredictInterface: no visible global function definition for
  'predict'
crissCrossPlot: no visible binding for global variable 'params'
crissCrossPlot: no visible binding for global variable 'real'
crissCrossPlot: no visible binding for global variable 'Var1'
crissCrossPlot: no visible binding for global variable 'Var2'
crissCrossPlot: no visible binding for global variable 'value'
crissCrossPlot: no visible binding for global variable 'random'
crissCrossValidate : <anonymous> : <anonymous>: no visible global
  function definition for 'predict'
crissCrossValidate : <anonymous> : <anonymous>: no visible global
  function definition for 'na.omit'
differentMeansRanking : <anonymous>: no visible global function
  definition for 'chisq.test'
edgeRranking: no visible global function definition for 'model.matrix'
elasticNetGLMpredictInterface: no visible global function definition
  for 'predict'
elasticNetGLMtrainInterface : <anonymous>: no visible global function
  definition for 'predict'
extremeGradientBoostingPredictInterface: no visible global function
  definition for 'predict'
fastCox: no visible global function definition for 'pnorm'
fisherDiscriminant: no visible binding for global variable
  'trainingMatrix'
fisherDiscriminant: no visible binding for global variable 'var'
getLocationsAndScales: no visible global function definition for
  'setNames'
getLocationsAndScales: no visible binding for global variable 'median'
getLocationsAndScales: no visible binding for global variable 'sd'
getLocationsAndScales: no visible binding for global variable 'mad'
kNNinterface: no visible global function definition for 'setNames'
kTSPclassifier : <anonymous>: no visible binding for global variable
  'trainingMatrix'
kTSPclassifier : <anonymous>: no visible global function definition for
  'Pairs'
kTSPclassifier: no visible binding for global variable 'testingMatrix'
likelihoodRatioRanking : <anonymous>: no visible global function
  definition for 'dnorm'
likelihoodRatioRanking : <anonymous> : <anonymous>: no visible global
  function definition for 'dnorm'
limmaRanking: no visible global function definition for 'model.matrix'
mixModelsPredict : <anonymous>: no visible global function definition
  for 'setNames'
mixModelsPredict : <anonymous> : <anonymous> : <anonymous>: no visible
  global function definition for 'dnorm'
mixModelsPredict : <anonymous> : <anonymous>: no visible global
  function definition for 'splinefun'
mixModelsTrain: no visible global function definition for 'setNames'
naiveBayesKernel: no visible binding for global variable 'density'
naiveBayesKernel : <anonymous> : <anonymous>: no visible global
  function definition for 'splinefun'
naiveBayesKernel: no visible binding for global variable 'test'
naiveBayesKernel : <anonymous>: no visible global function definition
  for 'setNames'
pcaPredictInterface : <anonymous>: no visible global function
  definition for 'predict'
pcaTrainInterface : <anonymous>: no visible global function definition
  for 'prcomp'
randomForestPredictInterface: no visible global function definition for
  'predict'
rfsrcPredictInterface: no visible global function definition for
  'predict'
subtractFromLocation: no visible binding for global variable 'median'
train.DataFrame : <anonymous> : <anonymous> : <anonymous>: no visible
  global function definition for 'na.omit'
train.DataFrame: no visible binding for global variable
  'crossValParams'
ROCplot,list : <anonymous> : <anonymous> : <anonymous>: no visible
  global function definition for 'quantile'
ROCplot,list : <anonymous>: no visible binding for global variable
  'FPR'
ROCplot,list : <anonymous>: no visible binding for global variable
  'TPR'
ROCplot,list : <anonymous>: no visible binding for global variable
  'lower'
ROCplot,list : <anonymous>: no visible binding for global variable
  'upper'
crossValidate,DataFrame: no visible global function definition for
  'runif'
distribution,ClassifyResult: no visible binding for global variable
  'allPredictions'
distribution,ClassifyResult: no visible global function definition for
  'first'
distribution,ClassifyResult: no visible global function definition for
  'second'
distribution,ClassifyResult: no visible global function definition for
  'aggregate'
distribution,ClassifyResult: no visible global function definition for
  'mcols<-'
featureSetSummary,DataFrame: no visible binding for global variable
  'median'
featureSetSummary,MultiAssayExperiment: no visible binding for global
  variable 'median'
featureSetSummary,matrix: no visible binding for global variable
  'median'
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
  global variable 'measurement'
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
  global variable '..density..'
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
  global variable 'legends grouping'
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
  global variable 'key'
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
  global variable 'value'
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
  global variable 'ID'
prepareData,DataFrame: no visible binding for global variable 'var'
rankingPlot,list: no visible binding for global variable 'top'
rankingPlot,list: no visible binding for global variable 'overlap'
runTest,DataFrame: no visible global function definition for 'na.omit'
runTest,DataFrame : <anonymous>: no visible global function definition
  for 'na.omit'
runTest,MultiAssayExperiment: no visible binding for global variable
  'extrasInputs'
runTest,MultiAssayExperiment: no visible binding for global variable
  'prepArgs'
samplesMetricMap,list: no visible binding for global variable 'Class'
samplesMetricMap,list: no visible binding for global variable 'Group'
samplesMetricMap,list: no visible binding for global variable
  'measurements'
samplesMetricMap,list: no visible binding for global variable 'name'
samplesMetricMap,list: no visible binding for global variable 'type'
samplesMetricMap,list: no visible binding for global variable 'Metric'
samplesMetricMap,matrix: no visible binding for global variable 'Class'
samplesMetricMap,matrix: no visible binding for global variable 'Group'
samplesMetricMap,matrix: no visible binding for global variable
  'measurements'
samplesMetricMap,matrix: no visible binding for global variable 'name'
samplesMetricMap,matrix: no visible binding for global variable 'type'
samplesMetricMap,matrix: no visible binding for global variable
  'Metric'
selectionPlot,list: no visible binding for global variable 'overlap'
selectionPlot,list: no visible binding for global variable 'median'
selectionPlot,list : <anonymous>: no visible binding for global
  variable 'feature'
selectionPlot,list: no visible binding for global variable 'feature'
selectionPlot,list: no visible binding for global variable
  'colourVariable'
selectionPlot,list: no visible binding for global variable 'size'
selectionPlot,list: no visible binding for global variable 'Freq'
show,PredictParams: no visible global function definition for 'na.omit'
show,SelectParams: no visible global function definition for 'na.omit'
show,TrainParams: no visible global function definition for 'na.omit'
show,TransformParams: no visible global function definition for
  'na.omit'
Undefined global functions or variables:
  ..density.. Class FPR Freq Group ID Metric Pairs TPR Var1 Var2
  aResult aggregate allPredictions binomial chisq.test classes
  colourVariable coxph crossValParams density dist dmvnorm dnorm
  extrasInputs feature featuresLists first glm key legends grouping
  lower mad mcols<- measurement measurements measurementsSubset median
  model.matrix na.omit name overlap params pnorm prcomp predict
  predictParams prepArgs quantile random real runif sd second setNames
  size splinefun test testingMatrix top trainParams trainingMatrix type
  upper value var
Consider adding
  importFrom("base", "grouping")
  importFrom("stats", "aggregate", "binomial", "chisq.test", "density",
             "dist", "dnorm", "glm", "mad", "median", "model.matrix",
             "na.omit", "pnorm", "prcomp", "predict", "quantile",
             "runif", "sd", "setNames", "splinefun", "var")
to your NAMESPACE file.
* checking Rd files ... WARNING
checkRd: (5) ClassifyResult-class.Rd:73-75: \item in \describe must have non-empty label
checkRd: (5) FeatureSetCollection.Rd:21-22: \item in \describe must have non-empty label
checkRd: (5) FeatureSetCollection.Rd:36-38: \item in \describe must have non-empty label
checkRd: (5) FeatureSetCollection.Rd:39-41: \item in \describe must have non-empty label
checkRd: (5) FeatureSetCollection.Rd:51-55: \item in \describe must have non-empty label
checkRd: (5) FeatureSetCollection.Rd:56-60: \item in \describe must have non-empty label
checkRd: (5) PredictParams-class.Rd:22-27: \item in \describe must have non-empty label
checkRd: (5) PredictParams-class.Rd:43-45: \item in \describe must have non-empty label
checkRd: (5) SelectParams-class.Rd:19-44: \item in \describe must have non-empty label
checkRd: (5) SelectParams-class.Rd:51-53: \item in \describe must have non-empty label
checkRd: (5) TrainParams-class.Rd:18-44: \item in \describe must have non-empty label
checkRd: (5) TrainParams-class.Rd:51-53: \item in \describe must have non-empty label
checkRd: (5) TransformParams-class.Rd:17-34: \item in \describe must have non-empty label
checkRd: (5) TransformParams-class.Rd:41-43: \item in \describe must have non-empty label
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/ClassifyR/libs/x64/ClassifyR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
crossValidate        1051.63 142.36  651.46
distribution          245.67  37.35  132.95
ClassifyResult-class  239.38  37.39  128.89
runTests                2.29   0.11   30.79
selectionPlot           1.45   0.04   10.75
rankingPlot             1.00   0.05    9.46
* 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 WARNING, 2 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/ClassifyR.Rcheck/00check.log'
for details.

Installation output

ClassifyR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL ClassifyR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'ClassifyR' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
using C++11
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c coxformatrices.cpp -o coxformatrices.o
g++ -shared -s -static-libgcc -o ClassifyR.dll tmp.def coxformatrices.o -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-ClassifyR/00new/ClassifyR/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for 'ROCplot' with signature '"ClassifyResult"': no definition for class "ClassifyResult"
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ClassifyR)

Tests output

Example timings

ClassifyR.Rcheck/ClassifyR-Ex.timings

nameusersystemelapsed
ClassifyResult-class239.38 37.39128.89
CrossValParams-class1.570.001.58
FeatureSetCollection000
ModellingParams-class0.140.000.14
PredictParams-class000
ROCplot0.580.020.60
SelectParams-class0.030.000.03
TrainParams-class0.020.000.01
TransformParams-class000
available000
calcPerformance0.010.000.01
colCoxTests0.340.000.35
crossValidate1051.63 142.36 651.46
distribution245.67 37.35132.95
edgesToHubNetworks0.010.000.02
featureSetSummary000
interactorDifferences0.020.000.01
performancePlot0.250.000.25
plotFeatureClasses2.010.022.06
rankingPlot1.000.059.46
runTest1.600.041.64
runTests 2.29 0.1130.79
samplesMetricMap2.350.032.38
selectionPlot 1.45 0.0410.75