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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings ClassifyR_3.3.15.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ClassifyR.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘ClassifyR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ClassifyR’ version ‘3.3.15’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ClassifyR’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 ... WARNING
summary:
  function(object, ...)
summary.PrecisionPathways:
  function(object, weights)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* 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’
.getEdgeLabel: no visible binding for '<<-' assignment to ‘nSamples’
.getEdgeLabel: no visible binding for global variable ‘samplesTiers’
.getEdgeLabel: no visible binding for global variable ‘nSamples’
.getFeaturesStrings : <anonymous>: no visible global function
  definition for ‘first’
.getFeaturesStrings : <anonymous>: no visible global function
  definition for ‘second’
.getFillColour: no visible binding for global variable ‘nodeColours’
.posterior_probs : <anonymous>: no visible global function definition
  for ‘dmvnorm’
.precisionPathwaysPredict: no visible binding for global variable ‘PPT’
.precisionPathwaysPredict: no visible binding for global variable
  ‘clinicalPredictors’
.precisionPathwaysTrain: no visible global function definition for
  ‘setNames’
.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’
bubblePlot.PrecisionPathways: no visible binding for global variable
  ‘accuracy’
bubblePlot.PrecisionPathways: no visible binding for global variable
  ‘cost’
bubblePlot.PrecisionPathways: no visible binding for global variable
  ‘Sequence’
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’
flowchart.PrecisionPathways: no visible binding for global variable
  ‘Node’
flowchart.PrecisionPathways: no visible binding for global variable
  ‘Predicted’
flowchart.PrecisionPathways: no visible binding for global variable
  ‘Tier’
flowchart.PrecisionPathways: no visible global function definition for
  ‘SetGraphStyle’
flowchart.PrecisionPathways: no visible global function definition for
  ‘SetEdgeStyle’
flowchart.PrecisionPathways: no visible global function definition for
  ‘SetNodeStyle’
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’
strataPlot.PrecisionPathways: no visible binding for global variable
  ‘Tier’
strataPlot.PrecisionPathways: no visible binding for global variable
  ‘trueClass’
strataPlot.PrecisionPathways: no visible binding for global variable
  ‘Accuracy’
strataPlot.PrecisionPathways: no visible binding for global variable
  ‘ID’
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’
precisionPathwaysTrain,MultiAssayExperimentOrList: no visible global
  function definition for ‘setNames’
prepareData,DataFrame: no visible global function definition for
  ‘unqiue’
prepareData,DataFrame : <anonymous>: 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.. Accuracy Class FPR Freq Group ID Metric Node PPT Pairs
  Predicted Sequence SetEdgeStyle SetGraphStyle SetNodeStyle TPR Tier
  Var1 Var2 aResult accuracy aggregate allPredictions binomial
  chisq.test classes clinicalPredictors colourVariable cost coxph
  crossValParams density dist dmvnorm dnorm extrasInputs feature
  featuresLists first glm key legends grouping lower mad mcols<-
  measurement measurements measurementsSubset median model.matrix
  nSamples na.omit name nodeColours overlap params pnorm prcomp predict
  predictParams prepArgs quantile random real runif samplesTiers sd
  second setNames size splinefun test testingMatrix top trainParams
  trainingMatrix trueClass type unqiue 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 ... 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 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user  system elapsed
crossValidate        1188.239 142.834 969.149
ClassifyResult-class  247.779 240.140 619.773
distribution          246.854  21.187 165.636
runTests               11.580   2.469   6.193
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘ClassifyR.Rmd’ using ‘UTF-8’... OK
  ‘DevelopersGuide.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘ClassifyR.Rmd’ using rmarkdown

WARNING: reaching max number of iterations

WARNING: reaching max number of iterations
Quitting from lines 252-257 (ClassifyR.Rmd) 
Error: processing vignette 'ClassifyR.Rmd' failed with diagnostics:
wrong args for environment subassignment
--- failed re-building ‘ClassifyR.Rmd’

--- re-building ‘DevelopersGuide.Rmd’ using rmarkdown
--- finished re-building ‘DevelopersGuide.Rmd’

SUMMARY: processing the following file failed:
  ‘ClassifyR.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Missing \endgroup inserted.
<inserted text> 
                \endgroup 
l.2992 ]
         Creates a \code{SelectParams} object which stores the function(s) w...
! Missing \endgroup inserted.
<inserted text> 
                \endgroup 
l.2992 ]
         Creates a \code{SelectParams} object which stores the function(s) w...
! Missing } inserted.
<inserted text> 
                }
l.2992 ]
         Creates a \code{SelectParams} object which stores the function(s) w...
! LaTeX Error: \begin{description} on input line 2989 ended by \end{alltt}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
\sbox  ...box {\color@setgroup #2\color@endgroup }
                                                  
l.2992 ]
         Creates a \code{SelectParams} object which stores the function(s) w...
! LaTeX Error: \begin{Rdsection} on input line 2987 ended by \end{description}.


See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: \begin{Section} on input line 2987 ended by \end{list}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! LaTeX Error: \begin{document} ended by \end{Rdsection}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra \endgroup.
<recently read> \endgroup 
                          
l.3008 \end{Section}
                    
! LaTeX Error: \begin{document} ended by \end{Section}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra \endgroup.
<recently read> \endgroup 
                          
l.3008 \end{Section}
                    
! Missing \endgroup inserted.
<inserted text> 
                \endgroup 
l.3056 ]
        
! Missing \endgroup inserted.
<inserted text> 
                \endgroup 
l.3056 ]
        
! Missing } inserted.
<inserted text> 
                }
l.3056 ]
        
! LaTeX Error: \begin{description} on input line 3052 ended by \end{alltt}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
\sbox  ...box {\color@setgroup #2\color@endgroup }
                                                  
l.3056 ]
        
! LaTeX Error: \begin{Rdsection} on input line 3050 ended by \end{description}.


See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! LaTeX Error: \begin{Section} on input line 3050 ended by \end{list}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! LaTeX Error: \begin{document} ended by \end{Rdsection}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra \endgroup.
<recently read> \endgroup 
                          
l.3087 \end{Section}
                    
! LaTeX Error: \begin{document} ended by \end{Section}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra \endgroup.
<recently read> \endgroup 
                          
l.3087 \end{Section}
                    
* checking PDF version of manual without index ... ERROR
* DONE

Status: 2 ERRORs, 2 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/ClassifyR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ClassifyR
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘ClassifyR’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c coxformatrices.cpp -o coxformatrices.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o ClassifyR.so coxformatrices.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-ClassifyR/00new/ClassifyR/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ClassifyR)