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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ClassifyR_3.11.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ClassifyR.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ClassifyR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ClassifyR’ version ‘3.11.4’
* 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 ... WARNING
Found the following significant warnings:
  coxformatrices.cpp:528:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  coxformatrices.cpp:529:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  coxformatrices.cpp:569:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  coxformatrices.cpp:570:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  coxformatrices.cpp:656:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  coxformatrices.cpp:657:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/Users/biocbuild/bbs-3.21-bioc/meat/ClassifyR.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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 code 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
.addUserLevels: no visible binding for global variable ‘median’
.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’
.precisionPathwaysTrain: no visible global function definition for
  ‘setNames’
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
  ‘quasibinomial’
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’
calcCostsAndPerformance : <anonymous>: no visible global function
  definition for ‘na.omit’
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’
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
  ‘Predicted’
flowchart.PrecisionPathways: no visible binding for global variable
  ‘Tier’
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’
penalisedGLMpredictInterface: no visible global function definition for
  ‘predict’
penalisedGLMtrainInterface : <anonymous>: no visible global function
  definition for ‘predict’
performanceTable : <anonymous> : <anonymous>: no visible global
  function definition for ‘median’
performanceTable : <anonymous>: no visible binding for global variable
  ‘characteristic’
performanceTable : <anonymous>: no visible binding for global variable
  ‘value’
randomForestPredictInterface: no visible global function definition for
  ‘predict’
rfsrcPredictInterface: no visible global function definition for
  ‘predict’
samplesSplits : <anonymous>: no visible binding for global variable
  ‘classes’
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 : <anonymous>: no visible global function
  definition for ‘combn’
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 global function definition for ‘tail’
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:
  Accuracy Class FPR Freq Group ID Metric Pairs Predicted Sequence TPR
  Tier Var1 Var2 aResult accuracy aggregate characteristic chisq.test
  classes colourVariable combn cost 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 quasibinomial
  random real sd second setNames size splinefun tail test testingMatrix
  top trainParams trainingMatrix trueClass type unqiue upper value var
Consider adding
  importFrom("base", "grouping")
  importFrom("stats", "aggregate", "chisq.test", "density", "dist",
             "dnorm", "glm", "mad", "median", "model.matrix", "na.omit",
             "pnorm", "prcomp", "predict", "quantile", "quasibinomial",
             "sd", "setNames", "splinefun", "var")
  importFrom("utils", "combn", "tail")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ClassifyResult-class.Rd: DataFrame
  CrossValParams-class.Rd: BiocParallelParam, bpparam
  HuRI.Rd: Pairs
  METABRICclinical.Rd: DataFrame
  PredictParams-class.Rd: DataFrame
  SelectParams-class.Rd: DataFrame
  TrainParams-class.Rd: DataFrame
  TransformParams-class.Rd: DataFrame
  crissCrossValidate.Rd: DataFrame
  crossValidate.Rd: DataFrame, MultiAssayExperiment, Surv
  featureSetSummary.Rd: DataFrame, MultiAssayExperiment
  interactorDifferences.Rd: DataFrame, MultiAssayExperiment, Pairs
  plotFeatureClasses.Rd: Pairs, DataFrame, MultiAssayExperiment
  precisionPathways.Rd: MultiAssayExperiment
  prepareData.Rd: DataFrame, MultiAssayExperiment, Surv
  rankingPlot.Rd: MulticoreParam, SnowParam
  runTest.Rd: DataFrame, MultiAssayExperiment, Surv
  runTests.Rd: BiocParallel, DataFrame, MultiAssayExperiment, Surv
  samplesSplitting.Rd: Surv
  selectionPlot.Rd: MulticoreParam, SnowParam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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        100.224  6.347  82.519
ClassifyResult-class  26.883  1.791  22.307
distribution          23.907  1.776  19.122
runTests              11.111  3.702   7.048
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/ClassifyR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ClassifyR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘ClassifyR’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c coxformatrices.cpp -o coxformatrices.o
coxformatrices.cpp:24:16: warning: unused variable 'sclback3' [-Wunused-variable]
        double sclback3=*sctest3;
               ^
coxformatrices.cpp:23:16: warning: unused variable 'sclback2' [-Wunused-variable]
        double sclback2=*sctest2;
               ^
coxformatrices.cpp:81:9: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        NULL
        ^~~~
        {   }
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/stddef.h:84:18: note: expanded from macro 'NULL'
#    define NULL __null
                 ^~~~~~
coxformatrices.cpp:528:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int i,j;
    ^~~~~~~~~
coxformatrices.cpp:528:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int i,j;
    ^~~~~~~~~
coxformatrices.cpp:529:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register double temp;
    ^~~~~~~~~
coxformatrices.cpp:569:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register double temp;
    ^~~~~~~~~
coxformatrices.cpp:570:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int i,j,k;
    ^~~~~~~~~
coxformatrices.cpp:570:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int i,j,k;
    ^~~~~~~~~
coxformatrices.cpp:570:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int i,j,k;
    ^~~~~~~~~
coxformatrices.cpp:656:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int i;
    ^~~~~~~~~
coxformatrices.cpp:657:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register double **pointer;
    ^~~~~~~~~
12 warnings generated.
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o ClassifyR.so coxformatrices.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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)