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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 352/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ClassifyR 3.9.2  (landing page)
Dario Strbenac
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/ClassifyR
git_branch: devel
git_last_commit: c8738f1
git_last_commit_date: 2024-06-09 09:00:05 -0400 (Sun, 09 Jun 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  YES
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    TIMEOUT    OK  
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  YES


CHECK results for ClassifyR on palomino4

To the developers/maintainers of the ClassifyR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ClassifyR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: ClassifyR
Version: 3.9.2
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ClassifyR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ClassifyR_3.9.2.tar.gz
StartedAt: 2024-06-10 00:57:40 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 01:24:13 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 1592.9 seconds
RetCode: 0
Status:   OK  
CheckDir: ClassifyR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ClassifyR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ClassifyR_3.9.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/ClassifyR.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 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 '3.9.2'
* 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) 13.2.0'
* 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'
.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
  'useFeatures'
.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
  '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'
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
  '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'
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'
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'
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:
  Accuracy Class FPR Freq Group ID Metric Node Pairs Predicted Sequence
  SetEdgeStyle SetGraphStyle SetNodeStyle TPR Tier Var1 Var2 aResult
  accuracy aggregate characteristic chisq.test classes 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 quasibinomial random
  real samplesTiers sd second setNames size splinefun test
  testingMatrix top trainParams trainingMatrix trueClass type unqiue
  upper useFeatures 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")
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 for x64 is not available
File 'F:/biocbuild/bbs-3.20-bioc/R/library/ClassifyR/libs/x64/ClassifyR.dll':
  Found '_exit', possibly from '_exit' (C)
  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        1317.15 145.97  883.41
distribution          296.81  37.16  182.14
ClassifyResult-class  285.46  38.50  173.40
runTests                3.20   0.22   49.99
selectionPlot           1.80   0.06   16.87
rankingPlot             1.07   0.09   15.61
* 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: 3 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/ClassifyR.Rcheck/00check.log'
for details.


Installation output

ClassifyR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL ClassifyR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'ClassifyR' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
using C++11
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c coxformatrices.cpp -o coxformatrices.o
coxformatrices.cpp: In function 'void coxmat(double*, int*, int*, double*, double*, double*, int*, int*, int*, double*, int*, double*, double*, int*, double*, double*, double*, double*, double*, int*, double*, double*, double*, double*, double*, double*)':
coxformatrices.cpp:23:16: warning: unused variable 'sclback2' [-Wunused-variable]
   23 |         double sclback2=*sctest2;
      |                ^~~~~~~~
coxformatrices.cpp:24:16: warning: unused variable 'sclback3' [-Wunused-variable]
   24 |         double sclback3=*sctest3;
      |                ^~~~~~~~
g++ -shared -s -static-libgcc -o ClassifyR.dll tmp.def coxformatrices.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-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-class285.46 38.50173.40
CrossValParams-class2.330.002.33
FeatureSetCollection000
ModellingParams-class0.160.000.15
PredictParams-class0.010.000.02
ROCplot0.690.050.73
SelectParams-class0.080.000.08
TrainParams-class0.030.000.03
TransformParams-class000
available000
calcPerformance0.030.000.03
colCoxTests0.310.010.33
crossValidate1317.15 145.97 883.41
distribution296.81 37.16182.14
edgesToHubNetworks000
featureSetSummary000
interactorDifferences0.040.000.05
performancePlot0.50.00.5
plotFeatureClasses1.720.051.77
precisionPathways000
rankingPlot 1.07 0.0915.61
runTest2.370.102.46
runTests 3.20 0.2249.99
samplesMetricMap3.130.093.22
selectionPlot 1.80 0.0616.87