Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:05:00 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

CHECK results for ClassifyR on nebbiolo2


To the developers/maintainers of the ClassifyR package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 336/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ClassifyR 3.2.7  (landing page)
Dario Strbenac
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/ClassifyR
git_branch: RELEASE_3_16
git_last_commit: 04d9a3e
git_last_commit_date: 2023-02-03 05:20:20 -0400 (Fri, 03 Feb 2023)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: ClassifyR
Version: 3.2.7
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings ClassifyR_3.2.7.tar.gz
StartedAt: 2023-04-10 19:43:33 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 20:13:55 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 1821.9 seconds
RetCode: 0
Status:   OK  
CheckDir: ClassifyR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings ClassifyR_3.2.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/ClassifyR.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘ClassifyR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ClassifyR’ version ‘3.2.7’
* 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 ... NOTE
Found the following hidden files and directories:
  dump/.-package.R
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ClassifyR’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘BiocParallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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’
CrossValParams: no visible global function definition for ‘bpparam’
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’
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’
generateCrossValParams: no visible global function definition for
  ‘SerialParam’
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: no visible global function definition for
  ‘SerialParam’
pcaTrainInterface : <anonymous>: no visible global function definition
  for ‘prcomp’
prevalTrainInterface: no visible global function definition for
  ‘SerialParam’
prevalTrainInterface: no visible global function definition for
  ‘bpmapply’
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 global function definition for ‘bpparam’
rankingPlot,list: no visible global function definition for ‘bpmapply’
rankingPlot,list: no visible global function definition for ‘bplapply’
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’
runTests,DataFrame: no visible global function definition for
  ‘bpmapply’
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 ‘bpparam’
selectionPlot,list: no visible global function definition for
  ‘bpmapply’
selectionPlot,list: no visible global function definition for
  ‘bplapply’
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 SerialParam TPR
  aResult aggregate allPredictions binomial bplapply bpmapply bpparam
  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 pnorm
  prcomp predict predictParams prepArgs quantile 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 ... 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        1341.630 158.031 809.454
ClassifyResult-class  315.476  43.150 167.160
distribution          318.487  39.359 159.797
runTests               11.186   3.665   6.515
* 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 ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/ClassifyR.Rcheck/00check.log’
for details.



Installation output

ClassifyR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL ClassifyR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘ClassifyR’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-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-3.16-bioc/R/lib -L/usr/local/lib -o ClassifyR.so coxformatrices.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/site-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
** 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)

Tests output


Example timings

ClassifyR.Rcheck/ClassifyR-Ex.timings

nameusersystemelapsed
ClassifyResult-class315.476 43.150167.160
CrossValParams-class2.0570.3342.390
FeatureSetCollection0.0080.0000.008
ModellingParams-class0.1840.0070.191
PredictParams-class0.0100.0000.011
ROCplot1.2260.0581.283
SelectParams-class0.0520.0000.052
TrainParams-class0.020.000.02
TransformParams-class0.0100.0000.011
available0.0030.0000.003
calcPerformance0.0190.0000.019
colCoxTests0.2380.0070.246
crossValidate1341.630 158.031 809.454
distribution318.487 39.359159.797
edgesToHubNetworks0.0020.0000.002
featureSetSummary0.0060.0000.006
interactorDifferences0.0340.0000.034
performancePlot0.3290.0650.394
plotFeatureClasses2.7030.1402.843
rankingPlot0.3790.2580.487
runTest2.4980.1332.631
runTests11.186 3.665 6.515
samplesMetricMap4.0360.1614.198
selectionPlot1.2040.2461.340