Back to Multiple platform build/check report for BioC 3.20:   simplified   long
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-02-13 12:12 -0500 (Thu, 13 Feb 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4754
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4502
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4525
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4477
taishanLinux (openEuler 24.03 LTS)aarch644.4.2 (2024-10-31) -- "Pile of Leaves" 4414
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 359/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ClassifyR 3.10.6  (landing page)
Dario Strbenac
Snapshot Date: 2025-02-10 13:00 -0500 (Mon, 10 Feb 2025)
git_url: https://git.bioconductor.org/packages/ClassifyR
git_branch: RELEASE_3_20
git_last_commit: b501969
git_last_commit_date: 2025-01-30 23:20:05 -0500 (Thu, 30 Jan 2025)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


CHECK results for ClassifyR on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: ClassifyR
Version: 3.10.6
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ClassifyR_3.10.6.tar.gz
StartedAt: 2025-02-11 04:50:12 -0000 (Tue, 11 Feb 2025)
EndedAt: 2025-02-11 04:56:09 -0000 (Tue, 11 Feb 2025)
EllapsedTime: 356.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ClassifyR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ClassifyR_3.10.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ClassifyR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403)
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ClassifyR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ClassifyR’ version ‘3.10.6’
* 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: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘TOP’
'loadNamespace' or 'requireNamespace' call not declared from: ‘TOP’
* 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 : plotMatrix: no visible binding for global variable
  ‘Var1’
crissCrossPlot : plotMatrix: no visible binding for global variable
  ‘Var2’
crissCrossPlot : plotMatrix: no visible binding for global variable
  ‘value’
crissCrossPlot: no visible binding for global variable ‘real’
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<-’
easyHard,MultiAssayExperimentOrList : <anonymous>: no visible global
  function definition for ‘glm’
easyHard,MultiAssayExperimentOrList : <anonymous>: no visible binding
  for global variable ‘binomial’
easyHard,MultiAssayExperimentOrList : <anonymous>: no visible global
  function definition for ‘predict’
easyHard,MultiAssayExperimentOrList: no visible global function
  definition for ‘glm’
easyHard,MultiAssayExperimentOrList: no visible global function
  definition for ‘binomial’
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’
prepareData,DataFrame: no visible global function definition for
  ‘combn’
prepareData,DataFrame : <anonymous>: no visible global function
  definition for ‘fisher.test’
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 binomial characteristic
  chisq.test classes colourVariable combn cost coxph crossValParams
  density dist dmvnorm dnorm extrasInputs feature featuresLists first
  fisher.test 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", "binomial", "chisq.test", "density",
             "dist", "dnorm", "fisher.test", "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 ... 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        68.016  2.731  63.070
ClassifyResult-class 18.513  1.743  18.268
distribution         14.782  0.564  13.321
runTests             10.571  3.276   6.348
* 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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/ClassifyR.Rcheck/00check.log’
for details.


Installation output

ClassifyR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL ClassifyR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.2/site-library’
* installing *source* package ‘ClassifyR’ ...
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++11
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -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;
      |                ^~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o ClassifyR.so coxformatrices.o -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.4.2/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
*** 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)

Tests output


Example timings

ClassifyR.Rcheck/ClassifyR-Ex.timings

nameusersystemelapsed
ClassifyResult-class18.513 1.74318.268
CrossValParams-class3.3260.1443.481
FeatureSetCollection0.0070.0000.007
ModellingParams-class0.2130.0000.213
PredictParams-class0.0140.0000.014
ROCplot0.8610.0360.900
SelectParams-class0.0430.0000.043
TrainParams-class0.0240.0000.024
TransformParams-class0.0120.0000.012
available0.0000.0020.003
calcPerformance0.0230.0010.024
colCoxTests0.2220.0000.223
crossValidate68.016 2.73163.070
distribution14.782 0.56413.321
edgesToHubNetworks0.0020.0000.002
featureSetSummary0.0050.0000.005
interactorDifferences0.0340.0000.034
performancePlot0.4590.0080.469
plotFeatureClasses2.2410.0442.293
precisionPathways000
rankingPlot0.3640.2380.481
runTest3.3380.4463.809
runTests10.571 3.276 6.348
samplesMetricMap4.0410.4454.500
samplesSplitting0.0010.0000.002
selectionPlot1.1260.3591.349