Multiple platform build/check report for BioC 3.21 - CHECK results for ClassifyR on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"	4783
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"	4552
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4581
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4533
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4463
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 kunpeng2

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: 3.11.11

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_3.11.11.tar.gz

StartedAt: 2025-03-26 04:57:35 -0000 (Wed, 26 Mar 2025)

EndedAt: 2025-03-26 05:04:01 -0000 (Wed, 26 Mar 2025)

EllapsedTime: 386.3 seconds

RetCode: 0

Status: OK

CheckDir: ClassifyR.Rcheck

Warnings: 0

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_3.11.11.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ClassifyR.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ClassifyR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ClassifyR’ version ‘3.11.11’
* 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 ... 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 : 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’
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 ... 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
  calcPerformance.Rd: DataFrame, MultiAssayExperiment
  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        71.307  1.763  65.367
ClassifyResult-class 20.490  0.647  19.137
distribution         14.635  0.448  13.062
runTests             10.923  2.817   5.949
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-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-devel_2025-02-19/site-library’
* installing *source* package ‘ClassifyR’ ...
** this is package ‘ClassifyR’ version ‘3.11.11’
** 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-devel_2025-02-19/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

name	user	system	elapsed
ClassifyResult-class	20.490	0.647	19.137
CrossValParams-class	4.400	0.009	4.418
FeatureSetCollection	0.007	0.000	0.007
ModellingParams-class	0.218	0.000	0.219
PredictParams-class	0.014	0.000	0.014
ROCplot	0.912	0.008	0.923
SelectParams-class	0.044	0.000	0.044
TrainParams-class	0.024	0.000	0.024
TransformParams-class	0.012	0.000	0.012
available	0.003	0.000	0.002
calcPerformance	0.025	0.000	0.025
colCoxTests	0.254	0.004	0.257
crossValidate	71.307	1.763	65.367
distribution	14.635	0.448	13.062
edgesToHubNetworks	0.001	0.000	0.002
featureSetSummary	0.006	0.000	0.005
interactorDifferences	0.036	0.000	0.036
performancePlot	0.480	0.028	0.509
plotFeatureClasses	2.228	0.012	2.246
precisionPathways	0	0	0
rankingPlot	0.400	0.210	0.493
runTest	3.423	0.195	3.627
runTests	10.923	2.817	5.949
samplesMetricMap	4.206	0.349	4.568
samplesSplitting	0.001	0.000	0.001
selectionPlot	1.192	0.304	1.390