Dario Strbenac
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/ClassifyR |
| git_branch: RELEASE_3_20 |
| git_last_commit: 39dd7d4 |
| git_last_commit_date: 2024-12-12 23:45:16 -0500 (Thu, 12 Dec 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 359/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ClassifyR 3.10.4 (landing page) Dario Strbenac
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
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. |
| Package: ClassifyR |
| Version: 3.10.4 |
| 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_3.10.4.tar.gz |
| StartedAt: 2024-12-20 00:03:04 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 00:09:58 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 413.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ClassifyR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_3.10.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/ClassifyR.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* 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 '3.10.4'
* 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 whether package 'ClassifyR' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
* 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'
.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: no visible binding for global variable 'outcome'
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'
prepareData,MultiAssayExperiment: possible error in
union(useFeatures[["clinical"]], group, outcomeColumns): unused
argument (outcomeColumns)
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 outcome 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 ... 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 65.68 2.11 58.38
ClassifyResult-class 18.80 0.84 16.97
distribution 13.58 0.74 11.82
runTests 3.87 0.19 47.03
selectionPlot 1.86 0.03 14.28
rankingPlot 1.34 0.03 14.47
* 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.
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) 13.3.0'
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)
ClassifyR.Rcheck/ClassifyR-Ex.timings
| name | user | system | elapsed | |
| ClassifyResult-class | 18.80 | 0.84 | 16.97 | |
| CrossValParams-class | 2.62 | 0.02 | 2.64 | |
| FeatureSetCollection | 0 | 0 | 0 | |
| ModellingParams-class | 0.15 | 0.00 | 0.15 | |
| PredictParams-class | 0 | 0 | 0 | |
| ROCplot | 0.77 | 0.03 | 0.80 | |
| SelectParams-class | 0.00 | 0.02 | 0.01 | |
| TrainParams-class | 0.02 | 0.00 | 0.01 | |
| TransformParams-class | 0 | 0 | 0 | |
| available | 0 | 0 | 0 | |
| calcPerformance | 0.03 | 0.00 | 0.04 | |
| colCoxTests | 0.27 | 0.00 | 0.26 | |
| crossValidate | 65.68 | 2.11 | 58.38 | |
| distribution | 13.58 | 0.74 | 11.82 | |
| edgesToHubNetworks | 0 | 0 | 0 | |
| featureSetSummary | 0 | 0 | 0 | |
| interactorDifferences | 0.06 | 0.00 | 0.07 | |
| performancePlot | 0.49 | 0.00 | 0.48 | |
| plotFeatureClasses | 2.17 | 0.00 | 2.22 | |
| precisionPathways | 0 | 0 | 0 | |
| rankingPlot | 1.34 | 0.03 | 14.47 | |
| runTest | 2.46 | 0.06 | 2.53 | |
| runTests | 3.87 | 0.19 | 47.03 | |
| samplesMetricMap | 3.03 | 0.01 | 3.05 | |
| samplesSplitting | 0 | 0 | 0 | |
| selectionPlot | 1.86 | 0.03 | 14.28 | |