* using log directory ‘/srv/hornik/tmp/CRAN_pretest/MultiPhen.Rcheck’
* using R Under development (unstable) (2026-03-15 r89634)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 21.1.8 (3+b1)
    Debian flang version 21.1.8 (3+b1)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* current time: 2026-03-17 00:08:05 UTC
* checking for file ‘MultiPhen/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MultiPhen’ version ‘2.0.4’
* checking CRAN incoming feasibility ... [3s/5s] OK
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘MultiPhen’ can be installed ... [3s/3s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... NOTE
Author field differs from that derived from Authors@R
  Author:    ‘Lachlan Coin, Paul O'Reilly, Yotsawat Pompyen, Clive Hoggart and Federico Calboli’
  Authors@R: ‘Lachlan Coin [aut, cre], Paul O'Reilly [aut], Yotsawat Pompyen [aut], Clive Hoggart [aut], Federico Calboli [aut]’

* 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] OK
* checking whether startup messages can be suppressed ... [0s/0s] OK
* checking use of S3 registration ... 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 ... [8s/8s] NOTE
.hwep: no visible global function definition for ‘HWExact’
.metaresHetMeasure: no visible global function definition for ‘metagen’
.metaresInvVarianceFixed: no visible global function definition for
  ‘metagen’
Undefined global functions or variables:
  HWExact metagen
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘.abf’ ‘.abfSig’ ‘.allFreq’ ‘.applySidakCorrection’ ‘.applyTrans’
  ‘.as.numeric1’ ‘.backwardSelection’ ‘.bafratio’ ‘.calcExpectedGeno’
  ‘.calcOffset’ ‘.calcPPA’ ‘.centralise’ ‘.chol’ ‘.cholesky’
  ‘.closeGenoConnection’ ‘.cnt’ ‘.cntNa’ ‘.cntVec’ ‘.cnvdistr’
  ‘.convAvgToUnc’ ‘.convAvgToUncM’ ‘.convAvgToUncMat’
  ‘.convertFactorToMatrix’ ‘.convertMatrixToFactor’ ‘.countIn’
  ‘.destandardise’ ‘.entropy’ ‘.estSigma’ ‘.expDist’ ‘.expand’
  ‘.expand2’ ‘.expandCoeff’ ‘.expandDat’ ‘.expandGenoToDist’
  ‘.expandGenoToDistAll’ ‘.extractIds’ ‘.extractIdsMat’
  ‘.extractIdsVec’ ‘.extractNames’ ‘.extractSig’ ‘.extractSig1’
  ‘.extractSig1P’ ‘.extractSigExact’ ‘.extractSigP’ ‘.fillMissing’
  ‘.findIn’ ‘.findInclusion’ ‘.findInd’ ‘.findmax’ ‘.fisherPvalue’
  ‘.fixDuplicatesInTodo’ ‘.fixGenoCols’ ‘.fixNonNumeric’ ‘.flatten’
  ‘.flattenBetaX’ ‘.formatTable’ ‘.fprint’ ‘.genRandCovar’ ‘.getArray’
  ‘.getAvg’ ‘.getAvgAll’ ‘.getAvgWeights’ ‘.getCNProfile’ ‘.getDim’
  ‘.getFamily’ ‘.getGlm’ ‘.getHWE’ ‘.getHist’ ‘.getIMatrix’ ‘.getIncl’
  ‘.getLast’ ‘.getLimitMatrixFromList’ ‘.getMaf’ ‘.getOnes’ ‘.getPv’
  ‘.getPvLrr’ ‘.getPvLrrAllGen’ ‘.getPvLrrMult’ ‘.getPvLrrMultiGen’
  ‘.getPvLrrMultiGen1’ ‘.getPvLrrMultiGenNoVS’ ‘.getPvLrrMultiGenVS’
  ‘.getPvRev’ ‘.getPvRevPleio’ ‘.getPvRevPleioVS’ ‘.getPvRevPleio_’
  ‘.getPvTable’ ‘.getSuffix’ ‘.getSumBetaX’ ‘.getUNum1Matrix’
  ‘.getVCFDimNames’ ‘.getVCFProcess’ ‘.getVCFSplit’ ‘.getin’ ‘.getin1’
  ‘.getin2’ ‘.glm1’ ‘.gs’ ‘.heatm’ ‘.hwep’ ‘.hwepall’ ‘.hwestat’
  ‘.iscase’ ‘.joinRes’ ‘.joinResVec’ ‘.length’ ‘.lrt’ ‘.mPhen’ ‘.mabf’
  ‘.mafCount’ ‘.makeColsForBed’ ‘.makeFactor’ ‘.makeGenoWeights’
  ‘.makeNumeric’ ‘.makeQuantile’ ‘.makeThresh’ ‘.makeTopTail’ ‘.manh’
  ‘.manhattan’ ‘.manhattanBed’ ‘.mergeAlleleCols’ ‘.mergeFiles’
  ‘.mergeLists’ ‘.metaAnalysis’ ‘.metaresFisher’ ‘.metaresHetMeasure’
  ‘.metaresInvVarianceFixed’ ‘.minOneMinus’ ‘.mod’ ‘.mod1’
  ‘.nonNumeric’ ‘.nonNumeric1’ ‘.nullDim’ ‘.numLev’ ‘.nyholdtSidak’
  ‘.openGenoConnection’ ‘.openOutputConnection’ ‘.openPlinkConnection’
  ‘.openVCFConnection’ ‘.openZipConnection’ ‘.ordTest’ ‘.ordTest1’
  ‘.ordTest2’ ‘.ordTestUnivariate’ ‘.orthogonalise’ ‘.pFromSEBeta’
  ‘.parseOpts’ ‘.plotBaf’ ‘.plotFingerprint’ ‘.pow’ ‘.proc’ ‘.proc1’
  ‘.projOut’ ‘.pseudoInv’ ‘.qb’ ‘.qq’ ‘.qqplot’ ‘.readGenoConnection’
  ‘.readHeader’ ‘.readLimitFile’ ‘.readLinesPlink’ ‘.readPhen’
  ‘.readPlinkConnection’ ‘.readVCFConnection’ ‘.readZip’
  ‘.readZipConnection’ ‘.reduceWeightsToGeno’ ‘.reopenConnection’
  ‘.rescale’ ‘.sampDirichlet’ ‘.sampJoint’ ‘.sample1’ ‘.seFromPBeta’
  ‘.splitImputed’ ‘.standardise’ ‘.subSample’ ‘.sum1’
  ‘.summariseBootstrap’ ‘.tabulateWithWeights’ ‘.trL’ ‘.unchanged’
  ‘.updateRelatedness’ ‘.updateSampleQC’ ‘.writeBed’ ‘.writeTable’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [0s/0s] OK
* checking for unstated dependencies in ‘demo’ ... OK
* checking PDF version of manual ... [3s/2s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 WARNING, 2 NOTEs