* using log directory 'd:/RCompile/CRANincoming/R-devel/alakazam.Rcheck'
* using R Under development (unstable) (2026-04-27 r89967 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.3.0
    GNU Fortran (GCC) 14.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* current time: 2026-04-28 11:11:20 UTC
* checking for file 'alakazam/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'alakazam' version '1.4.3'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [19s] 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'alakazam' can be installed ... OK
* used C++ compiler: 'g++.exe (GCC) 14.3.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [11s] OK
* checking whether the package can be loaded with stated dependencies ... [11s] OK
* checking whether the package can be unloaded cleanly ... [13s] OK
* checking whether the namespace can be loaded with stated dependencies ... [11s] OK
* checking whether the namespace can be unloaded cleanly ... [12s] OK
* checking loading without being on the library search path ... [12s] OK
* checking whether startup messages can be suppressed ... [11s] 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 ... [60s] OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'ABBREV_AA' 'DNA_COLORS' 'DNA_IUPAC' 'Example10x' 'ExampleDb'
  'ExampleDbChangeo' 'ExampleTrees' 'IG_COLORS' 'IMGT_REGIONS'
  'IUPAC_AA' 'IUPAC_DNA' 'SingleDb' 'TR_COLORS' 'aliphatic'
  'alphaDiversity' 'aminoAcidProperties' 'baseTheme'
  'buildPhylipLineage' 'bulk' 'calcCoverage' 'calcDiversity' 'charge'
  'checkColumns' 'collapseDuplicates' 'combineIgphyml' 'countClones'
  'countGenes' 'countPatterns' 'cpuCount' 'estimateAbundance'
  'extractVRegion' 'getAAMatrix' 'getAllele' 'getChain' 'getDNAMatrix'
  'getFamily' 'getGene' 'getLocus' 'getMRCA' 'getPathLengths'
  'getPositionQuality' 'getSegment' 'graphToPhylo' 'gravy' 'gridPlot'
  'groupGenes' 'isValidAASeq' 'junctionAlignment' 'makeChangeoClone'
  'makeTempDir' 'maskPositionsByQuality' 'maskSeqEnds' 'maskSeqGaps'
  'nonsquareDist' 'padSeqEnds' 'pairwiseDist' 'pairwiseEqual'
  'permuteLabels' 'phyloToGraph' 'plotAbundanceCurve'
  'plotDiversityCurve' 'plotDiversityTest' 'plotEdgeTest'
  'plotMRCATest' 'plotSubtrees' 'polar' 'progressBar' 'rarefyDiversity'
  'readChangeoDb' 'readFastqDb' 'readIgphyml' 'seqDist' 'seqEqual'
  'sortGenes' 'stoufferMeta' 'summarizeSubtrees' 'tableEdges'
  'testDiversity' 'testEdges' 'testMRCA' 'translateDNA'
  'translateStrings' 'writeChangeoDb'
Undocumented data sets:
  'Example10x' 'ExampleDb' 'ExampleDbChangeo' 'ExampleTrees' 'SingleDb'
Undocumented S4 classes:
  'MRCATest' 'EdgeTest' 'DiversityCurve' 'AbundanceCurve'
  'ChangeoClone'
Undocumented S4 methods:
  generic 'plot' and siglist 'AbundanceCurve,missing'
  generic 'plot' and siglist 'DiversityCurve,missing'
  generic 'plot' and siglist 'DiversityCurve,numeric'
  generic 'plot' and siglist 'EdgeTest,missing'
  generic 'plot' and siglist 'MRCATest,missing'
  generic 'print' and siglist 'AbundanceCurve'
  generic 'print' and siglist 'DiversityCurve'
  generic 'print' and siglist 'EdgeTest'
  generic 'print' and siglist 'MRCATest'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... NONE
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [119s] OK
* checking PDF version of manual ... [11s] OK
* DONE
Status: 1 WARNING