* using log directory ‘/srv/hornik/tmp/CRAN_pretest/alakazam.Rcheck’
* using R Under development (unstable) (2026-04-27 r89967)
* 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: 2026-04-28 11:02:10 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 ... [4s/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 whether package ‘alakazam’ can be installed ... [27s/27s] OK
* used C++ compiler: ‘Debian clang version 21.1.8 (3+b1)’
* 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 ... [6s/6s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [6s/6s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
* checking loading without being on the library search path ... [6s/6s] OK
* checking whether startup messages can be suppressed ... [6s/6s] 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 ... [31s/31s] 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 ... [0s/0s] 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 ... [54s/54s] OK
* checking PDF version of manual ... [2s/2s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 WARNING