* using log directory ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/immunarch.Rcheck’
* using R Under development (unstable) (2025-02-25 r87824)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (Debian 14.2.0-16) 14.2.0
    GNU Fortran (Debian 14.2.0-16) 14.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘immunarch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘immunarch’ version ‘0.9.1’
* 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 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 ‘immunarch’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/immunarch-00install.html' for details.
* used C++ compiler: ‘g++-14 (Debian 14.2.0-16) 14.2.0’
* 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 ... [5s/6s] OK
* checking whether the package can be loaded with stated dependencies ... [4s/6s] OK
* checking whether the package can be unloaded cleanly ... [4s/5s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s/5s] OK
* checking whether the namespace can be unloaded cleanly ... [4s/5s] OK
* checking loading without being on the library search path ... [4s/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/40s] OK
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  coding.Rd: data.table, copy_to
  dbAnnotate.Rd: data.table, copy_to
  geneUsage.Rd: data.table, copy_to
  getKmers.Rd: data.table, copy_to
  immunr_hclust.Rd: fviz_nbclust, hcut, dbscan
  immunr_pca.Rd: isoMDS, Rtsne
  inc_overlap.Rd: data.table, copy_to
  pubRep.Rd: data.table, copy_to
  repAlignLineage.Rd: data.table
  repClonality.Rd: data.table, copy_to
  repDiversity.Rd: data.table, copy_to
  repExplore.Rd: data.table, copy_to
  repGermline.Rd: data.table
  repOverlap.Rd: data.table, copy_to
  repSample.Rd: data.table, copy_to
  select_barcodes.Rd: data.table, copy_to
  seqCluster.Rd: data.table
  seqDist.Rd: data.table
  spectratype.Rd: data.table, copy_to
  top.Rd: data.table, copy_to
  trackClonotypes.Rd: data.table, copy_to
  vis.immunr_gene_usage.Rd: chordDiagram
  vis.immunr_hclust.Rd: fviz_dend
  vis.immunr_kmeans.Rd: fviz_cluster
  vis.immunr_ov_matrix.Rd: chordDiagram
  vis.immunr_public_statistics.Rd: upset
  vis_box.Rd: melt
  vis_circos.Rd: chordDiagram
  vis_hist.Rd: melt
  vis_textlogo.Rd: geom_logo
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 ... [2s/2s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [103s/129s] OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
vis_public_clonotypes 7.553  0.128   7.117
repDiversity          4.218  0.014   5.938
vis.immunr_gene_usage 3.816  0.059   5.020
repSave               1.636  0.295   9.569
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [8s/12s] OK
* checking PDF version of manual ... [6s/8s] OK
* checking HTML version of manual ... [2s/4s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 NOTE