• using R version 4.5.1 Patched (2025-09-24 r88883)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.3.0-8) 14.3.0     GNU Fortran (Debian 14.3.0-8) 14.3.0
• running under: Debian GNU/Linux forky/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 the install log for details.
• used C++ compiler: ‘g++-14 (Debian 14.3.0-8) 14.3.0’
• 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 ... [7s/9s] OK
• checking whether the package can be loaded with stated dependencies ... [7s/9s] OK
• checking whether the package can be unloaded cleanly ... [7s/8s] OK
• checking whether the namespace can be loaded with stated dependencies ... [6s/8s] OK
• checking whether the namespace can be unloaded cleanly ... [6s/7s] OK
• checking loading without being on the library search path ... [7s/9s] 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 ... [48s/60s] 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 ... [144s/190s] OK Examples with CPU (user + system) or elapsed time > 5s                               user system elapsed repDiversity 7.278 0.012 10.365 vis.immunr_gene_usage 7.059 0.000 8.506 vis.immunr_dynamics 6.193 0.034 6.915 trackClonotypes 5.771 0.081 7.387 vis_public_frequencies 5.521 0.088 7.628 vis_public_clonotypes 5.500 0.023 6.304 seqCluster 4.912 0.095 6.119 vis.immunr_public_repertoire 4.947 0.015 6.166 vis_textlogo 4.540 0.014 6.380 vis 4.354 0.019 6.147
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [10s/15s] OK
• checking PDF version of manual ... [9s/12s] OK
• checking HTML version of manual ... [3s/6s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 NOTE