• using R version 4.5.0 (2025-04-11)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.2.0-19) 14.2.0     GNU Fortran (Debian 14.2.0-19) 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 the install log for details.
• used C++ compiler: ‘g++-14 (Debian 14.2.0-19) 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 ... [6s/8s] OK
• checking whether the package can be loaded with stated dependencies ... [5s/6s] OK
• checking whether the package can be unloaded cleanly ... [6s/7s] OK
• checking whether the namespace can be loaded with stated dependencies ... [6s/7s] OK
• checking whether the namespace can be unloaded cleanly ... [6s/8s] OK
• checking loading without being on the library search path ... [6s/8s] 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 ... [47s/67s] 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 ... [124s/157s] OK Examples with CPU (user + system) or elapsed time > 5s                         user system elapsed repDiversity 6.216 0.189 8.225 vis.immunr_gene_usage 5.956 0.121 7.471 vis.immunr_dynamics 5.359 0.157 6.366 seqCluster 4.949 0.160 6.216 vis_public_clonotypes 5.019 0.026 5.889 vis_public_frequencies 4.457 0.150 5.699 trackClonotypes 4.409 0.034 5.401 vis_textlogo 4.035 0.119 5.879 vis 3.706 0.047 5.184
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [10s/14s] OK
• checking PDF version of manual ... [7s/10s] OK
• checking HTML version of manual ... [3s/5s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 NOTE