* 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