* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’ * installing *source* package ‘immunarch’ ... ** this is package ‘immunarch’ version ‘0.9.1’ ** package ‘immunarch’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpCsYYZL/R.INSTALL358f6a1ae7770a/immunarch/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c fill_functions.cpp -o fill_functions.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o immunarch.so RcppExports.o fill_functions.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpCsYYZL/R.INSTALL358f6a1ae7770a/immunarch/src' make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpCsYYZL/R.INSTALL358f6a1ae7770a/immunarch/src' make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpCsYYZL/R.INSTALL358f6a1ae7770a/immunarch/src' installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-immunarch/00new/immunarch/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package ‘immunarch’ finding HTML links ... done aa_properties html aa_table html add_class html apply_symm html bcrdata html bunch_translate html check_distribution html coding html Rd warning: coding.Rd:20: missing link ‘data.table’ Rd warning: coding.Rd:26: missing link ‘copy_to’ dbAnnotate html Rd warning: dbAnnotate.Rd:11: missing link ‘data.table’ Rd warning: dbAnnotate.Rd:17: missing link ‘copy_to’ dbLoad html dot-quant_column_choice html entropy html fixVis html geneUsage html Rd warning: geneUsage.Rd:20: missing link ‘data.table’ Rd warning: geneUsage.Rd:26: missing link ‘copy_to’ geneUsageAnalysis html gene_segments html gene_stats html getKmers html Rd warning: getKmers.Rd:13: missing link ‘data.table’ Rd warning: getKmers.Rd:19: missing link ‘copy_to’ group_from_metadata html has_class html immdata html immunr_data_format html immunr_hclust html Rd warning: immunr_hclust.Rd:21: missing link ‘fviz_nbclust’ Rd warning: immunr_hclust.Rd:23: missing link ‘fviz_nbclust’ Rd warning: immunr_hclust.Rd:27: missing link ‘fviz_nbclust’ Rd warning: immunr_hclust.Rd:34: missing link ‘hcut’ Rd warning: immunr_hclust.Rd:35: missing link ‘fviz_nbclust’ Rd warning: immunr_hclust.Rd:38: missing link ‘fviz_nbclust’ Rd warning: immunr_hclust.Rd:41: missing link ‘dbscan’ immunr_pca html Rd warning: immunr_pca.Rd:37: missing link ‘isoMDS’ Rd warning: immunr_pca.Rd:39: missing link ‘Rtsne’ inc_overlap html Rd warning: inc_overlap.Rd:20: missing link ‘data.table’ Rd warning: inc_overlap.Rd:26: missing link ‘copy_to’ matrixdiagcopy html pubRep html Rd warning: pubRep.Rd:20: missing link ‘data.table’ Rd warning: pubRep.Rd:26: missing link ‘copy_to’ pubRepApply html pubRepFilter html pubRepStatistics html public_matrix html repAlignLineage html Rd warning: repAlignLineage.Rd:10: missing link ‘data.table’ repClonalFamily html repClonality html Rd warning: repClonality.Rd:25: missing link ‘data.table’ Rd warning: repClonality.Rd:31: missing link ‘copy_to’ repDiversity html Rd warning: repDiversity.Rd:33: missing link ‘data.table’ Rd warning: repDiversity.Rd:39: missing link ‘copy_to’ repExplore html Rd warning: repExplore.Rd:16: missing link ‘data.table’ Rd warning: repExplore.Rd:22: missing link ‘copy_to’ repFilter html repGermline html Rd warning: repGermline.Rd:10: missing link ‘data.table’ repLoad html repOverlap html Rd warning: repOverlap.Rd:25: missing link ‘data.table’ Rd warning: repOverlap.Rd:31: missing link ‘copy_to’ repOverlapAnalysis html repSample html Rd warning: repSample.Rd:16: missing link ‘data.table’ Rd warning: repSample.Rd:22: missing link ‘copy_to’ repSave html repSomaticHypermutation html scdata html select_barcodes html Rd warning: select_barcodes.Rd:11: missing link ‘data.table’ Rd warning: select_barcodes.Rd:17: missing link ‘copy_to’ select_clusters html seqCluster html Rd warning: seqCluster.Rd:11: missing link ‘data.table’ seqDist html Rd warning: seqDist.Rd:12: missing link ‘data.table’ set_pb html spectratype html Rd warning: spectratype.Rd:11: missing link ‘data.table’ Rd warning: spectratype.Rd:17: missing link ‘copy_to’ split_to_kmers html switch_type html top html Rd warning: top.Rd:11: missing link ‘data.table’ Rd warning: top.Rd:17: missing link ‘copy_to’ trackClonotypes html Rd warning: trackClonotypes.Rd:11: missing link ‘data.table’ Rd warning: trackClonotypes.Rd:17: missing link ‘copy_to’ vis html vis.clonal_family html vis.clonal_family_tree html vis.immunr_chao1 html vis.immunr_clonal_prop html vis.immunr_dynamics html vis.immunr_exp_vol html vis.immunr_gene_usage html Rd warning: vis.immunr_gene_usage.Rd:32: missing link ‘chordDiagram’ vis.immunr_hclust html Rd warning: vis.immunr_hclust.Rd:12: missing link ‘fviz_dend’ vis.immunr_inc_overlap html vis.immunr_kmeans html Rd warning: vis.immunr_kmeans.Rd:22: missing link ‘fviz_cluster’ Rd warning: vis.immunr_kmeans.Rd:24: missing link ‘fviz_cluster’ Rd warning: vis.immunr_kmeans.Rd:26: missing link ‘fviz_cluster’ Rd warning: vis.immunr_kmeans.Rd:28: missing link ‘fviz_cluster’ Rd warning: vis.immunr_kmeans.Rd:30: missing link ‘fviz_cluster’ vis.immunr_kmer_table html vis.immunr_mds html vis.immunr_ov_matrix html Rd warning: vis.immunr_ov_matrix.Rd:27: missing link ‘chordDiagram’ vis.immunr_public_repertoire html vis.immunr_public_statistics html Rd warning: vis.immunr_public_statistics.Rd:12: missing link ‘upset’ vis.step_failure_ignored html vis_bar html vis_box html Rd warning: vis_box.Rd:41: missing link ‘melt’ vis_circos html Rd warning: vis_circos.Rd:20: missing link ‘chordDiagram’ Rd warning: vis_circos.Rd:14: missing link ‘chordDiagram’ vis_heatmap html vis_heatmap2 html vis_hist html Rd warning: vis_hist.Rd:55: missing link ‘melt’ vis_immunr_kmer_profile_main html vis_public_clonotypes html vis_public_frequencies html vis_textlogo html Rd warning: vis_textlogo.Rd:23: missing link ‘geom_logo’ ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (immunarch)