* 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/RtmpNZOQsi/R.INSTALL36f28d1e8dcbb4/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/RtmpNZOQsi/R.INSTALL36f28d1e8dcbb4/immunarch/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpNZOQsi/R.INSTALL36f28d1e8dcbb4/immunarch/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpNZOQsi/R.INSTALL36f28d1e8dcbb4/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)