fix: pkgdown and CRAN

Author: vadimnazarov

.github/workflows/pkgdown.yaml

@@ -37,7 +37,7 @@ jobs:
           needs: website
 
       - name: Build site
-        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE, run_dont_run = FALSE)
         shell: Rscript {0}
 
       - name: Deploy to GitHub pages 🚀

DESCRIPTION

@@ -19,7 +19,7 @@ Description: A comprehensive analytics framework for building reproducible pipel
     Think Scanpy or Seurat, but for AIRR data, a.k.a. Adaptive Immune Receptor Repertoire, VDJ-seq, RepSeq, or 
     VDJ sequencing data. A successor to our previously published "tcR" R package (Nazarov 2015).
 License: Apache License (>= 2.0)
-URL: https://immunomind.github.io/docs/, https://github.com/immunomind/immunarch
+URL: https://immunomind.github.io/docs/, https://github.com/immunomind/immunarch/, https://immunarch.com/
 BugReports: https://github.com/immunomind/immunarch/issues
 Depends:
     R (>= 4.2.0),

R/v0_filters.R

@@ -45,29 +45,6 @@
 #' - substring: matches all strings containing the specified substring.
 #' Default value: 'exact'.
 #'
-#' @examples
-#' data(immdata)
-#'
-#' # Select samples with status "MS"
-#' repFilter(immdata, "by.meta", list(Status = include("MS")))
-#'
-#' # Select samples without status "MS"
-#' repFilter(immdata, "by.meta", list(Status = exclude("MS")))
-#'
-#' # Select samples from lanes "A" and "B" with age > 15
-#' repFilter(immdata, "by.meta", list(Lane = include("A", "B"), Age = morethan(15)))
-#'
-#' # Select samples that are not from lanes "A" and "B"
-#' repFilter(immdata, "by.meta", list(Lane = exclude("A", "B")))
-#'
-#' # Select samples with a number of clonotypes from 1000 to 5000
-#' repFilter(immdata, "by.repertoire", list(n_clonotypes = interval(1000, 5000)))
-#'
-#' # Select clonotypes in all samples with alpha chains
-#' repFilter(immdata, "by.clonotype",
-#'   list(V.name = include("AV"), J.name = include("AJ")),
-#'   .match = "substring"
-#' )
 #' @export repFilter include exclude lessthan morethan interval
 repFilter <- function(.data, .method = "by.clonotype",
                       .query = list(CDR3.aa = exclude("partial", "out_of_frame")),

R/v1_clonality_airr.R

@@ -23,8 +23,11 @@
 #' # Limit the number of threads used by the underlying DB for this session.
 #' # Change this only if you know what you're doing (e.g., multi-user machines, shared CI/servers).
 #' db_exec("SET threads TO 1")
+#'
 #' # Load data
+#' \dontrun{
 #' immdata <- get_test_idata() |> agg_repertoires("Therapy")
+#' }
 #'
 #' @name airr_clonality
 #' @concept Clonality
@@ -82,7 +85,9 @@ airr_clonality_line_impl <- function(idata, limit = 100000) {
 #' #
 #' # airr_clonality_line
 #' #
+#' \dontrun{
 #' top_line <- airr_clonality_line(immdata, limit = 1000)
+#' }
 #'
 #' @rdname airr_clonality
 #' @concept Clonality
@@ -133,7 +138,9 @@ airr_clonality_rank_impl <- function(idata,
 #' #
 #' # airr_clonality_rank
 #' #
+#' \dontrun{
 #' rank_stat <- airr_clonality_rank(immdata, bins = c(10, 100))
+#' }
 #'
 #' @rdname airr_clonality
 #' @concept Clonality
@@ -191,7 +198,9 @@ airr_clonality_prop_impl <- function(
 #' #
 #' # airr_clonality_prop
 #' #
+#' \dontrun{
 #' prop_stat <- airr_clonality_prop(immdata)
+#' }
 #'
 #' @rdname airr_clonality
 #' @concept Clonality

R/v1_diversity_airr.R

@@ -25,7 +25,9 @@
 #' # Change this only if you know what you're doing (e.g., multi-user machines, shared CI/servers).
 #' db_exec("SET threads TO 1")
 #' # Load data
+#' \dontrun{
 #' immdata <- get_test_idata() |> agg_repertoires("Therapy")
+#' }
 #'
 #' @name airr_diversity
 #' @concept Diversity
@@ -103,8 +105,10 @@ airr_diversity_dxx_impl <- function(idata, perc = 50) {
 #' #
 #' # airr_diversity_dxx
 #' #
+#' \dontrun{
 #' d50 <- airr_diversity_dxx(immdata, perc = 50)
 #' d_multi <- airr_diversity_dxx(immdata, perc = c(20, 50, 80))
+#' }
 #'
 #' @rdname airr_diversity
 #' @concept Diversity
@@ -154,7 +158,9 @@ airr_diversity_chao1_impl <- function(idata) {
 #' #
 #' # airr_diversity_chao1
 #' #
+#' \dontrun{
 #' chao <- airr_diversity_chao1(immdata)
+#' }
 #'
 #' @rdname airr_diversity
 #' @concept Diversity
@@ -197,7 +203,9 @@ airr_diversity_shannon_impl <- function(idata) {
 #' #
 #' # airr_diversity_shannon
 #' #
+#' \dontrun{
 #' sh <- airr_diversity_shannon(immdata)
+#' }
 #'
 #' @rdname airr_diversity
 #' @concept Diversity
@@ -236,7 +244,9 @@ airr_diversity_pielou_impl <- function(idata) {
 #' #
 #' # airr_diversity_pielou
 #' #
+#' \dontrun{
 #' pj <- airr_diversity_pielou(immdata)
+#' }
 #'
 #' @rdname airr_diversity
 #' @concept Diversity
@@ -267,7 +277,9 @@ airr_diversity_index_impl <- function(idata) {
 #' #
 #' # airr_diversity_index
 #' #
+#' \dontrun{
 #' idx <- airr_diversity_index(immdata)
+#' }
 #'
 #' @rdname airr_diversity
 #' @concept Diversity
@@ -351,7 +363,9 @@ airr_diversity_hill_impl <- function(idata, q = 0:5) {
 #' #
 #' # airr_diversity_hill
 #' #
+#' \dontrun{
 #' hill <- airr_diversity_hill(immdata, q = c(0, 1, 2))
+#' }
 #'
 #' @rdname airr_diversity
 #' @concept Diversity

R/v1_public_airr.R

@@ -86,7 +86,9 @@ airr_public_intersection_impl <- function(idata) {
 #' #
 #' # airr_public_intersection
 #' #
+#' \dontrun{
 #' m_pub <- airr_public_intersection(immdata)
+#' }
 #'
 #' @rdname airr_public
 #' @concept Public indices
@@ -165,7 +167,9 @@ airr_public_jaccard_impl <- function(idata) {
 #' #
 #' # airr_public_jaccard
 #' #
+#' \dontrun{
 #' m_jac <- airr_public_jaccard(immdata)
+#' }
 #'
 #' @rdname airr_public
 #' @concept Public indices

R/v1_stats_airr.R

@@ -23,7 +23,9 @@
 #' db_exec("SET threads TO 2")
 #'
 #' # Load data
+#' \dontrun{
 #' immdata <- get_test_idata() |> agg_repertoires("Therapy")
+#' }
 #'
 #' @name airr_stats
 #' @concept Key AIRR statistics
@@ -94,7 +96,10 @@ airr_stats_chains_impl <- function(idata, locus_col = NA) {
 #' #
 #' # airr_stats_chains
 #' #
+#'
+#' \dontrun{
 #' airr_stats_chains(immdata)
+#' }
 #'
 #' @rdname airr_stats
 #' @concept Key AIRR statistics
@@ -144,7 +149,10 @@ airr_stats_lengths_impl <- function(idata, seq_col = "cdr3_aa") {
 #' #
 #' # airr_stats_lengths
 #' #
+#'
+#' \dontrun{
 #' airr_stats_lengths(immdata)
+#' }
 #'
 #' @rdname airr_stats
 #' @concept Key AIRR statistics
@@ -217,6 +225,8 @@ airr_stats_genes_impl <- function(idata, gene_col = "v_call", level = c("recepto
 #' #
 #' # airr_stats_genes
 #' #
+#'
+#' \dontrun{
 #' # V gene usage by receptor count
 #' airr_stats_genes(immdata, gene_col = "v_call", level = "receptor")
 #'
@@ -225,6 +235,7 @@ airr_stats_genes_impl <- function(idata, gene_col = "v_call", level = c("recepto
 #'
 #' # Split by locus (TRA/TRB/... if locus column exists)
 #' airr_stats_genes(immdata, gene_col = "v_call", level = "receptor", by = "locus")
+#' }
 #'
 #' @rdname airr_stats
 #' @concept Key AIRR statistics

_pkgdown.yml

@@ -22,6 +22,7 @@ articles:
   subtitle: "Deprecated"
   desc: ~
   contents:
+  - '`immunarch_threads`'
   - '`web_only_v0/introduction`'
   - '`web_only_v0/data`'
   - '`web_only_v0/v21_singlecell`'
@@ -35,7 +36,6 @@ articles:
   - '`web_only_v0/v8_tracking`'
   - '`web_only_v0/v9_kmers`'
   - '`web_only_v0/v11_db`'
-  - '`web_only_v0/community`'
   - '`web_only_v0/repFilter_v3`'
   - '`web_only_v0/v10_prop`'
   - '`web_only_v0/BCRpipeline`'