Field fixes from building the demo fixture (0.8.1)

From running the full audit stack against a realistic 20-page synthetic
manuscript with a planted-defect ledger:

- reconcile_values: bibliography lines (DOI/arXiv or APA year+page-range
  shape) are quarantined as reference_meta instead of flooding the
  registry with volume/page/DOI fragments (86 such values on the test
  manuscript); the structured extractor own [Table k, row j] markers are
  stripped before tokenizing so row indices are no longer treated as
  document values
- crossref_get: base R reports HTTP status in a warning, so 404s were
  invisible to the error-message check and got retried for ~7s each;
  warnings are now sniffed and 404s return immediately (0.3s)
- check_arxiv_impl: retries with a longer timeout (arXiv API is slow on
  cold requests) and reports lookup failure explicitly instead of
  returning nothing

CI: reconcile quarantine/marker-stripping functional test.
R CMD check: Status OK.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

Author: IMNMV

.github/scripts/checks.R

@@ -229,6 +229,24 @@ r <- tryCatch({
 }, error = function(e) conditionMessage(e))
 if (isTRUE(r)) pass("reconcile_values end-to-end: only planted value unmatched") else fail("reconcile e2e:", r)
 
+# --- 9b. reconcile: reference-line quarantine + extractor-marker stripping ---
+r <- tryCatch({
+  doc <- tempfile(fileext = ".txt")
+  writeLines(c(
+    "The effect was significant, d = 0.53.",
+    "[Table 1, row 5] condition | 44.2 | 78.6",
+    "Leroy, S. (2009). Why is it so hard? Journal, 109(2), 168-181. https://doi.org/10.1016/j.obhdp.2009.04.002"
+  ), doc)
+  src <- tempfile(fileext = ".txt")
+  writeLines(c("d 0.5337", "diff 44.1678", "sd 78.6487"), src)
+  invisible(capture.output(env$reconcile_values(doc, src)))
+  reg <- get("values_registry", envir = .GlobalEnv)
+  sum(reg$status == "reference_meta") >= 4 &&        # 109, 2, 168, 181, DOI bits
+    !any(reg$raw == "5" & reg$status == "unmatched") &&  # row marker stripped
+    all(reg$status[reg$value %in% c(0.53, 44.2, 78.6)] == "matched")
+}, error = function(e) conditionMessage(e))
+if (isTRUE(r)) pass("reconcile: reference lines quarantined, cell markers stripped") else fail("reconcile v2:", r)
+
 # --- 10. docx extractor: tables row-wise, headings marked (needs officer) ---
 if (requireNamespace("officer", quietly = TRUE)) {
   r <- tryCatch({

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ClaudeR
 Title: R Integration for Claude AI
-Version: 0.8.0
+Version: 0.8.1
 Authors@R: person("Nykko", "Vitali", email = "nykvt@icloud.com", role = c("aut", "cre"))
 Description: Connects RStudio with Claude AI to enable interactive coding sessions.
 License: MIT + file LICENSE

R/citations.R

@@ -82,11 +82,20 @@ crossref_get <- function(url, simplify = FALSE) {
   waits <- c(0, 1.5, 5)
   for (k in seq_along(waits)) {
     if (waits[k] > 0) Sys.sleep(waits[k])
-    res <- tryCatch(jsonlite::fromJSON(url, simplifyVector = simplify),
-                    error = function(e) e)
+    # base R surfaces the HTTP status in a *warning* ("HTTP status was '404
+    # Not Found'") while the error message only says "cannot open URL", so
+    # both conditions must be sniffed to tell a real 404 from rate limiting.
+    saw_404 <- FALSE
+    res <- withCallingHandlers(
+      tryCatch(jsonlite::fromJSON(url, simplifyVector = simplify),
+               error = function(e) e),
+      warning = function(w) {
+        if (grepl("404", conditionMessage(w))) saw_404 <<- TRUE
+        invokeRestart("muffleWarning")
+      }
+    )
     if (!inherits(res, "error")) return(res)
-    # 404 is a real answer (no such DOI/filter result), not rate limiting
-    if (grepl("404", conditionMessage(res))) return(NULL)
+    if (saw_404 || grepl("404", conditionMessage(res))) return(NULL)
   }
   NULL
 }
@@ -142,12 +151,24 @@ match_reference_impl <- function(ref_text) {
 # published (journal/proceedings) version so preprint citations of published
 # work get flagged. Atom parsed with regex to avoid an xml2 hard dependency.
 check_arxiv_impl <- function(arxiv_id) {
-  res <- tryCatch({
-    con <- url(paste0("https://export.arxiv.org/api/query?id_list=", arxiv_id))
-    on.exit(try(close(con), silent = TRUE), add = TRUE)
-    paste(readLines(con, warn = FALSE), collapse = "\n")
-  }, error = function(e) NULL)
-  if (is.null(res)) return(NULL)
+  # export.arxiv.org is slow enough to trip a 10s timeout on cold requests;
+  # retry with a longer allowance before giving up.
+  res <- NULL
+  for (k in 1:3) {
+    if (k > 1) Sys.sleep(2)
+    old_t <- options(timeout = if (k == 1) 10 else 25)
+    res <- tryCatch({
+      con <- url(paste0("https://export.arxiv.org/api/query?id_list=", arxiv_id))
+      txt <- suppressWarnings(paste(readLines(con, warn = FALSE), collapse = "\n"))
+      try(close(con), silent = TRUE)
+      txt
+    }, error = function(e) NULL)
+    options(old_t)
+    if (!is.null(res) && nzchar(res)) break
+  }
+  if (is.null(res) || !nzchar(res)) {
+    return(sprintf("arXiv:%s -- lookup failed (arXiv API unreachable); verify manually.", arxiv_id))
+  }
 
   title <- regmatches(res, regexpr("<title>[^<]+</title>", res))
   # First <title> is the feed's own; the entry title is the second match

R/reconcile.R

@@ -58,12 +58,25 @@ extract_numbers_from_line <- function(line) {
   do.call(rbind, out)
 }
 
+# A bibliography line: contains a DOI/arXiv id, or looks like an APA entry
+# (a parenthesized year followed later by a page range). Values on such lines
+# are citation metadata (volumes, issues, pages, DOI fragments), not results.
+is_reference_line <- function(line) {
+  grepl("doi\\.org/|\\barXiv:", line, ignore.case = TRUE) ||
+    grepl("\\((17|18|19|20)\\d\\d[a-z]?\\)\\..*\\d+-\\d+\\.?$", line, perl = TRUE)
+}
+
 # Extract all numbers from a character vector, with line numbers and context.
 extract_numbers_impl <- function(lines, label = "text") {
   res <- lapply(seq_along(lines), function(i) {
-    d <- extract_numbers_from_line(lines[i])
+    # Strip the structured-extractor cell markers ("[Table 2, row 5] ...")
+    # before tokenizing: the table and row indices are our own metadata, not
+    # values the document states.
+    clean <- sub("^\\[Table \\d+, (row \\d+|header)\\] ", "", lines[i])
+    d <- extract_numbers_from_line(clean)
     if (nrow(d) == 0) return(NULL)
     d$line <- i
+    d$is_reference <- is_reference_line(lines[i])
     ctx <- trimws(lines[i])
     if (nchar(ctx) > 160) ctx <- paste0(substr(ctx, 1, 157), "...")
     d$context <- ctx
@@ -74,6 +87,7 @@ extract_numbers_impl <- function(lines, label = "text") {
     return(data.frame(raw = character(0), value = numeric(0), ulp = numeric(0),
                       is_threshold = logical(0), threshold_dir = character(0),
                       is_percent = logical(0), line = integer(0),
+                      is_reference = logical(0),
                       context = character(0), source = character(0),
                       stringsAsFactors = FALSE))
   }
@@ -146,7 +160,11 @@ reconcile_values <- function(document, sources, ignore_years = TRUE,
   for (i in seq_len(nrow(doc_nums))) {
     v <- doc_nums$value[i]
     u <- doc_nums$ulp[i]
-    if (ignore_years && !doc_nums$is_percent[i] && !doc_nums$is_threshold[i] &&
+    if (isTRUE(doc_nums$is_reference[i])) {
+      # Volumes, issues, pages, and DOI fragments on bibliography lines are
+      # citation metadata; verify_references audits those, not the sweep.
+      status[i] <- "reference_meta"
+    } else if (ignore_years && !doc_nums$is_percent[i] && !doc_nums$is_threshold[i] &&
         u == 1 && v >= 1900 && v <= 2100 && v == floor(v)) {
       status[i] <- "year_skipped"
     } else if (doc_nums$is_threshold[i]) {
@@ -179,7 +197,7 @@ reconcile_values <- function(document, sources, ignore_years = TRUE,
   n <- nrow(registry)
   counts <- table(factor(registry$status,
                          levels = c("matched", "matched_scaled", "threshold_ok",
-                                    "unmatched", "year_skipped")))
+                                    "unmatched", "year_skipped", "reference_meta")))
   unmatched <- registry[registry$status == "unmatched", , drop = FALSE]
   shown <- utils::head(unmatched, max_unmatched_shown)
 
@@ -188,9 +206,9 @@ reconcile_values <- function(document, sources, ignore_years = TRUE,
     sprintf("Document: %s (%d numeric values)\n", basename(document), n),
     sprintf("Corpus: %d unique values from %d source file(s)\n",
             length(corpus), length(sources)),
-    sprintf("matched: %d | matched_scaled: %d | threshold_ok: %d | unmatched: %d | year_skipped: %d\n",
+    sprintf("matched: %d | matched_scaled: %d | threshold_ok: %d | unmatched: %d | year_skipped: %d | reference_meta: %d\n",
             counts["matched"], counts["matched_scaled"], counts["threshold_ok"],
-            counts["unmatched"], counts["year_skipped"]),
+            counts["unmatched"], counts["year_skipped"], counts["reference_meta"]),
     "\n'values_registry' has been assigned to the global environment.\n",
     if (nrow(unmatched) == 0) {
       "\nEvery non-year value is accounted for.\n"