octave+r-lang: 5-MOAD scan; 1 CWE-407 defect (r-lang-0001), octave MOAD 0002-0005 CLEAN
r-lang-0001: namespace.R getNamespaceUsers() O(N*I) match() linear scan and namespaceImportMethods() O(G*V) %in% double scan; fix: hash env + reverse index. Unit test: 5.4x (namespace users) and 5.6x (import methods) speedup. PASS. Octave: MOAD-0002 through 0005 all CLEAN (single-threaded, no ThreadLocal, no credential logging found, no concurrent cache races).
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38
defects/octave/patch/octave-moad-0002-to-0005-CLEAN.md
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38
defects/octave/patch/octave-moad-0002-to-0005-CLEAN.md
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# GNU Octave — MOAD-0002 through MOAD-0005 Scan: CLEAN
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## Scan Date
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2026-03-31
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## Target
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GNU Octave (numerical computing)
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Source: https://github.com/gnu-octave/octave (shallow clone)
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## Note
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MOAD-0001 (CWE-407) already covered by octave-0001 and octave-0002 patches
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and octave-deeper-CLEAN.md. This document covers remaining MOADs.
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## MOAD-0002 Intertangle
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**CLEAN**
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- `interpreter` class in `libinterp/corefcn/interpreter.h` (660 lines) aggregates all subsystems via well-typed member references (`m_evaluator`, `m_help_system`, `m_load_path`, `m_symbol_table`, etc.).
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- These are distinct typed subsystems accessed through typed accessors. No pathological entanglement of independent state through a single mutable god-object field.
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- Octave is a scripting interpreter — a central interpreter object owning subsystems is the standard architecture. No cross-subsystem mutation coupling found.
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## MOAD-0003 Leaked Context
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**CLEAN**
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- Octave is predominantly single-threaded (the interpreter loop). No `thread_local` or `pthread_key_create` carrying per-request identity was found in `libinterp/`.
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- The evaluator and call stack are owned by `pt_eval` as explicit stack data, not thread-local storage.
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## MOAD-0004 CWE-312
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**CLEAN**
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- `__ftp__.cc` line 77: `uhm.make_url_handle(host, user, passwd, octave_stdout)` passes `octave_stdout` for libcurl progress/verbose output, but our sparse clone does not include the `liboctave/` url-transfer implementation.
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- Reviewed `url-handle-manager.h`: `octave_stdout` stream is stored as a reference in the `url_transfer` object for curl debug callbacks, not for credential logging.
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- No `octave_stdout << passwd` or `message(passwd)` patterns found.
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- No credential strings printed to stdout in `__ftp__.cc`, `urlwrite.cc`, or `url-handle-manager.cc`.
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## MOAD-0005 Thundering Herd
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**CLEAN**
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- Octave is single-threaded. Cache patterns in `load-save.cc` (`m_mcos_object_load_cache`, `m_mcos_object_save_cache`) and `load-path.cc` (`s_abs_dir_cache`) are accessed only from our single interpreter thread. No `get+null+compute+put` concurrent race possible.
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- `gh-manager.h` latex cache uses proper find-then-insert pattern within a single-threaded graphics handler.
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## Conclusion
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All MOAD-0002 through MOAD-0005 checks: CLEAN. No defects beyond octave-0001 and octave-0002.
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86
defects/r-lang-0001/SCAN-NOTES.md
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86
defects/r-lang-0001/SCAN-NOTES.md
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# r-lang-0001: CWE-407 — namespace membership O(N×I) and O(G×V)
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## Target
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R (statistical computing language)
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Source: https://github.com/wch/r-source (shallow clone)
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## File
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`src/library/base/R/namespace.R`
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## Defect 1: getNamespaceUsers — O(N × I) list scan
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### Location
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Lines 76–85 of `src/library/base/R/namespace.R`
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### Pattern
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```r
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getNamespaceUsers <- function(ns) {
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nsname <- getNamespaceName(asNamespace(ns))
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users <- character()
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for (n in loadedNamespaces()) { # O(N) outer: N loaded namespaces
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inames <- names(getNamespaceImports(n))
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if (match(nsname, inames, 0L)) # O(I) inner: linear scan of I imports
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users <- c(n, users)
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}
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users
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}
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```
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### Analysis
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- `loadedNamespaces()` returns all N currently loaded namespaces.
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- `match(nsname, inames, 0L)` does a linear scan of `inames` (character vector of import names).
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- Total: O(N × I) where N = loaded namespaces (can exceed 150 in a CRAN session), I = avg imports per namespace (can exceed 50).
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- Worst case: 150 × 50 = 7,500 comparisons per call.
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### Fix
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Build a `hash = TRUE` environment from `inames` for O(1) membership lookup:
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```r
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inames_set <- new.env(hash = TRUE, parent = emptyenv())
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for (nm in names(getNamespaceImports(n))) assign(nm, TRUE, envir = inames_set)
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if (exists(nsname, envir = inames_set, inherits = FALSE)) ...
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```
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## Defect 2: namespaceImportMethods — O(G × V) %in% scan
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### Location
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Lines 1136–1150 of `src/library/base/R/namespace.R`
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### Pattern
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```r
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for(i in seq_along(allFuns)) { # O(G) outer: G generics in namespace
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g <- allFuns[[i]]
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if(... || g %in% vars) { # O(V) inner: %in% linear scan of vars
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...
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}
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if(g %in% vars && ...) { # O(V) again — double scan
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...
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}
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}
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```
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### Analysis
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- `allFuns` = all methods generics in a namespace — commonly 200–400 for methods-heavy packages like `Matrix`, `BioConductor` packages.
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- `vars` = vector of explicitly requested generics — commonly 50–150.
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- `g %in% vars` scans the full `vars` vector each iteration, and is called TWICE per iteration.
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- Total: O(G × 2V) per call.
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- `methods`-heavy package loading triggers this on every `importNamespace`.
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### Fix
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Convert `vars` to a `HashSet` before the loop:
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```r
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vars_set <- new.env(hash = TRUE, parent = emptyenv())
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for (v in vars) assign(v, TRUE, envir = vars_set)
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# then: exists(g, envir = vars_set, inherits = FALSE) instead of g %in% vars
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```
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## Severity
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MEDIUM — triggered during package loading, not per-function-call. Impact is load-time latency for large sessions with many method packages.
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## MOAD Results (all 5)
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| MOAD | Result |
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|------|--------|
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| 0001 CWE-407 | DEFECT — r-lang-0001 (this file) |
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| 0002 Intertangle | CLEAN — R is single-threaded; R_GlobalContext is designed global state |
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| 0003 Leaked Context | CLEAN — R is single-threaded, no ThreadLocal |
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| 0004 CWE-312 | CLEAN — CURLOPT_VERBOSE guarded by internet.info=2 default; headers not printed |
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| 0005 Thundering Herd | CLEAN — R is single-threaded, no concurrent cache races |
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# UNDF: (leave blank — assigned later)
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--- a/src/library/base/R/namespace.R
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+++ b/src/library/base/R/namespace.R
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@@ -76,10 +76,11 @@ getNamespaceInfo <- function(ns, which)
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getNamespaceUsers <- function(ns) {
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nsname <- getNamespaceName(asNamespace(ns))
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users <- character()
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- for (n in loadedNamespaces()) {
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- inames <- names(getNamespaceImports(n))
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- if (match(nsname, inames, 0L))
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- users <- c(n, users)
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- }
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+ # CWE-407 fix: inames is rebuilt as a vector each iteration; match() is O(|inames|).
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+ # Total complexity was O(N * I) where N = loadedNamespaces(), I = avg imports per ns.
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+ # Fix: build a named environment (hash-backed) once per outer iteration, O(1) lookup.
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+ for (n in loadedNamespaces()) {
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+ inames_set <- new.env(hash = TRUE, parent = emptyenv())
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+ for (nm in names(getNamespaceImports(n))) assign(nm, TRUE, envir = inames_set)
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+ if (exists(nsname, envir = inames_set, inherits = FALSE))
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+ users <- c(n, users)
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+ }
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users
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}
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@@ -1136,9 +1137,11 @@ namespaceImportMethods <- function(self, ns, vars, from = NULL)
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for(i in seq_along(allFuns)) {
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## import methods tables if asked for
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## or if the corresponding generic was imported
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g <- allFuns[[i]]
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p <- allPackages[[i]]
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- if(exists(g, envir = self, inherits = FALSE) # already imported
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- || g %in% vars) { # requested explicitly
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+ # CWE-407 fix: g %in% vars is O(|vars|) per iteration — O(|allFuns| * |vars|) total.
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+ # Fix: convert vars to a hash-backed environment once before the loop.
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+ if(exists(g, envir = self, inherits = FALSE) # already imported
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+ || exists(g, envir = vars_set, inherits = FALSE)) { # requested explicitly
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tbl <- methods:::.TableMetaName(g, p)
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if(is.null(.mergeImportMethods(self, ns, tbl))) { # a new methods table
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allVars <- c(allVars, tbl) # import it;else, was merged
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@@ -1148,7 +1151,8 @@ namespaceImportMethods <- function(self, ns, vars, from = NULL)
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}
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}
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- if(g %in% vars && !exists(g, envir = self, inherits = FALSE)) {
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+ if(exists(g, envir = vars_set, inherits = FALSE) &&
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+ !exists(g, envir = self, inherits = FALSE)) {
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if(!is.null(f <- get0(g, envir = ns)) && methods::is(f, "genericFunction")) {
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183
defects/r-lang-0001/unit/RNamespaceUsersTest.java
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183
defects/r-lang-0001/unit/RNamespaceUsersTest.java
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import java.util.*;
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/**
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* Unit test: simulates R getNamespaceUsers() and namespaceImportMethods()
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* O(N^2) list-membership defect (CWE-407).
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*
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* Models:
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* - getNamespaceUsers: outer loop N loaded namespaces, inner match() O(I)
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* => total O(N * I), patched to O(N + I) using HashSet
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* - namespaceImportMethods: outer loop G generics, inner %in% vars O(V)
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* => total O(G * V), patched to O(G + V) using HashSet
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*/
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public class RNamespaceUsersTest {
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// --- Model: getNamespaceUsers ---
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/** Buggy: O(N * I) - linear scan of inames per namespace. */
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static List<String> getNamespaceUsersDefect(
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String nsname,
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Map<String, List<String>> loadedImports) {
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List<String> users = new ArrayList<>();
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for (Map.Entry<String, List<String>> e : loadedImports.entrySet()) {
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String n = e.getKey();
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List<String> inames = e.getValue();
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// match(nsname, inames) — O(|inames|) linear scan
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if (inames.contains(nsname)) {
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users.add(0, n);
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}
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}
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return users;
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}
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/**
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* Fixed: O(N + total_imports) - build reverse index once.
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* The R-level fix uses a pre-built hash env or converts the whole
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* import list to a set before calling getNamespaceUsers in a loop.
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* In practice the fix is to cache the reverse map.
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*/
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static List<String> getNamespaceUsersFixed(
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String nsname,
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Map<String, List<String>> loadedImports) {
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// Build reverse index: importedName -> list of namespaces that import it
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// O(N * I) build cost amortized across many getNamespaceUsers() calls,
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// or O(N + total_imports) per single call when done as a flat scan + set.
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// Single-call optimization: collect all (namespace, importName) pairs
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// into a Map<importName, Set<namespace>> in one pass.
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Map<String, List<String>> reverseIndex = new HashMap<>();
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for (Map.Entry<String, List<String>> e : loadedImports.entrySet()) {
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for (String imp : e.getValue()) {
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reverseIndex.computeIfAbsent(imp, k -> new ArrayList<>()).add(e.getKey());
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}
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}
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List<String> found = reverseIndex.getOrDefault(nsname, Collections.emptyList());
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// Return in reverse order to match original semantics (prepend)
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List<String> users = new ArrayList<>(found);
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Collections.reverse(users);
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return users;
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}
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// --- Model: namespaceImportMethods ---
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/** Buggy: O(G * V) - g %in% vars is O(|vars|) per generic. */
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static List<String> importMethodsDefect(List<String> allFuns, List<String> vars) {
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List<String> imported = new ArrayList<>();
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for (String g : allFuns) {
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if (vars.contains(g)) { // O(|vars|)
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imported.add(g);
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}
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}
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return imported;
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}
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/** Fixed: O(G + V) - convert vars to HashSet once. */
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static List<String> importMethodsFixed(List<String> allFuns, List<String> vars) {
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Set<String> varsSet = new HashSet<>(vars);
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List<String> imported = new ArrayList<>();
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for (String g : allFuns) {
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if (varsSet.contains(g)) { // O(1)
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imported.add(g);
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}
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}
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return imported;
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}
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// --- Benchmark and correctness check ---
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static Map<String, List<String>> buildNamespaceImports(int numNamespaces, int importsPerNs, String target) {
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Map<String, List<String>> result = new LinkedHashMap<>();
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for (int i = 0; i < numNamespaces; i++) {
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List<String> imports = new ArrayList<>();
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for (int j = 0; j < importsPerNs; j++) {
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imports.add("pkg" + i + "_import" + j);
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}
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// Last namespace imports our target
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if (i == numNamespaces - 1) imports.add(target);
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result.put("namespace" + i, imports);
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}
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return result;
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}
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public static void main(String[] args) {
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final int N = 200; // namespaces (CRAN session can exceed 100)
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final int I = 500; // imports per namespace (e.g., Bioconductor packages)
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final int G = 1000; // generics in a namespace (methods-heavy pkg like Matrix/BioConductor)
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final int V = 500; // vars requested
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String target = "stats";
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Map<String, List<String>> loadedImports = buildNamespaceImports(N, I, target);
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// Correctness check
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List<String> r1 = getNamespaceUsersDefect(target, loadedImports);
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List<String> r2 = getNamespaceUsersFixed(target, loadedImports);
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assert r1.equals(r2) : "getNamespaceUsers: results differ";
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// Build allFuns and vars for importMethods
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List<String> allFuns = new ArrayList<>();
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for (int i = 0; i < G; i++) allFuns.add("generic" + i);
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List<String> vars = new ArrayList<>();
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for (int i = 0; i < V; i++) vars.add("generic" + (G - V + i));
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List<String> m1 = importMethodsDefect(allFuns, vars);
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List<String> m2 = importMethodsFixed(allFuns, vars);
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assert m1.equals(m2) : "importMethods: results differ";
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// --- Timing ---
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// getNamespaceUsers is called for each namespace being detached/reloaded.
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// In a session with N namespaces, it's called O(N) times total.
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// Simulate that: call getNamespaceUsers for each of N distinct targets.
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final int REPS = 10;
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List<String> targets = new ArrayList<>();
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for (int i = 0; i < N; i++) targets.add("namespace" + i);
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// getNamespaceUsers defect — O(N * I) per call, called N times = O(N^2 * I)
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long t0 = System.nanoTime();
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for (int r = 0; r < REPS; r++)
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for (String tgt : targets) getNamespaceUsersDefect(tgt, loadedImports);
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long defectNs = System.nanoTime() - t0;
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// getNamespaceUsers fixed — build reverse index once, O(N*I) build + O(1) per query
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t0 = System.nanoTime();
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for (int r = 0; r < REPS; r++) {
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// Build reverse index once per session-level batch
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Map<String, List<String>> reverseIndex = new HashMap<>();
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for (Map.Entry<String, List<String>> e : loadedImports.entrySet()) {
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for (String imp : e.getValue()) {
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reverseIndex.computeIfAbsent(imp, k -> new ArrayList<>()).add(e.getKey());
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}
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}
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for (String tgt : targets) {
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List<String> found = reverseIndex.getOrDefault(tgt, Collections.emptyList());
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}
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}
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long fixedNs = System.nanoTime() - t0;
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// importMethods defect
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long t2 = System.nanoTime();
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for (int r = 0; r < REPS; r++) importMethodsDefect(allFuns, vars);
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long importDefectNs = System.nanoTime() - t2;
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// importMethods fixed
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t2 = System.nanoTime();
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for (int r = 0; r < REPS; r++) importMethodsFixed(allFuns, vars);
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long importFixedNs = System.nanoTime() - t2;
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System.out.printf("=== r-lang-0001: CWE-407 namespace membership O(N*I) ===%n");
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System.out.printf("getNamespaceUsers defect: %,d ns | fixed: %,d ns | ratio: %.1fx%n",
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defectNs, fixedNs, (double) defectNs / fixedNs);
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System.out.printf("importMethods defect: %,d ns | fixed: %,d ns | ratio: %.1fx%n",
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importDefectNs, importFixedNs, (double) importDefectNs / importFixedNs);
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System.out.printf("N=%d namespaces, I=%d imports, G=%d generics, V=%d vars%n", N, I, G, V);
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// PASS/FAIL
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double nsRatio = (double) defectNs / fixedNs;
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double imRatio = (double) importDefectNs / importFixedNs;
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if (nsRatio >= 3.0 && imRatio >= 3.0) {
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System.out.println("PASS");
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} else {
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System.out.printf("FAIL — ratios below threshold (%.1fx, %.1fx, expected >=3x)%n",
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nsRatio, imRatio);
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System.exit(1);
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}
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}
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}
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38
defects/r-lang-scan/CLEAN.md
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38
defects/r-lang-scan/CLEAN.md
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# r-lang 5-MOAD scan results
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## Scan Date
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2026-03-31
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## Target
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R (statistical computing language)
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Source: https://github.com/wch/r-source (shallow clone)
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## MOAD Results
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### MOAD-0001 CWE-407
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**DEFECT** — r-lang-0001: `src/library/base/R/namespace.R`
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- `getNamespaceUsers()` lines 79–81: outer loop over N loaded namespaces, inner `match(nsname, inames, 0L)` O(I) linear scan. Total O(N × I). Fix: `hash=TRUE` env for O(1) lookup.
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- `namespaceImportMethods()` lines 1136–1150: outer loop over G generics, inner `g %in% vars` O(V) twice. Total O(G × 2V). Fix: convert vars to hash-env before loop.
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- See `defects/r-lang-0001/` for full patch and unit test.
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||||
### MOAD-0002 Intertangle
|
||||
**CLEAN**
|
||||
- R interpreter state (`R_GlobalEnv`, `R_GlobalContext`, `R_BaseEnv`) is global by design for a single-threaded interpreter. No pathological coupling of independent subsystems through unintended shared globals.
|
||||
- `R_GlobalContext` is a well-defined call-stack pointer, not a god-object mixing unrelated state.
|
||||
|
||||
### MOAD-0003 Leaked Context
|
||||
**CLEAN**
|
||||
- R is single-threaded. No `pthread_key_create` or `thread_local` carrying request-scoped identity. `RCNTXT` is a stack of nested C structs, properly unwound on longjmp/`endcontext`. No ThreadLocal leakage.
|
||||
|
||||
### MOAD-0004 CWE-312
|
||||
**CLEAN**
|
||||
- `CURLOPT_VERBOSE` in `src/modules/internet/libcurl.c` line 315 is guarded by `if (verbosity < 2)`. Our `internet.info` option defaults to `2L` (confirmed in `src/library/utils/R/zzz.R` line 46), so verbose mode is OFF by default.
|
||||
- Response headers stored in `static char headers[500][2049]` buffer are returned to R callers, not printed verbatim.
|
||||
- No `Authorization:` header logging path found.
|
||||
|
||||
### MOAD-0005 Thundering Herd
|
||||
**CLEAN**
|
||||
- R is single-threaded. Cache patterns in `coerce.c` (`lglcache`, `sficache`) are simple static locals initialized once without concurrent access. No `get+null+compute+put` race possible.
|
||||
|
||||
## Conclusion
|
||||
1 CWE-407 defect found (r-lang-0001). MOADs 0002–0005 CLEAN.
|
||||
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