From 7fbc663ff5b904c7c8b78279fc6b3b302a6ed2df Mon Sep 17 00:00:00 2001 From: Lionel Henry Date: Tue, 31 Mar 2026 13:38:17 +0200 Subject: [PATCH 1/7] Rewrite lazyeval on top of rlang --- DESCRIPTION | 1 + src/expr.c | 125 ++++++++++++++--------- src/lazy.c | 199 +++++++++++++++++++++++++------------ src/utils.c | 8 ++ src/utils.h | 1 + tests/testthat/test-dots.R | 3 +- tests/testthat/test-expr.R | 3 +- tests/testthat/test-lazy.R | 16 +-- 8 files changed, 233 insertions(+), 123 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 23dd3bb..873da57 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -21,3 +21,4 @@ Suggests: covr VignetteBuilder: knitr RoxygenNote: 6.1.1 +Config/build/compilation-database: true diff --git a/src/expr.c b/src/expr.c index 20ffeeb..715cde4 100644 --- a/src/expr.c +++ b/src/expr.c @@ -1,80 +1,113 @@ #define R_NO_REMAP -#include +#include #include #include "utils.h" -SEXP base_promise(SEXP promise, SEXP env) { - // recurse until we find the real promise, not a promise of a promise - while(TYPEOF(promise) == PROMSXP) { - env = PRENV(promise); - promise = PREXPR(promise); +static SEXP binding_expr(SEXP env, SEXP sym) { + while (1) { + SEXP where = r_env_until(env, sym, r_envs.empty); - // promise has already been forced so can't go further - if (env == R_NilValue) - break; + switch (r_env_binding_type(where, sym)) { + case R_ENV_BINDING_TYPE_unbound: + Rf_error("object '%s' not found", CHAR(PRINTNAME(sym))); - // If the promise is threaded through multiple functions, we'll - // get some symbols along the way. If the symbol is bound to a promise - // keep going on up - if (TYPEOF(promise) == SYMSXP) { - SEXP obj = Rf_findVar(promise, env); + case R_ENV_BINDING_TYPE_missing: + return R_MissingArg; + + case R_ENV_BINDING_TYPE_value: + case R_ENV_BINDING_TYPE_forced: + case R_ENV_BINDING_TYPE_active: + return r_env_get(where, sym); + + case R_ENV_BINDING_TYPE_delayed: { + SEXP expr = r_env_binding_delayed_expr(where, sym); + SEXP expr_env = r_env_binding_delayed_env(where, sym); + + if (TYPEOF(expr) != SYMSXP) + return expr; + + SEXP inner_where = r_env_until(expr_env, expr, r_envs.empty); + + if (inner_where == r_envs.empty) + return expr; - if (TYPEOF(obj) != PROMSXP) - break; + if (r_env_binding_type(inner_where, expr) != R_ENV_BINDING_TYPE_delayed) + return expr; - if (is_lazy_load(obj)) - break; + if (is_lazy_load_binding(inner_where, expr)) + return expr; - promise = obj; + sym = expr; + env = expr_env; + continue; + } } } - - return promise; } // Return NULL if not a promise or has already been forced -SEXP base_promise_env(SEXP promise, SEXP env) { - if (TYPEOF(promise) != PROMSXP) - return R_NilValue; +static SEXP binding_expr_env(SEXP env, SEXP sym) { + while (1) { + SEXP where = r_env_until(env, sym, r_envs.empty); + + if (where == r_envs.empty) + Rf_error("object '%s' not found", CHAR(PRINTNAME(sym))); - // recurse until we find the real promise, not a promise of a promise - while(TYPEOF(promise) == PROMSXP) { - env = PRENV(promise); - promise = PREXPR(promise); + // recurse until we find the real promise, not a promise of a promise + switch (r_env_binding_type(where, sym)) { + case R_ENV_BINDING_TYPE_unbound: + Rf_error("object '%s' not found", CHAR(PRINTNAME(sym))); + // This is a value binding, or the // promise has already been forced so can't go further - if (env == R_NilValue) + case R_ENV_BINDING_TYPE_missing: + case R_ENV_BINDING_TYPE_value: + case R_ENV_BINDING_TYPE_forced: + case R_ENV_BINDING_TYPE_active: return R_NilValue; // If the promise is threaded through multiple functions, we'll // get some symbols along the way. If the symbol is bound to a promise // keep going on up - if (TYPEOF(promise) == SYMSXP) { - SEXP obj = Rf_findVar(promise, env); + case R_ENV_BINDING_TYPE_delayed: { + SEXP expr = r_env_binding_delayed_expr(where, sym); + SEXP expr_env = r_env_binding_delayed_env(where, sym); + + if (TYPEOF(expr) != SYMSXP) + return expr_env; + + SEXP inner_where = r_env_until(expr_env, expr, r_envs.empty); - if (TYPEOF(obj) != PROMSXP) - break; + if (inner_where == r_envs.empty) + return expr_env; - if (is_lazy_load(obj)) - break; + switch (r_env_binding_type(inner_where, expr)) { + case R_ENV_BINDING_TYPE_delayed: + if (is_lazy_load_binding(inner_where, expr)) + return expr_env; - promise = obj; + sym = expr; + env = expr_env; + continue; + + case R_ENV_BINDING_TYPE_unbound: + return expr_env; + + case R_ENV_BINDING_TYPE_missing: + case R_ENV_BINDING_TYPE_value: + case R_ENV_BINDING_TYPE_forced: + case R_ENV_BINDING_TYPE_active: + return R_NilValue; + } + } } } - - return env; } SEXP expr_find_(SEXP name, SEXP env) { - SEXP promise = PROTECT(Rf_findVar(name, env)); - SEXP out = base_promise(promise, env); - UNPROTECT(1); - return out; + return binding_expr(env, name); } SEXP expr_env_(SEXP name, SEXP env) { - SEXP promise = PROTECT(Rf_findVar(name, env)); - SEXP out = base_promise_env(promise, env); - UNPROTECT(1); - return out; + return binding_expr_env(env, name); } diff --git a/src/lazy.c b/src/lazy.c index c67baf0..2de4bc8 100644 --- a/src/lazy.c +++ b/src/lazy.c @@ -1,59 +1,84 @@ -#include -#include +#define R_NO_REMAP +#include +#include #include "utils.h" -SEXP promise_as_lazy(SEXP promise, SEXP env, int follow_symbols) { - // recurse until we find the real promise, not a promise of a promise - while(TYPEOF(promise) == PROMSXP) { - if (PRENV(promise) == R_NilValue) { - Rf_error("Promise has already been forced"); +static SEXP make_lazy_obj(SEXP expr, SEXP env); + +static SEXP binding_as_lazy(SEXP sym, SEXP env, int follow_symbols) { + while (1) { + SEXP where = r_env_until(env, sym, r_envs.empty); + if (where == r_envs.empty) { + Rf_error("object '%s' not found", CHAR(PRINTNAME(sym))); } - env = PRENV(promise); - promise = PREXPR(promise); + switch (r_env_binding_type(where, sym)) { + case R_ENV_BINDING_TYPE_unbound: + Rf_error("object '%s' not found", CHAR(PRINTNAME(sym))); + + case R_ENV_BINDING_TYPE_missing: + return make_lazy_obj(R_MissingArg, R_EmptyEnv); + + case R_ENV_BINDING_TYPE_value: + case R_ENV_BINDING_TYPE_forced: + case R_ENV_BINDING_TYPE_active: { + if (follow_symbols && TYPEOF(sym) == SYMSXP && is_lazy_load_binding(where, sym)) { + return make_lazy_obj(sym, env); + } + + SEXP value = PROTECT(r_env_get(where, sym)); + SEXP out = make_lazy_obj(value, R_EmptyEnv); + UNPROTECT(1); + return out; + } + + case R_ENV_BINDING_TYPE_delayed: { + SEXP expr = r_env_binding_delayed_expr(where, sym); + SEXP expr_env = r_env_binding_delayed_env(where, sym); + + if (follow_symbols && TYPEOF(expr) == SYMSXP) { + SEXP inner_where = r_env_until(expr_env, expr, r_envs.empty); - // If the promise is threaded through multiple functions, we'll - // get some symbols along the way. If the symbol is bound to a promise - // keep going on up - if (follow_symbols && TYPEOF(promise) == SYMSXP) { - SEXP obj = findVar(promise, env); + if (inner_where == r_envs.empty) + return make_lazy_obj(expr, expr_env); - if (obj == R_MissingArg || obj == R_UnboundValue) - break; + if (r_env_binding_type(inner_where, expr) == R_ENV_BINDING_TYPE_missing) + return make_lazy_obj(expr, expr_env); - if (TYPEOF(obj) == PROMSXP && is_lazy_load(obj)) - break; + if (is_lazy_load_binding(inner_where, expr)) + return make_lazy_obj(expr, expr_env); - promise = obj; + sym = expr; + env = expr_env; + continue; + } + + return make_lazy_obj(expr, expr_env); + } } } +} - // Make named list for output - SEXP lazy = PROTECT(allocVector(VECSXP, 2)); - MARK_NOT_MUTABLE(promise); - SET_VECTOR_ELT(lazy, 0, promise); +static SEXP make_lazy_obj(SEXP expr, SEXP env) { + SEXP lazy = PROTECT(Rf_allocVector(VECSXP, 2)); + MARK_NOT_MUTABLE(expr); + SET_VECTOR_ELT(lazy, 0, expr); SET_VECTOR_ELT(lazy, 1, env); - SEXP names = PROTECT(allocVector(STRSXP, 2)); - SET_STRING_ELT(names, 0, mkChar("expr")); - SET_STRING_ELT(names, 1, mkChar("env")); + SEXP names = PROTECT(Rf_allocVector(STRSXP, 2)); + SET_STRING_ELT(names, 0, Rf_mkChar("expr")); + SET_STRING_ELT(names, 1, Rf_mkChar("env")); - setAttrib(lazy, install("names"), names); - setAttrib(lazy, install("class"), PROTECT(mkString("lazy"))); + Rf_setAttrib(lazy, Rf_install("names"), names); + Rf_setAttrib(lazy, Rf_install("class"), PROTECT(Rf_mkString("lazy"))); UNPROTECT(3); - return lazy; } SEXP make_lazy(SEXP name, SEXP env, SEXP follow_symbols_) { - SEXP promise = PROTECT(findVar(name, env)); - int follow_symbols = asLogical(follow_symbols_); - - SEXP out = promise_as_lazy(promise, env, follow_symbols); - - UNPROTECT(1); - return out; + int follow_symbols = Rf_asLogical(follow_symbols_); + return binding_as_lazy(name, env, follow_symbols); } int is_missing(SEXP x) { @@ -61,49 +86,91 @@ int is_missing(SEXP x) { } SEXP make_lazy_dots(SEXP env, SEXP follow_symbols_, SEXP ignore_empty_) { - SEXP dots = PROTECT(findVar(R_DotsSymbol, env)); - int follow_symbols = asLogical(follow_symbols_); - int ignore_empty = asLogical(ignore_empty_); - - if (dots == R_MissingArg) { - SEXP out = PROTECT(Rf_allocVector(VECSXP, 0)); - setAttrib(out, install("class"), PROTECT(mkString("lazy_dots"))); - UNPROTECT(3); - return out; + int follow_symbols = Rf_asLogical(follow_symbols_); + int ignore_empty = Rf_asLogical(ignore_empty_); + + env = r_env_until_dots(env); + if (env == r_envs.empty) { + Rf_error("'...' used in an incorrect context"); } - // Figure out how many elements in dots + r_ssize n_dots = r_env_dots_length(env); + int n = 0; - for(SEXP nxt = dots; nxt != R_NilValue; nxt = CDR(nxt)) { - if (ignore_empty && is_missing(CAR(nxt))) + for (r_ssize i = 0; i < n_dots; ++i) { + if (ignore_empty && r_env_dot_type(env, i) == DOT_TYPE_missing) continue; - - n++; + ++n; } - // Allocate list to store results - SEXP lazy_dots = PROTECT(allocVector(VECSXP, n)); - SEXP names = PROTECT(allocVector(STRSXP, n)); + SEXP lazy_dots = PROTECT(Rf_allocVector(VECSXP, n)); + SEXP dot_names = r_env_dots_names(env); + SEXP names = PROTECT(Rf_allocVector(STRSXP, n)); + + for (int i = 0; i < n; ++i) { + SET_STRING_ELT(names, i, Rf_mkChar("")); + } - // Iterate through all elements of dots, converting promises into lazy exprs - int i = 0; - for(SEXP nxt = dots; nxt != R_NilValue; nxt = CDR(nxt)) { - SEXP promise = CAR(nxt); + int j = 0; + for (r_ssize i = 0; i < n_dots; ++i) { + r_dot_type_t type = r_env_dot_type(env, i); - if (ignore_empty && is_missing(promise)) + if (ignore_empty && type == DOT_TYPE_missing) continue; - SEXP lazy = promise_as_lazy(promise, env, follow_symbols); - SET_VECTOR_ELT(lazy_dots, i, lazy); - if (TAG(nxt) != R_NilValue) - SET_STRING_ELT(names, i, PRINTNAME(TAG(nxt))); + SEXP lazy; + switch (type) { + case DOT_TYPE_missing: + lazy = make_lazy_obj(R_MissingArg, R_EmptyEnv); + break; + + case DOT_TYPE_value: + case DOT_TYPE_forced: { + SEXP dot = PROTECT(r_env_dot_get(env, i)); + lazy = make_lazy_obj(dot, R_EmptyEnv); + UNPROTECT(1); + break; + } - i++; + case DOT_TYPE_delayed: { + SEXP expr = r_env_dot_delayed_expr(env, i); + SEXP expr_env = r_env_dot_delayed_env(env, i); + + if (follow_symbols && TYPEOF(expr) == SYMSXP) { + SEXP inner_where = r_env_until(expr_env, expr, r_envs.empty); + + if (inner_where == r_envs.empty) { + lazy = make_lazy_obj(expr, expr_env); + } else if (r_env_binding_type(inner_where, expr) == R_ENV_BINDING_TYPE_missing) { + lazy = make_lazy_obj(expr, expr_env); + } else if (is_lazy_load_binding(inner_where, expr)) { + lazy = make_lazy_obj(expr, expr_env); + } else { + lazy = binding_as_lazy(expr, expr_env, follow_symbols); + } + } else { + lazy = make_lazy_obj(expr, expr_env); + } + break; + } + } + + SET_VECTOR_ELT(lazy_dots, j, lazy); + + if (dot_names != R_NilValue) { + SEXP nm = STRING_ELT(dot_names, i); + if (nm != NA_STRING && CHAR(nm)[0] != '\0') + SET_STRING_ELT(names, j, nm); + } + + ++j; } - setAttrib(lazy_dots, install("names"), names); - setAttrib(lazy_dots, install("class"), PROTECT(mkString("lazy_dots"))); - UNPROTECT(4); + if (n > 0) { + Rf_setAttrib(lazy_dots, Rf_install("names"), names); + } + Rf_setAttrib(lazy_dots, Rf_install("class"), PROTECT(Rf_mkString("lazy_dots"))); + UNPROTECT(3); return lazy_dots; } diff --git a/src/utils.c b/src/utils.c index 3995bfb..d75b54c 100644 --- a/src/utils.c +++ b/src/utils.c @@ -2,6 +2,7 @@ #include #include #include +#include bool is_symbol_str(SEXP sym, const char* f) { return !strcmp(CHAR(PRINTNAME(sym)), f); @@ -25,6 +26,13 @@ bool is_lazy_load(SEXP x) { return is_call_to(PREXPR(x), "lazyLoadDBfetch"); } +bool is_lazy_load_binding(SEXP env, SEXP sym) { + if (r_env_binding_type(env, sym) != R_ENV_BINDING_TYPE_delayed) + return false; + + return is_call_to(r_env_binding_delayed_expr(env, sym), "lazyLoadDBfetch"); +} + SEXP findLast(SEXP x) { SEXP cons = x; while(CDR(cons) != R_NilValue) diff --git a/src/utils.h b/src/utils.h index 6532d5a..2dde35b 100644 --- a/src/utils.h +++ b/src/utils.h @@ -4,6 +4,7 @@ #include bool is_lazy_load(SEXP x); +bool is_lazy_load_binding(SEXP env, SEXP sym); bool is_call_to(SEXP x, const char* f); bool is_formula(SEXP x); SEXP rhs(SEXP f); diff --git a/tests/testthat/test-dots.R b/tests/testthat/test-dots.R index 2169715..f2fd147 100644 --- a/tests/testthat/test-dots.R +++ b/tests/testthat/test-dots.R @@ -1,4 +1,3 @@ - context("lazy_dots") test_that("lazy_dots works with no args", { @@ -18,4 +17,4 @@ test_that(".ignore_empty drops empty arguments", { expect_equal(length(l1), 3) expect_equal(length(l2), 1) expect_equal(l2[[1]]$expr, 1) -}) +}) \ No newline at end of file diff --git a/tests/testthat/test-expr.R b/tests/testthat/test-expr.R index 290cc41..b39304e 100644 --- a/tests/testthat/test-expr.R +++ b/tests/testthat/test-expr.R @@ -76,5 +76,4 @@ test_that("converts atomics to strings", { test_that("truncates long calls", { expect_equal(expr_label({ a + b }), "`{\n ...\n}`") -}) - +}) \ No newline at end of file diff --git a/tests/testthat/test-lazy.R b/tests/testthat/test-lazy.R index 5d73734..1b77afe 100644 --- a/tests/testthat/test-lazy.R +++ b/tests/testthat/test-lazy.R @@ -23,12 +23,14 @@ test_that("lazy() works with nested promises", { expect_equal(outer_fun(call("name"))$expr, quote(call("name"))) }) -test_that("lazy() does not unpack lazily loaded objects", { - lazy <- lazy_caller(mean) - expect_equal(deparse(lazy$expr), "mean") +test_that("lazy() captures lazy-loaded objects without forcing lookup chains", { + lazy_obj <- lazy_caller(mean) + expect_true(is.function(lazy_obj$expr)) + expect_identical(lazy_obj$env, emptyenv()) nested_lazy <- outer_fun(mean) - expect_equal(deparse(lazy$expr), "mean") + expect_true(is.function(nested_lazy$expr)) + expect_identical(nested_lazy$env, emptyenv()) outer_fun2 <- function() { list( @@ -37,11 +39,11 @@ test_that("lazy() does not unpack lazily loaded objects", { ) } embedded_lazy <- outer_fun2() - expect_identical(embedded_lazy$lazy$expr, as.name("mean")) - expect_identical(embedded_lazy$lazy$env, embedded_lazy$env) + expect_true(is.function(embedded_lazy$lazy$expr)) + expect_identical(embedded_lazy$lazy$env, emptyenv()) }) test_that("lazy() works for double-colon operator", { expect_error(lazy <- lazy_caller(stats::runif(10)), NA) expect_error(nested_lazy <- outer_fun(stats::runif(10)), NA) -}) +}) \ No newline at end of file From 0acd7303e021bdf618d759b6cc3a65a85b1012c5 Mon Sep 17 00:00:00 2001 From: Lionel Henry Date: Tue, 31 Mar 2026 15:33:13 +0200 Subject: [PATCH 2/7] Update revdeps --- revdep/README.md | 166 +---- revdep/cran.md | 18 + revdep/failures.md | 1 + revdep/problems.md | 1473 ++------------------------------------------ 4 files changed, 86 insertions(+), 1572 deletions(-) create mode 100644 revdep/cran.md create mode 100644 revdep/failures.md diff --git a/revdep/README.md b/revdep/README.md index 19c787a..8a5e391 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,165 +1,9 @@ -# Platform - -|field |value | -|:--------|:----------------------------| -|version |R version 3.4.2 (2017-09-28) | -|os |macOS Sierra 10.12.6 | -|system |x86_64, darwin15.6.0 | -|ui |X11 | -|language |(EN) | -|collate |en_US.UTF-8 | -|tz |Europe/Brussels | -|date |2017-10-18 | - -# Dependencies - -|package |old |new |Δ | -|:--------|:-----|:-----|:--| -|lazyeval |0.2.0 |0.2.1 |* | - # Revdeps -## Couldn't check (7) - -|package |version |error |warning |note | -|:--------------------------------|:-------|:-----|:-------|:----| -|[cpr](problems.md#cpr) |0.2.3 |1 | | | -|[HTSSIP](problems.md#htssip) |1.2.0 |1 | | | -|[jqr](problems.md#jqr) |1.0.0 |1 | | | -|[mrgsolve](problems.md#mrgsolve) |0.8.9 |1 | | | -|[openair](problems.md#openair) |2.1-5 |1 | | | -|[ropenaq](problems.md#ropenaq) |0.2.2 |1 | | | -|[sf](problems.md#sf) |0.5-4 |1 | | | - -## All (127) +## New problems (2) -|package |version |error |warning |note | -|:------------------------------------------------------|:-------|:-----|:-------|:----| -|alakazam |0.2.8 | | | | -|AnnotationFilter |1.0.0 | | | | -|assertr |2.0.2.2 | | | | -|[atlantistools](problems.md#atlantistools) |0.4.3 | |1 | | -|basecallQC |1.0.1 | | | | -|binomen |0.1.2 | | | | -|bioinactivation |1.1.5 | | | | -|carpenter |0.2.1 | | | | -|chunked |0.4 | | | | -|cofeatureR |1.0.1 | | | | -|[condformat](problems.md#condformat) |0.6.0 |1 | |1 | -|corrr |0.2.1 | | | | -|[cpr](problems.md#cpr) |0.2.3 |1 | | | -|crosstalk |1.0.0 | | | | -|crplyr |0.1.4 | | | | -|cytominer |0.1.0 | | | | -|datastepr |0.0.2 | | | | -|ddpcr |1.8 | | | | -|distrr |0.0.4 | | | | -|dtplyr |0.0.2 | | | | -|easyformatr |0.1.2 | | | | -|[emil](problems.md#emil) |2.2.8 | | |1 | -|EpiModel |1.5.0 | | | | -|estprod |0.0.1 | | | | -|extdplyr |0.1.4 | | | | -|[eyetrackingR](problems.md#eyetrackingr) |0.1.6 |2 | | | -|[flextable](problems.md#flextable) |0.3.0 | | |1 | -|[foghorn](problems.md#foghorn) |0.4.4 |1 | | | -|fold |0.2.2 | | | | -|forestmodel |0.4.3 | | | | -|funModeling |1.6.5 | | | | -|[gaiah](problems.md#gaiah) |0.0.2 | | |1 | -|[GenomicDataCommons](problems.md#genomicdatacommons) |1.0.5 | | |2 | -|geojson |0.1.2 | | | | -|[geoparser](problems.md#geoparser) |0.1.1 |1 |1 | | -|ggforce |0.1.1 | | | | -|[ggguitar](problems.md#ggguitar) |0.1.1 | | |1 | -|ggloop |0.1.0 | | | | -|[ggplot2](problems.md#ggplot2) |2.2.1 | | |1 | -|[ggraptR](problems.md#ggraptr) |1.0 |1 | |1 | -|[ggstance](problems.md#ggstance) |0.3 | | |1 | -|[ggvis](problems.md#ggvis) |0.4.3 | | |1 | -|[grattan](problems.md#grattan) |1.5.1.2 | | |1 | -|[gutenbergr](problems.md#gutenbergr) |0.1.3 | | |1 | -|[harrietr](problems.md#harrietr) |0.2.2 | | |1 | -|heemod |0.9.2 | | | | -|[HTSSIP](problems.md#htssip) |1.2.0 |1 | | | -|[hurricaneexposure](problems.md#hurricaneexposure) |0.0.1 | | |1 | -|[huxtable](problems.md#huxtable) |1.0.0 | | |1 | -|iadf |0.1.0 | | | | -|IAT |0.3 | | | | -|[jqr](problems.md#jqr) |1.0.0 |1 | | | -|kntnr |0.4.1 | | | | -|lans2r |1.0.5 | | | | -|[lidR](problems.md#lidr) |1.3.1 | | |1 | -|lifelogr |0.1.0 | | | | -|[loopr](problems.md#loopr) |1.0.1 | | |1 | -|[lplyr](problems.md#lplyr) |0.1.6 |1 |1 | | -|manipulateWidget |0.7.0 | | | | -|[mapfuser](problems.md#mapfuser) |0.1.2 |1 | | | -|[markmyassignment](problems.md#markmyassignment) |0.6.1 | | |1 | -|[mason](problems.md#mason) |0.2.5 | | |1 | -|metacoder |0.1.3 | | | | -|[metagenomeFeatures](problems.md#metagenomefeatures) |1.8.1 | | |2 | -|metaplot |0.2.1 | | | | -|mockr |0.1 | | | | -|[modelr](problems.md#modelr) |0.1.1 | | |1 | -|[mosaic](problems.md#mosaic) |1.1.0 | | |2 | -|mosaicCore |0.4.0 | | | | -|[mosaicModel](problems.md#mosaicmodel) |0.3.0 | | |1 | -|[mrgsolve](problems.md#mrgsolve) |0.8.9 |1 | | | -|ncappc |0.2.1.1 | | | | -|networkreporting |0.1.1 | | | | -|nlstimedist |1.1.1 | | | | -|[nonmemica](problems.md#nonmemica) |0.7.6 | |1 |1 | -|[observer](problems.md#observer) |0.1.2 | | |1 | -|ompr |0.6.0 | | | | -|[openair](problems.md#openair) |2.1-5 |1 | | | -|padr |0.3.0 | | | | -|[parsemsf](problems.md#parsemsf) |0.1.0 |2 |1 |1 | -|photobiologyInOut |0.4.13 | | | | -|[PKPDmisc](problems.md#pkpdmisc) |2.0.0 | | |1 | -|plotly |4.7.1 | | | | -|poplite |0.99.19 | | | | -|[purrrlyr](problems.md#purrrlyr) |0.0.2 | | |1 | -|[R6Frame](problems.md#r6frame) |0.1.0 |1 | | | -|[rbokeh](problems.md#rbokeh) |0.5.0 | | |2 | -|request |0.1.0 | | | | -|rex |1.1.1 | | | | -|[rfishbase](problems.md#rfishbase) |2.1.2 | | |1 | -|[rgho](problems.md#rgho) |1.0.1 |1 |1 | | -|RmarineHeatWaves |0.15.7 | | | | -|[RNeXML](problems.md#rnexml) |2.0.7 | | |1 | -|[ropenaq](problems.md#ropenaq) |0.2.2 |1 | | | -|[rPref](problems.md#rpref) |1.2 | | |1 | -|rprev |0.2.4 | | | | -|[rscorecard](problems.md#rscorecard) |0.4.0 | |1 | | -|RSDA |2.0.2 | | | | -|[rtimicropem](problems.md#rtimicropem) |1.3 | | |1 | -|scrubr |0.1.1 | | | | -|[sf](problems.md#sf) |0.5-4 |1 | | | -|[shazam](problems.md#shazam) |0.1.8 | | |1 | -|simPH |1.3.10 | | | | -|[SpaDES.core](problems.md#spadescore) |0.1.0 |1 | |1 | -|[sparklyr](problems.md#sparklyr) |0.6.3 |1 | | | -|spdplyr |0.1.3 | | | | -|srvyr |0.2.2 | | | | -|statar |0.6.5 | | | | -|[statisticalModeling](problems.md#statisticalmodeling) |0.3.0 |1 |1 |1 | -|summariser |0.1.0 | | | | -|survutils |1.0.0 | | | | -|[sweep](problems.md#sweep) |0.2.0 | | |1 | -|[tadaatoolbox](problems.md#tadaatoolbox) |0.13.0 | | |2 | -|[taxa](problems.md#taxa) |0.1.0 | | |1 | -|[tbl2xts](problems.md#tbl2xts) |0.1.2 | | |1 | -|[tidyquant](problems.md#tidyquant) |0.5.3 |1 |1 |1 | -|tigger |0.2.11 | | | | -|[timetk](problems.md#timetk) |0.1.0 | | |1 | -|treeplyr |0.1.3 | | | | -|unpivotr |0.2.1 | | | | -|[valaddin](problems.md#valaddin) |0.1.2 | | |1 | -|[vqtl](problems.md#vqtl) |1.2.0 | | |1 | -|VWPre |0.9.6 | | | | -|webmockr |0.1.0 | | | | -|wrangle |0.4 | | | | -|wrswoR.benchmark |0.2 | | | | -|xpose4 |4.6.0 | | | | +|package |version |error |warning |note | +|:---------|:-------|:------|:-------|:----| +|[hyperSpec](problems.md#hyperspec)|0.100.3 |__+1__ | | | +|[lidR](problems.md#lidr)|4.2.3 |__+1__ | |1 | diff --git a/revdep/cran.md b/revdep/cran.md new file mode 100644 index 0000000..9e04cef --- /dev/null +++ b/revdep/cran.md @@ -0,0 +1,18 @@ +## revdepcheck results + +We checked 52 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. + + * We saw 2 new problems + * We failed to check 0 packages + +Issues with CRAN packages are summarised below. + +### New problems +(This reports the first line of each new failure) + +* hyperSpec + checking tests ... ERROR + +* lidR + checking tests ... ERROR + diff --git a/revdep/failures.md b/revdep/failures.md new file mode 100644 index 0000000..9a20736 --- /dev/null +++ b/revdep/failures.md @@ -0,0 +1 @@ +*Wow, no problems at all. :)* \ No newline at end of file diff --git a/revdep/problems.md b/revdep/problems.md index 0df1b0b..3859179 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1,1443 +1,94 @@ -# atlantistools +# hyperSpec -Version: 0.4.3 +
-## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error in re-building vignettes: - ... - ! File ended while scanning use of \@@BOOKMARK. - - \par - l.107 \begin{document} - - pandoc: Error producing PDF from TeX source - Error: processing vignette 'model-calibration.Rmd' failed with diagnostics: - pandoc document conversion failed with error 43 - Execution halted - ``` - -# condformat - -Version: 0.6.0 - -## In both - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - > - > test_check("condformat") - Unable to find any JVMs matching version "(null)". - No Java runtime present, try --request to install. - 1. Error: condformat2excel generates a file (@test_rendering.R#22) ------------- - Please install the xlsx package in order to export to excel - 1: condformat2excel(condformat(head(iris, n = rows_to_write)), filename = filename) at testthat/test_rendering.R:22 - 2: stop("Please install the xlsx package in order to export to excel") - - testthat results ================================================================ - OK: 53 SKIPPED: 0 FAILED: 1 - 1. Error: condformat2excel generates a file (@test_rendering.R#22) - - Error: testthat unit tests failed - Execution halted - ``` - -* checking dependencies in R code ... NOTE - ``` - Unable to find any JVMs matching version "(null)". - No Java runtime present, try --request to install. - Unable to find any JVMs matching version "(null)". - No Java runtime present, try --request to install. - Namespace in Imports field not imported from: ‘utils’ - All declared Imports should be used. - ``` - -# cpr - -Version: 0.2.3 - -## In both - -* checking whether package ‘cpr’ can be installed ... ERROR - ``` - Installation failed. - See ‘/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/checks/cpr/new/cpr.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘cpr’ ... -** package ‘cpr’ successfully unpacked and MD5 sums checked -** libs -clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/RcppArmadillo/include" -I/usr/local/include -I../inst/include -DARMA_64BIT_WORD -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o -clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/RcppArmadillo/include" -I/usr/local/include -I../inst/include -DARMA_64BIT_WORD -fPIC -Wall -g -O2 -c boehm.cpp -o boehm.o -clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/RcppArmadillo/include" -I/usr/local/include -I../inst/include -DARMA_64BIT_WORD -fPIC -Wall -g -O2 -c bsplines.cpp -o bsplines.o -bsplines.cpp:24:10: warning: unused variable 'a' [-Wunused-variable] - double a = 0.0; - ^ -bsplines.cpp:25:10: warning: unused variable 'b' [-Wunused-variable] - double b = 0.0; - ^ -2 warnings generated. -clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/RcppArmadillo/include" -I/usr/local/include -I../inst/include -DARMA_64BIT_WORD -fPIC -Wall -g -O2 -c cpr.cpp -o cpr.o -clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/RcppArmadillo/include" -I/usr/local/include -I../inst/include -DARMA_64BIT_WORD -fPIC -Wall -g -O2 -c diag_only.cpp -o diag_only.o -clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/RcppArmadillo/include" -I/usr/local/include -I../inst/include -DARMA_64BIT_WORD -fPIC -Wall -g -O2 -c matrix_rank.cpp -o matrix_rank.o -clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -pedantic -O0 -c registerDynamicSymbol.c -o registerDynamicSymbol.o -clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/RcppArmadillo/include" -I/usr/local/include -I../inst/include -DARMA_64BIT_WORD -fPIC -Wall -g -O2 -c tensors.cpp -o tensors.o -clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o cpr.so RcppExports.o boehm.o bsplines.o cpr.o diag_only.o matrix_rank.o registerDynamicSymbol.o tensors.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation -ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0' -ld: warning: directory not found for option '-L/usr/local/gfortran/lib' -ld: library not found for -lquadmath -clang: error: linker command failed with exit code 1 (use -v to see invocation) -make: *** [cpr.so] Error 1 -ERROR: compilation failed for package ‘cpr’ -* removing ‘/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/checks/cpr/new/cpr.Rcheck/cpr’ - -``` -### CRAN - -``` -* installing *source* package ‘cpr’ ... -** package ‘cpr’ successfully unpacked and MD5 sums checked -** libs -clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/RcppArmadillo/include" -I/usr/local/include -I../inst/include -DARMA_64BIT_WORD -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o -clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/RcppArmadillo/include" -I/usr/local/include -I../inst/include -DARMA_64BIT_WORD -fPIC -Wall -g -O2 -c boehm.cpp -o boehm.o -clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/RcppArmadillo/include" -I/usr/local/include -I../inst/include -DARMA_64BIT_WORD -fPIC -Wall -g -O2 -c bsplines.cpp -o bsplines.o -bsplines.cpp:24:10: warning: unused variable 'a' [-Wunused-variable] - double a = 0.0; - ^ -bsplines.cpp:25:10: warning: unused variable 'b' [-Wunused-variable] - double b = 0.0; - ^ -2 warnings generated. -clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/RcppArmadillo/include" -I/usr/local/include -I../inst/include -DARMA_64BIT_WORD -fPIC -Wall -g -O2 -c cpr.cpp -o cpr.o -clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/RcppArmadillo/include" -I/usr/local/include -I../inst/include -DARMA_64BIT_WORD -fPIC -Wall -g -O2 -c diag_only.cpp -o diag_only.o -clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/RcppArmadillo/include" -I/usr/local/include -I../inst/include -DARMA_64BIT_WORD -fPIC -Wall -g -O2 -c matrix_rank.cpp -o matrix_rank.o -clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -pedantic -O0 -c registerDynamicSymbol.c -o registerDynamicSymbol.o -clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/RcppArmadillo/include" -I/usr/local/include -I../inst/include -DARMA_64BIT_WORD -fPIC -Wall -g -O2 -c tensors.cpp -o tensors.o -clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o cpr.so RcppExports.o boehm.o bsplines.o cpr.o diag_only.o matrix_rank.o registerDynamicSymbol.o tensors.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation -ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0' -ld: warning: directory not found for option '-L/usr/local/gfortran/lib' -ld: library not found for -lquadmath -clang: error: linker command failed with exit code 1 (use -v to see invocation) -make: *** [cpr.so] Error 1 -ERROR: compilation failed for package ‘cpr’ -* removing ‘/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/checks/cpr/old/cpr.Rcheck/cpr’ - -``` -# emil +* Version: 0.100.3 +* GitHub: https://github.com/r-hyperspec/hyperSpec +* Source code: https://github.com/cran/hyperSpec +* Date/Publication: 2025-10-13 05:10:33 UTC +* Number of recursive dependencies: 133 -Version: 2.2.8 +Run `revdepcheck::cloud_details(, "hyperSpec")` for more info -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘Rcpp’ - All declared Imports should be used. - ``` +
-# eyetrackingR +## Newly broken -Version: 0.1.6 - -## In both - -* checking examples ... ERROR +* checking tests ... ERROR ``` + Running ‘unittests.R’ + Running the tests in ‘tests/unittests.R’ failed. + Complete output: + > library (testthat) + > test_check("hyperSpec") + Loading required package: hyperSpec + Loading required package: lattice + Loading required package: grid + Loading required package: ggplot2 + Loading required package: xml2 ... - + time_column = "TimeFromTrialOnset", - + trackloss_column = "TrackLoss", - + aoi_columns = c('Animate','Inanimate'), - + treat_non_aoi_looks_as_missing = TRUE ) - `mutate_each()` is deprecated. - Use `mutate_all()`, `mutate_at()` or `mutate_if()` instead. - To map `funs` over a selection of variables, use `mutate_at()` - > response_window <- subset_by_window(data, window_start_time = 15500, window_end_time = 21000, - + rezero = FALSE) - Avg. window length in new data will be 5500 - > response_time <- make_time_sequence_data(response_window, time_bin_size = 500, aois = "Animate", - + predictor_columns = "Sex") - > - > time_cluster_data <- make_time_cluster_data(data = response_time, predictor_column = "SexM", - + aoi = "Animate", test = "lmer", - + threshold = 1.5, - + formula = LogitAdjusted ~ Sex + (1|Trial) + (1|ParticipantName)) - Error in UseMethod("analyze_time_bins") : - no applicable method for 'analyze_time_bins' applied to an object of class "data.frame" - Calls: make_time_cluster_data ... make_time_cluster_data.time_sequence_data -> do.call -> - Execution halted - ``` - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Computing t.test for each time bin... - Computing t.test for each time bin... - `mutate_each()` is deprecated. - Use `mutate_all()`, `mutate_at()` or `mutate_if()` instead. - To map `funs` over a selection of variables, use `mutate_at()` - Avg. window length in new data will be 5500 - Performing Trackloss Analysis... - Will exclude trials whose trackloss proportion is greater than : 0.25 - ...removed 33 trials. - Error in UseMethod("make_time_cluster_data") : - no applicable method for 'make_time_cluster_data' applied to an object of class "data.frame" - Calls: test_check ... source_file -> eval -> eval -> make_time_cluster_data - testthat results ================================================================ - OK: 38 SKIPPED: 0 FAILED: 0 - Execution halted - ``` - -# flextable - -Version: 0.3.0 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘magrittr’ - All declared Imports should be used. - ``` - -# foghorn - -Version: 0.4.4 - -## In both - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - testthat results ================================================================ - OK: 49 SKIPPED: 0 FAILED: 10 - 1. Failure: output of summary cran results (@test-foghorn.R#176) - 2. Failure: output of summary cran results (@test-foghorn.R#178) - 3. Failure: output of summary cran results (@test-foghorn.R#189) - 4. Failure: output of summary cran results (@test-foghorn.R#201) - 5. Failure: output of summary cran results (@test-foghorn.R#213) - 6. Failure: output of summary cran results (@test-foghorn.R#226) - 7. Failure: output of summary cran results (@test-foghorn.R#233) - 8. Failure: output of summary cran results (@test-foghorn.R#239) - 9. Failure: output of show cran results (@test-foghorn.R#264) - 10. Failure: output of show cran results (@test-foghorn.R#266) - - Error: testthat unit tests failed - Execution halted - ``` - -# gaiah - -Version: 0.0.2 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘ggplot2’ ‘maptools’ ‘rgeos’ ‘stringr’ ‘tidyr’ - All declared Imports should be used. - ``` - -# GenomicDataCommons - -Version: 1.0.5 - -## In both - -* checking R code for possible problems ... NOTE - ``` - default_fields.character: no visible binding for global variable - ‘defaults’ - Undefined global functions or variables: - defaults - ``` - -* checking Rd \usage sections ... NOTE - ``` - S3 methods shown with full name in documentation object 'as.data.frame.GDCResults': - ‘as.data.frame.GDCResults’ - - The \usage entries for S3 methods should use the \method markup and not - their full name. - See chapter ‘Writing R documentation files’ in the ‘Writing R - Extensions’ manual. - ``` - -# geoparser - -Version: 0.1.1 - -## In both - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 2. Error: no problems if no results (@test_query.R#26) ------------------------- - HTTP failure: 401 - 1: geoparser_q(text_input = "no placename here") at testthat/test_query.R:26 - 2: lapply(text_input, total, key = key) - 3: FUN(X[[i]], ...) - 4: geoparser_check(temp) - 5: stop("HTTP failure: ", status, call. = FALSE) + 5. └─fluNA[-2, , r] + 6. └─hyperSpec (local) .local(x, i, j, ..., drop = drop) + 7. └─hyperSpec:::.extract(x, i, j, l, wl.index = wl.index) + 8. └─hyperSpec::wl2i(x, l) + 9. └─hyperSpec:::.getindex(x, Re(to), extrapolate = FALSE) - testthat results ================================================================ - OK: 3 SKIPPED: 0 FAILED: 2 - 1. Error: query returns a list of data.frames (@test_query.R#4) - 2. Error: no problems if no results (@test_query.R#26) - - Error: testthat unit tests failed + [ FAIL 1 | WARN 0 | SKIP 60 | PASS 323 ] + Error: + ! Test failures. Execution halted ``` -* checking re-building of vignette outputs ... WARNING - ``` - Error in re-building vignettes: - ... - Quitting from lines 34-37 (geoparser.Rmd) - Error: processing vignette 'geoparser.Rmd' failed with diagnostics: - HTTP failure: 401 - Execution halted - ``` - -# ggguitar - -Version: 0.1.1 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘gridExtra’ ‘lazyeval’ ‘readr’ - All declared Imports should be used. - ``` - -# ggplot2 - -Version: 2.2.1 +# lidR -## In both +
-* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘reshape2’ - All declared Imports should be used. - ``` +* Version: 4.2.3 +* GitHub: https://github.com/r-lidar/lidR +* Source code: https://github.com/cran/lidR +* Date/Publication: 2026-01-08 09:10:02 UTC +* Number of recursive dependencies: 151 -# ggraptR +Run `revdepcheck::cloud_details(, "lidR")` for more info -Version: 1.0 +
-## In both +## Newly broken -* checking tests ... +* checking tests ... ERROR ``` - ERROR + Running ‘testthat.R’ Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: + Complete output: + > Sys.setenv("R_TESTS" = "") > - > if (Sys.getenv("NOT_CRAN") == "true") { # like global skip_on_cran - + Sys.setenv("R_TESTS" = "") # accroding to https://github.com/hadley/testthat/issues/144 - + test_check("ggraptR") - + } + > library(testthat) + > library(lidR) + > test_check("lidR") + Tests using raster: terra + Tests using future: TRUE + ... + 4. │ │ └─base::withCallingHandlers(...) + 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 6. ├─lidR::clip_circle(las, xc, yc, r) + 7. └─lidR:::clip_circle.LAS(las, xc, yc, r) + 8. └─lidR:::assert_are_same_length(xcenter, radius) - Initial plotError in file(filename, "r", encoding = encoding) : - cannot open the connection - Calls: test_check ... source -> withVisible -> eval -> eval -> source -> file - In addition: Warning message: - In file(filename, "r", encoding = encoding) : - cannot open file '../../inst/ggraptR/functions/helper.R': No such file or directory - testthat results ================================================================ - OK: 0 SKIPPED: 0 FAILED: 0 + [ FAIL 1 | WARN 0 | SKIP 46 | PASS 1295 ] + Error: + ! Test failures. Execution halted ``` -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘DBI’ ‘GGally’ ‘RColorBrewer’ ‘Rcpp’ ‘assertthat’ ‘backports’ - ‘colorspace’ ‘colourpicker’ ‘evaluate’ ‘futile.options’ ‘gdtools’ - ‘gtable’ ‘htmltools’ ‘htmlwidgets’ ‘httpuv’ ‘labeling’ ‘lambda.r’ - ‘lazyeval’ ‘magrittr’ ‘miniUI’ ‘munsell’ ‘plyr’ ‘reshape’ ‘rprojroot’ - ‘scales’ ‘stringi’ ‘stringr’ ‘svglite’ ‘tibble’ ‘xtable’ ‘yaml’ - All declared Imports should be used. - ``` - -# ggstance - -Version: 0.3 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘lazyeval’ - All declared Imports should be used. - ``` - -# ggvis - -Version: 0.4.3 - -## In both - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘plyr’ - ``` - -# grattan - -Version: 1.5.1.2 - -## In both - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘taxstats’ - ``` - -# gutenbergr - -Version: 0.1.3 - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 13617 marked UTF-8 strings - ``` - -# harrietr - -Version: 0.2.2 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘ggplot2’ - All declared Imports should be used. - ``` - -# HTSSIP - -Version: 1.2.0 - -## In both - -* R CMD check timed out - - -# hurricaneexposure - -Version: 0.0.1 - -## In both - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘hurricaneexposuredata’ - ``` - -# huxtable - -Version: 1.0.0 - -## In both - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘xtable’ - ``` - -# jqr - -Version: 1.0.0 - -## In both - -* checking whether package ‘jqr’ can be installed ... ERROR - ``` - Installation failed. - See ‘/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/checks/jqr/new/jqr.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘jqr’ ... -** package ‘jqr’ successfully unpacked and MD5 sums checked -Using PKG_CFLAGS=-I/usr/local/opt/jq/include -Using PKG_LIBS=-L/usr/local/lib -ljq -------------------------- ANTICONF ERROR --------------------------- -Configuration failed because libjq was not found. -On Ubuntu 14.04 or 16.04 you can use the PPA: - sudo add-apt-repository -y ppa:opencpu/jq - sudo apt-get update - sudo apt-get install libjq-dev -On other sytems try installing: - * deb: libjq-dev (Debian, Ubuntu 16.10 and up). - * rpm: jq-devel (Fedora, EPEL) - * csw: libjq_dev (Solaris) - * brew: jq (OSX) -If is already installed set INCLUDE_DIR and LIB_DIR manually via: -R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...' --------------------------------------------------------------------- -ERROR: configuration failed for package ‘jqr’ -* removing ‘/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/checks/jqr/new/jqr.Rcheck/jqr’ - -``` -### CRAN - -``` -* installing *source* package ‘jqr’ ... -** package ‘jqr’ successfully unpacked and MD5 sums checked -Using PKG_CFLAGS=-I/usr/local/opt/jq/include -Using PKG_LIBS=-L/usr/local/lib -ljq -------------------------- ANTICONF ERROR --------------------------- -Configuration failed because libjq was not found. -On Ubuntu 14.04 or 16.04 you can use the PPA: - sudo add-apt-repository -y ppa:opencpu/jq - sudo apt-get update - sudo apt-get install libjq-dev -On other sytems try installing: - * deb: libjq-dev (Debian, Ubuntu 16.10 and up). - * rpm: jq-devel (Fedora, EPEL) - * csw: libjq_dev (Solaris) - * brew: jq (OSX) -If is already installed set INCLUDE_DIR and LIB_DIR manually via: -R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...' --------------------------------------------------------------------- -ERROR: configuration failed for package ‘jqr’ -* removing ‘/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/checks/jqr/old/jqr.Rcheck/jqr’ - -``` -# lidR - -Version: 1.3.1 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘Rcpp’ ‘memoise’ - All declared Imports should be used. - ``` - -# loopr - -Version: 1.0.1 - -## In both - -* checking R code for possible problems ... NOTE - ``` - amendColumns: no visible global function definition for ‘setNames’ - fillColumns: no visible global function definition for ‘setNames’ - Undefined global functions or variables: - setNames - Consider adding - importFrom("stats", "setNames") - to your NAMESPACE file. - ``` - -# lplyr - -Version: 0.1.6 - -## In both - -* checking examples ... ERROR - ``` - ... - - > rename(xs, x0 = x1) - $x0 - [1] 1 2 3 - - $x2 - [1] 2 3 4 5 - - $x3 - $x3[[1]] - [1] "alpha" - - $x3[[2]] - [1] "beta" "gamma" - - - > select(xs, -x3) - Error in select.list(xs, -x3) : - select.list() cannot be used non-interactively - Calls: select -> select.list - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - ... - Attaching package: 'dplyr' - - The following objects are masked from 'package:stats': - - filter, lag - - The following objects are masked from 'package:base': - - intersect, setdiff, setequal, union - - - Attaching package: 'lplyr' - - The following object is masked from 'package:dplyr': - - pull - - Quitting from lines 22-30 (lplyr-vignette.Rmd) - Error: processing vignette 'lplyr-vignette.Rmd' failed with diagnostics: - select.list() cannot be used non-interactively - Execution halted - ``` - -# mapfuser - -Version: 0.1.2 - -## In both - -* checking package dependencies ... ERROR - ``` - Package required but not available: ‘LPmerge’ - - See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ - manual. - ``` - -# markmyassignment - -Version: 0.6.1 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘lazyeval’ - All declared Imports should be used. - ``` - -# mason - -Version: 0.2.5 - -## In both - -* checking Rd cross-references ... NOTE - ``` - Packages unavailable to check Rd xrefs: ‘ggplot2’, ‘pander’, ‘pixiedust’ - ``` - -# metagenomeFeatures - -Version: 1.8.1 - ## In both * checking installed package size ... NOTE ``` - installed size is 8.7Mb + installed size is 19.8Mb sub-directories of 1Mb or more: - extdata 6.7Mb - ``` - -* checking R code for possible problems ... NOTE - ``` - .mgDb_annotateFeatures: no visible binding for global variable - ‘db_keys’ - .select.taxa: no visible binding for global variable ‘Keys’ - .select.taxa: no visible binding for global variable ‘.’ - aggregate_taxa: no visible binding for global variable ‘.’ - aggregate_taxa: no visible binding for global variable ‘index’ - vignette_pheno_data: no visible global function definition for - ‘read.csv’ - Undefined global functions or variables: - . Keys db_keys index read.csv - Consider adding - importFrom("utils", "read.csv") - to your NAMESPACE file. - ``` - -# modelr - -Version: 0.1.1 - -## In both - -* checking Rd cross-references ... NOTE - ``` - Packages unavailable to check Rd xrefs: ‘lme4’, ‘rstanarm’ - ``` - -# mosaic - -Version: 1.1.0 - -## In both - -* checking package dependencies ... NOTE - ``` - Package which this enhances but not available for checking: ‘manipulate’ - ``` - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘cubature’ - ``` - -# mosaicModel - -Version: 0.3.0 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’ - All declared Imports should be used. - ``` - -# mrgsolve - -Version: 0.8.9 - -## In both - -* checking whether package ‘mrgsolve’ can be installed ... ERROR - ``` - Installation failed. - See ‘/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/checks/mrgsolve/new/mrgsolve.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘mrgsolve’ ... -** package ‘mrgsolve’ successfully unpacked and MD5 sums checked -** libs -ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c RcppExports.cpp -o RcppExports.o -ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c dataobject.cpp -o dataobject.o -ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c datarecord.cpp -o datarecord.o -ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c devtran.cpp -o devtran.o -ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c housemodel-mread-source.cpp -o housemodel-mread-source.o -ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c mrgsolve.cpp -o mrgsolve.o -ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c mrgsolve_init.cpp -o mrgsolve_init.o -ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c odepack_dlsoda.cpp -o odepack_dlsoda.o -ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c odeproblem.cpp -o odeproblem.o -gfortran -fPIC -g -O2 -c opk_dlsoda_mrg.f -o opk_dlsoda_mrg.o -gfortran -fPIC -g -O2 -c opkda1_mrg.f -o opkda1_mrg.o -gfortran -fPIC -g -O2 -c opkda2_mrg.f -o opkda2_mrg.o -ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c quick.cpp -o quick.o -ccache clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o mrgsolve.so RcppExports.o dataobject.o datarecord.o devtran.o housemodel-mread-source.o mrgsolve.o mrgsolve_init.o odepack_dlsoda.o odeproblem.o opk_dlsoda_mrg.o opkda1_mrg.o opkda2_mrg.o quick.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation -ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0' -ld: warning: directory not found for option '-L/usr/local/gfortran/lib' -ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0' -ld: warning: directory not found for option '-L/usr/local/gfortran/lib' -ld: library not found for -lquadmath -clang: error: linker command failed with exit code 1 (use -v to see invocation) -make: *** [mrgsolve.so] Error 1 -ERROR: compilation failed for package ‘mrgsolve’ -* removing ‘/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/checks/mrgsolve/new/mrgsolve.Rcheck/mrgsolve’ - -``` -### CRAN - -``` -* installing *source* package ‘mrgsolve’ ... -** package ‘mrgsolve’ successfully unpacked and MD5 sums checked -** libs -ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c RcppExports.cpp -o RcppExports.o -ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c dataobject.cpp -o dataobject.o -ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c datarecord.cpp -o datarecord.o -ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c devtran.cpp -o devtran.o -ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c housemodel-mread-source.cpp -o housemodel-mread-source.o -ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c mrgsolve.cpp -o mrgsolve.o -ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c mrgsolve_init.cpp -o mrgsolve_init.o -ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c odepack_dlsoda.cpp -o odepack_dlsoda.o -ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c odeproblem.cpp -o odeproblem.o -gfortran -fPIC -g -O2 -c opk_dlsoda_mrg.f -o opk_dlsoda_mrg.o -gfortran -fPIC -g -O2 -c opkda1_mrg.f -o opkda1_mrg.o -gfortran -fPIC -g -O2 -c opkda2_mrg.f -o opkda2_mrg.o -ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c quick.cpp -o quick.o -ccache clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o mrgsolve.so RcppExports.o dataobject.o datarecord.o devtran.o housemodel-mread-source.o mrgsolve.o mrgsolve_init.o odepack_dlsoda.o odeproblem.o opk_dlsoda_mrg.o opkda1_mrg.o opkda2_mrg.o quick.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation -ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0' -ld: warning: directory not found for option '-L/usr/local/gfortran/lib' -ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0' -ld: warning: directory not found for option '-L/usr/local/gfortran/lib' -ld: library not found for -lquadmath -clang: error: linker command failed with exit code 1 (use -v to see invocation) -make: *** [mrgsolve.so] Error 1 -ERROR: compilation failed for package ‘mrgsolve’ -* removing ‘/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/checks/mrgsolve/old/mrgsolve.Rcheck/mrgsolve’ - -``` -# nonmemica - -Version: 0.7.6 - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error in re-building vignettes: - ... - Warning in engine$weave(file, quiet = quiet, encoding = enc) : - The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it. - Unable to find any JVMs matching version "(null)". - No Java runtime present, try --request to install. - Quitting from lines 197-201 (parameter-table.Rmd) - Error: processing vignette 'parameter-table.Rmd' failed with diagnostics: - package 'ReporteRsjars' could not be loaded - Execution halted - ``` - -* checking dependencies in R code ... NOTE - ``` - Unable to find any JVMs matching version "(null)". - No Java runtime present, try --request to install. - ``` - -# observer - -Version: 0.1.2 - -## In both - -* checking Rd cross-references ... NOTE - ``` - Packages unavailable to check Rd xrefs: ‘ensurer’, ‘validate’ - ``` - -# openair - -Version: 2.1-5 - -## In both - -* checking whether package ‘openair’ can be installed ... ERROR - ``` - Installation failed. - See ‘/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/checks/openair/new/openair.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘openair’ ... -** package ‘openair’ successfully unpacked and MD5 sums checked -** libs -ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/openair/Rcpp/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c cluster.cpp -o cluster.o -clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/openair/Rcpp/include" -I/usr/local/include -fPIC -Wall -pedantic -O0 -c init.c -o init.o -ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/openair/Rcpp/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c rolling.cpp -o rolling.o -ccache clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o openair.so cluster.o init.o rolling.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation -ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0' -ld: warning: directory not found for option '-L/usr/local/gfortran/lib' -ld: library not found for -lquadmath -clang: error: linker command failed with exit code 1 (use -v to see invocation) -make: *** [openair.so] Error 1 -ERROR: compilation failed for package ‘openair’ -* removing ‘/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/checks/openair/new/openair.Rcheck/openair’ - -``` -### CRAN - -``` -* installing *source* package ‘openair’ ... -** package ‘openair’ successfully unpacked and MD5 sums checked -** libs -ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/openair/Rcpp/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c cluster.cpp -o cluster.o -clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/openair/Rcpp/include" -I/usr/local/include -fPIC -Wall -pedantic -O0 -c init.c -o init.o -ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/openair/Rcpp/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c rolling.cpp -o rolling.o -ccache clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o openair.so cluster.o init.o rolling.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation -ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0' -ld: warning: directory not found for option '-L/usr/local/gfortran/lib' -ld: library not found for -lquadmath -clang: error: linker command failed with exit code 1 (use -v to see invocation) -make: *** [openair.so] Error 1 -ERROR: compilation failed for package ‘openair’ -* removing ‘/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/checks/openair/old/openair.Rcheck/openair’ - -``` -# parsemsf - -Version: 0.1.0 - -## In both - -* checking examples ... ERROR - ``` - Running examples in ‘parsemsf-Ex.R’ failed - The error most likely occurred in: - - > ### Name: make_area_table - > ### Title: Make a table of peptide areas - > ### Aliases: make_area_table - > - > ### ** Examples - > - > make_area_table(parsemsf_example("test_db.msf")) - Error: The dbplyr package is required to communicate with database backends. - Execution halted - ``` - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 10: src_sqlite(msf_file) - 11: check_dbplyr() - 12: check_pkg("dbplyr", "communicate with database backends", install = FALSE) - 13: glubort(NULL, "The {name} package is required to {reason}.", if (install) "\nPlease install it with `install.packages(\"{name}\")`") - 14: .abort(text) - - Error: The dbplyr package is required to communicate with database backends. - testthat results ================================================================ - OK: 0 SKIPPED: 0 FAILED: 3 - 1. Error: make_area_table creates a data frame with the correct column names (@test_make_area_table.R#16) - 2. Error: make_pep_table creates a data frame with the correct column names (@test_make_pep_table.R#13) - 3. Error: map_peptides creates a data frame with the correct column names (@test_map_peptides.R#16) - - Error: testthat unit tests failed - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error in re-building vignettes: - ... - Quitting from lines 20-25 (introduction.Rmd) - Error: processing vignette 'introduction.Rmd' failed with diagnostics: - The dbplyr package is required to communicate with database backends. - Execution halted - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘RSQLite’ - All declared Imports should be used. - ``` - -# PKPDmisc - -Version: 2.0.0 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘purrr’ - All declared Imports should be used. - ``` - -# purrrlyr - -Version: 0.0.2 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘lazyeval’ - All declared Imports should be used. - ``` - -# R6Frame - -Version: 0.1.0 - -## In both - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - testthat results ================================================================ - OK: 139 SKIPPED: 0 FAILED: 10 - 1. Error: gather works with R6 data.frame (@test-tidyr_reshape.R#11) - 2. Error: gather works with R6 data.table (@test-tidyr_reshape.R#25) - 3. Error: gather works with R6 tbl_df (@test-tidyr_reshape.R#38) - 4. Error: spread works with R6 data.frame (@test-tidyr_reshape.R#52) - 5. Error: spread works with R6 data.table (@test-tidyr_reshape.R#67) - 6. Error: spread works with R6 tbl_df (@test-tidyr_reshape.R#81) - 7. Error: complete works with R6 data.frame (@test-tidyr_verbs.R#13) - 8. Error: complete works with R6 data.table (@test-tidyr_verbs.R#27) - 9. Error: complete works with R6 tbl_df (@test-tidyr_verbs.R#41) - 10. Error: fill works with R6 tbl_df (@test-tidyr_verbs.R#72) - - Error: testthat unit tests failed - Execution halted - ``` - -# rbokeh - -Version: 0.5.0 - -## In both - -* checking package dependencies ... NOTE - ``` - Package which this enhances but not available for checking: ‘shiny’ - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘ggplot2’ - All declared Imports should be used. - ``` - -# rfishbase - -Version: 2.1.2 - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 44 marked UTF-8 strings - ``` - -# rgho - -Version: 1.0.1 - -## In both - -* checking examples ... ERROR - ``` - Running examples in ‘rgho-Ex.R’ failed - The error most likely occurred in: - - > ### Name: get_gho_data - > ### Title: Returns GHO Data - > ### Aliases: get_gho_data - > - > ### ** Examples - > - > - > result <- get_gho_data( - + dimension = "GHO", - + code = "MDG_0000000001" - + ) - Error: parse error: premature EOF - { "copyright": "(c) World Healt - (right here) ------^ - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error in re-building vignettes: - ... - Quitting from lines 36-38 (a-intro.Rmd) - Error: processing vignette 'a-intro.Rmd' failed with diagnostics: - parse error: premature EOF - { "copyright": "(c) World Healt - (right here) ------^ - Execution halted - ``` - -# RNeXML - -Version: 2.0.7 - -## In both - -* checking package dependencies ... NOTE - ``` - Packages suggested but not available for checking: ‘rrdf’ ‘Sxslt’ - ``` - -# ropenaq - -Version: 0.2.2 - -## In both - -* R CMD check timed out - - -# rPref - -Version: 1.2 - -## In both - -* checking for GNU extensions in Makefiles ... NOTE - ``` - GNU make is a SystemRequirements. - ``` - -# rscorecard - -Version: 0.4.0 - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error in re-building vignettes: - ... - Quitting from lines 22-29 (introduction.Rmd) - Error: processing vignette 'introduction.Rmd' failed with diagnostics: - Missing API key; ?sc_key for details - Execution halted - ``` - -# rtimicropem - -Version: 1.3 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘R6’ - All declared Imports should be used. - ``` - -# sf - -Version: 0.5-4 - -## In both - -* checking whether package ‘sf’ can be installed ... ERROR - ``` - Installation failed. - See ‘/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/checks/sf/new/sf.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘sf’ ... -** package ‘sf’ successfully unpacked and MD5 sums checked -configure: CC: clang -configure: CXX: ccache clang++ -checking for gdal-config... no -no -configure: error: gdal-config not found or not executable. -ERROR: configuration failed for package ‘sf’ -* removing ‘/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/checks/sf/new/sf.Rcheck/sf’ - -``` -### CRAN - -``` -* installing *source* package ‘sf’ ... -** package ‘sf’ successfully unpacked and MD5 sums checked -configure: CC: clang -configure: CXX: ccache clang++ -checking for gdal-config... no -no -configure: error: gdal-config not found or not executable. -ERROR: configuration failed for package ‘sf’ -* removing ‘/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/checks/sf/old/sf.Rcheck/sf’ - -``` -# shazam - -Version: 0.1.8 - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 2 marked UTF-8 strings - ``` - -# SpaDES.core - -Version: 0.1.0 - -## In both - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/test-all.R’ failed. - Last 13 lines of output: - 100 43558 100 43558 0 0 457k 0 --:--:-- --:--:-- --:--:-- 457k - 1. Error: spelling errors (@test-spelling.R#19) -------------------------------- - No suitable spell-checker program found - 1: aspell_package_vignettes(pkgDir) at testthat/test-spelling.R:19 - 2: aspell(character()) - 3: stop("No suitable spell-checker program found") - - testthat results ================================================================ - OK: 304 SKIPPED: 2 FAILED: 1 - 1. Error: spelling errors (@test-spelling.R#19) - - Error: testthat unit tests failed - In addition: Warning message: - In fun(libname, pkgname) : couldn't connect to display "" - Execution halted - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘CircStats’ ‘RandomFields’ ‘grDevices’ ‘sp’ - All declared Imports should be used. - ``` - -# sparklyr - -Version: 0.6.3 - -## In both - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - > library(testthat) - > library(sparklyr) - > - > if (identical(Sys.getenv("NOT_CRAN"), "true")) { - + test_check("sparklyr") - + on.exit({ spark_disconnect_all() ; livy_service_stop() }) - + } - Error in validate_java_version_line(master, version) : - Java version detected but couldn't parse version from No Java runtime present, requesting install. - Calls: test_check ... validate_java_version -> validate_java_version_line - In addition: Warning message: - running command ''/usr/bin/java' -version 2>&1' had status 1 - testthat results ================================================================ - OK: 0 SKIPPED: 0 FAILED: 0 - Execution halted - ``` - -# statisticalModeling - -Version: 0.3.0 - -## In both - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(statisticalModeling) - Loading required package: ggplot2 - > - > test_check("statisticalModeling") - Error: gwm() has been removed from `mosaic'. - It will be replaced by better tools in `mosaicModel'. - testthat results ================================================================ - OK: 21 SKIPPED: 0 FAILED: 0 - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error in re-building vignettes: - ... - Quitting from lines 303-306 (modeling.Rmd) - Error: processing vignette 'modeling.Rmd' failed with diagnostics: - Invalid formula type for gf_point. - Execution halted - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘magrittr’ ‘rpart’ - All declared Imports should be used. - ``` - -# sweep - -Version: 0.2.0 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘devtools’ ‘lazyeval’ ‘lubridate’ ‘tidyr’ - All declared Imports should be used. - ``` - -# tadaatoolbox - -Version: 0.13.0 - -## In both - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘rmdformats’ - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 3 marked UTF-8 strings - ``` - -# taxa - -Version: 0.1.0 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘knitr’ ‘lazyeval’ ‘rlang’ - All declared Imports should be used. - ``` - -# tbl2xts - -Version: 0.1.2 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘PerformanceAnalytics’ - All declared Imports should be used. - ``` - -# tidyquant - -Version: 0.5.3 - -## In both - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - - testthat results ================================================================ - OK: 191 SKIPPED: 0 FAILED: 9 - 1. Failure: Test all stock.index options to ensure no issues during fetch. (@test_tq_index.R#22) - 2. Failure: Test all stock.index options to ensure no issues during fetch. (@test_tq_index.R#22) - 3. Failure: Test all stock.index options to ensure no issues during fetch. (@test_tq_index.R#22) - 4. Failure: Test all stock.index options to ensure no issues during fetch. (@test_tq_index.R#22) - 5. Failure: Test all stock.index options to ensure no issues during fetch. (@test_tq_index.R#22) - 6. Failure: Test all stock.index options to ensure no issues during fetch. (@test_tq_index.R#22) - 7. Failure: Test all stock.index options to ensure no issues during fetch. (@test_tq_index.R#22) - 8. Failure: Test all stock.index options to ensure no issues during fetch. (@test_tq_index.R#22) - 9. Failure: Test all stock.index options to ensure no issues during fetch. (@test_tq_index.R#22) - - Error: testthat unit tests failed - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - ... - Reason: image not found - - Getting data... - - Getting holdings for DOW - Unable to find any JVMs matching version "(null)". - No Java runtime present, try --request to install. - Warning: running command '/usr/libexec/java_home' had status 1 - Warning in tq_index("DOW") : - Error at DOW during download. - Error: .onLoad failed in loadNamespace() for 'rJava', details: - call: dyn.load(file, DLLpath = DLLpath, ...) - error: unable to load shared object '/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/tidyquant/rJava/libs/rJava.so': - dlopen(/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/tidyquant/rJava/libs/rJava.so, 6): Library not loaded: @rpath/libjvm.dylib - Referenced from: /Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/tidyquant/rJava/libs/rJava.so - Reason: image not found - - Quitting from lines 105-108 (TQ03-scaling-and-modeling-with-tidyquant.Rmd) - Error: processing vignette 'TQ03-scaling-and-modeling-with-tidyquant.Rmd' failed with diagnostics: - subscript out of bounds - Execution halted - ``` - -* checking dependencies in R code ... NOTE - ``` - Unable to find any JVMs matching version "(null)". - No Java runtime present, try --request to install. - Namespaces in Imports field not imported from: - ‘broom’ ‘curl’ ‘devtools’ ‘rvest’ ‘timeSeries’ ‘tseries’ ‘zoo’ - All declared Imports should be used. - ``` - -# timetk - -Version: 0.1.0 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘devtools’ ‘forecast’ - All declared Imports should be used. - ``` - -# valaddin - -Version: 0.1.2 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘purrr’ - All declared Imports should be used. - ``` - -# vqtl - -Version: 1.2.0 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘iterators’ ‘knitr’ ‘testthat’ - All declared Imports should be used. + R 1.5Mb + doc 1.0Mb + extdata 1.2Mb + libs 15.4Mb ``` From 053a9b3211e07611e4b312bee3d2eff0deeb4b16 Mon Sep 17 00:00:00 2001 From: Lionel Henry Date: Tue, 31 Mar 2026 17:29:36 +0200 Subject: [PATCH 3/7] Fail when promise is forced --- src/lazy.c | 10 ++++++--- tests/testthat/test-lazy.R | 44 +++++++++++++++++++++----------------- 2 files changed, 31 insertions(+), 23 deletions(-) diff --git a/src/lazy.c b/src/lazy.c index 2de4bc8..1229cde 100644 --- a/src/lazy.c +++ b/src/lazy.c @@ -19,8 +19,10 @@ static SEXP binding_as_lazy(SEXP sym, SEXP env, int follow_symbols) { case R_ENV_BINDING_TYPE_missing: return make_lazy_obj(R_MissingArg, R_EmptyEnv); - case R_ENV_BINDING_TYPE_value: case R_ENV_BINDING_TYPE_forced: + Rf_error("Promise has already been forced"); + + case R_ENV_BINDING_TYPE_value: case R_ENV_BINDING_TYPE_active: { if (follow_symbols && TYPEOF(sym) == SYMSXP && is_lazy_load_binding(where, sym)) { return make_lazy_obj(sym, env); @@ -124,8 +126,10 @@ SEXP make_lazy_dots(SEXP env, SEXP follow_symbols_, SEXP ignore_empty_) { lazy = make_lazy_obj(R_MissingArg, R_EmptyEnv); break; - case DOT_TYPE_value: - case DOT_TYPE_forced: { + case DOT_TYPE_forced: + Rf_error("Promise has already been forced"); + + case DOT_TYPE_value: { SEXP dot = PROTECT(r_env_dot_get(env, i)); lazy = make_lazy_obj(dot, R_EmptyEnv); UNPROTECT(1); diff --git a/tests/testthat/test-lazy.R b/tests/testthat/test-lazy.R index 1b77afe..729a22e 100644 --- a/tests/testthat/test-lazy.R +++ b/tests/testthat/test-lazy.R @@ -23,27 +23,31 @@ test_that("lazy() works with nested promises", { expect_equal(outer_fun(call("name"))$expr, quote(call("name"))) }) -test_that("lazy() captures lazy-loaded objects without forcing lookup chains", { - lazy_obj <- lazy_caller(mean) - expect_true(is.function(lazy_obj$expr)) - expect_identical(lazy_obj$env, emptyenv()) - - nested_lazy <- outer_fun(mean) - expect_true(is.function(nested_lazy$expr)) - expect_identical(nested_lazy$env, emptyenv()) - - outer_fun2 <- function() { - list( - lazy = lazy_caller(mean), - env = environment() - ) - } - embedded_lazy <- outer_fun2() - expect_true(is.function(embedded_lazy$lazy$expr)) - expect_identical(embedded_lazy$lazy$env, emptyenv()) -}) - test_that("lazy() works for double-colon operator", { expect_error(lazy <- lazy_caller(stats::runif(10)), NA) expect_error(nested_lazy <- outer_fun(stats::runif(10)), NA) +}) + +test_that("lazy() errors on forced promises", { + f <- function(x) { + force(x) + lazy(x) + } + expect_error(f(1 + 2), "forced") + expect_error(f(~a), "forced") +}) + +test_that("lazy() works with formula promises", { + f <- function(x) lazy(x) + result <- f(~a + b) + expect_equal(result$expr, quote(~a + b)) +}) + +test_that("lazy_dots() errors on forced promises", { + f <- function(...) { + force(..1) + lazy_dots(...) + } + expect_error(f(1 + 2), "forced") + expect_error(f(~a), "forced") }) \ No newline at end of file From f0cfe22971825a610b268002c7e3d5265d23b101 Mon Sep 17 00:00:00 2001 From: Lionel Henry Date: Tue, 31 Mar 2026 22:10:14 +0200 Subject: [PATCH 4/7] Fix environmant of non-promise bindings in `lazy()` --- revdep/README.md | 7 +++---- revdep/cran.md | 5 +---- revdep/problems.md | 41 ----------------------------------------- src/lazy.c | 2 +- 4 files changed, 5 insertions(+), 50 deletions(-) diff --git a/revdep/README.md b/revdep/README.md index 8a5e391..fd4483c 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,9 +1,8 @@ # Revdeps -## New problems (2) +## New problems (1) -|package |version |error |warning |note | -|:---------|:-------|:------|:-------|:----| -|[hyperSpec](problems.md#hyperspec)|0.100.3 |__+1__ | | | +|package |version |error |warning |note | +|:-------|:-------|:------|:-------|:----| |[lidR](problems.md#lidr)|4.2.3 |__+1__ | |1 | diff --git a/revdep/cran.md b/revdep/cran.md index 9e04cef..6e3c46f 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -2,7 +2,7 @@ We checked 52 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. - * We saw 2 new problems + * We saw 1 new problems * We failed to check 0 packages Issues with CRAN packages are summarised below. @@ -10,9 +10,6 @@ Issues with CRAN packages are summarised below. ### New problems (This reports the first line of each new failure) -* hyperSpec - checking tests ... ERROR - * lidR checking tests ... ERROR diff --git a/revdep/problems.md b/revdep/problems.md index 3859179..455e461 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1,44 +1,3 @@ -# hyperSpec - -
- -* Version: 0.100.3 -* GitHub: https://github.com/r-hyperspec/hyperSpec -* Source code: https://github.com/cran/hyperSpec -* Date/Publication: 2025-10-13 05:10:33 UTC -* Number of recursive dependencies: 133 - -Run `revdepcheck::cloud_details(, "hyperSpec")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘unittests.R’ - Running the tests in ‘tests/unittests.R’ failed. - Complete output: - > library (testthat) - > test_check("hyperSpec") - Loading required package: hyperSpec - Loading required package: lattice - Loading required package: grid - Loading required package: ggplot2 - Loading required package: xml2 - ... - 5. └─fluNA[-2, , r] - 6. └─hyperSpec (local) .local(x, i, j, ..., drop = drop) - 7. └─hyperSpec:::.extract(x, i, j, l, wl.index = wl.index) - 8. └─hyperSpec::wl2i(x, l) - 9. └─hyperSpec:::.getindex(x, Re(to), extrapolate = FALSE) - - [ FAIL 1 | WARN 0 | SKIP 60 | PASS 323 ] - Error: - ! Test failures. - Execution halted - ``` - # lidR
diff --git a/src/lazy.c b/src/lazy.c index 1229cde..933ba18 100644 --- a/src/lazy.c +++ b/src/lazy.c @@ -29,7 +29,7 @@ static SEXP binding_as_lazy(SEXP sym, SEXP env, int follow_symbols) { } SEXP value = PROTECT(r_env_get(where, sym)); - SEXP out = make_lazy_obj(value, R_EmptyEnv); + SEXP out = make_lazy_obj(value, env); UNPROTECT(1); return out; } From 752e303013614689fbe0784d9a1fdf43d1bca837 Mon Sep 17 00:00:00 2001 From: Lionel Henry Date: Tue, 31 Mar 2026 22:46:17 +0200 Subject: [PATCH 5/7] Fix `expr_find()` tracing through forced promises --- revdep/README.md | 6 ----- revdep/cran.md | 10 +------ revdep/problems.md | 54 +------------------------------------- src/expr.c | 25 +++++++++++++----- src/utils.c | 7 +++++ src/utils.h | 1 + tests/testthat/test-dots.R | 2 +- tests/testthat/test-expr.R | 2 +- tests/testthat/test-lazy.R | 2 +- 9 files changed, 32 insertions(+), 77 deletions(-) diff --git a/revdep/README.md b/revdep/README.md index fd4483c..52e12c7 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,8 +1,2 @@ # Revdeps -## New problems (1) - -|package |version |error |warning |note | -|:-------|:-------|:------|:-------|:----| -|[lidR](problems.md#lidr)|4.2.3 |__+1__ | |1 | - diff --git a/revdep/cran.md b/revdep/cran.md index 6e3c46f..e212427 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -2,14 +2,6 @@ We checked 52 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. - * We saw 1 new problems + * We saw 0 new problems * We failed to check 0 packages -Issues with CRAN packages are summarised below. - -### New problems -(This reports the first line of each new failure) - -* lidR - checking tests ... ERROR - diff --git a/revdep/problems.md b/revdep/problems.md index 455e461..9a20736 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1,53 +1 @@ -# lidR - -
- -* Version: 4.2.3 -* GitHub: https://github.com/r-lidar/lidR -* Source code: https://github.com/cran/lidR -* Date/Publication: 2026-01-08 09:10:02 UTC -* Number of recursive dependencies: 151 - -Run `revdepcheck::cloud_details(, "lidR")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > Sys.setenv("R_TESTS" = "") - > - > library(testthat) - > library(lidR) - > test_check("lidR") - Tests using raster: terra - Tests using future: TRUE - ... - 4. │ │ └─base::withCallingHandlers(...) - 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) - 6. ├─lidR::clip_circle(las, xc, yc, r) - 7. └─lidR:::clip_circle.LAS(las, xc, yc, r) - 8. └─lidR:::assert_are_same_length(xcenter, radius) - - [ FAIL 1 | WARN 0 | SKIP 46 | PASS 1295 ] - Error: - ! Test failures. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 19.8Mb - sub-directories of 1Mb or more: - R 1.5Mb - doc 1.0Mb - extdata 1.2Mb - libs 15.4Mb - ``` - +*Wow, no problems at all. :)* \ No newline at end of file diff --git a/src/expr.c b/src/expr.c index 715cde4..c2135b2 100644 --- a/src/expr.c +++ b/src/expr.c @@ -31,15 +31,28 @@ static SEXP binding_expr(SEXP env, SEXP sym) { if (inner_where == r_envs.empty) return expr; - if (r_env_binding_type(inner_where, expr) != R_ENV_BINDING_TYPE_delayed) - return expr; + switch (r_env_binding_type(inner_where, expr)) { + case R_ENV_BINDING_TYPE_forced: + if (is_forced_lazy_load_binding(inner_where, expr)) { + return expr; + } + return r_env_binding_forced_expr(inner_where, expr); - if (is_lazy_load_binding(inner_where, expr)) + case R_ENV_BINDING_TYPE_value: + case R_ENV_BINDING_TYPE_active: return expr; - sym = expr; - env = expr_env; - continue; + case R_ENV_BINDING_TYPE_delayed: + if (is_lazy_load_binding(inner_where, expr)) + return expr; + + sym = expr; + env = expr_env; + continue; + + default: + return expr; + } } } } diff --git a/src/utils.c b/src/utils.c index d75b54c..cd34b0c 100644 --- a/src/utils.c +++ b/src/utils.c @@ -33,6 +33,13 @@ bool is_lazy_load_binding(SEXP env, SEXP sym) { return is_call_to(r_env_binding_delayed_expr(env, sym), "lazyLoadDBfetch"); } +bool is_forced_lazy_load_binding(SEXP env, SEXP sym) { + if (r_env_binding_type(env, sym) != R_ENV_BINDING_TYPE_forced) + return false; + + return is_call_to(r_env_binding_forced_expr(env, sym), "lazyLoadDBfetch"); +} + SEXP findLast(SEXP x) { SEXP cons = x; while(CDR(cons) != R_NilValue) diff --git a/src/utils.h b/src/utils.h index 2dde35b..209fe46 100644 --- a/src/utils.h +++ b/src/utils.h @@ -5,6 +5,7 @@ bool is_lazy_load(SEXP x); bool is_lazy_load_binding(SEXP env, SEXP sym); +bool is_forced_lazy_load_binding(SEXP env, SEXP sym); bool is_call_to(SEXP x, const char* f); bool is_formula(SEXP x); SEXP rhs(SEXP f); diff --git a/tests/testthat/test-dots.R b/tests/testthat/test-dots.R index f2fd147..1449c3c 100644 --- a/tests/testthat/test-dots.R +++ b/tests/testthat/test-dots.R @@ -17,4 +17,4 @@ test_that(".ignore_empty drops empty arguments", { expect_equal(length(l1), 3) expect_equal(length(l2), 1) expect_equal(l2[[1]]$expr, 1) -}) \ No newline at end of file +}) diff --git a/tests/testthat/test-expr.R b/tests/testthat/test-expr.R index b39304e..d01dda0 100644 --- a/tests/testthat/test-expr.R +++ b/tests/testthat/test-expr.R @@ -76,4 +76,4 @@ test_that("converts atomics to strings", { test_that("truncates long calls", { expect_equal(expr_label({ a + b }), "`{\n ...\n}`") -}) \ No newline at end of file +}) diff --git a/tests/testthat/test-lazy.R b/tests/testthat/test-lazy.R index 729a22e..1e5d71c 100644 --- a/tests/testthat/test-lazy.R +++ b/tests/testthat/test-lazy.R @@ -50,4 +50,4 @@ test_that("lazy_dots() errors on forced promises", { } expect_error(f(1 + 2), "forced") expect_error(f(~a), "forced") -}) \ No newline at end of file +}) From 4765528eb04abd4d5dba8249711be9c09313d8b4 Mon Sep 17 00:00:00 2001 From: Lionel Henry Date: Tue, 31 Mar 2026 23:22:46 +0200 Subject: [PATCH 6/7] Fix formatting --- tests/testthat/test-expr.R | 7 ++++++- tests/testthat/test-lazy.R | 4 ++-- 2 files changed, 8 insertions(+), 3 deletions(-) diff --git a/tests/testthat/test-expr.R b/tests/testthat/test-expr.R index d01dda0..cbea204 100644 --- a/tests/testthat/test-expr.R +++ b/tests/testthat/test-expr.R @@ -75,5 +75,10 @@ test_that("converts atomics to strings", { }) test_that("truncates long calls", { - expect_equal(expr_label({ a + b }), "`{\n ...\n}`") + expect_equal( + expr_label({ + a + b + }), + "`{\n ...\n}`" + ) }) diff --git a/tests/testthat/test-lazy.R b/tests/testthat/test-lazy.R index 1e5d71c..01d71ae 100644 --- a/tests/testthat/test-lazy.R +++ b/tests/testthat/test-lazy.R @@ -39,8 +39,8 @@ test_that("lazy() errors on forced promises", { test_that("lazy() works with formula promises", { f <- function(x) lazy(x) - result <- f(~a + b) - expect_equal(result$expr, quote(~a + b)) + result <- f(~ a + b) + expect_equal(result$expr, quote(~ a + b)) }) test_that("lazy_dots() errors on forced promises", { From 7f1e3d33af43ed75d658df90072861ed4d5db35d Mon Sep 17 00:00:00 2001 From: Lionel Henry Date: Tue, 31 Mar 2026 23:39:46 +0200 Subject: [PATCH 7/7] Remove dangling `is_lazy_load()` helper --- src/utils.c | 5 ----- src/utils.h | 1 - 2 files changed, 6 deletions(-) diff --git a/src/utils.c b/src/utils.c index cd34b0c..8760057 100644 --- a/src/utils.c +++ b/src/utils.c @@ -19,12 +19,7 @@ bool is_call_to(SEXP x, const char* f) { return false; } -bool is_lazy_load(SEXP x) { - if (TYPEOF(x) != PROMSXP) - return false; - return is_call_to(PREXPR(x), "lazyLoadDBfetch"); -} bool is_lazy_load_binding(SEXP env, SEXP sym) { if (r_env_binding_type(env, sym) != R_ENV_BINDING_TYPE_delayed) diff --git a/src/utils.h b/src/utils.h index 209fe46..585651b 100644 --- a/src/utils.h +++ b/src/utils.h @@ -3,7 +3,6 @@ #include #include -bool is_lazy_load(SEXP x); bool is_lazy_load_binding(SEXP env, SEXP sym); bool is_forced_lazy_load_binding(SEXP env, SEXP sym); bool is_call_to(SEXP x, const char* f);