diff --git a/R/structural.properties.R b/R/structural.properties.R
index c9e0575732..898a595bdc 100644
--- a/R/structural.properties.R
+++ b/R/structural.properties.R
@@ -292,12 +292,13 @@ graph.knn <- function(graph, vids = V(graph), mode = c("all", "out", "in", "tota
#'
#' `graph.dfs()` was renamed to `dfs()` to create a more
#' consistent API.
+#' @param father Logical scalar, whether to return the father of the vertices.
#' @inheritParams dfs
#' @keywords internal
#' @export
graph.dfs <- function(graph, root, mode = c("out", "in", "all", "total"), unreachable = TRUE, order = TRUE, order.out = FALSE, father = FALSE, dist = FALSE, in.callback = NULL, out.callback = NULL, extra = NULL, rho = parent.frame(), neimode) { # nocov start
lifecycle::deprecate_soft("2.0.0", "graph.dfs()", "dfs()")
- dfs(graph = graph, root = root, mode = mode, unreachable = unreachable, order = order, order.out = order.out, father = father, dist = dist, in.callback = in.callback, out.callback = out.callback, extra = extra, rho = rho, neimode = neimode)
+ dfs(graph = graph, root = root, mode = mode, unreachable = unreachable, order = order, order.out = order.out, parent = father, dist = dist, in.callback = in.callback, out.callback = out.callback, extra = extra, rho = rho, neimode = neimode)
} # nocov end
#' Graph density
@@ -338,11 +339,12 @@ graph.coreness <- function(graph, mode = c("all", "out", "in")) { # nocov start
#' `graph.bfs()` was renamed to `bfs()` to create a more
#' consistent API.
#' @inheritParams bfs
+#' @param father Logical scalar, whether to return the father of the vertices.
#' @keywords internal
#' @export
graph.bfs <- function(graph, root, mode = c("out", "in", "all", "total"), unreachable = TRUE, restricted = NULL, order = TRUE, rank = FALSE, father = FALSE, pred = FALSE, succ = FALSE, dist = FALSE, callback = NULL, extra = NULL, rho = parent.frame(), neimode) { # nocov start
lifecycle::deprecate_soft("2.0.0", "graph.bfs()", "bfs()")
- bfs(graph = graph, root = root, mode = mode, unreachable = unreachable, restricted = restricted, order = order, rank = rank, father = father, pred = pred, succ = succ, dist = dist, callback = callback, extra = extra, rho = rho, neimode = neimode)
+ bfs(graph = graph, root = root, mode = mode, unreachable = unreachable, restricted = restricted, order = order, rank = rank, parent = father, pred = pred, succ = succ, dist = dist, callback = callback, extra = extra, rho = rho, neimode = neimode)
} # nocov end
#' Diameter of a graph
@@ -2084,7 +2086,8 @@ any_loop <- has_loop_impl
#' given vertices.
#' @param order Logical scalar, whether to return the ordering of the vertices.
#' @param rank Logical scalar, whether to return the rank of the vertices.
-#' @param father Logical scalar, whether to return the father of the vertices.
+#' @param father `r lifecycle::badge("deprecated")` Use `parent` instead.
+#' @param parent Logical scalar, whether to return the parent of the vertices.
#' @param pred Logical scalar, whether to return the predecessors of the
#' vertices.
#' @param succ Logical scalar, whether to return the successors of the
@@ -2097,6 +2100,7 @@ any_loop <- has_loop_impl
#' @param rho The environment in which the callback function is evaluated.
#' @param neimode `r lifecycle::badge("deprecated")` This argument is deprecated
#' from igraph 1.3.0; use `mode` instead.
+#' @inheritParams rlang::args_dots_empty
#' @return A named list with the following entries:
#' \item{root}{Numeric scalar.
#' The root vertex that was used as the starting point of the search.}
@@ -2106,8 +2110,9 @@ any_loop <- has_loop_impl
#' \item{order}{Numeric vector. The
#' vertex ids, in the order in which they were visited by the search.}
#' \item{rank}{Numeric vector. The rank for each vertex, zero for unreachable vertices.}
-#' \item{father}{Numeric
-#' vector. The father of each vertex, i.e. the vertex it was discovered from.}
+#' \item{parent}{Numeric
+#' vector. The parent of each vertex, i.e. the vertex it was discovered from.}
+#' \item{father}{Like parent, kept for compatibility for now.}
#' \item{pred}{Numeric vector. The previously visited vertex for each vertex,
#' or 0 if there was no such vertex.}
#' \item{succ}{Numeric vector. The next
@@ -2117,7 +2122,7 @@ any_loop <- has_loop_impl
#' root of the search tree. Unreachable vertices have a negative distance
#' as of igraph 1.6.0, this used to be `NaN`.}
#'
-#' Note that `order`, `rank`, `father`, `pred`, `succ`
+#' Note that `order`, `rank`, `parent`, `pred`, `succ`
#' and `dist` might be `NULL` if their corresponding argument is
#' `FALSE`, i.e. if their calculation is not requested.
#' @author Gabor Csardi \email{csardi.gabor@@gmail.com}
@@ -2130,7 +2135,7 @@ any_loop <- has_loop_impl
#' ## Two rings
#' bfs(make_ring(10) %du% make_ring(10),
#' root = 1, "out",
-#' order = TRUE, rank = TRUE, father = TRUE, pred = TRUE,
+#' order = TRUE, rank = TRUE, parent = TRUE, pred = TRUE,
#' succ = TRUE, dist = TRUE
#' )
#'
@@ -2155,28 +2160,40 @@ bfs <- function(
graph,
root,
mode = c("out", "in", "all", "total"),
+ ...,
unreachable = TRUE,
restricted = NULL,
order = TRUE,
rank = FALSE,
- father = FALSE,
+ parent = FALSE,
pred = FALSE,
succ = FALSE,
dist = FALSE,
callback = NULL,
extra = NULL,
rho = parent.frame(),
- neimode = deprecated()) {
+ neimode = deprecated(),
+ father = deprecated()) {
+
+ rlang::check_dots_empty()
+
ensure_igraph(graph)
if (lifecycle::is_present(neimode)) {
lifecycle::deprecate_stop(
"1.3.0",
- "bfs(neimode)",
- "bfs(mode)"
+ "bfs(neimode = )",
+ "bfs(mode = )"
)
}
+ if (lifecycle::is_present(father)) {
+ lifecycle::deprecate_warn("2.2.0", "bfs(father = )", "bfs(parent = )")
+ if (missing(parent)) {
+ parent <- father
+ }
+ }
+
if (length(root) == 1) {
root <- as_igraph_vs(graph, root) - 1
roots <- NULL
@@ -2202,7 +2219,7 @@ bfs <- function(
res <- .Call(
R_igraph_bfs, graph, root, roots, mode, unreachable,
restricted,
- as.logical(order), as.logical(rank), as.logical(father),
+ as.logical(order), as.logical(rank), as.logical(parent),
as.logical(pred), as.logical(succ), as.logical(dist),
callback, extra, rho
)
@@ -2212,13 +2229,13 @@ bfs <- function(
if (order) res$order <- res$order + 1
if (rank) res$rank <- res$rank + 1
- if (father) res$father <- res$father + 1
+ if (parent) res$parent <- res$parent + 1
if (pred) res$pred <- res$pred + 1
if (succ) res$succ <- res$succ + 1
if (igraph_opt("return.vs.es")) {
if (order) res$order <- V(graph)[.env$res$order, na_ok = TRUE]
- if (father) res$father <- create_vs(graph, res$father, na_ok = TRUE)
+ if (parent) res$parent <- create_vs(graph, res$parent, na_ok = TRUE)
if (pred) res$pred <- create_vs(graph, res$pred, na_ok = TRUE)
if (succ) res$succ <- create_vs(graph, res$succ, na_ok = TRUE)
} else {
@@ -2227,7 +2244,7 @@ bfs <- function(
if (igraph_opt("add.vertex.names") && is_named(graph)) {
if (rank) names(res$rank) <- V(graph)$name
- if (father) names(res$father) <- V(graph)$name
+ if (parent) names(res$parent) <- V(graph)$name
if (pred) names(res$pred) <- V(graph)$name
if (succ) names(res$succ) <- V(graph)$name
if (dist) names(res$dist) <- V(graph)$name
@@ -2241,6 +2258,9 @@ bfs <- function(
res$dist[is.nan(res$dist)] <- -3
}
+ # Remove this later? https://github.com/igraph/rigraph/issues/1576
+ res$father <- res$parent
+
res
}
@@ -2273,7 +2293,8 @@ bfs <- function(
#' vertices.
#' @param order.out Logical scalar, whether to return the ordering based on
#' leaving the subtree of the vertex.
-#' @param father Logical scalar, whether to return the father of the vertices.
+#' @param father `r lifecycle::badge("deprecated")`, use `parent` instead.
+#' @param parent Logical scalar, whether to return the parent of the vertices.
#' @param dist Logical scalar, whether to return the distance from the root of
#' the search tree.
#' @param in.callback If not `NULL`, then it must be callback function.
@@ -2285,6 +2306,7 @@ bfs <- function(
#' @param rho The environment in which the callback function is evaluated.
#' @param neimode `r lifecycle::badge("deprecated")` This argument is deprecated from igraph 1.3.0; use
#' `mode` instead.
+#' @inheritParams rlang::args_dots_empty
#' @return A named list with the following entries: \item{root}{Numeric scalar.
#' The root vertex that was used as the starting point of the search.}
#' \item{neimode}{Character scalar. The `mode` argument of the function
@@ -2292,11 +2314,13 @@ bfs <- function(
#' irrespectively of the supplied value.} \item{order}{Numeric vector. The
#' vertex ids, in the order in which they were visited by the search.}
#' \item{order.out}{Numeric vector, the vertex ids, in the order of the
-#' completion of their subtree.} \item{father}{Numeric vector. The father of
-#' each vertex, i.e. the vertex it was discovered from.} \item{dist}{Numeric
+#' completion of their subtree.} \item{parent}{Numeric vector. The parent of
+#' each vertex, i.e. the vertex it was discovered from.}
+#' \item{father}{Like parent, kept for compatibility for now.}
+#' \item{dist}{Numeric
#' vector, for each vertex its distance from the root of the search tree.}
#'
-#' Note that `order`, `order.out`, `father`, and `dist`
+#' Note that `order`, `order.out`, `parent`, and `dist`
#' might be `NULL` if their corresponding argument is `FALSE`, i.e.
#' if their calculation is not requested.
#' @author Gabor Csardi \email{csardi.gabor@@gmail.com}
@@ -2307,9 +2331,13 @@ bfs <- function(
#' @examples
#'
#' ## A graph with two separate trees
-#' dfs(make_tree(10) %du% make_tree(10),
-#' root = 1, "out",
-#' TRUE, TRUE, TRUE, TRUE
+#' dfs(
+#' graph = make_tree(10) %du% make_tree(10),
+#' root = 1, mode = "out",
+#' unreachable = TRUE,
+#' order = TRUE,
+#' order.out = TRUE,
+#' parent = TRUE
#' )
#'
#' ## How to use a callback
@@ -2321,8 +2349,9 @@ bfs <- function(
#' cat("out:", paste(collapse = ", ", data), "\n")
#' FALSE
#' }
-#' tmp <- dfs(make_tree(10),
-#' root = 1, "out",
+#' tmp <- dfs(
+#' graph = make_tree(10),
+#' root = 1, mode = "out",
#' in.callback = f.in, out.callback = f.out
#' )
#'
@@ -2330,25 +2359,39 @@ bfs <- function(
#' f.out <- function(graph, data, extra) {
#' data["vid"] == 1
#' }
-#' tmp <- dfs(make_tree(10) %du% make_tree(10),
+#' tmp <- dfs(
+#' graph = make_tree(10) %du% make_tree(10),
#' root = 1,
#' out.callback = f.out
#' )
#'
dfs <- function(graph, root, mode = c("out", "in", "all", "total"),
+ ...,
unreachable = TRUE,
- order = TRUE, order.out = FALSE, father = FALSE, dist = FALSE,
+ order = TRUE, order.out = FALSE,
+ parent = FALSE, dist = FALSE,
in.callback = NULL, out.callback = NULL, extra = NULL,
- rho = parent.frame(), neimode = deprecated()) {
+ rho = parent.frame(), neimode = deprecated(),
+ father = deprecated()) {
+
+ rlang::check_dots_empty()
+
ensure_igraph(graph)
if (lifecycle::is_present(neimode)) {
lifecycle::deprecate_stop(
"1.3.0",
- "dfs(neimode)",
- "dfs(mode)"
+ "dfs(neimode = )",
+ "dfs(mode = )"
)
}
+ if (lifecycle::is_present(father)) {
+ lifecycle::deprecate_warn("2.2.0", "dfs(father = )", "dfs(parent = )")
+ if (missing(parent)) {
+ parent <- father
+ }
+ }
+
root <- as_igraph_vs(graph, root) - 1
mode <- switch(igraph.match.arg(mode),
"out" = 1,
@@ -2367,7 +2410,7 @@ dfs <- function(graph, root, mode = c("out", "in", "all", "total"),
on.exit(.Call(R_igraph_finalizer))
res <- .Call(
R_igraph_dfs, graph, root, mode, unreachable,
- as.logical(order), as.logical(order.out), as.logical(father),
+ as.logical(order), as.logical(order.out), as.logical(parent),
as.logical(dist), in.callback, out.callback, extra, rho
)
@@ -2376,22 +2419,25 @@ dfs <- function(graph, root, mode = c("out", "in", "all", "total"),
if (order) res$order <- res$order + 1
if (order.out) res$order.out <- res$order.out + 1
- if (father) res$father <- res$father + 1
+ if (parent) res$parent <- res$parent + 1
if (igraph_opt("return.vs.es")) {
if (order) res$order <- V(graph)[.env$res$order, na_ok = TRUE]
if (order.out) res$order.out <- V(graph)[.env$res$order.out, na_ok = TRUE]
- if (father) res$father <- create_vs(graph, res$father, na_ok = TRUE)
+ if (parent) res$parent <- create_vs(graph, res$parent, na_ok = TRUE)
} else {
if (order) res$order <- res$order[res$order != 0]
if (order.out) res$order.out <- res$order.out[res$order.out != 0]
}
if (igraph_opt("add.vertex.names") && is_named(graph)) {
- if (father) names(res$father) <- V(graph)$name
+ if (parent) names(res$parent) <- V(graph)$name
if (dist) names(res$dist) <- V(graph)$name
}
+ # Remove this later? https://github.com/igraph/rigraph/issues/1576
+ res$father <- res$parent
+
res
}
diff --git a/man/bfs.Rd b/man/bfs.Rd
index aeba03dfdb..ba2c1b0210 100644
--- a/man/bfs.Rd
+++ b/man/bfs.Rd
@@ -8,18 +8,20 @@ bfs(
graph,
root,
mode = c("out", "in", "all", "total"),
+ ...,
unreachable = TRUE,
restricted = NULL,
order = TRUE,
rank = FALSE,
- father = FALSE,
+ parent = FALSE,
pred = FALSE,
succ = FALSE,
dist = FALSE,
callback = NULL,
extra = NULL,
rho = parent.frame(),
- neimode = deprecated()
+ neimode = deprecated(),
+ father = deprecated()
)
}
\arguments{
@@ -33,6 +35,8 @@ vertices to start the search from.}
ignores edge directions completely. \sQuote{total} is a synonym for
\sQuote{all}. This argument is ignored for undirected graphs.}
+\item{...}{These dots are for future extensions and must be empty.}
+
\item{unreachable}{Logical scalar, whether the search should visit the
vertices that are unreachable from the given root vertex (or vertices). If
\code{TRUE}, then additional searches are performed until all vertices are
@@ -46,7 +50,7 @@ given vertices.}
\item{rank}{Logical scalar, whether to return the rank of the vertices.}
-\item{father}{Logical scalar, whether to return the father of the vertices.}
+\item{parent}{Logical scalar, whether to return the parent of the vertices.}
\item{pred}{Logical scalar, whether to return the predecessors of the
vertices.}
@@ -66,6 +70,8 @@ is called whenever a vertex is visited. See details below.}
\item{neimode}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} This argument is deprecated
from igraph 1.3.0; use \code{mode} instead.}
+
+\item{father}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Use \code{parent} instead.}
}
\value{
A named list with the following entries:
@@ -77,8 +83,9 @@ irrespectively of the supplied value.}
\item{order}{Numeric vector. The
vertex ids, in the order in which they were visited by the search.}
\item{rank}{Numeric vector. The rank for each vertex, zero for unreachable vertices.}
-\item{father}{Numeric
-vector. The father of each vertex, i.e. the vertex it was discovered from.}
+\item{parent}{Numeric
+vector. The parent of each vertex, i.e. the vertex it was discovered from.}
+\item{father}{Like parent, kept for compatibility for now.}
\item{pred}{Numeric vector. The previously visited vertex for each vertex,
or 0 if there was no such vertex.}
\item{succ}{Numeric vector. The next
@@ -88,7 +95,7 @@ vertex.}
root of the search tree. Unreachable vertices have a negative distance
as of igraph 1.6.0, this used to be \code{NaN}.}
-Note that \code{order}, \code{rank}, \code{father}, \code{pred}, \code{succ}
+Note that \code{order}, \code{rank}, \code{parent}, \code{pred}, \code{succ}
and \code{dist} might be \code{NULL} if their corresponding argument is
\code{FALSE}, i.e. if their calculation is not requested.
}
@@ -118,7 +125,7 @@ use the callback function.
## Two rings
bfs(make_ring(10) \%du\% make_ring(10),
root = 1, "out",
- order = TRUE, rank = TRUE, father = TRUE, pred = TRUE,
+ order = TRUE, rank = TRUE, parent = TRUE, pred = TRUE,
succ = TRUE, dist = TRUE
)
diff --git a/man/dfs.Rd b/man/dfs.Rd
index b906bd2ec2..a9c24fa71a 100644
--- a/man/dfs.Rd
+++ b/man/dfs.Rd
@@ -8,16 +8,18 @@ dfs(
graph,
root,
mode = c("out", "in", "all", "total"),
+ ...,
unreachable = TRUE,
order = TRUE,
order.out = FALSE,
- father = FALSE,
+ parent = FALSE,
dist = FALSE,
in.callback = NULL,
out.callback = NULL,
extra = NULL,
rho = parent.frame(),
- neimode = deprecated()
+ neimode = deprecated(),
+ father = deprecated()
)
}
\arguments{
@@ -30,6 +32,8 @@ dfs(
ignores edge directions completely. \sQuote{total} is a synonym for
\sQuote{all}. This argument is ignored for undirected graphs.}
+\item{...}{These dots are for future extensions and must be empty.}
+
\item{unreachable}{Logical scalar, whether the search should visit the
vertices that are unreachable from the given root vertex (or vertices). If
\code{TRUE}, then additional searches are performed until all vertices are
@@ -41,7 +45,7 @@ vertices.}
\item{order.out}{Logical scalar, whether to return the ordering based on
leaving the subtree of the vertex.}
-\item{father}{Logical scalar, whether to return the father of the vertices.}
+\item{parent}{Logical scalar, whether to return the parent of the vertices.}
\item{dist}{Logical scalar, whether to return the distance from the root of
the search tree.}
@@ -59,6 +63,8 @@ algorithm. See details below.}
\item{neimode}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} This argument is deprecated from igraph 1.3.0; use
\code{mode} instead.}
+
+\item{father}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}, use \code{parent} instead.}
}
\value{
A named list with the following entries: \item{root}{Numeric scalar.
@@ -68,11 +74,13 @@ call. Note that for undirected graphs this is always \sQuote{all},
irrespectively of the supplied value.} \item{order}{Numeric vector. The
vertex ids, in the order in which they were visited by the search.}
\item{order.out}{Numeric vector, the vertex ids, in the order of the
-completion of their subtree.} \item{father}{Numeric vector. The father of
-each vertex, i.e. the vertex it was discovered from.} \item{dist}{Numeric
+completion of their subtree.} \item{parent}{Numeric vector. The parent of
+each vertex, i.e. the vertex it was discovered from.}
+\item{father}{Like parent, kept for compatibility for now.}
+\item{dist}{Numeric
vector, for each vertex its distance from the root of the search tree.}
-Note that \code{order}, \code{order.out}, \code{father}, and \code{dist}
+Note that \code{order}, \code{order.out}, \code{parent}, and \code{dist}
might be \code{NULL} if their corresponding argument is \code{FALSE}, i.e.
if their calculation is not requested.
}
@@ -92,9 +100,13 @@ to terminate it. See examples below on how to use the callback functions.
\examples{
## A graph with two separate trees
-dfs(make_tree(10) \%du\% make_tree(10),
- root = 1, "out",
- TRUE, TRUE, TRUE, TRUE
+dfs(
+ graph = make_tree(10) \%du\% make_tree(10),
+ root = 1, mode = "out",
+ unreachable = TRUE,
+ order = TRUE,
+ order.out = TRUE,
+ parent = TRUE
)
## How to use a callback
@@ -106,8 +118,9 @@ f.out <- function(graph, data, extra) {
cat("out:", paste(collapse = ", ", data), "\n")
FALSE
}
-tmp <- dfs(make_tree(10),
- root = 1, "out",
+tmp <- dfs(
+ graph = make_tree(10),
+ root = 1, mode = "out",
in.callback = f.in, out.callback = f.out
)
@@ -115,7 +128,8 @@ tmp <- dfs(make_tree(10),
f.out <- function(graph, data, extra) {
data["vid"] == 1
}
-tmp <- dfs(make_tree(10) \%du\% make_tree(10),
+tmp <- dfs(
+ graph = make_tree(10) \%du\% make_tree(10),
root = 1,
out.callback = f.out
)
diff --git a/revdep/README.md b/revdep/README.md
index 19d1b1129d..75a14fe209 100644
--- a/revdep/README.md
+++ b/revdep/README.md
@@ -1,6 +1,6 @@
# Revdeps
-## Failed to check (8)
+## Failed to check (7)
|package |version |error |warning |note |
|:---------------|:-------|:-----|:-------|:----|
@@ -11,12 +11,10 @@
|multinma |0.7.2 |1 | | |
|randomForestSRC |? | | | |
|streamDAG |? | | | |
-|TDA |1.9.1 |1 | | |
-## New problems (2)
+## New problems (1)
-|package |version |error |warning |note |
-|:-------------|:-------|:------|:-------|:----|
-|[grainscape](problems.md#grainscape)|0.4.4 |__+1__ | | |
-|[multilaterals](problems.md#multilaterals)|1.0 |__+1__ | | |
+|package |version |error |warning |note |
+|:-------|:-------|:------|:-------|:----|
+|[pomdp](problems.md#pomdp)|1.2.3 |__+3__ | |1 |
diff --git a/revdep/cran.md b/revdep/cran.md
index f340edd4cd..bd85c04952 100644
--- a/revdep/cran.md
+++ b/revdep/cran.md
@@ -1,20 +1,19 @@
## revdepcheck results
-We checked 13 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
+We checked 2118 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
- * We saw 2 new problems
- * We failed to check 8 packages
+ * We saw 1 new problems
+ * We failed to check 7 packages
Issues with CRAN packages are summarised below.
### New problems
(This reports the first line of each new failure)
-* grainscape
- checking tests ... ERROR
-
-* multilaterals
+* pomdp
checking examples ... ERROR
+ checking tests ... ERROR
+ checking re-building of vignette outputs ... ERROR
### Failed to check
@@ -25,4 +24,3 @@ Issues with CRAN packages are summarised below.
* multinma (NA)
* randomForestSRC (NA)
* streamDAG (NA)
-* TDA (NA)
diff --git a/revdep/failures.md b/revdep/failures.md
index d3a3f44284..2c2271f9e8 100644
--- a/revdep/failures.md
+++ b/revdep/failures.md
@@ -29,180 +29,13 @@ Run `revdepcheck::cloud_details(, "bnlearn")` for more info
** package ‘bnlearn’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
-using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
+using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c arcs/arcs2amat.c -o arcs/arcs2amat.o
gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c arcs/arcs2elist.c -o arcs/arcs2elist.o
gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c arcs/bind.c -o arcs/bind.o
gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c arcs/filter.arcs.c -o arcs/filter.arcs.o
gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c arcs/hash.c -o arcs/hash.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c arcs/is.row.equal.c -o arcs/is.row.equal.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c bnlearn/bayesian.network.c -o bnlearn/bayesian.network.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c bnlearn/bn.recovery.c -o bnlearn/bn.recovery.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c bnlearn/cache.structure.c -o bnlearn/cache.structure.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c bnlearn/cextend.c -o bnlearn/cextend.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c bnlearn/colliders.c -o bnlearn/colliders.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c bnlearn/cpdag.c -o bnlearn/cpdag.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c bnlearn/fitted.c -o bnlearn/fitted.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c bnlearn/nparams.c -o bnlearn/nparams.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c bnlearn/shd.c -o bnlearn/shd.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c core/allocations.c -o core/allocations.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c core/contingency.tables.c -o core/contingency.tables.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c core/correlation.c -o core/correlation.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c core/covariance.matrix.c -o core/covariance.matrix.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c core/data.table.c -o core/data.table.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c core/math.functions.c -o core/math.functions.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c core/moments.c -o core/moments.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c core/sampling.c -o core/sampling.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c core/sets.c -o core/sets.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c core/uppertriangular.c -o core/uppertriangular.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c fitted/enums.c -o fitted/enums.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c fitted/fitted.c -o fitted/fitted.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c fitted/nparams.c -o fitted/nparams.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c fitted/rinterface/nparams.c -o fitted/rinterface/nparams.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c foreign/parse.c -o foreign/parse.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c globals.c -o globals.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c graphs/acyclic.c -o graphs/acyclic.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c graphs/is.dag.c -o graphs/is.dag.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c graphs/path.c -o graphs/path.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c graphs/pdag2dag.c -o graphs/pdag2dag.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c graphs/random/graph.generation.c -o graphs/random/graph.generation.o
-In file included from graphs/random/../../include/rcore.h:3,
- from graphs/random/graph.generation.c:1:
-graphs/random/graph.generation.c: In function ‘print_modelstring’:
-graphs/random/graph.generation.c:719:19: warning: implicit declaration of function ‘allocLang’; did you mean ‘alloca’? [-Wimplicit-function-declaration]
- 719 | PROTECT(t = s = allocLang(2));
- | ^~~~~~~~~
-/opt/R/4.4.0/lib/R/include/Rinternals.h:371:36: note: in definition of macro ‘PROTECT’
- 371 | #define PROTECT(s) Rf_protect(s)
- | ^
-graphs/random/graph.generation.c:719:17: warning: assignment to ‘SEXP’ {aka ‘struct SEXPREC *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
- 719 | PROTECT(t = s = allocLang(2));
- | ^
-/opt/R/4.4.0/lib/R/include/Rinternals.h:371:36: note: in definition of macro ‘PROTECT’
- 371 | #define PROTECT(s) Rf_protect(s)
- | ^
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c graphs/topological.ordering.c -o graphs/topological.ordering.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c inference/likelihood.weighting.c -o inference/likelihood.weighting.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c inference/loglikelihood/common.c -o inference/loglikelihood/common.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c inference/loglikelihood/discrete.c -o inference/loglikelihood/discrete.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c inference/loglikelihood/gaussian.c -o inference/loglikelihood/gaussian.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c inference/loglikelihood/conditional.gaussian.c -o inference/loglikelihood/conditional.gaussian.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c inference/loss.c -o inference/loss.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c inference/rbn.c -o inference/rbn.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c inference/rinterface/loglikelihood.c -o inference/rinterface/loglikelihood.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c inference/rinterface/cpdist.c -o inference/rinterface/cpdist.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c inference/rinterface/rbn.c -o inference/rinterface/rbn.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c inference/rinterface/likelihood.weighting.c -o inference/rinterface/likelihood.weighting.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c learning/averaging/averaging.c -o learning/averaging/averaging.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c learning/averaging/bootstrap.c -o learning/averaging/bootstrap.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c learning/local/mi.matrix.c -o learning/local/mi.matrix.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c learning/score/hc.cache.lookup.c -o learning/score/hc.cache.lookup.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c learning/score/score.delta.c -o learning/score/score.delta.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c learning/score/tabu.c -o learning/score/tabu.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c math/conditional.least.squares.c -o math/conditional.least.squares.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c math/least.squares.c -o math/least.squares.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c math/linear.algebra.c -o math/linear.algebra.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c minimal/common.c -o minimal/common.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c minimal/data.frame.c -o minimal/data.frame.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c minimal/strings.c -o minimal/strings.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c minimal/table.c -o minimal/table.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c minimal/tiers.c -o minimal/tiers.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c minimal/unique.c -o minimal/unique.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c parameters/discrete/classic_discrete.c -o parameters/discrete/classic_discrete.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c parameters/discrete/hierarchical_dirichlet.c -o parameters/discrete/hierarchical_dirichlet.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c parameters/rinterface/classic_discrete.c -o parameters/rinterface/classic_discrete.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c parameters/rinterface/hierarchical_dirichlet.c -o parameters/rinterface/hierarchical_dirichlet.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c parameters/rinterface/mixture_ordinary_least_squares.c -o parameters/rinterface/mixture_ordinary_least_squares.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c parameters/rinterface/ordinary_least_squares.c -o parameters/rinterface/ordinary_least_squares.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c predict/map.lw.c -o predict/map.lw.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c predict/predict.c -o predict/predict.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c preprocessing/dedup.c -o preprocessing/dedup.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c preprocessing/discretize.c -o preprocessing/discretize.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c preprocessing/enums.c -o preprocessing/enums.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sanitization/cg.assumptions.c -o sanitization/cg.assumptions.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sanitization/covariance.c -o sanitization/covariance.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sanitization/data.c -o sanitization/data.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/alpha.star.c -o scores/alpha.star.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/cg.loglikelihood.c -o scores/cg.loglikelihood.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/cg.predictive.loglikelihood.c -o scores/cg.predictive.loglikelihood.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/cg.nal.c -o scores/cg.nal.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/custom.score.c -o scores/custom.score.o
-In file included from scores/../include/rcore.h:3,
- from scores/custom.score.c:1:
-scores/custom.score.c: In function ‘custom_score_function’:
-scores/custom.score.c:12:34: warning: implicit declaration of function ‘allocLang’; did you mean ‘alloca’? [-Wimplicit-function-declaration]
- 12 | PROTECT(args_iterator = call = allocLang(5));
- | ^~~~~~~~~
-/opt/R/4.4.0/lib/R/include/Rinternals.h:371:36: note: in definition of macro ‘PROTECT’
- 371 | #define PROTECT(s) Rf_protect(s)
- | ^
-scores/custom.score.c:12:32: warning: assignment to ‘SEXP’ {aka ‘struct SEXPREC *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
- 12 | PROTECT(args_iterator = call = allocLang(5));
- | ^
-/opt/R/4.4.0/lib/R/include/Rinternals.h:371:36: note: in definition of macro ‘PROTECT’
- 371 | #define PROTECT(s) Rf_protect(s)
- | ^
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/dirichlet.averaged.posterior.c -o scores/dirichlet.averaged.posterior.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/dirichlet.posterior.c -o scores/dirichlet.posterior.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/discrete.loglikelihood.c -o scores/discrete.loglikelihood.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/discrete.nal.c -o scores/discrete.nal.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/discrete.predictive.loglikelihood.c -o scores/discrete.predictive.loglikelihood.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/enum.c -o scores/enum.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/gaussian.loglikelihood.c -o scores/gaussian.loglikelihood.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/gaussian.nal.c -o scores/gaussian.nal.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/gaussian.predictive.loglikelihood.c -o scores/gaussian.predictive.loglikelihood.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/graph.priors.c -o scores/graph.priors.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/nml_regret.c -o scores/nml_regret.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/nml_regret_table.c -o scores/nml_regret_table.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/normalized.maximum.likelihood.c -o scores/normalized.maximum.likelihood.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/per.node.score.c -o scores/per.node.score.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/wishart.posterior.c -o scores/wishart.posterior.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c test.counter.c -o test.counter.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/conditional.gaussian/cg.mutual.information.c -o tests/conditional.gaussian/cg.mutual.information.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/discrete/df.adjust.c -o tests/discrete/df.adjust.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/discrete/discrete.tests.c -o tests/discrete/discrete.tests.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/discrete/jonckheere.c -o tests/discrete/jonckheere.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/discrete/shrinkage.c -o tests/discrete/shrinkage.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/enums.c -o tests/enums.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/gaussian/df.adjust.c -o tests/gaussian/df.adjust.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/gaussian/gaussian.tests.c -o tests/gaussian/gaussian.tests.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/gaussian/shrinkage.c -o tests/gaussian/shrinkage.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/omnibus/custom.test.c -o tests/omnibus/custom.test.o
-In file included from tests/omnibus/../../include/rcore.h:3,
- from tests/omnibus/custom.test.c:1:
-tests/omnibus/custom.test.c: In function ‘custom_test_function’:
-tests/omnibus/custom.test.c:11:34: warning: implicit declaration of function ‘allocLang’; did you mean ‘alloca’? [-Wimplicit-function-declaration]
- 11 | PROTECT(args_iterator = call = allocLang(6));
- | ^~~~~~~~~
-/opt/R/4.4.0/lib/R/include/Rinternals.h:371:36: note: in definition of macro ‘PROTECT’
- 371 | #define PROTECT(s) Rf_protect(s)
- | ^
-tests/omnibus/custom.test.c:11:32: warning: assignment to ‘SEXP’ {aka ‘struct SEXPREC *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
- 11 | PROTECT(args_iterator = call = allocLang(6));
- | ^
-/opt/R/4.4.0/lib/R/include/Rinternals.h:371:36: note: in definition of macro ‘PROTECT’
- 371 | #define PROTECT(s) Rf_protect(s)
- | ^
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/patterns/allsubs.test.c -o tests/patterns/allsubs.test.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/patterns/ctest.c -o tests/patterns/ctest.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/patterns/roundrobin.test.c -o tests/patterns/roundrobin.test.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/patterns/utest.c -o tests/patterns/utest.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/permutation/discrete.monte.carlo.c -o tests/permutation/discrete.monte.carlo.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/permutation/gaussian.monte.carlo.c -o tests/permutation/gaussian.monte.carlo.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/rinterface/allsubs.test.c -o tests/rinterface/allsubs.test.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/rinterface/ctest.c -o tests/rinterface/ctest.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/rinterface/htest.c -o tests/rinterface/htest.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/rinterface/indep.test.c -o tests/rinterface/indep.test.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/rinterface/roundrobin.test.c -o tests/rinterface/roundrobin.test.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/rinterface/utest.c -o tests/rinterface/utest.o
-gcc -std=gnu17 -shared -L/opt/R/4.4.0/lib/R/lib -L/usr/local/lib -o bnlearn.so arcs/arcs2amat.o arcs/arcs2elist.o arcs/bind.o arcs/filter.arcs.o arcs/hash.o arcs/is.row.equal.o bnlearn/bayesian.network.o bnlearn/bn.recovery.o bnlearn/cache.structure.o bnlearn/cextend.o bnlearn/colliders.o bnlearn/cpdag.o bnlearn/fitted.o bnlearn/nparams.o bnlearn/shd.o core/allocations.o core/contingency.tables.o core/correlation.o core/covariance.matrix.o core/data.table.o core/math.functions.o core/moments.o core/sampling.o core/sets.o core/uppertriangular.o fitted/enums.o fitted/fitted.o fitted/nparams.o fitted/rinterface/nparams.o foreign/parse.o globals.o graphs/acyclic.o graphs/is.dag.o graphs/path.o graphs/pdag2dag.o graphs/random/graph.generation.o graphs/topological.ordering.o inference/likelihood.weighting.o inference/loglikelihood/common.o inference/loglikelihood/discrete.o inference/loglikelihood/gaussian.o inference/loglikelihood/conditional.gaussian.o inference/loss.o inference/rbn.o inference/rinterface/loglikelihood.o inference/rinterface/cpdist.o inference/rinterface/rbn.o inference/rinterface/likelihood.weighting.o learning/averaging/averaging.o learning/averaging/bootstrap.o learning/local/mi.matrix.o learning/score/hc.cache.lookup.o learning/score/score.delta.o learning/score/tabu.o math/conditional.least.squares.o math/least.squares.o math/linear.algebra.o minimal/common.o minimal/data.frame.o minimal/strings.o minimal/table.o minimal/tiers.o minimal/unique.o parameters/discrete/classic_discrete.o parameters/discrete/hierarchical_dirichlet.o parameters/rinterface/classic_discrete.o parameters/rinterface/hierarchical_dirichlet.o parameters/rinterface/mixture_ordinary_least_squares.o parameters/rinterface/ordinary_least_squares.o predict/map.lw.o predict/predict.o preprocessing/dedup.o preprocessing/discretize.o preprocessing/enums.o sanitization/cg.assumptions.o sanitization/covariance.o sanitization/data.o scores/alpha.star.o scores/cg.loglikelihood.o scores/cg.predictive.loglikelihood.o scores/cg.nal.o scores/custom.score.o scores/dirichlet.averaged.posterior.o scores/dirichlet.posterior.o scores/discrete.loglikelihood.o scores/discrete.nal.o scores/discrete.predictive.loglikelihood.o scores/enum.o scores/gaussian.loglikelihood.o scores/gaussian.nal.o scores/gaussian.predictive.loglikelihood.o scores/graph.priors.o scores/nml_regret.o scores/nml_regret_table.o scores/normalized.maximum.likelihood.o scores/per.node.score.o scores/wishart.posterior.o test.counter.o tests/conditional.gaussian/cg.mutual.information.o tests/discrete/df.adjust.o tests/discrete/discrete.tests.o tests/discrete/jonckheere.o tests/discrete/shrinkage.o tests/enums.o tests/gaussian/df.adjust.o tests/gaussian/gaussian.tests.o tests/gaussian/shrinkage.o tests/omnibus/custom.test.o tests/patterns/allsubs.test.o tests/patterns/ctest.o tests/patterns/roundrobin.test.o tests/patterns/utest.o tests/permutation/discrete.monte.carlo.o tests/permutation/gaussian.monte.carlo.o tests/rinterface/allsubs.test.o tests/rinterface/ctest.o tests/rinterface/htest.o tests/rinterface/indep.test.o tests/rinterface/roundrobin.test.o tests/rinterface/utest.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.4.0/lib/R/lib -lR
-installing to /tmp/workdir/bnlearn/new/bnlearn.Rcheck/00LOCK-bnlearn/00new/bnlearn/libs
-** R
-** data
-*** moving datasets to lazyload DB
-** inst
-** byte-compile and prepare package for lazy loading
-** help
+...
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
@@ -223,180 +56,13 @@ ERROR: loading failed
** package ‘bnlearn’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
-using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
+using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c arcs/arcs2amat.c -o arcs/arcs2amat.o
gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c arcs/arcs2elist.c -o arcs/arcs2elist.o
gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c arcs/bind.c -o arcs/bind.o
gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c arcs/filter.arcs.c -o arcs/filter.arcs.o
gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c arcs/hash.c -o arcs/hash.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c arcs/is.row.equal.c -o arcs/is.row.equal.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c bnlearn/bayesian.network.c -o bnlearn/bayesian.network.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c bnlearn/bn.recovery.c -o bnlearn/bn.recovery.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c bnlearn/cache.structure.c -o bnlearn/cache.structure.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c bnlearn/cextend.c -o bnlearn/cextend.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c bnlearn/colliders.c -o bnlearn/colliders.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c bnlearn/cpdag.c -o bnlearn/cpdag.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c bnlearn/fitted.c -o bnlearn/fitted.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c bnlearn/nparams.c -o bnlearn/nparams.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c bnlearn/shd.c -o bnlearn/shd.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c core/allocations.c -o core/allocations.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c core/contingency.tables.c -o core/contingency.tables.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c core/correlation.c -o core/correlation.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c core/covariance.matrix.c -o core/covariance.matrix.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c core/data.table.c -o core/data.table.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c core/math.functions.c -o core/math.functions.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c core/moments.c -o core/moments.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c core/sampling.c -o core/sampling.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c core/sets.c -o core/sets.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c core/uppertriangular.c -o core/uppertriangular.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c fitted/enums.c -o fitted/enums.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c fitted/fitted.c -o fitted/fitted.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c fitted/nparams.c -o fitted/nparams.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c fitted/rinterface/nparams.c -o fitted/rinterface/nparams.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c foreign/parse.c -o foreign/parse.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c globals.c -o globals.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c graphs/acyclic.c -o graphs/acyclic.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c graphs/is.dag.c -o graphs/is.dag.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c graphs/path.c -o graphs/path.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c graphs/pdag2dag.c -o graphs/pdag2dag.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c graphs/random/graph.generation.c -o graphs/random/graph.generation.o
-In file included from graphs/random/../../include/rcore.h:3,
- from graphs/random/graph.generation.c:1:
-graphs/random/graph.generation.c: In function ‘print_modelstring’:
-graphs/random/graph.generation.c:719:19: warning: implicit declaration of function ‘allocLang’; did you mean ‘alloca’? [-Wimplicit-function-declaration]
- 719 | PROTECT(t = s = allocLang(2));
- | ^~~~~~~~~
-/opt/R/4.4.0/lib/R/include/Rinternals.h:371:36: note: in definition of macro ‘PROTECT’
- 371 | #define PROTECT(s) Rf_protect(s)
- | ^
-graphs/random/graph.generation.c:719:17: warning: assignment to ‘SEXP’ {aka ‘struct SEXPREC *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
- 719 | PROTECT(t = s = allocLang(2));
- | ^
-/opt/R/4.4.0/lib/R/include/Rinternals.h:371:36: note: in definition of macro ‘PROTECT’
- 371 | #define PROTECT(s) Rf_protect(s)
- | ^
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c graphs/topological.ordering.c -o graphs/topological.ordering.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c inference/likelihood.weighting.c -o inference/likelihood.weighting.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c inference/loglikelihood/common.c -o inference/loglikelihood/common.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c inference/loglikelihood/discrete.c -o inference/loglikelihood/discrete.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c inference/loglikelihood/gaussian.c -o inference/loglikelihood/gaussian.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c inference/loglikelihood/conditional.gaussian.c -o inference/loglikelihood/conditional.gaussian.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c inference/loss.c -o inference/loss.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c inference/rbn.c -o inference/rbn.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c inference/rinterface/loglikelihood.c -o inference/rinterface/loglikelihood.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c inference/rinterface/cpdist.c -o inference/rinterface/cpdist.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c inference/rinterface/rbn.c -o inference/rinterface/rbn.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c inference/rinterface/likelihood.weighting.c -o inference/rinterface/likelihood.weighting.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c learning/averaging/averaging.c -o learning/averaging/averaging.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c learning/averaging/bootstrap.c -o learning/averaging/bootstrap.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c learning/local/mi.matrix.c -o learning/local/mi.matrix.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c learning/score/hc.cache.lookup.c -o learning/score/hc.cache.lookup.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c learning/score/score.delta.c -o learning/score/score.delta.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c learning/score/tabu.c -o learning/score/tabu.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c math/conditional.least.squares.c -o math/conditional.least.squares.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c math/least.squares.c -o math/least.squares.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c math/linear.algebra.c -o math/linear.algebra.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c minimal/common.c -o minimal/common.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c minimal/data.frame.c -o minimal/data.frame.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c minimal/strings.c -o minimal/strings.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c minimal/table.c -o minimal/table.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c minimal/tiers.c -o minimal/tiers.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c minimal/unique.c -o minimal/unique.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c parameters/discrete/classic_discrete.c -o parameters/discrete/classic_discrete.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c parameters/discrete/hierarchical_dirichlet.c -o parameters/discrete/hierarchical_dirichlet.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c parameters/rinterface/classic_discrete.c -o parameters/rinterface/classic_discrete.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c parameters/rinterface/hierarchical_dirichlet.c -o parameters/rinterface/hierarchical_dirichlet.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c parameters/rinterface/mixture_ordinary_least_squares.c -o parameters/rinterface/mixture_ordinary_least_squares.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c parameters/rinterface/ordinary_least_squares.c -o parameters/rinterface/ordinary_least_squares.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c predict/map.lw.c -o predict/map.lw.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c predict/predict.c -o predict/predict.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c preprocessing/dedup.c -o preprocessing/dedup.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c preprocessing/discretize.c -o preprocessing/discretize.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c preprocessing/enums.c -o preprocessing/enums.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sanitization/cg.assumptions.c -o sanitization/cg.assumptions.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sanitization/covariance.c -o sanitization/covariance.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sanitization/data.c -o sanitization/data.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/alpha.star.c -o scores/alpha.star.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/cg.loglikelihood.c -o scores/cg.loglikelihood.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/cg.predictive.loglikelihood.c -o scores/cg.predictive.loglikelihood.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/cg.nal.c -o scores/cg.nal.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/custom.score.c -o scores/custom.score.o
-In file included from scores/../include/rcore.h:3,
- from scores/custom.score.c:1:
-scores/custom.score.c: In function ‘custom_score_function’:
-scores/custom.score.c:12:34: warning: implicit declaration of function ‘allocLang’; did you mean ‘alloca’? [-Wimplicit-function-declaration]
- 12 | PROTECT(args_iterator = call = allocLang(5));
- | ^~~~~~~~~
-/opt/R/4.4.0/lib/R/include/Rinternals.h:371:36: note: in definition of macro ‘PROTECT’
- 371 | #define PROTECT(s) Rf_protect(s)
- | ^
-scores/custom.score.c:12:32: warning: assignment to ‘SEXP’ {aka ‘struct SEXPREC *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
- 12 | PROTECT(args_iterator = call = allocLang(5));
- | ^
-/opt/R/4.4.0/lib/R/include/Rinternals.h:371:36: note: in definition of macro ‘PROTECT’
- 371 | #define PROTECT(s) Rf_protect(s)
- | ^
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/dirichlet.averaged.posterior.c -o scores/dirichlet.averaged.posterior.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/dirichlet.posterior.c -o scores/dirichlet.posterior.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/discrete.loglikelihood.c -o scores/discrete.loglikelihood.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/discrete.nal.c -o scores/discrete.nal.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/discrete.predictive.loglikelihood.c -o scores/discrete.predictive.loglikelihood.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/enum.c -o scores/enum.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/gaussian.loglikelihood.c -o scores/gaussian.loglikelihood.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/gaussian.nal.c -o scores/gaussian.nal.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/gaussian.predictive.loglikelihood.c -o scores/gaussian.predictive.loglikelihood.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/graph.priors.c -o scores/graph.priors.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/nml_regret.c -o scores/nml_regret.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/nml_regret_table.c -o scores/nml_regret_table.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/normalized.maximum.likelihood.c -o scores/normalized.maximum.likelihood.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/per.node.score.c -o scores/per.node.score.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scores/wishart.posterior.c -o scores/wishart.posterior.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c test.counter.c -o test.counter.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/conditional.gaussian/cg.mutual.information.c -o tests/conditional.gaussian/cg.mutual.information.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/discrete/df.adjust.c -o tests/discrete/df.adjust.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/discrete/discrete.tests.c -o tests/discrete/discrete.tests.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/discrete/jonckheere.c -o tests/discrete/jonckheere.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/discrete/shrinkage.c -o tests/discrete/shrinkage.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/enums.c -o tests/enums.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/gaussian/df.adjust.c -o tests/gaussian/df.adjust.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/gaussian/gaussian.tests.c -o tests/gaussian/gaussian.tests.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/gaussian/shrinkage.c -o tests/gaussian/shrinkage.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/omnibus/custom.test.c -o tests/omnibus/custom.test.o
-In file included from tests/omnibus/../../include/rcore.h:3,
- from tests/omnibus/custom.test.c:1:
-tests/omnibus/custom.test.c: In function ‘custom_test_function’:
-tests/omnibus/custom.test.c:11:34: warning: implicit declaration of function ‘allocLang’; did you mean ‘alloca’? [-Wimplicit-function-declaration]
- 11 | PROTECT(args_iterator = call = allocLang(6));
- | ^~~~~~~~~
-/opt/R/4.4.0/lib/R/include/Rinternals.h:371:36: note: in definition of macro ‘PROTECT’
- 371 | #define PROTECT(s) Rf_protect(s)
- | ^
-tests/omnibus/custom.test.c:11:32: warning: assignment to ‘SEXP’ {aka ‘struct SEXPREC *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
- 11 | PROTECT(args_iterator = call = allocLang(6));
- | ^
-/opt/R/4.4.0/lib/R/include/Rinternals.h:371:36: note: in definition of macro ‘PROTECT’
- 371 | #define PROTECT(s) Rf_protect(s)
- | ^
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/patterns/allsubs.test.c -o tests/patterns/allsubs.test.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/patterns/ctest.c -o tests/patterns/ctest.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/patterns/roundrobin.test.c -o tests/patterns/roundrobin.test.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/patterns/utest.c -o tests/patterns/utest.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/permutation/discrete.monte.carlo.c -o tests/permutation/discrete.monte.carlo.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/permutation/gaussian.monte.carlo.c -o tests/permutation/gaussian.monte.carlo.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/rinterface/allsubs.test.c -o tests/rinterface/allsubs.test.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/rinterface/ctest.c -o tests/rinterface/ctest.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/rinterface/htest.c -o tests/rinterface/htest.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/rinterface/indep.test.c -o tests/rinterface/indep.test.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/rinterface/roundrobin.test.c -o tests/rinterface/roundrobin.test.o
-gcc -std=gnu17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tests/rinterface/utest.c -o tests/rinterface/utest.o
-gcc -std=gnu17 -shared -L/opt/R/4.4.0/lib/R/lib -L/usr/local/lib -o bnlearn.so arcs/arcs2amat.o arcs/arcs2elist.o arcs/bind.o arcs/filter.arcs.o arcs/hash.o arcs/is.row.equal.o bnlearn/bayesian.network.o bnlearn/bn.recovery.o bnlearn/cache.structure.o bnlearn/cextend.o bnlearn/colliders.o bnlearn/cpdag.o bnlearn/fitted.o bnlearn/nparams.o bnlearn/shd.o core/allocations.o core/contingency.tables.o core/correlation.o core/covariance.matrix.o core/data.table.o core/math.functions.o core/moments.o core/sampling.o core/sets.o core/uppertriangular.o fitted/enums.o fitted/fitted.o fitted/nparams.o fitted/rinterface/nparams.o foreign/parse.o globals.o graphs/acyclic.o graphs/is.dag.o graphs/path.o graphs/pdag2dag.o graphs/random/graph.generation.o graphs/topological.ordering.o inference/likelihood.weighting.o inference/loglikelihood/common.o inference/loglikelihood/discrete.o inference/loglikelihood/gaussian.o inference/loglikelihood/conditional.gaussian.o inference/loss.o inference/rbn.o inference/rinterface/loglikelihood.o inference/rinterface/cpdist.o inference/rinterface/rbn.o inference/rinterface/likelihood.weighting.o learning/averaging/averaging.o learning/averaging/bootstrap.o learning/local/mi.matrix.o learning/score/hc.cache.lookup.o learning/score/score.delta.o learning/score/tabu.o math/conditional.least.squares.o math/least.squares.o math/linear.algebra.o minimal/common.o minimal/data.frame.o minimal/strings.o minimal/table.o minimal/tiers.o minimal/unique.o parameters/discrete/classic_discrete.o parameters/discrete/hierarchical_dirichlet.o parameters/rinterface/classic_discrete.o parameters/rinterface/hierarchical_dirichlet.o parameters/rinterface/mixture_ordinary_least_squares.o parameters/rinterface/ordinary_least_squares.o predict/map.lw.o predict/predict.o preprocessing/dedup.o preprocessing/discretize.o preprocessing/enums.o sanitization/cg.assumptions.o sanitization/covariance.o sanitization/data.o scores/alpha.star.o scores/cg.loglikelihood.o scores/cg.predictive.loglikelihood.o scores/cg.nal.o scores/custom.score.o scores/dirichlet.averaged.posterior.o scores/dirichlet.posterior.o scores/discrete.loglikelihood.o scores/discrete.nal.o scores/discrete.predictive.loglikelihood.o scores/enum.o scores/gaussian.loglikelihood.o scores/gaussian.nal.o scores/gaussian.predictive.loglikelihood.o scores/graph.priors.o scores/nml_regret.o scores/nml_regret_table.o scores/normalized.maximum.likelihood.o scores/per.node.score.o scores/wishart.posterior.o test.counter.o tests/conditional.gaussian/cg.mutual.information.o tests/discrete/df.adjust.o tests/discrete/discrete.tests.o tests/discrete/jonckheere.o tests/discrete/shrinkage.o tests/enums.o tests/gaussian/df.adjust.o tests/gaussian/gaussian.tests.o tests/gaussian/shrinkage.o tests/omnibus/custom.test.o tests/patterns/allsubs.test.o tests/patterns/ctest.o tests/patterns/roundrobin.test.o tests/patterns/utest.o tests/permutation/discrete.monte.carlo.o tests/permutation/gaussian.monte.carlo.o tests/rinterface/allsubs.test.o tests/rinterface/ctest.o tests/rinterface/htest.o tests/rinterface/indep.test.o tests/rinterface/roundrobin.test.o tests/rinterface/utest.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.4.0/lib/R/lib -lR
-installing to /tmp/workdir/bnlearn/old/bnlearn.Rcheck/00LOCK-bnlearn/00new/bnlearn/libs
-** R
-** data
-*** moving datasets to lazyload DB
-** inst
-** byte-compile and prepare package for lazy loading
-** help
+...
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
@@ -409,68 +75,6 @@ ERROR: loading failed
* removing ‘/tmp/workdir/bnlearn/old/bnlearn.Rcheck/bnlearn’
-```
-# dataone
-
-
-
-* Version: 2.2.2
-* GitHub: https://github.com/DataONEorg/rdataone
-* Source code: https://github.com/cran/dataone
-* Date/Publication: 2022-06-10 19:30:02 UTC
-* Number of recursive dependencies: 63
-
-Run `revdepcheck::cloud_details(, "dataone")` for more info
-
-
-
-## In both
-
-* checking whether package ‘dataone’ can be installed ... ERROR
- ```
- Installation failed.
- See ‘/tmp/workdir/dataone/new/dataone.Rcheck/00install.out’ for details.
- ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘dataone’ ...
-** package ‘dataone’ successfully unpacked and MD5 sums checked
-** using staged installation
-** R
-** inst
-** byte-compile and prepare package for lazy loading
-Error in dyn.load(file, DLLpath = DLLpath, ...) :
- unable to load shared object '/usr/local/lib/R/site-library/redland/libs/redland.so':
- librdf.so.0: cannot open shared object file: No such file or directory
-Calls: ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
-Execution halted
-ERROR: lazy loading failed for package ‘dataone’
-* removing ‘/tmp/workdir/dataone/new/dataone.Rcheck/dataone’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘dataone’ ...
-** package ‘dataone’ successfully unpacked and MD5 sums checked
-** using staged installation
-** R
-** inst
-** byte-compile and prepare package for lazy loading
-Error in dyn.load(file, DLLpath = DLLpath, ...) :
- unable to load shared object '/usr/local/lib/R/site-library/redland/libs/redland.so':
- librdf.so.0: cannot open shared object file: No such file or directory
-Calls: ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
-Execution halted
-ERROR: lazy loading failed for package ‘dataone’
-* removing ‘/tmp/workdir/dataone/old/dataone.Rcheck/dataone’
-
-
```
# datapack
@@ -480,7 +84,7 @@ ERROR: lazy loading failed for package ‘dataone’
* GitHub: https://github.com/ropensci/datapack
* Source code: https://github.com/cran/datapack
* Date/Publication: 2022-06-10 19:40:01 UTC
-* Number of recursive dependencies: 63
+* Number of recursive dependencies: 68
Run `revdepcheck::cloud_details(, "datapack")` for more info
@@ -506,7 +110,7 @@ Run `revdepcheck::cloud_details(, "datapack")` for more info
** inst
** byte-compile and prepare package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) :
- unable to load shared object '/usr/local/lib/R/site-library/redland/libs/redland.so':
+ unable to load shared object '/opt/R/4.4.0/lib/R/site-library/redland/libs/redland.so':
librdf.so.0: cannot open shared object file: No such file or directory
Calls: ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
Execution halted
@@ -525,7 +129,7 @@ ERROR: lazy loading failed for package ‘datapack’
** inst
** byte-compile and prepare package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) :
- unable to load shared object '/usr/local/lib/R/site-library/redland/libs/redland.so':
+ unable to load shared object '/opt/R/4.4.0/lib/R/site-library/redland/libs/redland.so':
librdf.so.0: cannot open shared object file: No such file or directory
Calls: ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
Execution halted
@@ -533,232 +137,6 @@ ERROR: lazy loading failed for package ‘datapack’
* removing ‘/tmp/workdir/datapack/old/datapack.Rcheck/datapack’
-```
-# FAIRmaterials
-
-
-
-* Version: 0.4.2.1
-* GitHub: NA
-* Source code: https://github.com/cran/FAIRmaterials
-* Date/Publication: 2024-06-27 15:40:02 UTC
-* Number of recursive dependencies: 93
-
-Run `revdepcheck::cloud_details(, "FAIRmaterials")` for more info
-
-
-
-## In both
-
-* checking whether package ‘FAIRmaterials’ can be installed ... ERROR
- ```
- Installation failed.
- See ‘/tmp/workdir/FAIRmaterials/new/FAIRmaterials.Rcheck/00install.out’ for details.
- ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘FAIRmaterials’ ...
-** package ‘FAIRmaterials’ successfully unpacked and MD5 sums checked
-** using staged installation
-** R
-** inst
-** byte-compile and prepare package for lazy loading
-Error in dyn.load(file, DLLpath = DLLpath, ...) :
- unable to load shared object '/usr/local/lib/R/site-library/redland/libs/redland.so':
- librdf.so.0: cannot open shared object file: No such file or directory
-Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
-Execution halted
-ERROR: lazy loading failed for package ‘FAIRmaterials’
-* removing ‘/tmp/workdir/FAIRmaterials/new/FAIRmaterials.Rcheck/FAIRmaterials’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘FAIRmaterials’ ...
-** package ‘FAIRmaterials’ successfully unpacked and MD5 sums checked
-** using staged installation
-** R
-** inst
-** byte-compile and prepare package for lazy loading
-Error in dyn.load(file, DLLpath = DLLpath, ...) :
- unable to load shared object '/usr/local/lib/R/site-library/redland/libs/redland.so':
- librdf.so.0: cannot open shared object file: No such file or directory
-Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
-Execution halted
-ERROR: lazy loading failed for package ‘FAIRmaterials’
-* removing ‘/tmp/workdir/FAIRmaterials/old/FAIRmaterials.Rcheck/FAIRmaterials’
-
-
-```
-# randomForestSRC
-
-
-
-* Version: 3.3.1
-* GitHub: https://github.com/kogalur/randomForestSRC
-* Source code: https://github.com/cran/randomForestSRC
-* Date/Publication: 2024-07-25 14:30:02 UTC
-* Number of recursive dependencies: 156
-
-Run `revdepcheck::cloud_details(, "randomForestSRC")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/randomForestSRC/new/randomForestSRC.Rcheck’
-* using R version 4.4.0 (2024-04-24)
-* using platform: x86_64-pc-linux-gnu
-* R was compiled by
- gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
- GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
-* running under: Ubuntu 24.04.1 LTS
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘randomForestSRC/DESCRIPTION’ ... OK
-* this is package ‘randomForestSRC’ version ‘3.3.1’
-* checking package namespace information ... OK
-* checking package dependencies ... NOTE
-Package suggested but not available for checking: ‘imbalance’
-* checking if this is a source package ... OK
-* checking if there is a namespace ... OK
-* checking for executable files ... OK
-* checking for hidden files and directories ... OK
-* checking for portable file names ... OK
-* checking for sufficient/correct file permissions ... OK
-* checking whether package ‘randomForestSRC’ can be installed ... OK
-* used C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
-* checking installed package size ... OK
-* checking package directory ... OK
-* checking DESCRIPTION meta-information ... OK
-* checking top-level files ... OK
-* checking for left-over files ... OK
-* checking index information ... OK
-* checking package subdirectories ... OK
-* checking code files for non-ASCII characters ... OK
-* checking R files for syntax errors ... OK
-* checking whether the package can be loaded ... OK
-* checking whether the package can be loaded with stated dependencies ... OK
-* checking whether the package can be unloaded cleanly ... OK
-* checking whether the namespace can be loaded with stated dependencies ... OK
-* checking whether the namespace can be unloaded cleanly ... OK
-* checking loading without being on the library search path ... OK
-* checking whether startup messages can be suppressed ... OK
-* checking dependencies in R code ... OK
-* checking S3 generic/method consistency ... OK
-* checking replacement functions ... OK
-* checking foreign function calls ... OK
-* checking R code for possible problems ... OK
-* checking Rd files ... OK
-* checking Rd metadata ... OK
-* checking Rd cross-references ... OK
-* checking for missing documentation entries ... OK
-* checking for code/documentation mismatches ... OK
-* checking Rd \usage sections ... OK
-* checking Rd contents ... OK
-* checking for unstated dependencies in examples ... OK
-* checking contents of ‘data’ directory ... OK
-* checking data for non-ASCII characters ... OK
-* checking data for ASCII and uncompressed saves ... OK
-* checking line endings in shell scripts ... OK
-* checking line endings in C/C++/Fortran sources/headers ... OK
-* checking line endings in Makefiles ... OK
-* checking compilation flags in Makevars ... OK
-* checking for GNU extensions in Makefiles ... OK
-* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
-* checking use of PKG_*FLAGS in Makefiles ... OK
-* checking compiled code ... OK
-* checking examples ... OK
-* DONE
-Status: 1 NOTE
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/randomForestSRC/old/randomForestSRC.Rcheck’
-* using R version 4.4.0 (2024-04-24)
-* using platform: x86_64-pc-linux-gnu
-* R was compiled by
- gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
- GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
-* running under: Ubuntu 24.04.1 LTS
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘randomForestSRC/DESCRIPTION’ ... OK
-* this is package ‘randomForestSRC’ version ‘3.3.1’
-* checking package namespace information ... OK
-* checking package dependencies ... NOTE
-Package suggested but not available for checking: ‘imbalance’
-* checking if this is a source package ... OK
-* checking if there is a namespace ... OK
-* checking for executable files ... OK
-* checking for hidden files and directories ... OK
-* checking for portable file names ... OK
-* checking for sufficient/correct file permissions ... OK
-* checking whether package ‘randomForestSRC’ can be installed ... OK
-* used C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
-* checking installed package size ... OK
-* checking package directory ... OK
-* checking DESCRIPTION meta-information ... OK
-* checking top-level files ... OK
-* checking for left-over files ... OK
-* checking index information ... OK
-* checking package subdirectories ... OK
-* checking code files for non-ASCII characters ... OK
-* checking R files for syntax errors ... OK
-* checking whether the package can be loaded ... OK
-* checking whether the package can be loaded with stated dependencies ... OK
-* checking whether the package can be unloaded cleanly ... OK
-* checking whether the namespace can be loaded with stated dependencies ... OK
-* checking whether the namespace can be unloaded cleanly ... OK
-* checking loading without being on the library search path ... OK
-* checking whether startup messages can be suppressed ... OK
-* checking dependencies in R code ... OK
-* checking S3 generic/method consistency ... OK
-* checking replacement functions ... OK
-* checking foreign function calls ... OK
-* checking R code for possible problems ... OK
-* checking Rd files ... OK
-* checking Rd metadata ... OK
-* checking Rd cross-references ... OK
-* checking for missing documentation entries ... OK
-* checking for code/documentation mismatches ... OK
-* checking Rd \usage sections ... OK
-* checking Rd contents ... OK
-* checking for unstated dependencies in examples ... OK
-* checking contents of ‘data’ directory ... OK
-* checking data for non-ASCII characters ... OK
-* checking data for ASCII and uncompressed saves ... OK
-* checking line endings in shell scripts ... OK
-* checking line endings in C/C++/Fortran sources/headers ... OK
-* checking line endings in Makefiles ... OK
-* checking compilation flags in Makevars ... OK
-* checking for GNU extensions in Makefiles ... OK
-* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
-* checking use of PKG_*FLAGS in Makefiles ... OK
-* checking compiled code ... OK
-* checking examples ... OK
-* DONE
-Status: 1 NOTE
-
-
-
-
-
```
# streamDAG
@@ -768,7 +146,7 @@ Status: 1 NOTE
* GitHub: NA
* Source code: https://github.com/cran/streamDAG
* Date/Publication: 2023-10-06 18:50:02 UTC
-* Number of recursive dependencies: 131
+* Number of recursive dependencies: 132
Run `revdepcheck::cloud_details(, "streamDAG")` for more info
@@ -783,9 +161,9 @@ Run `revdepcheck::cloud_details(, "streamDAG")` for more info
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
- gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
- GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
-* running under: Ubuntu 24.04.1 LTS
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using option ‘--no-manual’
* checking for file ‘streamDAG/DESCRIPTION’ ... OK
@@ -811,9 +189,9 @@ Status: 1 ERROR
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
- gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
- GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
-* running under: Ubuntu 24.04.1 LTS
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using option ‘--no-manual’
* checking for file ‘streamDAG/DESCRIPTION’ ... OK
@@ -831,8246 +209,4 @@ Status: 1 ERROR
-```
-# TDA
-
-
-
-* Version: 1.9.1
-* GitHub: NA
-* Source code: https://github.com/cran/TDA
-* Date/Publication: 2024-01-24 15:42:47 UTC
-* Number of recursive dependencies: 54
-
-Run `revdepcheck::cloud_details(, "TDA")` for more info
-
-
-
-## In both
-
-* checking whether package ‘TDA’ can be installed ... ERROR
- ```
- Installation failed.
- See ‘/tmp/workdir/TDA/new/TDA.Rcheck/00install.out’ for details.
- ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘TDA’ ...
-** package ‘TDA’ successfully unpacked and MD5 sums checked
-** using staged installation
-** libs
-/bin/sh: 1: clang++: not found
-expr: syntax error: unexpected argument ‘50000’
-using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
-using C++17
-/bin/sh: 1: clang++: not found
-expr: syntax error: unexpected argument ‘50000’
-g++ -std=gnu++17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I. -I'/usr/local/lib/R/site-library/BH/include' -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppEigen/include' -I/usr/local/include -DBOOST_DISABLE_THREADS -DCGAL_EIGEN3_ENABLED -DCGAL_HEADER_ONLY -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
-In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:205,
- from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
- from /usr/local/lib/R/site-library/RcppEigen/include/RcppEigenForward.h:28,
- from /usr/local/lib/R/site-library/RcppEigen/include/RcppEigen.h:25,
- from RcppExports.cpp:4:
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:46:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes]
- 46 | typedef eigen_packet_wrapper<__m128i, 0> Packet4i;
- | ^
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:47:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes]
- 47 | typedef eigen_packet_wrapper<__m128i, 1> Packet16b;
- | ^
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:49:39: warning: ignoring attributes on template argument ‘__m128’ [-Wignored-attributes]
- 49 | template<> struct is_arithmetic<__m128> { enum { value = true }; };
- | ^
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:50:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes]
- 50 | template<> struct is_arithmetic<__m128i> { enum { value = true }; };
- | ^
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:51:40: warning: ignoring attributes on template argument ‘__m128d’ [-Wignored-attributes]
- 51 | template<> struct is_arithmetic<__m128d> { enum { value = true }; };
- | ^
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:222:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes]
- 222 | template<> struct unpacket_traits {
- | ^
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:228:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes]
- 228 | template<> struct unpacket_traits {
- | ^
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1124:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes]
- 1124 | ptranspose(PacketBlock& kernel) {
- | ^
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1129:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes]
- 1129 | ptranspose(PacketBlock& kernel) {
- | ^
-In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:174:
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes]
- 16 | struct conj_helper { \
- | ^
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
- 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f)
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes]
- 29 | struct conj_helper { \
- | ^
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
- 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f)
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes]
- 16 | struct conj_helper { \
- | ^
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
- 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d)
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes]
- 29 | struct conj_helper { \
- | ^
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
- 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d)
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:165:
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet’:
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits >’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from ‘struct Eigen::internal::traits >’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:24:46: required from here
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes]
- 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value>
- | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes]
- 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value>
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes]
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(4) float>::half’ {aka ‘__m128’} [-Wignored-attributes]
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes]
- 208 | typedef typename find_best_packet_helper::type>::type type;
- | ^~~~
-In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:271:
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’:
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from ‘class Eigen::DenseCoeffsBase, 1>’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from ‘class Eigen::DenseCoeffsBase, 3>’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase >’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase >’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase >’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase >’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from ‘class Eigen::Quaternion’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:27:3: required from here
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes]
- 56 | >::type PacketReturnType;
- | ^~~~~~~~~~~~~~~~
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet’:
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits >’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from ‘struct Eigen::internal::traits >’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:98:47: required from here
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes]
- 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value>
- | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes]
- 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value>
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes]
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(2) double>::half’ {aka ‘__m128d’} [-Wignored-attributes]
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes]
- 208 | typedef typename find_best_packet_helper::type>::type type;
- | ^~~~
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’:
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from ‘class Eigen::DenseCoeffsBase, 1>’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from ‘class Eigen::DenseCoeffsBase, 3>’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase >’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase >’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase >’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase >’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from ‘class Eigen::Quaternion’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:102:3: required from here
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes]
- 56 | >::type PacketReturnType;
- | ^~~~~~~~~~~~~~~~
-In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/SparseCore:37,
- from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Sparse:26,
- from /usr/local/lib/R/site-library/RcppEigen/include/RcppEigenForward.h:29:
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of ‘class Eigen::SparseMatrixBase >’:
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7: required from ‘class Eigen::SparseCompressedBase >’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7: required from ‘class Eigen::SparseMatrix’
-/usr/local/lib/R/site-library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h:61:25: required from here
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes]
- 47 | >::type PacketReturnType;
- | ^~~~~~~~~~~~~~~~
-g++ -std=gnu++17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG -I. -I'/usr/local/lib/R/site-library/BH/include' -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppEigen/include' -I/usr/local/include -DBOOST_DISABLE_THREADS -DCGAL_EIGEN3_ENABLED -DCGAL_HEADER_ONLY -fpic -g -O2 -c diag.cpp -o diag.o
-In file included from ./CGAL/license/Triangulation.h:17,
- from ./CGAL/Delaunay_triangulation.h:15,
- from ./gudhi/Alpha_complex.h:26,
- from ./tdautils/gudhiUtils.h:13,
- from diag.cpp:19:
-./CGAL/config.h:124: warning: "BOOST_PARAMETER_MAX_ARITY" redefined
- 124 | #define BOOST_PARAMETER_MAX_ARITY 12
- |
-In file included from /usr/local/lib/R/site-library/BH/include/boost/parameter/aux_/is_tagged_argument.hpp:17,
- from /usr/local/lib/R/site-library/BH/include/boost/parameter/is_argument_pack.hpp:9,
- from /usr/local/lib/R/site-library/BH/include/boost/graph/named_function_params.hpp:20,
- from /usr/local/lib/R/site-library/BH/include/boost/graph/depth_first_search.hpp:21,
- from /usr/local/lib/R/site-library/BH/include/boost/graph/max_cardinality_matching.hpp:21,
- from ./topology/persistence-diagram.hpp:144,
- from ./topology/persistence-diagram.h:176,
- from ./tdautils/ripsL2.h:9,
- from diag.cpp:9:
-/usr/local/lib/R/site-library/BH/include/boost/parameter/config.hpp:61: note: this is the location of the previous definition
- 61 | #define BOOST_PARAMETER_MAX_ARITY BOOST_MPL_LIMIT_VECTOR_SIZE
- |
-In file included from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
- from /usr/local/lib/R/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
- from /usr/local/lib/R/site-library/BH/include/boost/property_map/property_map.hpp:598,
- from ./utilities/property-maps.h:6,
- from ./topology/complex-traits.h:6,
- from ./topology/filtration.h:7,
- from ./tdautils/ripsL2.h:6:
-/usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
- 326 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
- | ^~~~~~~~
-In file included from /usr/include/c++/13/memory:78,
- from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
- from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:23:
-/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
- 65 | template class auto_ptr;
- | ^~~~~~~~
-/usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
- 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
- | ^~~~~~~~
-/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
- 65 | template class auto_ptr;
- | ^~~~~~~~
-/usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
- 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
- | ^~~~~~~~
-/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
- 65 | template class auto_ptr;
- | ^~~~~~~~
-/usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
- 423 | shared_ptr & operator=( std::auto_ptr & r )
- | ^~~~~~~~
-/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
- 65 | template class auto_ptr;
- | ^~~~~~~~
-/usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
- 430 | shared_ptr & operator=( std::auto_ptr && r )
- | ^~~~~~~~
-/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
- 65 | template class auto_ptr;
- | ^~~~~~~~
-/usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
-/usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
- 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
- | ^~~~~~~~
-/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
- 65 | template class auto_ptr;
- | ^~~~~~~~
-In file included from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:23,
- from /usr/local/lib/R/site-library/BH/include/boost/bind/bind.hpp:23,
- from /usr/local/lib/R/site-library/BH/include/boost/multi_index/detail/ord_index_impl.hpp:82,
- from /usr/local/lib/R/site-library/BH/include/boost/multi_index/ordered_index.hpp:17,
- from ./topology/filtration.h:14:
-/usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp: At global scope:
-/usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
- 48 | template T * get_pointer(std::auto_ptr const& p)
- | ^~~~~~~~
-/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
- 65 | template class auto_ptr;
- | ^~~~~~~~
-In file included from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/deprecated_macros.hpp:8,
- from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/sp_counted_base.hpp:22,
- from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:22:
-/usr/local/lib/R/site-library/BH/include/boost/config/pragma_message.hpp:24:34: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’
- 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
- | ^~~~~~~
-/usr/local/lib/R/site-library/BH/include/boost/bind.hpp:36:1: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’
- 36 | BOOST_PRAGMA_MESSAGE(
- | ^~~~~~~~~~~~~~~~~~~~
-In file included from /usr/local/lib/R/site-library/BH/include/boost/scoped_ptr.hpp:13,
- from /usr/local/lib/R/site-library/BH/include/boost/graph/adjacency_list.hpp:22,
- from ./topology/persistence-diagram.hpp:143:
-/usr/local/lib/R/site-library/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
- 75 | explicit scoped_ptr( std::auto_ptr p ) noexcept : px( p.release() )
- | ^~~~~~~~
-/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
- 65 | template class auto_ptr;
- | ^~~~~~~~
-In file included from ./boost/container/detail/flat_tree.hpp:30,
- from ./boost/container/flat_map.hpp:29,
- from ./gudhi/Simplex_tree/Simplex_tree_siblings.h:16,
- from ./gudhi/Simplex_tree.h:15,
- from ./tdautils/gudhiUtils.h:10:
-./boost/container/vector.hpp:3173:1: error: ‘BOOST_MOVE_STD_NS_BEG’ does not name a type; did you mean ‘BOOST_MATH_STD_USING’?
- 3173 | BOOST_MOVE_STD_NS_BEG
- | ^~~~~~~~~~~~~~~~~~~~~
- | BOOST_MATH_STD_USING
-./boost/container/vector.hpp:3180:1: error: ‘BOOST_MOVE_STD_NS_END’ does not name a type; did you mean ‘BOOST_MOVE_CATCH_END’?
- 3180 | BOOST_MOVE_STD_NS_END
- | ^~~~~~~~~~~~~~~~~~~~~
- | BOOST_MOVE_CATCH_END
-./boost/container/detail/flat_tree.hpp: In function ‘void boost::container::dtl::flat_tree_container_inplace_merge(SequenceContainer&, typename SequenceContainer::iterator, Compare, boost::move_detail::true_)’:
-./boost/container/detail/flat_tree.hpp:148:38: error: ‘back_free_capacity’ was not declared in this scope
- 148 | (braw, iraw, eraw, comp, eraw, back_free_capacity::get(dest));
- | ^~~~~~~~~~~~~~~~~~
-./boost/container/detail/flat_tree.hpp:148:74: error: expected primary-expression before ‘>’ token
- 148 | (braw, iraw, eraw, comp, eraw, back_free_capacity::get(dest));
- | ^
-./boost/container/detail/flat_tree.hpp: In function ‘void boost::container::dtl::flat_tree_container_inplace_sort_ending(SequenceContainer&, typename SequenceContainer::iterator, Compare, boost::move_detail::true_)’:
-./boost/container/detail/flat_tree.hpp:175:32: error: ‘back_free_capacity’ was not declared in this scope
- 175 | (iraw, eraw, comp, eraw, back_free_capacity::get(dest));
- | ^~~~~~~~~~~~~~~~~~
-./boost/container/detail/flat_tree.hpp:175:68: error: expected primary-expression before ‘>’ token
- 175 | (iraw, eraw, comp, eraw, back_free_capacity::get(dest));
- | ^
-In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:205,
- from ./gudhi/Alpha_complex/Alpha_kernel_d.h:16,
- from ./gudhi/Alpha_complex.h:15:
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h: At global scope:
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:46:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes]
- 46 | typedef eigen_packet_wrapper<__m128i, 0> Packet4i;
- | ^
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:47:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes]
- 47 | typedef eigen_packet_wrapper<__m128i, 1> Packet16b;
- | ^
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:49:39: warning: ignoring attributes on template argument ‘__m128’ [-Wignored-attributes]
- 49 | template<> struct is_arithmetic<__m128> { enum { value = true }; };
- | ^
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:50:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes]
- 50 | template<> struct is_arithmetic<__m128i> { enum { value = true }; };
- | ^
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:51:40: warning: ignoring attributes on template argument ‘__m128d’ [-Wignored-attributes]
- 51 | template<> struct is_arithmetic<__m128d> { enum { value = true }; };
- | ^
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:222:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes]
- 222 | template<> struct unpacket_traits {
- | ^
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:228:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes]
- 228 | template<> struct unpacket_traits {
- | ^
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1124:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes]
- 1124 | ptranspose(PacketBlock& kernel) {
- | ^
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1129:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes]
- 1129 | ptranspose(PacketBlock& kernel) {
- | ^
-In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:174:
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes]
- 16 | struct conj_helper { \
- | ^
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
- 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f)
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes]
- 29 | struct conj_helper { \
- | ^
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
- 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f)
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes]
- 16 | struct conj_helper { \
- | ^
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
- 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d)
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes]
- 29 | struct conj_helper { \
- | ^
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
- 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d)
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:165:
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet’:
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits >’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from ‘struct Eigen::internal::traits >’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:24:46: required from here
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes]
- 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value>
- | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes]
- 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value>
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes]
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(4) float>::half’ {aka ‘__m128’} [-Wignored-attributes]
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes]
- 208 | typedef typename find_best_packet_helper::type>::type type;
- | ^~~~
-In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:271:
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’:
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from ‘class Eigen::DenseCoeffsBase, 1>’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from ‘class Eigen::DenseCoeffsBase, 3>’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase >’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase >’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase >’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase >’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from ‘class Eigen::Quaternion’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:27:3: required from here
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes]
- 56 | >::type PacketReturnType;
- | ^~~~~~~~~~~~~~~~
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet’:
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits >’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from ‘struct Eigen::internal::traits >’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:98:47: required from here
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes]
- 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value>
- | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes]
- 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value>
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes]
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(2) double>::half’ {aka ‘__m128d’} [-Wignored-attributes]
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes]
- 208 | typedef typename find_best_packet_helper::type>::type type;
- | ^~~~
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’:
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from ‘class Eigen::DenseCoeffsBase, 1>’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from ‘class Eigen::DenseCoeffsBase, 3>’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase >’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase >’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase >’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase >’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from ‘class Eigen::Quaternion’
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:102:3: required from here
-/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes]
- 56 | >::type PacketReturnType;
- | ^~~~~~~~~~~~~~~~
-In file included from /usr/local/lib/R/site-library/BH/include/boost/concept/assert.hpp:35,
- from /usr/local/lib/R/site-library/BH/include/boost/property_map/property_map.hpp:19:
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/general.hpp: In instantiation of ‘static void boost::concepts::requirement::failed() [with Model = boost::concepts::usage_requirements > >*, false> > >]’:
-/usr/local/lib/R/site-library/BH/include/boost/concept_check.hpp:167:5: required from ‘struct boost::CopyConstructible > >*, false> >’
-/usr/local/lib/R/site-library/BH/include/boost/range/concepts.hpp:125:16: required from ‘struct boost::range_detail::IncrementableIteratorConcept > >*, false> >’
-/usr/local/lib/R/site-library/BH/include/boost/range/concepts.hpp:147:16: required from ‘struct boost::range_detail::SinglePassIteratorConcept > >*, false> >’
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:32:62: required by substitution of ‘template boost::concepts::detail::yes boost::concepts::detail::has_constraints_(Model*, wrap_constraints*) [with Model = boost::range_detail::SinglePassIteratorConcept > >*, false> >]’
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:42:5: required from ‘const bool boost::concepts::not_satisfied > >*, false> > >::value’
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:45:51: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/general.hpp:72:8: required from ‘struct boost::concepts::requirement_ >, std::less, void> >)>’
-/usr/local/lib/R/site-library/BH/include/boost/range/adaptor/reversed.hpp:52:13: required from ‘boost::range_detail::reversed_range boost::adaptors::reverse(BidirectionalRange&) [with BidirectionalRange = boost::container::flat_map >, std::less, void>]’
-./gudhi/Simplex_tree.h:1400:50: required from ‘bool Gudhi::Simplex_tree::make_filtration_non_decreasing() [with SimplexTreeOptions = Gudhi::Simplex_tree_options_full_featured]’
-./gudhi/Alpha_complex.h:463:47: required from ‘bool Gudhi::alpha_complex::Alpha_complex::create_complex(SimplicialComplexForAlpha&, Filtration_value, bool, bool) [with SimplicialComplexForAlpha = Gudhi::Simplex_tree<>; Filtration_value = double; Kernel = CGAL::Epick_d; bool Weighted = false]’
-./tdautils/gudhiUtils.h:390:45: required from ‘SimplexTree AlphaComplexFiltrationGudhi(const RealMatrix&, bool, Print&) [with SimplexTree = Gudhi::Simplex_tree<>; RealMatrix = Rcpp::Matrix<14>; Print = void(const char*, ...)]’
-diag.cpp:492:59: required from here
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/general.hpp:50:47: warning: ‘this’ pointer is null [-Wnonnull]
- 50 | static void failed() { ((Model*)0)->~Model(); }
- | ~~~~~~~~~~~~~~~~~~~^~
-In file included from /usr/local/lib/R/site-library/BH/include/boost/concept_check.hpp:31,
- from /usr/local/lib/R/site-library/BH/include/boost/property_map/property_map.hpp:20:
-/usr/local/lib/R/site-library/BH/include/boost/concept/usage.hpp:20:5: note: in a call to non-static member function ‘boost::concepts::usage_requirements::~usage_requirements() [with Model = boost::CopyConstructible > >*, false> >]’
- 20 | ~usage_requirements() { ((Model*)0)->~Model(); }
- | ^
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/general.hpp: In instantiation of ‘static void boost::concepts::requirement::failed() [with Model = boost::concepts::usage_requirements >]’:
-/usr/local/lib/R/site-library/BH/include/boost/concept_check.hpp:208:5: required from ‘struct boost::Convertible’
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:32:62: required by substitution of ‘template boost::concepts::detail::yes boost::concepts::detail::has_constraints_(Model*, wrap_constraints*) [with Model = boost::Convertible]’
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:42:5: required from ‘const bool boost::concepts::not_satisfied >::value’
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:45:51: required from ‘struct boost::concepts::not_satisfied >’
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/general.hpp:72:8: required from ‘struct boost::concepts::requirement_)>’
-/usr/local/lib/R/site-library/BH/include/boost/iterator/iterator_concepts.hpp:114:7: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/general.hpp:72:8: required from ‘struct boost::concepts::requirement_ >, std::less, void> >)>’
-/usr/local/lib/R/site-library/BH/include/boost/range/adaptor/reversed.hpp:52:13: required from ‘boost::range_detail::reversed_range boost::adaptors::reverse(BidirectionalRange&) [with BidirectionalRange = boost::container::flat_map >, std::less, void>]’
-./gudhi/Simplex_tree.h:1400:50: required from ‘bool Gudhi::Simplex_tree::make_filtration_non_decreasing() [with SimplexTreeOptions = Gudhi::Simplex_tree_options_full_featured]’
-./gudhi/Alpha_complex.h:463:47: required from ‘bool Gudhi::alpha_complex::Alpha_complex::create_complex(SimplicialComplexForAlpha&, Filtration_value, bool, bool) [with SimplicialComplexForAlpha = Gudhi::Simplex_tree<>; Filtration_value = double; Kernel = CGAL::Epick_d; bool Weighted = false]’
-./tdautils/gudhiUtils.h:390:45: required from ‘SimplexTree AlphaComplexFiltrationGudhi(const RealMatrix&, bool, Print&) [with SimplexTree = Gudhi::Simplex_tree<>; RealMatrix = Rcpp::Matrix<14>; Print = void(const char*, ...)]’
-diag.cpp:492:59: required from here
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/general.hpp:50:47: warning: ‘this’ pointer is null [-Wnonnull]
- 50 | static void failed() { ((Model*)0)->~Model(); }
- | ~~~~~~~~~~~~~~~~~~~^~
-/usr/local/lib/R/site-library/BH/include/boost/concept/usage.hpp:20:5: note: in a call to non-static member function ‘boost::concepts::usage_requirements::~usage_requirements() [with Model = boost::Convertible]’
- 20 | ~usage_requirements() { ((Model*)0)->~Model(); }
- | ^
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/general.hpp: In instantiation of ‘static void boost::concepts::requirement::failed() [with Model = boost::Convertible]’:
-/usr/local/lib/R/site-library/BH/include/boost/iterator/iterator_concepts.hpp:114:7: required from ‘struct boost::range_detail::IncrementableIteratorConcept > >*, false> >’
-/usr/local/lib/R/site-library/BH/include/boost/range/concepts.hpp:147:16: required from ‘struct boost::range_detail::SinglePassIteratorConcept > >*, false> >’
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:32:62: required by substitution of ‘template boost::concepts::detail::yes boost::concepts::detail::has_constraints_(Model*, wrap_constraints*) [with Model = boost::range_detail::SinglePassIteratorConcept > >*, false> >]’
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:42:5: required from ‘const bool boost::concepts::not_satisfied > >*, false> > >::value’
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:45:51: required from ‘struct boost::concepts::not_satisfied > >*, false> > >’
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/general.hpp:72:8: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/general.hpp:72:8: required from ‘struct boost::concepts::requirement_ >, std::less, void> >)>’
-/usr/local/lib/R/site-library/BH/include/boost/range/adaptor/reversed.hpp:52:13: required from ‘boost::range_detail::reversed_range boost::adaptors::reverse(BidirectionalRange&) [with BidirectionalRange = boost::container::flat_map >, std::less, void>]’
-./gudhi/Simplex_tree.h:1400:50: required from ‘bool Gudhi::Simplex_tree::make_filtration_non_decreasing() [with SimplexTreeOptions = Gudhi::Simplex_tree_options_full_featured]’
-./gudhi/Alpha_complex.h:463:47: required from ‘bool Gudhi::alpha_complex::Alpha_complex::create_complex(SimplicialComplexForAlpha&, Filtration_value, bool, bool) [with SimplicialComplexForAlpha = Gudhi::Simplex_tree<>; Filtration_value = double; Kernel = CGAL::Epick_d; bool Weighted = false]’
-./tdautils/gudhiUtils.h:390:45: required from ‘SimplexTree AlphaComplexFiltrationGudhi(const RealMatrix&, bool, Print&) [with SimplexTree = Gudhi::Simplex_tree<>; RealMatrix = Rcpp::Matrix<14>; Print = void(const char*, ...)]’
-diag.cpp:492:59: required from here
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/general.hpp:50:47: warning: ‘this’ pointer is null [-Wnonnull]
- 50 | static void failed() { ((Model*)0)->~Model(); }
- | ~~~~~~~~~~~~~~~~~~~^~
-/usr/local/lib/R/site-library/BH/include/boost/concept/usage.hpp:37:7: note: in a call to non-static member function ‘boost::Convertible::~Convertible() [with X = boost::iterators::random_access_traversal_tag; Y = boost::iterators::incrementable_traversal_tag]’
- 37 | ~model()
- | ^
-/usr/local/lib/R/site-library/BH/include/boost/concept_check.hpp:208:5: note: in expansion of macro ‘BOOST_CONCEPT_USAGE’
- 208 | BOOST_CONCEPT_USAGE(Convertible) {
- | ^~~~~~~~~~~~~~~~~~~
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/general.hpp: In instantiation of ‘static void boost::concepts::requirement::failed() [with Model = boost::concepts::usage_requirements > >*, false> > >]’:
-/usr/local/lib/R/site-library/BH/include/boost/range/concepts.hpp:136:13: required from ‘struct boost::range_detail::IncrementableIteratorConcept > >*, false> >’
-/usr/local/lib/R/site-library/BH/include/boost/range/concepts.hpp:147:16: required from ‘struct boost::range_detail::SinglePassIteratorConcept > >*, false> >’
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:32:62: required by substitution of ‘template boost::concepts::detail::yes boost::concepts::detail::has_constraints_(Model*, wrap_constraints*) [with Model = boost::range_detail::SinglePassIteratorConcept > >*, false> >]’
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:42:5: required from ‘const bool boost::concepts::not_satisfied > >*, false> > >::value’
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:45:51: required from ‘struct boost::concepts::not_satisfied > >*, false> > >’
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/general.hpp:72:8: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/general.hpp:72:8: required from ‘struct boost::concepts::requirement_ >, std::less, void> >)>’
-/usr/local/lib/R/site-library/BH/include/boost/range/adaptor/reversed.hpp:52:13: required from ‘boost::range_detail::reversed_range boost::adaptors::reverse(BidirectionalRange&) [with BidirectionalRange = boost::container::flat_map >, std::less, void>]’
-./gudhi/Simplex_tree.h:1400:50: required from ‘bool Gudhi::Simplex_tree::make_filtration_non_decreasing() [with SimplexTreeOptions = Gudhi::Simplex_tree_options_full_featured]’
-./gudhi/Alpha_complex.h:463:47: required from ‘bool Gudhi::alpha_complex::Alpha_complex::create_complex(SimplicialComplexForAlpha&, Filtration_value, bool, bool) [with SimplicialComplexForAlpha = Gudhi::Simplex_tree<>; Filtration_value = double; Kernel = CGAL::Epick_d; bool Weighted = false]’
-./tdautils/gudhiUtils.h:390:45: required from ‘SimplexTree AlphaComplexFiltrationGudhi(const RealMatrix&, bool, Print&) [with SimplexTree = Gudhi::Simplex_tree<>; RealMatrix = Rcpp::Matrix<14>; Print = void(const char*, ...)]’
-diag.cpp:492:59: required from here
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/general.hpp:50:47: warning: ‘this’ pointer is null [-Wnonnull]
- 50 | static void failed() { ((Model*)0)->~Model(); }
- | ~~~~~~~~~~~~~~~~~~~^~
-/usr/local/lib/R/site-library/BH/include/boost/concept/usage.hpp:20:5: note: in a call to non-static member function ‘boost::concepts::usage_requirements::~usage_requirements() [with Model = boost::range_detail::IncrementableIteratorConcept > >*, false> >]’
- 20 | ~usage_requirements() { ((Model*)0)->~Model(); }
- | ^
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/general.hpp: In instantiation of ‘static void boost::concepts::requirement::failed() [with Model = boost::concepts::usage_requirements > >*, false> > >]’:
-/usr/local/lib/R/site-library/BH/include/boost/concept_check.hpp:233:5: required from ‘struct boost::EqualityComparable > >*, false> >’
-/usr/local/lib/R/site-library/BH/include/boost/range/concepts.hpp:147:16: required from ‘struct boost::range_detail::SinglePassIteratorConcept > >*, false> >’
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:32:62: required by substitution of ‘template boost::concepts::detail::yes boost::concepts::detail::has_constraints_(Model*, wrap_constraints*) [with Model = boost::range_detail::SinglePassIteratorConcept > >*, false> >]’
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:42:5: required from ‘const bool boost::concepts::not_satisfied > >*, false> > >::value’
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:45:51: required from ‘struct boost::concepts::not_satisfied > >*, false> > >’
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/general.hpp:72:8: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/general.hpp:72:8: required from ‘struct boost::concepts::requirement_ >, std::less, void> >)>’
-/usr/local/lib/R/site-library/BH/include/boost/range/adaptor/reversed.hpp:52:13: required from ‘boost::range_detail::reversed_range boost::adaptors::reverse(BidirectionalRange&) [with BidirectionalRange = boost::container::flat_map >, std::less, void>]’
-./gudhi/Simplex_tree.h:1400:50: required from ‘bool Gudhi::Simplex_tree::make_filtration_non_decreasing() [with SimplexTreeOptions = Gudhi::Simplex_tree_options_full_featured]’
-./gudhi/Alpha_complex.h:463:47: required from ‘bool Gudhi::alpha_complex::Alpha_complex::create_complex(SimplicialComplexForAlpha&, Filtration_value, bool, bool) [with SimplicialComplexForAlpha = Gudhi::Simplex_tree<>; Filtration_value = double; Kernel = CGAL::Epick_d; bool Weighted = false]’
-./tdautils/gudhiUtils.h:390:45: required from ‘SimplexTree AlphaComplexFiltrationGudhi(const RealMatrix&, bool, Print&) [with SimplexTree = Gudhi::Simplex_tree<>; RealMatrix = Rcpp::Matrix<14>; Print = void(const char*, ...)]’
-diag.cpp:492:59: required from here
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/general.hpp:50:47: warning: ‘this’ pointer is null [-Wnonnull]
- 50 | static void failed() { ((Model*)0)->~Model(); }
- | ~~~~~~~~~~~~~~~~~~~^~
-/usr/local/lib/R/site-library/BH/include/boost/concept/usage.hpp:20:5: note: in a call to non-static member function ‘boost::concepts::usage_requirements::~usage_requirements() [with Model = boost::EqualityComparable > >*, false> >]’
- 20 | ~usage_requirements() { ((Model*)0)->~Model(); }
- | ^
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/general.hpp: In instantiation of ‘static void boost::concepts::requirement::failed() [with Model = boost::concepts::usage_requirements >]’:
-/usr/local/lib/R/site-library/BH/include/boost/concept_check.hpp:208:5: required from ‘struct boost::Convertible’
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:32:62: required by substitution of ‘template boost::concepts::detail::yes boost::concepts::detail::has_constraints_(Model*, wrap_constraints*) [with Model = boost::Convertible]’
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:42:5: required from ‘const bool boost::concepts::not_satisfied >::value’
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:45:51: required from ‘struct boost::concepts::not_satisfied >’
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/general.hpp:72:8: required from ‘struct boost::concepts::requirement_)>’
-/usr/local/lib/R/site-library/BH/include/boost/range/concepts.hpp:152:13: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-/usr/local/lib/R/site-library/BH/include/boost/concept/detail/general.hpp:72:8: required from ‘struct boost::concepts::requirement_ >, std::less, void> >)>’
-/usr/local/lib/R/site-library/BH/include/boost/range/adaptor/reversed.hpp:52:13: required from ‘boost::range_detail::reversed_range boost::adaptors::reverse(BidirectionalRange&) [with BidirectionalRange = boost::container::flat_map