as.matrix sometimes gives warning on HPC

iflint1 · Oct 29, 2023 · 32c7e65 · 32c7e65
1 parent 783409e
commit 32c7e65
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Showing 4 changed files with 4 additions and 4 deletions.
diff --git a/R/compute_A1.R b/R/compute_A1.R
@@ -51,7 +51,7 @@ compute_A1 <- function(..., list, nthreads = NULL, debug = FALSE, time_limit = I
     }, error = function(e) e, warning = function(w) w)
 
     # If we don't have enough RAM to call Matrix::as.matrix.Matrix, use custom function instead.
-    if(is(tt, "error")) {
+    if(is(tt, "error") | is(tt, "warning")) {
       # Ref: https://programmerah.com/the-sparse-matrix-of-r-language-is-too-large-to-be-used-as-matrix-8856/
       as_matrix <- function(mat) {
         tmp <- matrix(data = 0L, nrow = mat@Dim[1], ncol = mat@Dim[2])

diff --git a/R/compute_A2_plus_A3.R b/R/compute_A2_plus_A3.R
@@ -51,7 +51,7 @@ compute_A2_plus_A3 <- function(..., list, nthreads = NULL, debug = FALSE, npoint
   }, error = function(e) e, warning = function(w) w)
 
   # If we don't have enough RAM to call Matrix::as.matrix.Matrix, use custom function instead.
-  if(is(tt, "error")) {
+  if(is(tt, "error") | is(tt, "warning")) {
     # Ref: https://programmerah.com/the-sparse-matrix-of-r-language-is-too-large-to-be-used-as-matrix-8856/
     as_matrix <- function(mat) {
       tmp <- matrix(data = 0L, nrow = mat@Dim[1], ncol = mat@Dim[2])

diff --git a/R/compute_G2.R b/R/compute_G2.R
@@ -52,7 +52,7 @@ compute_G2 <- function(..., list, nthreads = NULL, debug = FALSE, time_limit = I
     }, error = function(e) e, warning = function(w) w)
 
     # If we don't have enough RAM to call Matrix::as.matrix.Matrix, use custom function instead.
-    if(is(tt, "error")) {
+    if(is(tt, "error") | is(tt, "warning")) {
       # Ref: https://programmerah.com/the-sparse-matrix-of-r-language-is-too-large-to-be-used-as-matrix-8856/
       as_matrix <- function(mat) {
         tmp <- matrix(data = 0L, nrow = mat@Dim[1], ncol = mat@Dim[2])

diff --git a/R/compute_S.R b/R/compute_S.R
@@ -52,7 +52,7 @@ compute_S <- function(..., list, nthreads = NULL, debug = FALSE, time_limit = In
     }, error = function(e) e, warning = function(w) w)
 
     # If we don't have enough RAM to call Matrix::as.matrix.Matrix, use custom function instead.
-    if(is(tt, "error")) {
+    if(is(tt, "error") | is(tt, "warning")) {
       # Ref: https://programmerah.com/the-sparse-matrix-of-r-language-is-too-large-to-be-used-as-matrix-8856/
       as_matrix <- function(mat) {
         tmp <- matrix(data = 0L, nrow = mat@Dim[1], ncol = mat@Dim[2])