Avoid integer overflow for indptr when incrementally saving a sparse …

…matrix.

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: alabaster.matrix
 Title: Load and Save Artifacts from File
-Version: 1.5.2
-Date: 2024-05-28
+Version: 1.5.3
+Date: 2024-06-07
 Authors@R: person("Aaron", "Lun", role=c("aut", "cre"), email="[email protected]")
 License: MIT + file LICENSE
 Description: 

R/saveSparseMatrix.R

@@ -146,8 +146,8 @@ setMethod("h5_write_sparse_matrix", "SVT_SparseMatrix", function(x, handle, deta
         column.counts <- integer(ncol(x))
 
     } else {
-        start <- 1L
-        cached <- 0
+        start <- 1 # don't use integers to avoid overflow
+        cached <- 0 # don't use integers to avoid overflow
         last.cleared <- 0L
 
         tstr <- type(x)
@@ -241,7 +241,7 @@ setMethod("h5_write_sparse_matrix", "ANY", function(x, handle, details, ...) {
     mhandle <- H5Screate_simple(1)
     on.exit(H5Sclose(mhandle), add=TRUE, after=FALSE)
 
-    start <- 1L
+    start <- 1 # don't use integers to avoid overflow
     pointers <- list(0)
     for (i in seq_along(grid)) {
         block <- read_sparse_block(x, grid[[i]])

inst/NEWS.Rd

@@ -7,4 +7,6 @@
 However, note that this was not implemented for the soft-deprecated \code{writeSparseMatrix}, which now errors if such objects are passed in.
 
 \item Added a \code{extract_sparse_array()} method for the \code{WrapperArraySeed} class, for some future-proofing when the seeds eventually make the switch.
+
+\item Bugfix for integer overflow when saving large sparse matrices in \code{saveObject()}.
 }}