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[r] Improve handling of arrays with with domains greater than 2^31 - 1 #1504

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merged 16 commits into from
Jun 26, 2023
+152 −47
Merged

[r] Improve handling of arrays with with domains greater than 2^31 - 1 #1504

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4df98e3
Temporarily stop erroring out on 32bit shape
aaronwolen Jun 20, 2023
36baff5
Truncate dims/coords to 31bit
aaronwolen Jun 20, 2023
6eda833
Avoid creation of CsparseMatrix with full array domain
aaronwolen Jun 20, 2023
0309a21
Remove 32bit warning from SOMASparseNDArray$read()
aaronwolen Jun 22, 2023
8c5d740
Truncate >=32bit array shapes in SOMASparseNDArrayRead$sparse_matrix()
aaronwolen Jun 22, 2023
802c086
Restore shape size assertions lower in the stack
aaronwolen Jun 22, 2023
642f8b6
Fix shape truncation
aaronwolen Jun 22, 2023
818729d
Stop removing 32bit coordinates from SOMASparseNDArray$convert_coords()
aaronwolen Jun 22, 2023
3390c45
Warn immediately
aaronwolen Jun 22, 2023
904dd5e
Refine assertion messages
aaronwolen Jun 23, 2023
939b2d6
Fix code alignment
aaronwolen Jun 23, 2023
eaf57eb
Refine sparse matrix creation
aaronwolen Jun 23, 2023
0e71ed8
Add tests for 32-bit arrays
aaronwolen Jun 23, 2023
82c2812
Fix assertions again
aaronwolen Jun 23, 2023
a7e8ae0
Bump version
aaronwolen Jun 23, 2023
20d00ce
Restore assertion that nnz < 2^31-1
aaronwolen Jun 23, 2023
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Restore assertion that nnz < 2^31-1
@aaronwolen
aaronwolen committed Jun 23, 2023
commit 20d00ce931c5ff68d8987a42875c0f7d7ca45b02
9 changes: 6 additions & 3 deletions apis/r/R/utils-readerTransformers.R
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Original file line number Diff line number Diff line change
@@ -37,9 +37,12 @@ arrow_table_to_sparse <- function(tbl, repr = c("C", "T", "R"), shape = NULL, ze
shape <- c(max(tbl$soma_dim_0)$as_vector(), max(tbl$soma_dim_1)$as_vector())
}

if (any(shape > .Machine$integer.max)) {
stop("'shape' must not exceed '.Machine$integer.max'.", call. = FALSE)
}
stopifnot(
"'shape' must not exceed '.Machine$integer.max'." =
all(shape <= .Machine$integer.max),
"A Matrix::sparseMatrix cannot hold more than 2^31 - 1 non-zero values" =
nrow(tbl) <= .Machine$integer.max
)

exceedsInt32Limit <- (
tbl$soma_dim_0 >= .Machine$integer.max | tbl$soma_dim_1 >= .Machine$integer.max