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`graph_from_incidence_matrix()` errors when a dense matrix contains `NA`s and `weighted = TRUE`
Describe the bug
This line doesn't handle NAs in the incidence matrix:
https://github.com/igraph/rigraph/blob/da27d5b5f79efb9e0a5bf1d9e5bdd91c24d30ca7/R/incidence.R#L89
... and so this line chokes trying to convert NA to numeric:
https://github.com/igraph/rigraph/blob/da27d5b5f79efb9e0a5bf1d9e5bdd91c24d30ca7/R/incidence.R#L93
To reproduce
library(igraph)
#>
#> Attaching package: 'igraph'
#> The following objects are masked from 'package:stats':
#>
#> decompose, spectrum
#> The following object is masked from 'package:base':
#>
#> union
library(Matrix)
m <- matrix(c(1:6), 2, 3)
n <- replace(m, m == 3, NA)
N <- Matrix(n, sparse = TRUE)
## Weighted dense with no NA runs
graph_from_incidence_matrix(m, weighted = TRUE)
#> IGRAPH 0ba9564 U-WB 5 6 --
#> + attr: type (v/l), weight (e/n)
#> + edges from 0ba9564:
#> [1] 1--3 1--4 1--5 2--3 2--4 2--5
## Unweighted dense with NA runs
graph_from_incidence_matrix(n)
#> IGRAPH 3bca128 U--B 5 6 --
#> + attr: type (v/l)
#> + edges from 3bca128:
#> [1] 1--3 1--4 1--5 2--3 2--4 2--5
## Weighted sparse with NA runs
graph_from_incidence_matrix(N, weighted = TRUE)
#> IGRAPH 5cc6a14 U-WB 5 6 --
#> + attr: type (v/l), weight (e/n)
#> + edges from 5cc6a14:
#> [1] 1--3 2--3 1--4 2--4 1--5 2--5
## Weighted dense with NA crashes
graph_from_incidence_matrix(n, weighted = TRUE)
#> Error in numeric(2 * no.edges): vector size cannot be NA/NaN
Created on 2023-10-25 with reprex v2.0.2
Version information
- R/igraph version: 1.5.1
- R version: 4.1.2
- Operating system: Ubuntu 20.04.6 LTS
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Matrix_1.6-1.1 igraph_1.5.1
loaded via a namespace (and not attached):
[1] rstudioapi_0.15.0 knitr_1.44 magrittr_2.0.3 lattice_0.20-45
[5] R.cache_0.16.0 R6_2.5.1 rlang_1.1.1 fastmap_1.1.1
[9] fansi_1.0.5 styler_1.10.2 tools_4.1.2 grid_4.1.2
[13] xfun_0.40 R.oo_1.25.0 utf8_1.2.3 cli_3.6.1
[17] clipr_0.8.0 withr_2.5.1 htmltools_0.5.6.1 yaml_2.3.7
[21] digest_0.6.33 tibble_3.2.1 lifecycle_1.0.3 processx_3.8.2
[25] callr_3.7.3 purrr_1.0.2 ps_1.7.5 vctrs_0.6.4
[29] R.utils_2.12.2 fs_1.6.3 glue_1.6.2 evaluate_0.22
[33] rmarkdown_2.25 unix_1.5.5 reprex_2.0.2 compiler_4.1.2
[37] pillar_1.9.0 R.methodsS3_1.8.2 pkgconfig_2.0.3
@szhorvat what should happen when incidence contains NA values? Should the function error earlier with an informative message, or should it be tweaked "somehow" to ignore the NAs for instance?
