`[<-` method return wrong results for `ConvertMatrixType` object

library(BPCells)
mock_matrix <- function(ngenes, ncells) {
    cell.means <- 2^stats::runif(ngenes, 2, 10)
    cell.disp <- 100 / cell.means + 0.5
    cell.data <- matrix(stats::rnbinom(ngenes * ncells,
        mu = cell.means,
        size = 1 / cell.disp
    ), ncol = ncells)
    rownames(cell.data) <- sprintf("Gene_%s", formatC(seq_len(ngenes),
        width = 4, flag = 0
    ))
    colnames(cell.data) <- sprintf("Cell_%s", formatC(seq_len(ncells),
        width = 3, flag = 0
    ))
    cell.data
}
mat <- mock_matrix(2000, 200)
path <- normalizePath(tempfile(tmpdir = tempdir()), mustWork = FALSE)
obj <- BPCells::write_matrix_dir(mat = as(mat, "dgCMatrix"), dir = path)
#> Warning: Matrix compression performs poorly with non-integers.
#> • Consider calling convert_matrix_type if a compressed integer matrix is intended.
#> This message is displayed once every 8 hours.
obj <- BPCells::convert_matrix_type(obj, "uint32_t")
value <- matrix(sample(mat, length(mat)), nrow = nrow(mat))
obj[1:10, ] <- value[1:10, ]
mat[1:10, ] <- value[1:10, ]
testthat::expect_equal(as.matrix(obj), mat)
#> Warning: Converting to a dense matrix may use excessive memory
#> This message is displayed once every 8 hours.
#> Error: as.matrix(obj) not equal to `mat`.
#> 298499/400000 mismatches (average diff: 242)
#> [11] 4.31e-312 -  113 ==  -113
#> [12] 3.56e-311 -  203 ==  -203
#> [13] 4.75e-312 - 1139 == -1139
#> [15] 2.97e-313 - 1678 == -1678
#> [16] 8.45e-312 -   47 ==   -47
#> [17] 1.91e-312 -  224 ==  -224
#> [18] 2.12e-313 -   56 ==   -56
#> [19] 5.20e-312 -   14 ==   -14
#> [21] 3.46e-312 -   76 ==   -76
#> ...

^{Created on 2024-01-29 with reprex v2.0.2}

Session info

``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.3.1 (2023-06-16) #> os Ubuntu 22.04.3 LTS #> system x86_64, linux-gnu #> ui X11 #> language en #> collate C.UTF-8 #> ctype C.UTF-8 #> tz Asia/Shanghai #> date 2024-01-29 #> pandoc 2.9.2.1 @ /usr/bin/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> BiocGenerics 0.46.0 2023-04-25 [1] Bioconductor #> bitops 1.0-7 2021-04-24 [1] CRAN (R 4.3.1) #> BPCells * 0.1.0 2024-01-25 [1] Github (bnprks/BPCells@0d56524) #> brio 1.1.4 2023-12-10 [1] CRAN (R 4.3.1) #> cli 3.6.2 2023-12-11 [1] CRAN (R 4.3.1) #> desc 1.4.3 2023-12-10 [1] CRAN (R 4.3.1) #> digest 0.6.33 2023-07-07 [1] CRAN (R 4.3.1) #> evaluate 0.23 2023-11-01 [1] CRAN (R 4.3.1) #> fansi 1.0.6 2023-12-08 [1] CRAN (R 4.3.1) #> fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.1) #> fs 1.6.3 2023-07-20 [1] CRAN (R 4.3.1) #> GenomeInfoDb 1.36.1 2023-06-21 [1] Bioconductor #> GenomeInfoDbData 1.2.10 2023-08-08 [1] Bioconductor #> GenomicRanges 1.52.0 2023-04-25 [1] Bioconductor #> glue 1.6.2 2022-02-24 [1] CRAN (R 4.3.1) #> htmltools 0.5.7 2023-11-03 [1] CRAN (R 4.3.1) #> IRanges 2.34.1 2023-06-22 [1] Bioconductor #> knitr 1.45 2023-10-30 [1] CRAN (R 4.3.1) #> lattice 0.22-5 2023-10-24 [1] CRAN (R 4.3.1) #> lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.3.1) #> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.1) #> Matrix 1.6-4 2023-11-30 [1] CRAN (R 4.3.1) #> pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.1) #> pkgload 1.3.3 2023-09-22 [1] CRAN (R 4.3.1) #> purrr 1.0.2 2023-08-10 [1] CRAN (R 4.3.1) #> R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.3.1) #> R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.3.1) #> R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.3.1) #> R.utils 2.12.2 2022-11-11 [1] CRAN (R 4.3.1) #> R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.1) #> Rcpp 1.0.11 2023-07-06 [1] CRAN (R 4.3.1) #> RCurl 1.98-1.12 2023-03-27 [1] CRAN (R 4.3.1) #> reprex 2.0.2 2022-08-17 [1] CRAN (R 4.3.1) #> rlang 1.1.2 2023-11-04 [1] CRAN (R 4.3.1) #> rmarkdown 2.25 2023-09-18 [1] CRAN (R 4.3.1) #> rprojroot 2.0.4 2023-11-05 [1] CRAN (R 4.3.1) #> RSpectra 0.16-1 2022-04-24 [1] CRAN (R 4.3.1) #> S4Vectors 0.38.1 2023-05-02 [1] Bioconductor #> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.1) #> styler 1.10.2 2024-01-13 [1] Github (r-lib/styler@17f91fc) #> testthat 3.2.1.9000 2024-01-19 [1] Github (r-lib/testthat@fe50a22) #> utf8 1.2.4 2023-10-22 [1] CRAN (R 4.3.1) #> vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.3.1) #> withr 2.5.2 2023-10-30 [1] CRAN (R 4.3.1) #> xfun 0.41 2023-11-01 [1] CRAN (R 4.3.1) #> XVector 0.40.0 2023-04-25 [1] Bioconductor #> yaml 2.3.8 2023-12-11 [1] CRAN (R 4.3.1) #> zlibbioc 1.46.0 2023-04-25 [1] Bioconductor #> #> [1] /home/yun/Rlibrary/4.3 #> [2] /usr/local/lib/R/site-library #> [3] /usr/lib/R/site-library #> [4] /usr/lib/R/library #> #> ────────────────────────────────────────────────────────────────────────────── ```

bnprks / BPCells

`[<-` method return wrong results for `ConvertMatrixType` object #68