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bug in setupX? #56

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tabpeter opened this issue Apr 25, 2024 · 1 comment
Open

bug in setupX? #56

tabpeter opened this issue Apr 25, 2024 · 1 comment

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@tabpeter
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sessionInfo()
#> R version 4.3.3 (2024-02-29)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 22.04.4 LTS
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
#> 
#> 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       
#> 
#> time zone: America/Chicago
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> loaded via a namespace (and not attached):
#>  [1] styler_1.10.3     digest_0.6.35     fastmap_1.1.1     xfun_0.41        
#>  [5] magrittr_2.0.3    glue_1.7.0        R.utils_2.12.3    knitr_1.45       
#>  [9] htmltools_0.5.7   rmarkdown_2.26.1  lifecycle_1.0.4   cli_3.6.2        
#> [13] R.methodsS3_1.8.2 vctrs_0.6.5       reprex_2.1.0      withr_3.0.0      
#> [17] compiler_4.3.3    R.oo_1.26.0       R.cache_0.16.0    purrr_1.0.2      
#> [21] rstudioapi_0.15.0 tools_4.3.3       evaluate_0.23     yaml_2.3.8       
#> [25] rlang_1.1.3       fs_1.6.3
X <- matrix(rnorm(1000*10000), nrow = 1000, ncol = 10000)
class(X); dim(X)
#> [1] "matrix" "array"
#> [1]  1000 10000

dir <- tempdir()              
write.table(X, file = paste0(dir, "/X.txt"),
            sep = "\t",
            quote = FALSE,
            row.names = FALSE,
            col.names = FALSE)

# attempt to create backing files (.bin, .desc)
bm_X <- biglasso::setupX(filename = paste0(dir, "/X.txt"),
                      dir = dir,
                      backingfile = paste0(dir, "/X.bin"),
                      descriptorfile = paste0(dir, "/X.desc"),
                      sep = '\t') 
#> Reading data from file, and creating file-backed big.matrix...
#> This should take a while if the data is very large...
#> Start time:  2024-04-25 11:33:59
#> Error in filebacked.big.matrix(nrow = nrow, ncol = ncol, type = type, : The path to the descriptor and backing file are specified with the backingpath option

Created on 2024-04-25 with reprex v2.1.0

@pbreheny
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pbreheny commented May 1, 2024

The correct syntax is:

bm_X <- biglasso::setupX(filename = paste0(dir, "/X.txt"),
                         dir = dir,
                         backingfile = "X.bin",
                         descriptorfile = "X.desc",
                         sep = '\t') 
  1. Does this work on your machine?
  2. Is this incorrectly documented somewhere in the package?

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