Changes in Matrix 1.6-2 breaking irlba: `function 'as_cholmod_sparse' not provided by package 'Matrix'`

[PeteHaitch]

Hi @bwlewis,

Changes in Matrix 1.6-2 seem to have broken irlba::irlba() for at least some types of sparse matrices.
I'm afraid I don't understand enough of Matrix and irlba to provide much help at this stage.

Cheers,
Pete

---

With Matrix 1.6-2

# Example taken from help("sparseMatrix", package = "Matrix").
i <- c(1,3:8); j <- c(2,9,6:10); x <- 7 * (1:7)
A <- Matrix::sparseMatrix(i, j, x = x)

irlba::irlba(A)
#> Warning in irlba::irlba(A): You're computing too large a percentage of total
#> singular values, use a standard svd instead.
#> Error in irlba::irlba(A): function 'as_cholmod_sparse' not provided by package 'Matrix'

Session info

sessionInfo()
#> R version 4.3.1 (2023-06-16)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: CentOS Linux 7 (Core)
#> 
#> Matrix products: default
#> BLAS:   /stornext/System/data/apps/R/R-4.3.1/lib64/R/lib/libRblas.so 
#> LAPACK: /stornext/System/data/apps/R/R-4.3.1/lib64/R/lib/libRlapack.so;  LAPACK version 3.11.0
#> 
#> 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: Australia/Melbourne
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> loaded via a namespace (and not attached):
#>  [1] digest_0.6.33     fastmap_1.1.1     Matrix_1.6-2      xfun_0.41        
#>  [5] lattice_0.21-8    glue_1.6.2        knitr_1.45        htmltools_0.5.7  
#>  [9] rmarkdown_2.25    lifecycle_1.0.4   cli_3.6.1         grid_4.3.1       
#> [13] reprex_2.0.2      withr_2.5.2       compiler_4.3.1    rstudioapi_0.15.0
#> [17] tools_4.3.1       irlba_2.3.5.1     evaluate_0.23     yaml_2.3.7       
#> [21] rlang_1.1.2       fs_1.6.3

---

With Matrix 1.6-1

# Example taken from help("sparseMatrix", package = "Matrix").
i <- c(1,3:8); j <- c(2,9,6:10); x <- 7 * (1:7)
A <- Matrix::sparseMatrix(i, j, x = x)

irlba::irlba(A)
#> Warning in irlba::irlba(A): You're computing too large a percentage of total
#> singular values, use a standard svd instead.
#> $d
#> [1] 49.00000 44.27189 35.00000 28.00000 21.00000
#> 
#> $u
#>               [,1]          [,2]          [,3]          [,4]          [,5]
#> [1,]  1.179612e-16 -6.418477e-17 -1.942890e-16  6.938894e-17  1.110223e-16
#> [2,]  0.000000e+00  0.000000e+00  0.000000e+00  0.000000e+00  0.000000e+00
#> [3,]  3.105155e-16  3.162278e-01 -6.245005e-17  1.110223e-16 -3.816392e-17
#> [4,] -1.734723e-16 -2.428613e-17 -3.885781e-16  5.273559e-16  1.000000e+00
#> [5,] -1.942890e-16 -2.602085e-16  9.436896e-16  1.000000e+00 -3.608225e-16
#> [6,] -2.498002e-16 -2.012279e-16 -1.000000e+00  1.054712e-15  2.775558e-17
#> [7,]  9.419548e-16  9.486833e-01 -1.318390e-16  2.914335e-16 -1.734723e-17
#> [8,]  1.000000e+00 -1.334002e-15 -3.885781e-16 -3.053113e-16  8.326673e-17
#> 
#> $v
#>                [,1]          [,2]          [,3]          [,4]          [,5]
#>  [1,] -6.938894e-17 -1.474515e-16 -1.665335e-16 -1.387779e-16  0.000000e+00
#>  [2,] -9.714451e-17 -9.020562e-17  2.220446e-16  5.551115e-17  1.665335e-16
#>  [3,]  6.071532e-18  1.192622e-17  2.081668e-17  1.040834e-17  1.734723e-18
#>  [4,]  1.127570e-17  1.474515e-17  3.122502e-17  2.775558e-17 -1.040834e-17
#>  [5,] -1.994932e-17 -4.770490e-17 -4.857226e-17 -1.734723e-17 -1.040834e-17
#>  [6,] -7.632783e-17  5.898060e-17 -3.330669e-16  6.938894e-16  1.000000e+00
#>  [7,] -8.326673e-17 -5.898060e-17  1.249001e-15  1.000000e+00 -3.053113e-16
#>  [8,] -3.816392e-16 -1.734723e-16 -1.000000e+00  9.714451e-16  2.775558e-17
#>  [9,]  1.065120e-15  1.000000e+00 -1.474515e-16  2.029626e-16 -1.908196e-16
#> [10,]  1.000000e+00 -1.234689e-15 -5.134781e-16  2.012279e-16  2.463307e-16
#> 
#> $iter
#> [1] 1
#> 
#> $mprod
#> [1] 16

Session info

sessionInfo()
#> R version 4.3.1 (2023-06-16)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: CentOS Linux 7 (Core)
#> 
#> Matrix products: default
#> BLAS:   /stornext/System/data/apps/R/R-4.3.1/lib64/R/lib/libRblas.so 
#> LAPACK: /stornext/System/data/apps/R/R-4.3.1/lib64/R/lib/libRlapack.so;  LAPACK version 3.11.0
#> 
#> 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: Australia/Melbourne
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> loaded via a namespace (and not attached):
#>  [1] digest_0.6.33     fastmap_1.1.1     Matrix_1.6-1      xfun_0.41        
#>  [5] lattice_0.21-8    glue_1.6.2        knitr_1.45        htmltools_0.5.7  
#>  [9] rmarkdown_2.25    lifecycle_1.0.4   cli_3.6.1         grid_4.3.1       
#> [13] reprex_2.0.2      withr_2.5.2       compiler_4.3.1    rstudioapi_0.15.0
#> [17] tools_4.3.1       irlba_2.3.5.1     evaluate_0.23     yaml_2.3.7       
#> [21] rlang_1.1.2       fs_1.6.3

[bwlewis]

Thanks for reporting this! This will force me to revisit a project we started a while back at re-implementing the sparse parts of the code in a more generic way. I'll try and get that ready as soon as I can.

…

On 11/8/23, Peter Hickey ***@***.***> wrote: Hi @bwlewis, Changes in **Matrix** 1.6-2 seem to have broken `irlba::irlba()` for at least some types of sparse matrices. I'm afraid I don't understand enough of **Matrix** and **irlba** to provide much help at this stage. Cheers, Pete --------- # With **Matrix** 1.6-2 ``` r # Example taken from help("sparseMatrix", package = "Matrix"). i <- c(1,3:8); j <- c(2,9,6:10); x <- 7 * (1:7) A <- Matrix::sparseMatrix(i, j, x = x) irlba::irlba(A) #> Warning in irlba::irlba(A): You're computing too large a percentage of total #> singular values, use a standard svd instead. #> Error in irlba::irlba(A): function 'as_cholmod_sparse' not provided by package 'Matrix' ``` <details style="margin-bottom:10px;"> <summary> Session info </summary> ``` r sessionInfo() #> R version 4.3.1 (2023-06-16) #> Platform: x86_64-pc-linux-gnu (64-bit) #> Running under: CentOS Linux 7 (Core) #> #> Matrix products: default #> BLAS: /stornext/System/data/apps/R/R-4.3.1/lib64/R/lib/libRblas.so #> LAPACK: /stornext/System/data/apps/R/R-4.3.1/lib64/R/lib/libRlapack.so; LAPACK version 3.11.0 #> #> 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: Australia/Melbourne #> tzcode source: system (glibc) #> #> attached base packages: #> [1] stats graphics grDevices utils datasets methods base #> #> loaded via a namespace (and not attached): #> [1] digest_0.6.33 fastmap_1.1.1 Matrix_1.6-2 xfun_0.41 #> [5] lattice_0.21-8 glue_1.6.2 knitr_1.45 htmltools_0.5.7 #> [9] rmarkdown_2.25 lifecycle_1.0.4 cli_3.6.1 grid_4.3.1 #> [13] reprex_2.0.2 withr_2.5.2 compiler_4.3.1 rstudioapi_0.15.0 #> [17] tools_4.3.1 irlba_2.3.5.1 evaluate_0.23 yaml_2.3.7 #> [21] rlang_1.1.2 fs_1.6.3 ``` </details> ------- # With **Matrix** 1.6-1 ``` r # Example taken from help("sparseMatrix", package = "Matrix"). i <- c(1,3:8); j <- c(2,9,6:10); x <- 7 * (1:7) A <- Matrix::sparseMatrix(i, j, x = x) irlba::irlba(A) #> Warning in irlba::irlba(A): You're computing too large a percentage of total #> singular values, use a standard svd instead. #> $d #> [1] 49.00000 44.27189 35.00000 28.00000 21.00000 #> #> $u #> [,1] [,2] [,3] [,4] [,5] #> [1,] 1.179612e-16 -6.418477e-17 -1.942890e-16 6.938894e-17 1.110223e-16 #> [2,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 #> [3,] 3.105155e-16 3.162278e-01 -6.245005e-17 1.110223e-16 -3.816392e-17 #> [4,] -1.734723e-16 -2.428613e-17 -3.885781e-16 5.273559e-16 1.000000e+00 #> [5,] -1.942890e-16 -2.602085e-16 9.436896e-16 1.000000e+00 -3.608225e-16 #> [6,] -2.498002e-16 -2.012279e-16 -1.000000e+00 1.054712e-15 2.775558e-17 #> [7,] 9.419548e-16 9.486833e-01 -1.318390e-16 2.914335e-16 -1.734723e-17 #> [8,] 1.000000e+00 -1.334002e-15 -3.885781e-16 -3.053113e-16 8.326673e-17 #> #> $v #> [,1] [,2] [,3] [,4] [,5] #> [1,] -6.938894e-17 -1.474515e-16 -1.665335e-16 -1.387779e-16 0.000000e+00 #> [2,] -9.714451e-17 -9.020562e-17 2.220446e-16 5.551115e-17 1.665335e-16 #> [3,] 6.071532e-18 1.192622e-17 2.081668e-17 1.040834e-17 1.734723e-18 #> [4,] 1.127570e-17 1.474515e-17 3.122502e-17 2.775558e-17 -1.040834e-17 #> [5,] -1.994932e-17 -4.770490e-17 -4.857226e-17 -1.734723e-17 -1.040834e-17 #> [6,] -7.632783e-17 5.898060e-17 -3.330669e-16 6.938894e-16 1.000000e+00 #> [7,] -8.326673e-17 -5.898060e-17 1.249001e-15 1.000000e+00 -3.053113e-16 #> [8,] -3.816392e-16 -1.734723e-16 -1.000000e+00 9.714451e-16 2.775558e-17 #> [9,] 1.065120e-15 1.000000e+00 -1.474515e-16 2.029626e-16 -1.908196e-16 #> [10,] 1.000000e+00 -1.234689e-15 -5.134781e-16 2.012279e-16 2.463307e-16 #> #> $iter #> [1] 1 #> #> $mprod #> [1] 16 ``` <details style="margin-bottom:10px;"> <summary> Session info </summary> ``` r sessionInfo() #> R version 4.3.1 (2023-06-16) #> Platform: x86_64-pc-linux-gnu (64-bit) #> Running under: CentOS Linux 7 (Core) #> #> Matrix products: default #> BLAS: /stornext/System/data/apps/R/R-4.3.1/lib64/R/lib/libRblas.so #> LAPACK: /stornext/System/data/apps/R/R-4.3.1/lib64/R/lib/libRlapack.so; LAPACK version 3.11.0 #> #> 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: Australia/Melbourne #> tzcode source: system (glibc) #> #> attached base packages: #> [1] stats graphics grDevices utils datasets methods base #> #> loaded via a namespace (and not attached): #> [1] digest_0.6.33 fastmap_1.1.1 Matrix_1.6-1 xfun_0.41 #> [5] lattice_0.21-8 glue_1.6.2 knitr_1.45 htmltools_0.5.7 #> [9] rmarkdown_2.25 lifecycle_1.0.4 cli_3.6.1 grid_4.3.1 #> [13] reprex_2.0.2 withr_2.5.2 compiler_4.3.1 rstudioapi_0.15.0 #> [17] tools_4.3.1 irlba_2.3.5.1 evaluate_0.23 yaml_2.3.7 #> [21] rlang_1.1.2 fs_1.6.3 ``` </details> -- Reply to this email directly or view it on GitHub: #70 You are receiving this because you were mentioned. Message ID: ***@***.***>

[PeteHaitch]

Re-installing irlba from source after upgrading to Matrix v1.6-2 seems to have resolved the error.

# Example taken from help("sparseMatrix", package = "Matrix").
i <- c(1,3:8); j <- c(2,9,6:10); x <- 7 * (1:7)
A <- Matrix::sparseMatrix(i, j, x = x)

irlba::irlba(A)
#> Warning in irlba::irlba(A): You're computing too large a percentage of total
#> singular values, use a standard svd instead.
#> $d
#> [1] 49.00000 44.27189 35.00000 28.00000 21.00000
#> 
#> $u
#>               [,1]          [,2]          [,3]          [,4]          [,5]
#> [1,] -4.076600e-17 -1.873501e-16 -1.387779e-17 -2.775558e-17  1.387779e-16
#> [2,]  0.000000e+00  0.000000e+00  0.000000e+00  0.000000e+00  0.000000e+00
#> [3,]  8.023096e-18 -3.162278e-01 -1.942890e-16 -1.873501e-16  1.040834e-16
#> [4,]  3.469447e-18 -1.665335e-16  7.216450e-16  1.426637e-14 -1.000000e+00
#> [5,] -3.122502e-17 -1.249001e-16 -4.440892e-16  1.000000e+00  1.459943e-14
#> [6,]  1.301043e-16  5.689893e-16 -1.000000e+00 -4.440892e-16 -8.881784e-16
#> [7,] -6.938894e-18 -9.486833e-01 -4.857226e-16 -5.273559e-16  8.326673e-17
#> [8,]  1.000000e+00 -1.656661e-16  1.578598e-16 -2.081668e-17 -5.551115e-17
#> 
#> $v
#>                [,1]          [,2]          [,3]          [,4]          [,5]
#>  [1,] -7.047314e-18  1.214306e-17  3.469447e-18  6.938894e-18  6.938894e-18
#>  [2,]  2.081668e-17 -9.020562e-17  3.053113e-16  1.110223e-16  1.110223e-16
#>  [3,]  8.890458e-18 -1.214306e-17  1.387779e-17 -3.469447e-18 -5.551115e-17
#>  [4,] -4.250073e-17  5.204170e-17 -3.469447e-17  6.938894e-18  0.000000e+00
#>  [5,] -2.222614e-17  3.122502e-17 -1.734723e-17 -3.469447e-18  1.387779e-17
#>  [6,] -3.729655e-17 -5.551115e-17  1.054712e-15  1.915135e-14 -1.000000e+00
#>  [7,] -1.175275e-16 -9.714451e-17 -6.522560e-16  1.000000e+00  1.948441e-14
#>  [8,] -2.211772e-17  3.920475e-16 -1.000000e+00 -7.563394e-16 -1.415534e-15
#>  [9,]  3.642919e-17 -1.000000e+00 -8.187895e-16 -3.677614e-16  2.012279e-16
#> [10,]  1.000000e+00 -5.204170e-18  1.600282e-16  5.854692e-17 -8.847090e-17
#> 
#> $iter
#> [1] 1
#> 
#> $mprod
#> [1] 16

Session info

sessionInfo()
#> R version 4.3.1 (2023-06-16)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: CentOS Linux 7 (Core)
#> 
#> Matrix products: default
#> BLAS:   /stornext/System/data/apps/R/R-4.3.1/lib64/R/lib/libRblas.so 
#> LAPACK: /stornext/System/data/apps/R/R-4.3.1/lib64/R/lib/libRlapack.so;  LAPACK version 3.11.0
#> 
#> 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: Australia/Melbourne
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> loaded via a namespace (and not attached):
#>  [1] digest_0.6.33     fastmap_1.1.1     Matrix_1.6-2      xfun_0.41        
#>  [5] lattice_0.22-5    glue_1.6.2        knitr_1.45        htmltools_0.5.7  
#>  [9] rmarkdown_2.25    lifecycle_1.0.4   cli_3.6.1         grid_4.3.1       
#> [13] reprex_2.0.2      withr_2.5.2       compiler_4.3.1    rstudioapi_0.15.0
#> [17] tools_4.3.1       irlba_2.3.5.1     evaluate_0.23     yaml_2.3.7       
#> [21] rlang_1.1.2       fs_1.6.3

I never fully understand when packages have to be re-built/re-installed when dependencies like Matrix update.
But if I had to guess, perhaps these remaps (https://github.com/cran/Matrix/blob/323f4d9b0722ba6f61682874a8d92ebdbf93d8fa/inst/include/Matrix/remap.h) are picked up when irlba is re-installed from source.

[bwlewis]

Also good to know. There is a re-write of the sparse/Matrix-dependency code that has been planned for a long time that will simplify installation and handle more special structured matrix cases. I will work on this this fall.

…

On 11/9/23, Peter Hickey ***@***.***> wrote: Re-installing *irlba* from source after upgrading to *Matrix* v1.6-2 seems to have resolved the error. ``` r # Example taken from help("sparseMatrix", package = "Matrix"). i <- c(1,3:8); j <- c(2,9,6:10); x <- 7 * (1:7) A <- Matrix::sparseMatrix(i, j, x = x) irlba::irlba(A) #> Warning in irlba::irlba(A): You're computing too large a percentage of total #> singular values, use a standard svd instead. #> $d #> [1] 49.00000 44.27189 35.00000 28.00000 21.00000 #> #> $u #> [,1] [,2] [,3] [,4] [,5] #> [1,] -4.076600e-17 -1.873501e-16 -1.387779e-17 -2.775558e-17 1.387779e-16 #> [2,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 #> [3,] 8.023096e-18 -3.162278e-01 -1.942890e-16 -1.873501e-16 1.040834e-16 #> [4,] 3.469447e-18 -1.665335e-16 7.216450e-16 1.426637e-14 -1.000000e+00 #> [5,] -3.122502e-17 -1.249001e-16 -4.440892e-16 1.000000e+00 1.459943e-14 #> [6,] 1.301043e-16 5.689893e-16 -1.000000e+00 -4.440892e-16 -8.881784e-16 #> [7,] -6.938894e-18 -9.486833e-01 -4.857226e-16 -5.273559e-16 8.326673e-17 #> [8,] 1.000000e+00 -1.656661e-16 1.578598e-16 -2.081668e-17 -5.551115e-17 #> #> $v #> [,1] [,2] [,3] [,4] [,5] #> [1,] -7.047314e-18 1.214306e-17 3.469447e-18 6.938894e-18 6.938894e-18 #> [2,] 2.081668e-17 -9.020562e-17 3.053113e-16 1.110223e-16 1.110223e-16 #> [3,] 8.890458e-18 -1.214306e-17 1.387779e-17 -3.469447e-18 -5.551115e-17 #> [4,] -4.250073e-17 5.204170e-17 -3.469447e-17 6.938894e-18 0.000000e+00 #> [5,] -2.222614e-17 3.122502e-17 -1.734723e-17 -3.469447e-18 1.387779e-17 #> [6,] -3.729655e-17 -5.551115e-17 1.054712e-15 1.915135e-14 -1.000000e+00 #> [7,] -1.175275e-16 -9.714451e-17 -6.522560e-16 1.000000e+00 1.948441e-14 #> [8,] -2.211772e-17 3.920475e-16 -1.000000e+00 -7.563394e-16 -1.415534e-15 #> [9,] 3.642919e-17 -1.000000e+00 -8.187895e-16 -3.677614e-16 2.012279e-16 #> [10,] 1.000000e+00 -5.204170e-18 1.600282e-16 5.854692e-17 -8.847090e-17 #> #> $iter #> [1] 1 #> #> $mprod #> [1] 16 ``` <details style="margin-bottom:10px;"> <summary> Session info </summary> ``` r sessionInfo() #> R version 4.3.1 (2023-06-16) #> Platform: x86_64-pc-linux-gnu (64-bit) #> Running under: CentOS Linux 7 (Core) #> #> Matrix products: default #> BLAS: /stornext/System/data/apps/R/R-4.3.1/lib64/R/lib/libRblas.so #> LAPACK: /stornext/System/data/apps/R/R-4.3.1/lib64/R/lib/libRlapack.so; LAPACK version 3.11.0 #> #> 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: Australia/Melbourne #> tzcode source: system (glibc) #> #> attached base packages: #> [1] stats graphics grDevices utils datasets methods base #> #> loaded via a namespace (and not attached): #> [1] digest_0.6.33 fastmap_1.1.1 Matrix_1.6-2 xfun_0.41 #> [5] lattice_0.22-5 glue_1.6.2 knitr_1.45 htmltools_0.5.7 #> [9] rmarkdown_2.25 lifecycle_1.0.4 cli_3.6.1 grid_4.3.1 #> [13] reprex_2.0.2 withr_2.5.2 compiler_4.3.1 rstudioapi_0.15.0 #> [17] tools_4.3.1 irlba_2.3.5.1 evaluate_0.23 yaml_2.3.7 #> [21] rlang_1.1.2 fs_1.6.3 ``` </details> I never fully understand when packages have to be re-built/re-installed when dependencies like *Matrix* update. But if I had to guess, perhaps these remaps (https://github.com/cran/Matrix/blob/323f4d9b0722ba6f61682874a8d92ebdbf93d8fa/inst/include/Matrix/remap.h) are picked up when *irlba* is re-installed from source. -- Reply to this email directly or view it on GitHub: #70 (comment) You are receiving this because you were mentioned. Message ID: ***@***.***>

[PeteHaitch]

And a bit more info now posted by the Matrix developers: https://stat.ethz.ch/pipermail/r-package-devel/2023q4/010051.html

[hpages]

Thanks @PeteHaitch.

@bwlewis Note that it's enough for you to bump irlba version and resubmit to CRAN. The new version will then propagate to the user machine which will trigger a reinstallation.

The problem affects any user who installed irlba before Matrix 1.6-2 got into the wild and landed on their machine. Unfortunately the info posted by the Matrix developers won't help them, and it's not realistic to expect that the thousands of users in that situation reinstall irlba manually. Most users will see the error in a context involving many packages and won't have a clue what package is actually the culprit. This is the case for Bioconductor users where 40+ Bioconductor packages are affected indirectly via irlba.

However, if a new version of irlba shows up on CRAN, then the problem will be solved for all the users and system admins that run update.packages() on a regular basis.

Thanks,
H.

[kvittingseerup]

Is there any update on how to solve this problem?

[sfplab]

I tried reinstalling irlba, but the issue persists with Matrix 1.6-3. Major issue for anyone running UMAP.