I've been having a series of issues that I tried to track down the origin of the problem and I think it's because I can't install Matrix 1.6-1.
I need to run a quickCluster function on a SingleCellExperiment object but I have the following error:
Error in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth = TRUE, : function 'as_cholmod_sparse' not provided by package 'Matrix'
Looking this error up, I found other people that had the same error and could get around it by installing an older version of Matrix. So I tried this:
install.packages("remotes")
remotes::install_version("Matrix", version = "1.6-1")
And got this:
ld: warning: directory not found for option '-L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0' ld: warning: directory not found for option '-L/opt/gfortran/lib' ld: library not found for -lgfortran clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [Matrix.so] Error 1 ERROR: compilation failed for package ‘Matrix’
- removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Matrix’
- restoring previous ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Matrix’ Warning message: In i.p(...) : installation of package ‘/var/folders/mx/spt7cbq57gn6ssxwq_yhzmqh0000gp/T//RtmpxuzZmQ/remotes2e406022dae6/Matrix’ had non-zero exit status
I have tried removing Matrix, removing irlba, removing Seurat, installing all over again and nothing works. Thoughts?
> sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.3.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] SummarizedExperiment_1.32.0 gtable_0.3.4 beeswarm_0.4.0 ggplot2_3.4.4
[5] remotes_2.4.2.1 processx_3.8.3 ggrepel_0.9.5 Biobase_2.62.0
[9] lattice_0.22-5 callr_3.7.3 ps_1.7.6 vctrs_0.6.5
[13] tools_4.3.2 bitops_1.0-7 generics_0.1.3 stats4_4.3.2
[17] parallel_4.3.2 tibble_3.2.1 fansi_1.0.6 pkgconfig_2.0.3
[21] BiocNeighbors_1.20.2 Matrix_1.6-5 S4Vectors_0.40.2 sparseMatrixStats_1.14.0
[25] lifecycle_1.0.4 GenomeInfoDbData_1.2.11 compiler_4.3.2 munsell_0.5.0
[29] codetools_0.2-19 vipor_0.4.7 GenomeInfoDb_1.38.5 RCurl_1.98-1.14
[33] pillar_1.9.0 crayon_1.5.2 BiocParallel_1.36.0 SingleCellExperiment_1.24.0
[37] DelayedArray_0.28.0 viridis_0.6.5 abind_1.4-5 tidyselect_1.2.0
[41] rsvd_1.0.5 BiocSingular_1.18.0 dplyr_1.1.4 grid_4.3.2
[45] colorspace_2.1-0 cli_3.6.2 SparseArray_1.2.3 scater_1.30.1
[49] magrittr_2.0.3 S4Arrays_1.2.0 pkgbuild_1.4.3 utf8_1.2.4
[53] DelayedMatrixStats_1.24.0 scales_1.3.0 ggbeeswarm_0.7.2 XVector_0.42.0
[57] matrixStats_1.2.0 gridExtra_2.3 reticulate_1.34.0 png_0.1-8
[61] ScaledMatrix_1.10.0 beachmat_2.18.0 GenomicRanges_1.54.1 IRanges_2.36.0
[65] viridisLite_0.4.2 irlba_2.3.5.1 rlang_1.1.3 Rcpp_1.0.12
[69] glue_1.7.0 scuttle_1.12.0 BiocGenerics_0.48.1 rstudioapi_0.15.0
[73] jsonlite_1.8.8 plyr_1.8.9 R6_2.5.1 MatrixGenerics_1.14.0
[77] zlibbioc_1.48.0