无法安装Matrix 1.6-1旧版本致函数报错，寻求解决方法
问题背景
在SingleCellExperiment对象上运行quickCluster函数时出现报错：
Error in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth = TRUE, :
function 'as_cholmod_sparse' not provided by package 'Matrix'
查阅资料得知安装Matrix旧版本（1.6-1）可解决该问题，但安装过程中出现编译失败。
尝试的安装命令及报错
执行以下命令安装指定版本的Matrix：
install.packages("remotes") remotes::install_version("Matrix", version = "1.6-1")
返回编译失败错误：
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
已尝试的无效操作
- 卸载Matrix、irlba、Seurat后重新安装，问题未解决
Session信息
> 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
解决思路建议
修复gfortran依赖：报错核心是找不到
libgfortran库，这是编译Matrix包的必需组件。在Apple Silicon Mac上，可通过Homebrew安装gcc（包含gfortran）：brew install gcc安装完成后重新运行Matrix的安装命令。
安装预编译二进制包：跳过源码编译，使用
pak包尝试安装适配系统的预编译版本：install.packages("pak") pak::pkg_install("Matrix@1.6-1")pak会自动寻找兼容的二进制包，降低编译失败概率。适配新版Matrix：检查
quickCluster所属的scran包是否有更新版本，确认是否已修复与Matrix 1.6-5的兼容问题，若有则直接升级scran：BiocManager::install("scran")创建隔离R环境：使用
renv搭建独立环境，在环境内安装指定版本的Matrix及依赖，避免干扰全局环境：install.packages("renv") renv::init() renv::install("Matrix@1.6-1")
内容的提问来源于stack exchange，提问作者Fernanda França
