服务器centos8安装monocle3包
2021-02-10 本文已影响0人
土豆学生信
最近在做单细胞的学习，跑拟时序分析代码（cds<- cluster_cells(cds）)的时候，莫名奇妙的Rstudio崩溃重启，本来以为python的原因，后来发现之前monocle3根本没有装上，神奇的是前面打代码可以运行！！！所以需要重新安装monocle3包。话不多说，上代码：
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# 一些依赖包，安装monocle3总是提示位置不存在，先安装几个依赖包解决
BiocManager::install(c('SummarizedExperiment', 'S4Vectors',
'limma', 'DelayedMatrixStats',
'DelayedArray', 'BiocGenerics',
'batchelor', 'SingleCellExperiment',
'Biobase',"GenomeInfoDb"))
# (可选)如果要在细胞聚类时设定分辨率参数(resolution)，就要安装一个python包
install.packages('reticulate') #为了调用Python
reticulate::py_install("louvain")
# 现在安装3版本，还是要通过github
devtools::install_github('cole-trapnell-lab/leidenbase')#必须先安装这个自家的产品
devtools::install_github('cole-trapnell-lab/monocle3', ref="develop")
网速不好，改为本地安装
先下载
https://github.com/cole-trapnell-lab/leidenbase
https://github.com/cole-trapnell-lab/monocle3
后上传相应的文件夹，注意路径
devtools::install_local("leidenbase-master.zip")
devtools::install_local("monocle3-master.zip")
# 重启Rstudio，检测是否成功
library(monocle3)
sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 8
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.3.so
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
attached base packages:
[1] stats4 parallel stats graphics grDevices utils
[7] datasets methods base
other attached packages:
[1] monocle3_0.2.3.0 SingleCellExperiment_1.12.0
[3] SummarizedExperiment_1.20.0 GenomicRanges_1.42.0
[5] GenomeInfoDb_1.26.2 IRanges_2.24.1
[7] S4Vectors_0.28.1 MatrixGenerics_1.2.1
[9] matrixStats_0.58.0 Biobase_2.50.0
[11] BiocGenerics_0.36.0
loaded via a namespace (and not attached):
[1] bitops_1.0-6 fs_1.5.0
[3] usethis_2.0.0 devtools_2.3.2
[5] bit64_4.0.5 RColorBrewer_1.1-2
[7] progress_1.2.2 httr_1.4.2
[9] rprojroot_2.0.2 tools_4.0.3
[11] R6_2.5.0 DBI_1.1.1
[13] colorspace_2.0-0 withr_2.4.1
[15] gridExtra_2.3 tidyselect_1.1.0
[17] prettyunits_1.1.1 processx_3.4.5
[19] bit_4.0.4 curl_4.3
[21] compiler_4.0.3 cli_2.3.0
[23] xml2_1.3.2 desc_1.2.0
[25] DelayedArray_0.16.1 scales_1.1.1
[27] callr_3.5.1 askpass_1.1
[29] rappdirs_0.3.3 stringr_1.4.0
[31] XVector_0.30.0 pkgconfig_2.0.3
[33] sessioninfo_1.1.1 dbplyr_2.1.0
[35] fastmap_1.1.0 rlang_0.4.10
[37] rstudioapi_0.13 RSQLite_2.2.3
[39] generics_0.1.0 jsonlite_1.7.2
[41] dplyr_1.0.4 RCurl_1.98-1.2
[43] magrittr_2.0.1 GenomeInfoDbData_1.2.4
[45] Matrix_1.3-2 Rcpp_1.0.6
[47] munsell_0.5.0 viridis_0.5.1
[49] reticulate_1.18 lifecycle_0.2.0
[51] stringi_1.5.3 zlibbioc_1.36.0
[53] pkgbuild_1.2.0 plyr_1.8.6
[55] BiocFileCache_1.14.0 grid_4.0.3
[57] blob_1.2.1 crayon_1.4.1
[59] lattice_0.20-41 hms_1.0.0
[61] ps_1.5.0 pillar_1.4.7
[63] reshape2_1.4.4 biomaRt_2.46.2
[65] pkgload_1.1.0 XML_3.99-0.5
[67] glue_1.4.2 remotes_2.2.0
[69] BiocManager_1.30.10 vctrs_0.3.6
[71] testthat_3.0.1 gtable_0.3.0
[73] openssl_1.4.3 purrr_0.3.4
[75] assertthat_0.2.1 cachem_1.0.3
[77] ggplot2_3.3.3 viridisLite_0.3.0
[79] tibble_3.0.6 pheatmap_1.0.12
[81] AnnotationDbi_1.52.0 memoise_2.0.0
[83] ellipsis_0.3.1
依赖包真多，所以不好装，随口吐槽一下！
