Bioconductor安装

ice-melt

Bioconductor安装

https://www.bioconductor.org/install/k

可能更新已有Bioconductor的版本

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.13")

R镜像源的切换

https://www.cnblogs.com/raisok/p/10967112.html

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错误记录

1. 使用 `BiocManager::install('scRNAseq')` 安装报错

* installing *source* package ‘BiocFileCache’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
错误: package ‘ rappdirs ’ was installed before R 4.0.0: please re-install it
停止执行
ERROR: lazy loading failed for package ‘BiocFileCache’
* removing ‘/data_raid/home/lx/R/x86_64-pc-linux-gnu-library/4.1/BiocFileCache’

# 查看安装lib路径
.libPaths()
[1] "/data_raid/home/lx/R/x86_64-pc-linux-gnu-library/4.1"
[2] "/usr/lib/R/site-library"   

# 找到 rappdirs 目录 ，删除
# 因为安装过之前的版本，需要删除后重新安装对应版本
rm -rf /usr/lib/R/site-library/rappdirs

ice-melt

@ice-melt

错误记录

> library(scRNAseq)
> sce <- MacoskoRetinaData()

snapshotDate(): 2021-05-18
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
loading from cache
错误: failed to load resource
  name: EH2690
  title: Macosko retina counts
  reason: 读取链结时发生了错误

原因：大陆用户在直接连接默认CRAN时由于网络问题无法正常连接
修改源

source("http://bioconductor.org/biocLite.R")
options(BioC_mirror="http://mirrors.ustc.edu.cn/bioc/")
biocLite("RGalaxy")##这样就用中科大的镜像来下载包啦
## bioconductor还有很多其它镜像：https://www.bioconductor.org/about/mirrors/
##https://stat.ethz.ch/R-manual/R-devel/library/utils/html/chooseBioCmirror.html
options(BioC_mirror="https://mirrors.tuna.tsinghua.edu.cn/bioconductor")
options("repos" = c(CRAN="https://mirrors.tuna.tsinghua.edu.cn/CRAN/"))

发现问依旧
通过debug源码定位到cache目录~/.cache/R,
该目录下ExperimentHub里的数据没完成，有文件处于LOCK状态，删除该目录
再次运行代码会重新下载数据，等待下载结束

Bioconductor安装

Bioconductor安装

R镜像源的切换

========================

错误记录

1. 使用 BiocManager::install('scRNAseq') 安装报错

错误记录

1. 使用 `BiocManager::install('scRNAseq')` 安装报错