geochina下载中出现的问题

1.首先是下载geochina、geomirror出现问题，后来各种搜索，反复尝试：

install.packages("Biobase")
install.packages("AnnoProbe")
if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("Biobase")
library("AnnoProbe") 
library("Biobase")
library(GEOmirror)
library(GEOquery)
#以上加载不出R包可以再尝试下面代码#
#安装bioconductor包GEOquery
if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
library(devtools)
install_github("jmzeng1314/GEOmirror")
BiocManager::install("GEOquery")
#安装github包GEOmirror和AnnoProbe
remotes::install_github("jmzeng1314/GEOmirror")
remotes::install_github("jmzeng1314/AnnoProbe")
#三个包同时加载
library(AnnoProbe)
library(GEOmirror)
library(GEOquery)
#下载获取GSE39582数据 
gset=AnnoProbe::geoChina('GSE39582')

2.下载gse数据集出现问题，好像是网速和时间设置的问题，在一位网友的帖子搜索到了答案：

Error in download.file(paste0(up, down), tpf, mode = "wb") : 
  download from 'http://49.235.27.111/GEOmirror/GSE39nnn/GSE39582_eSet.Rdata' failed
In addition: Warning messages:
1: In download.file(paste0(up, down), tpf, mode = "wb") :
  downloaded length 38156236 != reported length 155293160
2: In download.file(paste0(up, down), tpf, mode = "wb") :
  URL 'http://49.235.27.111/GEOmirror/GSE39nnn/GSE39582_eSet.Rdata': Timeout of 60 seconds was reached

##由于设置的时间问题（Timeout of 60 seconds was reached）会造成数据集下载失败，在下载gse之间检查一下
###查看timout时间
getOption('timeout')
#[1] 60
#设定timeout时间
options(timeout=100000)
##确认一下
getOption('timeout')
#[1] 1e+05

#后续可以继续下载gse了#
gset <- geoChina("GSE39582")
gse39582 <- gset[[1]]

还有一个转载的：使用Rstudio下载GEO芯片数据 - 简书 (jianshu.com) 如果上面不行可以尝试

> install.packages('AnnoProbe')
> library(AnnoProbe)
#更新镜像库
> devtools::install_git("https://gitee.com/jmzeng/GEOmirror")
#使用中国镜像下载GEO数据
> gset <- AnnoProbe::geoChina(gse='GSE87211', mirror = 'tencent', destdir = '.')
#此处mirror仅有企鹅源