getGEO()无法下载文件：InternetOpenUrl失败:’无法与服务器建立连接'

其实加载GEOquery包的时候就出现options()的这行代码

> library(GEOquery)
载入需要的程辑包：Biobase
载入需要的程辑包：BiocGenerics
载入需要的程辑包：parallel

载入程辑包：‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply,
    parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind,
    colnames, dirname, do.call, duplicated, eval, evalq,
    Filter, Find, get, grep, grepl, intersect, is.unsorted,
    lapply, Map, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce,
    rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages
    'citation("pkgname")'.

Setting options('download.file.method.GEOquery'='auto')  ####
Setting options('GEOquery.inmemory.gpl'=FALSE)

 其实不仅仅是在加载Bioconductor包的时候会有这样的连不上的报错，在下载有些数据的时候也会，比如下载GEO的数据：

> library(GEOquery)
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> if(!file.exists(f)){}
NULL
> if(!file.exists(f)){
+     gset <- getGEO("GSE42872",destdir = ".",AnnotGPL = F,getGPL = F)
+     save(gset,file = f)
+ }
Found 1 file(s)
GSE42872_series_matrix.txt.gz
试开URL’https://ftp.ncbi.nlm.nih.gov/geo/series/GSE42nnn/GSE42872/matrix/GSE42872_series_matrix.txt.gz'
 Error in download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s",  : 
  无法打开URL'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE42nnn/GSE42872/matrix/GSE42872_series_matrix.txt.gz' 
3.
download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s", 
    stub, GEO, b[i]), destfile = destfile, mode = "wb", method = getOption("download.file.method.GEOquery")) 
2.
getAndParseGSEMatrices(GEO, destdir, AnnotGPL = AnnotGPL, getGPL = getGPL, 
    parseCharacteristics = parseCharacteristics) 
1.
getGEO("GSE42872", destdir = ".", AnnotGPL = F, getGPL = F) 

当把options('download.file.method.GEOquery'='auto') 改成 options('download.file.method.GEOquery'='libcurl')的时候就可以下载了！、

> options('download.file.method.GEOquery'='libcurl')
> if(!file.exists(f)){
+     gset <- getGEO("GSE42872",destdir = ".",AnnotGPL = F,getGPL = F)
+     save(gset,file = f)
+ }
Found 1 file(s)
GSE42872_series_matrix.txt.gz
试开URL’https://ftp.ncbi.nlm.nih.gov/geo/series/GSE42nnn/GSE42872/matrix/GSE42872_series_matrix.txt.gz'
Content length 768865 bytes (750 KB)
downloaded 750 KB

Parsed with column specification:
cols(
  ID_REF = col_double(),
  GSM1052615 = col_double(),
  GSM1052616 = col_double(),
  GSM1052617 = col_double(),
  GSM1052618 = col_double(),
  GSM1052619 = col_double(),
  GSM1052620 = col_double()
)
|===========================================================| 100%    1 MB
> class(gset)
[1] "list"
> length(gset)
[1] 1
> gset
$GSE42872_series_matrix.txt.gz
ExpressionSet (storageMode: lockedEnvironment)
assayData: 33297 features, 6 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: GSM1052615 GSM1052616 ... GSM1052620 (6 total)
  varLabels: title geo_accession ... cell type:ch1 (34 total)
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
  pubMedIds: 24469106 
Annotation: GPL6244

 更正一下：有的时候也不定有用，咳咳。。。比如gpl6244 <- getGEO("GPL6244",destdir = ".")，下载个平台注释文件老是下部完整就完了，无奈！