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linux学习100篇3:Error in open.conne

linux学习100篇3:Error in open.conne

作者: Seurat_Satija | 来源:发表于2021-05-30 09:48 被阅读0次
    > library(tidyverse)
    > cell_markers <- vroom::vroom('http://bio-bigdata.hrbmu.edu.cn/CellMarker/download/Mouse_cell_markers.txt') %>%
    +   tidyr::unite("cellMarker", tissueType, cancerType, cellName, sep=", ") %>% 
    +   dplyr::select(cellMarker, geneID) %>%
    +   dplyr::mutate(geneID = strsplit(geneID, ', '))
    Error in open.connection(3L, "rb") : 
      Timeout was reached: [bio-bigdata.hrbmu.edu.cn] Connection timed out after 10001 milliseconds
    In addition: Warning messages:
    1: In for (i in seq_along(args)) { :
      closing unused connection 4 (http://bio-bigdata.hrbmu.edu.cn/CellMarker/download/Mouse_cell_markers.txt)
    2: In for (i in seq_along(args)) { :
      closing unused connection 3 (http://bio-bigdata.hrbmu.edu.cn/CellMarker/download/Mouse_cell_markers.txt)
    > 1+1
    [1] 2
    
    
    > .libPaths()
    [1] "/home/rstudio/R/x86_64-pc-linux-gnu-library/4.1"
    [2] "/usr/local/lib/R/site-library"                  
    [3] "/usr/lib/R/site-library"                        
    [4] "/usr/lib/R/library"                             
    > cell_markers <- vroom::vroom('http://bio-bigdata.hrbmu.edu.cn/CellMarker/download/Mouse_cell_markers.txt') %>%
    +   tidyr::unite("cellMarker", tissueType, cancerType, cellName, sep=", ") %>% 
    +   dplyr::select(cellMarker, geneID) %>%
    +   dplyr::mutate(geneID = strsplit(geneID, ', '))
    Rows: 1,255                                                                            
    Columns: 15
    Delimiter: "\t"
    chr [15]: speciesType, tissueType, UberonOntologyID, cancerType, cellType, cellName, CellOntologyID...
    
    Use `spec()` to retrieve the guessed column specification
    Pass a specification to the `col_types` argument to quiet this message
    > cell_markers
    # A tibble: 1,255 x 2
       cellMarker                                         geneID   
       <chr>                                              <list>   
     1 Bone marrow, Normal, Blastema cell                 <chr [3]>
     2 Taste bud, Normal, Type II taste bud cell          <chr [2]>
     3 Taste bud, Normal, Type III taste bud cell         <chr [5]>
     4 Adipose tissue, Normal, Adipose-derived stem cell  <chr [1]>
     5 Undefined, Normal, Regulatory T (Treg) cell        <chr [2]>
     6 Adipose tissue, Normal, White fat cell             <chr [1]>
     7 Meniscus, Normal, Meniscus-derived stem cell       <chr [6]>
     8 Meniscus, Normal, Meniscus-derived progenitor cell <chr [6]>
     9 Peyer patch, Normal, B cell                        <chr [1]>
    10 Peyer patch, Normal, T cell                        <chr [3]>
    # … with 1,245 more rows
    > y <- enricher(gene.df$ENTREZID, TERM2GENE=cell_markers, minGSSize=1)
    

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