R MetaboAnalystR пакет установки - PullRequest
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R MetaboAnalystR пакет установки

0 голосов
/ 16 апреля 2020

Я пытаюсь установить пакет в R версии 3.6.3. Это то, что я выполнил согласно инструкции, однако я получаю ошибку. Я не смог найти решение, обсуждаемое на сайте. Может ли кто-нибудь помочь мне с этой процедурой установки? Я не разбираюсь в кодировании. Спасибо. 

metanr_packages <- function(){

  metr_pkgs <- c("Rserve", "RSclient", "ellipse", "scatterplot3d", "Cairo", "randomForest", "caTools", "e1071", "som", "impute", "pcaMethods", "RJSONIO", "ROCR", "globaltest", "GlobalAncova", "Rgraphviz", "preprocessCore", "genefilter", "pheatmap", "SSPA", "sva", "Rcpp", "pROC", "data.table", "limma", "car", "fitdistrplus", "lars", "Hmisc", "magrittr", "methods", "xtable", "pls", "caret", "lattice", "igraph", "gplots", "KEGGgraph", "reshape", "RColorBrewer", "tibble", "siggenes", "plotly", "fgsea", "metap", "reshape2", "scales")

  list_installed <- installed.packages()

  new_pkgs <- subset(metr_pkgs, !(metr_pkgs %in% list_installed[, "Package"]))

  if(length(new_pkgs)!=0){

    if (!requireNamespace("BiocManager", quietly = TRUE))
      install.packages("BiocManager")
    BiocManager::install(new_pkgs)
    print(c(new_pkgs, " packages added..."))
  }

  if((length(new_pkgs)<1)){
    print("No new packages added...")
  }
}
metanr_packages()
library(devtools)

sessionInfo()
devtools::install_github("xia-lab/MetaboAnalystR", build = TRUE, build_opts = c("--no-resave-data", "--no-manual"))

I am getting an error like this warning while installing the dependencies packages

The downloaded source packages are in
    ‘c:\temp\RtmpkNe97i\downloaded_packages’
 [1] "RSclient"           "GlobalAncova"       "Rgraphviz"          "preprocessCore"     "pheatmap"          
 [6] "SSPA"               "sva"                "pROC"               "limma"              "car"               
[11] "fitdistrplus"       "lars"               "pls"                "caret"              "KEGGgraph"         
[16] "siggenes"           "plotly"             "fgsea"              "metap"              " packages added..."
Warning messages:
1: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Program Files\R\R-3.6.3\library\00LOCK\class\libs\x64\class.dll to C:\Program Files\R\R-3.6.3\library\class\libs\x64\class.dll: Permission denied
2: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Program Files\R\R-3.6.3\library\00LOCK\gtools\libs\x64\gtools.dll to C:\Program Files\R\R-3.6.3\library\gtools\libs\x64\gtools.dll: Permission denied
3: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Program Files\R\R-3.6.3\library\00LOCK\lattice\libs\x64\lattice.dll to C:\Program Files\R\R-3.6.3\library\lattice\libs\x64\lattice.dll: Permission denied
4: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Program Files\R\R-3.6.3\library\00LOCK\Rcpp\libs\x64\Rcpp.dll to C:\Program Files\R\R-3.6.3\library\Rcpp\libs\x64\Rcpp.dll: Permission denied
5: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Program Files\R\R-3.6.3\library\00LOCK\S4Vectors\libs\x64\S4Vectors.dll to C:\Program Files\R\R-3.6.3\library\S4Vectors\libs\x64\S4Vectors.dll: Permission denied

Installing 1 packages: spls
Error: Failed to install 'MetaboAnalystR' from GitHub:
  (converted from warning) unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.6:
  cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.6/PACKAGES'
...