setup microbiome error
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Entering edit mode
mafusa20 • 0
@mafusa20-19278
Last seen 2.6 years ago
setup_microbioma <- function(){

  .packages = c("ape", 
                "gridExtra", 
                "picante", 
                "data.table", 
                "RColorBrewer", 
                "DT", 
                "reshape", 
                "reshape2", 
                "magrittr", 
                "markdown",
                "ggpubr", 
                "tibble", 
                "pheatmap", 
                "dplyr", 
                "viridis", 
                "devtools", 
                "rmdformats",
                "intergraph",
                "network",
                "igraph",
                "ggplot2", 
                "gridExtra", 
                "knitr", 
                "vegan", 
                "plyr", 
                "dplyr",
                "ggrepel", 
                "ggnetwork", 
                "ade4", 
                "rmarkdown",
                "formatR",
                "caTools",
                "GGally",
                "clusterSim",
                "cluster")

  .bioc_packages <- c("phyloseq",
                      "microbiome", 
                      "phangorn", 
                      "genefilter",
                      "dada2",
                      "ggtree")

  # Instalar paquetes del CRAN (si no est?n instalados)
  .inst <- .packages %in% installed.packages()
  if(length(.packages[!.inst]) > 0) install.packages(.packages[!.inst])

  .inst <- .bioc_packages %in% installed.packages()
  if(any(!.inst)) {
    source("http://bioconductor.org/biocLite.R")
    biocLite(.bioc_packages[!.inst], ask = F, suppressUpdates=T)
  }

  # Instalar paquetes de github (si no est?n instalados)
  if (!("microbiomeutilities"  %in% installed.packages())) {
    library(devtools)
    devtools::install_github("microsud/microbiomeutilities")
  }

  if(!("microbiomeViz"  %in% installed.packages())){
    devtools::install_github("lch14forever/microbiomeViz")

  }

  if (!("SpiecEasi"  %in% installed.packages())) {
    devtools::install_github("zdk123/SpiecEasi")
  }

  if (!("microbiomeSeq"  %in% installed.packages())){
    install_github("umerijaz/microbiomeSeq")
  }
  if (!("ggnet"  %in% installed.packages())) {
    devtools::install_github("briatte/ggnet")
  }

  message("Ahora prueben cargar los paquetes del script con library(nombre_del_paquete)")

}

setup_microbioma()

  library(devtools) # Load the devtools package
  install_github("microbiome/microbiome", force = TRUE) # Install the package

**> setup_microbioma()
Error in install.packages : Updating loaded packages**

 **Error in read.dcf(path) :                                                                                                        Show Traceback
  Found continuation line starting '    person("Sudarsha ...' at begin of record.                     Rerun with Debug******


**> install.packages(.packages[!.inst])
Error in install.packages : object '.inst' not found**
help software error • 1.1k views
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0
Entering edit mode

The error comes from microbiomeutilities to install microbiomeutilites type this:

library(remotes)
install_url(url="https://github.com/microsud/microbiomeutilities/archive/master.zip", INSTALL_opt= "--no-multiarch")

lastarria taller?? Greetings!!!

a fixed seetup_microbioma.R may be this:

setup_microbioma <- function(){

  .packages = c("ape", 
                "gridExtra", 
                "picante", 
                "data.table", 
                "RColorBrewer", 
                "DT", 
                "reshape", 
                "reshape2", 
                "magrittr", 
                "markdown",
                "ggpubr", 
                "tibble", 
                "pheatmap", 
                "dplyr", 
                "viridis", 
                "devtools", 
                "rmdformats",
                "intergraph",
                "network",
                "igraph",
                "ggplot2", 
                "gridExtra", 
                "knitr", 
                "vegan", 
                "plyr", 
                "dplyr",
                "ggrepel", 
                "ggnetwork", 
                "ade4", 
                "rmarkdown",
                "formatR",
                "caTools",
                "GGally",
                "clusterSim",
                "cluster",
                "tidyverse")

  .bioc_packages <- c("phyloseq",
                      "microbiome",
                      "DECIPHER",
                      "phangorn", 
                      "genefilter",
                      "dada2",
                      "ggtree",
                      "microbiomeutilities")

  # Instalar paquetes del CRAN (si no están instalados)
  .inst <- .packages %in% installed.packages()
  if(length(.packages[!.inst]) > 0) install.packages(.packages[!.inst])

  .inst <- .bioc_packages %in% installed.packages()
  if(any(!.inst)) {
    source("http://bioconductor.org/biocLite.R")
    biocLite(.bioc_packages[!.inst], ask = F, suppressUpdates=T)
  }

  # Instalar paquetes de github (si no están instalados)
 # if (!("microbiomeutilities"  %in% installed.packages())) {
 #   library(devtools)
 #   devtools::install_github("microsud/microbiomeutilities")
 # }

  if(!("microbiomeViz"  %in% installed.packages())){
    devtools::install_github("lch14forever/microbiomeViz")

  }

  if (!("SpiecEasi"  %in% installed.packages())) {
    devtools::install_github("zdk123/SpiecEasi")
  }

  if (!("microbiomeSeq"  %in% installed.packages())){
    devtools::install_github("umerijaz/microbiomeSeq")
  }
  if (!("ggnet"  %in% installed.packages())) {
    devtools::install_github("briatte/ggnet")
  }

  message("Ahora prueben cargar los paquetes del script con library(nombre_del_paquete)")

}

setup_microbioma()

####para el microbiomeutilities
library(remotes)
install_url(url="https://github.com/microsud/microbiomeutilities/archive/master.zip", INSTALL_opt= "--no-multiarch")
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