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mafusa20
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@mafusa20-19278
Last seen 5.6 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**
The error comes from microbiomeutilities to install microbiomeutilites type this:
lastarria taller?? Greetings!!!
a fixed seetup_microbioma.R may be this: