I can´t install NetAct in R, I use got errors
I used this command:
library(devtools)
install_github("lusystemsbio/NetAct", dependencies=T, build_vignettes = T)
And got this:
library(devtools)
Loading required package: usethis
Error: package or namespace load failed for ‘devtools’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
namespace ‘htmltools’ 0.5.2 is already loaded, but >= 0.5.4 is required
In addition: Warning message:
package ‘usethis’ was built under R version 4.1.3
> install_github("lusystemsbio/NetAct", dependencies=T, build_vignettes = T)
Error in install_github("lusystemsbio/NetAct", dependencies = T, build_vignettes = T) :
could not find function "install_github"
Someone could help me? please
Related
In Rstudio I can't library any package now, the error message as below. But i can library R Gui.
Anyone can help ? Thanks!
> library(ggplot2)
Error: package or namespace load failed for ‘ggplot2’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
载入了名字空间‘rlang’ 0.4.11，但需要的是>= 1.0.0
> library(tidyverse)
Error: package or namespace load failed for ‘tidyverse’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
载入了名字空间‘rlang’ 0.4.11，但需要的是>= 1.0.1
In addition: Warning message:
程辑包‘tidyverse’是用R版本4.1.3 来建造的
In Rstudio:
> .libPaths()
[1] "C:/Users/Administrator/Documents/R/win-library/4.1"
[2] "C:/Program Files/R/R-4.1.0/library"
In Rgui:
> .libPaths()
[1] "C:/Users/andrewyang/Documents/R/win-library/4.1"
[2] "C:/Program Files/R/R-4.1.0/library"
I'm trying to run the Box-Cox Transformation function but I keep getting the below error message. Below the code and error I have listed some of the libraries and packages that I've installed to no avail. I'm using Jupyter notebook with R
Mycode:
caret::BoxCoxTrans(mydataframe$mycolumn)
The error in the console:
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called 'recipes'
Traceback:
caret::BoxCoxTrans
getExportedValue(pkg, name)
asNamespace(ns)
getNamespace(ns)
loadNamespace(name)
namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
. versionCheck = vI[[i]]), from = package)
loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
withRestarts(stop(cond), retry_loadNamespace = function() NULL)
withOneRestart(expr, restarts[[1L]])
doWithOneRestart(return(expr), restart)
I have done the following troubleshooting:
install.packages('caret', dependencies = TRUE)
install.packages("recipes", dependencies = TRUE)
install.packages(c('ddalpha', 'recipes'))
"Recipes" whatever that is seems to be downloaded as I got the following warning amongst others:
"installation of package 'recipes' had non-zero exit status"Warning message in install.packages("recipes", dependencies = TRUE):
Help would be very much appreciated I don't know what the problem is
Desired output:
Box-Cox Transformation
xx data points used to estimate Lambda
Input data summary:
Min. 1st Qu. Median Mean 3rd Qu. Max.
xx
Largest/Smallest: xx
Sample Skewness: xx
Estimated Lambda: xx
> library(ez)
Error: package or namespace load failed for ‘ez’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘zip’
You have to install the zip package manually and it will work.
install.packages("zip")
install.packages("ez")
library(ez)
Warning message:
Paket ‘ez’ wurde unter R Version 3.5.3 erstellt
Should work!
I used the same code every time to load necessary packages. But all of a sudden this stopped working.
library("knitr")
.cran_packages <- c("ggplot2", "tidyverse" ,"gridExtra", "Rcpp")
.bioc_packages <- c("dada2", "phyloseq", "DESeq2", "DECIPHER", "phangorn")
.inst <- .cran_packages %in% installed.packages()
if(any(!.inst)) {
install.packages(.cran_packages[!.inst], dependencies = TRUE)
}
.inst <- .bioc_packages %in% installed.packages()
if(any(!.inst)) {
source("http://bioconductor.org/biocLite.R")
biocLite(.bioc_packages[!.inst], dependencies = TRUE, ask = F)
}
sapply(c(.cran_packages, .bioc_packages), require, character.only = TRUE)
set.seed(100)
After running this chunk in RStudio, I get the following error message....
Loading required package: tidyverse
Error: package or namespace load failed for �tidyverse� in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called �glue�
Loading required package: dada2
Error: package or namespace load failed for �dada2� in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called �RcppParallel�
Loading required package: phyloseq
Error: package or namespace load failed for �phyloseq� in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called �stringi�
Loading required package: DESeq2
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Error: package or namespace load failed for �GenomeInfoDb� in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called �RCurl�
Failed with error: ‘package ‘GenomeInfoDb’ could not be loaded’
**ggplot2 tidyverse gridExtra Rcpp dada2 phyloseq DESeq2 DECIPHER phangorn
TRUE FALSE TRUE TRUE FALSE FALSE FALSE TRUE TRUE**
Could you please let me know how can I fix this to load all packages?
After installing ggplot2 I am trying to run the library.But it shows the error message :
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()),
versionCheck = vI[[j]]) :
there is no package called ‘Rcpp’
Error: package or namespace load failed for ‘ggplot2’
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()),
versionCheck = vI[[j]]) :
there is no package called ‘Rcpp’
Error: package or namespace load failed for ‘ggplot2’
Do this:
remove.packages(c("ggplot2", "data.table"))
install.packages('Rcpp', dependencies = TRUE)
install.packages('ggplot2', dependencies = TRUE)
install.packages('data.table', dependencies = TRUE)