I use R 3.4.3, And I need to install devtools::install_github("rstudio/rmarkdown"). But the following installation error comes up.
Downloading GitHub repo rstudio/rmarkdown#master
from URL https://api.github.com/repos/rstudio/rmarkdown/zipball/master
Installation failed: zip file 'C:\Users\Buster\AppData\Local\Temp\RtmpWyl4FP\file3bc6c571eec.zip' cannot be opened
Warning messages:
1: GitHub repo contains submodules, may not function as expected!
2: In utils::unzip(src, exdir = target) :
error 1 in extracting from zip file
How can I install this?
this has been resolved. I used devtools::install_url("http://cran.r-project.org/src/contrib/rmarkdown_1.9.tar.gz")
As explained in the README for rmarkdown:
If you are working within RStudio then you can simply install the
current release of RStudio (both the rmarkdown package and pandoc are
included).
If you want to use the rmarkdown package outside of RStudio then you
can install the package from CRAN as follows:
install.packages("rmarkdown")
This is a much more concise way of doing:
devtools::install_url("http://cran.r-project.org/src/contrib/rmarkdown_1.9.tar.gz")
Related
I just installed R studio and I was trying to install rmarkdown. However, I got the error as below. I unchecked the box ''Tools -> Global Options -> Packages -> Use secure download method for HTTP'' as someone suggested. No help. I tried other packages, I got the same error.
You should remove the package and reinstall it using dependencies = TRUE:
remove.packages("rmarkdown")
install.packages("rmarkdown", dependencies = TRUE)
library(rmarkdown)
Output:
Warning message:
package ‘rmarkdown’ was built under R version 4.1.2
I had the same issue and it was due to the newest version of the toolboxes include the names is under new package names. Go to the URL https://cran.rstudio.com/src/contrib/PACKAGES and search for "rmarkdown". Find the package name and try to install that instead. It's like a .zip file that includes several packages to your library. Try install.packages("accucor"). It worked for me at least, and then try to install the rmarkdown package.
I tried to install R packages using RStudio Package Manager using the following code:
install.packages("dplyr", type = "source")
and
install.packages("dplyr")
and it gives the following error:
Error in install.packages : invalid version specification 'r56550'
What should I do? I tried to google the error but nothing comes up. I have tried to delete and reinstall R and RStudio but i still received the error. I tried to download both the existing binary and the source file and neither ways worked. I tried to install different packages and repeated in both R and Rstudio and nothing worked.
Thank you!
Update 1: I'm using R version 4.0.5 and RStudio version 1.4.1106. I have also downloaded Rtools40 according to the instruction in the following website: https://cran.r-project.org/bin/windows/Rtools/. I'm using Windows. By 'R Manager' I meant the package manager console in RStudio.
Update 2: I'm not sure if there is no network issue or proxy. If I download the packages directly through the CRAN mirror, then it works. But we are trying to download packages in an offline environment, that's why I need RStudio Package Manager.
I installed Pandoc manually through this installation - link.
After restarting the system, I was able to locate the installation folder at C:/Users/YourUserName/AppData/Local/Pandoc
But when I'm trying to call the library:
library("pandoc", lib.loc = "C:/Users/YourUserName/AppData/Local/Pandoc")
I'm getting the following error:
Error in library("pandoc", lib.loc = "C:/Users/YourUserName/AppData/Local/Pandoc") :
no library trees found in 'lib.loc'
As i'm behind a firewall, I cannot install pandoc through github. So the install.pandoc() function is out.
Any ideas where I'm getting the installation process wrong?
Edit:
I've changed .LibPath to point to Pandoc's installation folder:
.libPaths('C:/Users/stefanj/AppData/Local/Pandoc')
And if I check, it seems to be ok:
> grep("pandoc", list.files(.libPaths()))
[1] 22 24
library(pandoc)
Error in library(pandoc) : there is no package called ‘pandoc’
Execution halted
I agree to #Dason's point that library in path : "C:/Users/YourUserName/AppData/Local/Pandoc" is not any library/package connected with R. It's just pandoc installed.
Other way to install pandoc would be using installr :
installr::install.pandoc()
Now, for performing for converting from one markup format to another, use the following package :
rmarkdown
The rmarkdown package includes high level functions for converting to a variety of formats. For
example:
render("input.Rmd", html_document())
render("input.Rmd", pdf_document())
Hope this helps.
I am on Windows 7 and I am using R Studio 0.99.902 with R3.3.1. When I am trying to install a package I get the Warnings:
Warning: unable to access index for repository http://cran.rstudio.com/src/contrib:
cannot open URL 'http://cran.rstudio.com/src/contrib/PACKAGES'
Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/src/contrib:
cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/src/contrib/PACKAGES'
It is the first time I see it and I cannot solve it. Can anyone help me ?
This issue is likely caused by the package being too old or too new for your R version. For example, if a package is released during R-3.4.1, it will not be available for R-3.3.1. Packages which are removed from CRAN before your R version are also not available. The package DESCRIPTION file shows if there is a hard restriction on which R versions the package will run.
Search for the package's CRAN page and see its status. You may still be able to install the package by downloading the package source (the tar.gz file) and in RStudio selecting Install from: Package Archive File in the Tools/Install Packages... menu (or using install.packages with repos = NULL). Beware that the package is not available from CRAN for a reason; you may need to make some changes to the package for it to work correctly.
Running options(download.file.method="libcurl") then installing packages did the trick for me. You may find an answer here.
Please note that compiling from source for Windows requires the appropriate version of Rtools that is compatible with the R version you are working with. This list is available at the Rtools site:
https://cran.r-project.org/src/contrib/Archive/
If compilation from source is complicated, it is also possible to find the Windows-compiled binaries (.zip files) for older versions of R at:
https://cran-archive.r-project.org/bin/windows/contrib
This link is referenced by the ReadMe file available at the "regular" repository for Windows binaries for different versions of R, namely at:
https://cran.r-project.org/bin/windows/contrib
Once the zip file is downloaded, you can run the following R code line to install the package:
# Use repos=NULL so that the first argument is a path to the local zip file
# containing the binary package to install
# (as opposed to just the name of the package to install from the web)
install.packages("<local-path-to-downloaded-zip-file>", repos=NULL)
I was trying to install RTextTools package for R, but failed. Here is the output from the screen
> > install.packages("RTextTools")
Warning in install.packages("RTextTools") :
argument 'lib' is missing: using 'C:\Users\datamining\Documents/R/win-library/2.10'
--- Please select a CRAN mirror for use in this session ---
Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.10
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
package ‘RTextTools’ is not available
What's the reason for this problem, and how to fix it? Thanks.
There are two distinct, but related, issues:
You are running version 2.10 of R which is two years old. CRAN supports only the current version with pre-built binaries. You could try installing from source.
RTextTools, as can be seen on its CRAN page also requires at least R version 2.13.
So in short: you should upgrade.
I have resolved the issue. I have Download RTextTools From Given Link.
https://cran.r-project.org/src/contrib/Archive/RTextTools/
and copy RTextTools_1.4.2.tar.gz file in project root folder then run this command in project folder in terminal
"R CMD INSTALL RTextTools_1.4.2.tar.gz"
After running this command I receive below error
"ERROR: dependencies ‘SparseM’, ‘randomForest’, ‘tree’, ‘e1071’, ‘ipred’, ‘caTools’, ‘maxent’, ‘glmnet’, ‘tau’ are not available for package ‘RTextTools’".
Now install each dependencies from RStudio or RConsole (Any Editor used by you) by simply running this code.
install.packages("caTools").
Install all 9 required packages One By One (In My Case it was 9 Packages Dependencies required by RTextTools) all packages will be installed except 'maxent'.
Now download maxent from the given link.
https://cran.r-project.org/src/contrib/Archive/maxent/.
and copy maxent_1.3.3.1.tar file in project folder then run this command in project folder in terminal.
"R CMD INSTALL maxent_1.3.3.1.tar"
Now For RTextTools Run this command again in Terminal.
"R CMD INSTALL RTextTools_1.4.2.tar.gz"
All is done Now..
But the Last Step is
Load the RTextTools using.
library(RTextTools)
You will see one more Error: Load SparseM Now Loading SparseM use code below.
library(SparseM)
and in the last Load RTextTools
library(RTextTools)
RTextTools is dependent on a number of packages, most of which require R 2.13+. You should always keep R updated to the latest version, since each update contains numerous bug fixes and performance enhancements.
If you can't install packages from repository or the packages are not available anymore, just follow this steps:
Install.packages("devtools")
check -- library("devtools")
install_github("cran/maxent")
install_github("cran/RTextTools")