I am working on R markdown script (RStudio). Individual code chunk works but when i try to Knit to HTML , it throws error as "Error in library(dplyr) : there is no package called 'dplyr' Calls: ... withCallingHandlers -> withVisible -> eval -> eval -> library"
code
##install library
```{r install pkg,include=FALSE,cache=TRUE}
install.packages("kableExtra",repos = "http://cran.us.r-project.org")
install.packages("dplyr", repos = "http://cran.us.r-project.org")
install.packages("ggplot2", repos = "http://cran.us.r-project.org")
```
```{r setup, include=FALSE}
library(knitr)
library(dplyr)
library(ggplot2)
```
Restart R
You should manually install packages and then knit to HDML. Click Tools > Install Packages and then type in the packages
Related
I'm working on a project in RStudio, and all the code runs well. but when I try to get a report in R Makdown, I constantly recieve this error on a chunk which contains installing needed packages:
```{r installing packages, include=FALSE}
install.packages("tidyverse")
library(tidyverse)
install.packages("lubridate")
library(lubridate)
install.packages("ggplot2")
library(ggplot2)
install.packages("dplyr")
library(dplyr)
```
this is the error message: (line 21-32 means all the mentioned chunk.)
Quitting from lines 21-32 (report.Rmd)
Error in contrib.url(repos, "source") :
trying to use CRAN without setting a mirror
Calls: <Anonymous> ... eval_with_user_handlers -> eval -> eval -> install.packages -> contrib.url
Execution halted
any recommendation??
I got the error on first chunk, but each chunk runs perfectly with no error when I run them separately.
It shows there is no package called 'flextable' even after installing the package.
install.packages("flextable")
library(flextable)
I keep getting this error when I try to knit to PDF using R Markdown. It has worked before, and I tried installing the package contrib.url but it says it is not available for my version. Any suggestions?
Error in contrib.url(repos, "source") : trying to use CRAN without setting a mirror calls : <Anonymous> ... with visible -> eval -> eval -> install.packages -> contrib.url Execution halted
The error usually comes when you don't set a mirror in the install.packages command. You probably have a call to install.packages somewhere in your markdown document.
Try the following:
install.packages("aPackage",repos = "http://cran.us.r-project.org")
So just add the repos part. You could of course also just install the package before usage and remove the install.packages line completely from your rmarkdown.
I'm using RStudio, and trying to knit my file to hand in my assignment. I installed the package "readxl" to read in a couple of excel files, and it worked fine in the actual coding of the assignment. But when I go to knit the file, I keep getting the error:
Error in library(readxl) : there is no package called 'readxl'
Calls: <Anonymous> ... withCallingHandlers -> withVisible -> eval -> eval ->
library
Execution halted
This is the code in question:
install.packages("tidyverse",repos = "http://cran.us.r-project.org")
library(tidyverse)
install.packages("readxl",repos = "http://cran.us.r-project.org")
library(readxl)
This has been frustrating me for over an hour and I just can't fix it. I can see the readxl package to the right of the console, in the "packages" tab. Any help will be much appreciated
I've been using knitr along with the showtext library to produce HTML files that use some Google fonts. It has worked fine until I upgraded R to 3.4. When I knit the document now, I get the following error:
Error: package 'sysfonts' could not be loaded Execution halted
This is reproducible by knitting:
---
title: "test"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(showtext)
```
It runs fine without the library(showtext).
Then, when I try running it with library(sysfonts) using the same template:
---
title: "test"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(sysfonts)
```
I get this error:
Error: package or namespace load failed for 'sysfonts': .onLoad failed in loadNamespace() for 'sysfonts', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared object '~/Library/R/3.4/library/sysfonts/libs/sysfonts.so': dlopen(~/Library/R/3.4/library/sysfonts/libs/sysfonts.so, 6): Library not loaded: /opt/X11/lib/libfreetype.6.dylib Reference from: ~/Library/R/3.4/library/sysfonts/libs/sysfonts.so Reason: image not found
It seems like an issue with the sysfonts library. However, I can load showtext and sysfonts just fine from the console. So I don't know if this is a sysfonts issue or a knitr issue. I'm running El Capitan 10.6 and again, recently upgraded R to 3.4. I tried downgrading back to 3.3, but still produced the same error.
A late reply, which yet might come useful to others (if working on a Mac):
1) remove all relevant R-packages
remove.packages("sysfonts")
remove.packages("showtext")
2) install XQuartz
3) reinstall and load all packages again
install.packages("sysfonts")
install.packages("showtext")
This solution provided by tcarnus on GitHub solved the issue for me.