R Version: 3.2.1; RStudio Version: 0.98.1103
I am trying to Knit a R Markdown file. But am getting the following warnings and error.
Warning messages:
1: In FUN(X[[i]], ...) :
Package 'plyr' not available in repository or locally
2: In FUN(X[[i]], ...) :
Package 'ggplot2' not available in repository or locally
3: In symlinkExternalPackages(project = project) :
The following external packages could not be located:
- "plyr", "ggplot2"
Loading required package: reshape2
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'reshape2'
Error in loadNamespace(name) : there is no package called 'rmarkdown'
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
I've made sure that all of the packages listed are installed, and I've added library(package) for each package listed (ggplot2, reshape2, rmarkdown). I assume I'm missing something simple.
I also tried moving all my packages back to the default directory: as suggested here, and checked my .libPaths() to be sure my library directory was there, which it is.
Below is a simplified version of my R markdown file:
---
title: "Gain Loss Plot - All Samples"
author: "Gaius"
date: "Thursday, September 24, 2015"
output:
html_document:
toc: yes
runtime: shiny
---
In order to more completely visualize how samples might be related, we are going to create a few interactive plots.
# Samples by Arm
```{r loadlibraries, echo=FALSE}
library(rmarkdown)
library(graphics)
library(ggvis)
library(ggplot2)
library(plyr)
library(reshape2)
library(data.table)
library(grDevices)
```
```{r prepdata, echo=FALSE}
C01p <- data.table(read.delim("~/_2015_CNV/2015-09-23_CCCC_GLredo_rmvdup-missedlowpurity/chr/01p.txt"))
#LOAD a bunch of other files just like the one above
C01p[,Chr.Arm := "01p"]
#Subset all files as shown in the line above
#bind all files together
All.Chrom.Stats <- rbind(C01p,C01q,C02p,C02q,C03p,C03q,C04p,C04q,C05p,C05q,C06p,C06q,C07p,C07q,C08p,C08q,C09p,C09q,C10p,C10q,C11p,C11q,C12p,C12q,C13q,C14q,C15q,C16p,C16q,C17p,C17q,C18p,C18q,C19p,C19q,C20p,C20q,C21q,C22q)
#Get just data necessary for creating plots
Prop.Gain.thresh <- All.Chrom.Stats[Prop.Gain > 0.50]
Prop.Loss.thresh <- All.Chrom.Stats[Prop.Loss > 0.50]
```
## Proportion Gained, Threshold > 0.5
```{r prop.gain, echo=FALSE}
all_values <- function(x) {
if(is.null(x)) return(NULL)
paste0(names(x), ": ", format(x), collapse = "<br />")
}
Prop.Gain.thresh %>%
ggvis(~Chr.Arm, ~Prop.Gain) %>%
layer_points( fill = ~Sample ) %>%
add_tooltip(all_values, "hover")
```
## Proportion Lost, Threshold > 0.5
```{r prop.gain, echo=FALSE}
all_values <- function(x) {
if(is.null(x)) return(NULL)
paste0(rev(names(x)), ": ", rev(format(x)), collapse = "<br />")
}
Prop.Loss.thresh %>%
ggvis(~Chr.Arm, ~Prop.Loss) %>%
layer_points( fill = ~Sample, shape = ~Sample ) %>%
add_tooltip(all_values, "hover")
```
UPDATE: I tried creating a new R markdown file and used the basic template given by RStudio to try to knit. It worked and output the file correctly.
Then I added runtime:shiny to the YAML header. It stopped working (giving same error as above).
I then removed runtime:shiny from the header via UNDO, and it still won't work. Error is the same as in my original question.
