Kernel

The issue seems to be that R is not found in your current PATH, which is necessary for running R from the terminal. This might be because R is not installed in the virtual environment or the path to the system-wide R installation is not included in your PATH.

Here are the steps to resolve this:

Step 1: Ensure R is Installed and Accessible

1. Check if R is installed system-wide:

   which R
   

   This should return the path to the R executable, such as /usr/local/bin/R. If it doesn’t, you may need to install R.

2. Install R (if not already installed):

   • Download and install R from CRAN.

Step 2: Add R to the PATH`

1. Find the path to the R executable:

   which R
   

   Assume it returns /usr/local/bin/R.

2. Add the R path to your PATH environment variable:

   export PATH=/usr/local/bin:$PATH`
   

3. Add the R path to your shell configuration file (~/.zshrc if you are using zsh):

   echo 'export PATH=/usr/local/bin:$PATH' >> ~/.zshrc
   

4. Reload the shell configuration file:

   source ~/.zshrc
   

Step 3: Register the IRKernel Again

1. Activate your virtual environment (if not already active):

   source /Users/apollo/documents/athena/myenv/bin/activate
   

2. Ensure Jupyter is installed:

   pip install jupyter jupyter-client
   

3. Open R from the terminal:

   R
   

4. Run the IRKernel installation command:

   IRkernel::installspec(user = TRUE)
   

Verify Kernel Registration

1. Check available Jupyter kernels:

   jupyter kernelspec list
   

These steps should ensure that R is accessible from the terminal and allow you to properly register the IRKernel for use in Jupyter Notebooks within VSCode.

Show code cell source Hide code cell source

# Install necessary packages if not already installed
if (!requireNamespace("IRkernel", quietly = TRUE)) {
  install.packages("IRkernel", repos = "http://cran.us.r-project.org")
  IRkernel::installspec()
}

if (!requireNamespace("ggplot2", quietly = TRUE)) {
  install.packages("ggplot2", repos = "http://cran.us.r-project.org")
}

if (!requireNamespace("dplyr", quietly = TRUE)) {
  install.packages("dplyr", repos = "http://cran.us.r-project.org")
}

# Load libraries with suppressed messages
suppressPackageStartupMessages(library(ggplot2))
suppressPackageStartupMessages(library(dplyr))

# Print a simple message
print("Hello, Jupyter!")

# Create a simple data frame
data <- data.frame(
  x = rnorm(100),
  y = rnorm(100)
)

# Display the first few rows of the data frame
head(data)

# Create a simple plot
ggplot(data, aes(x = x, y = y)) +
  geom_point() +
  ggtitle("Scatter Plot of Random Data")

# Perform a simple calculation
mean_x <- mean(data$x)
mean_y <- mean(data$y)

# Print the results
cat("Mean of x:", mean_x, "\n")
cat("Mean of y:", mean_y, "\n")

[1] "Hello, Jupyter!"

A data.frame: 6 × 2

	x	y
	<dbl>	<dbl>
1	1.4252539	-1.7111579
2	-0.1163045	1.1182317
3	0.8900219	0.4682633
4	-0.6654862	-1.0600062
5	0.4106440	-0.2861171
6	0.8183634	-1.1140323

Mean of x: 0.01360554 

Mean of y: -0.06021841 

1 + 1

2