Trying to publish an R notebook and keep getting the same error (error in contrib.url (repos, "source") trying to use CRAN without installing a mirror

Question

I use OSX Yosemite with XQuartz, as suggested in other questions, and I try to publish a laptop, but I get the same error every time. It looks like a .R file:

#' --- #' title: "MLB Payroll Analysis" #' author: "Steven Quartz Universe" #' date: "21 March 2015" #' output: pdf_document #' --- #loading the payroll data from the Python document payroll <- read.table("~/Documents/payroll.txt", header=TRUE, quote="\"") View(payroll) summary(payroll) bank <- payroll$PayrollMillions wins <- payroll$X2014Wins #loading the payroll data from the Python document payroll <- read.table("~/Documents/payroll.txt", header=TRUE, quote="\"") summary(payroll) bank <- payroll$PayrollMillions wins <- payroll$X2014Wins #displaying the mean and sd of payroll and wins (out of 162, of course) mean(bank) sd(bank) mean(wins) sd(wins) #setting a linear regression reg <- lm(wins ~ bank) summary(reg) #the regression is valid to significance < .10 (p-value .05072), #but the R-squared is only .1296, a weak correlation #a means of comparing the histogram to a normal distribution histNorm <- function(x, densCol = "darkblue"){ m <- mean(x) std <- sqrt(var(x)) h <- max(hist(x,plot=FALSE)$density) d <- dnorm(x, mean=m, sd=std) maxY <- max(h,d) hist(x, prob=TRUE, xlab="x", ylim=c(0, maxY), main="(Probability) Histogram with Normal Density") curve(dnorm(x, mean=m, sd=std), col=densCol, lwd=2, add=TRUE) } #showing the histogram with normal distribution line histNorm(reg$residuals, "purple") #QQplots and Shapiro-Wilk test qqnorm(reg$residuals) qqline(reg$residuals) shapiro.test(reg$residuals) #p-value is .383; this can be considered a normal distribution plot(reg$fitted.values,reg$residuals) abline(h = 0) #variances are wide, but in a channel install.packages("lmtest") library(lmtest) bptest(reg) #p-value of .849 given; we can assume variances are constant throughout the distribution hats <- hatvalues(reg) hatmu <- mean(hats) hats[hats > 2 * hatmu] #we get teams 14 and 19 with high leverage; the Dodgers and Yankees with their astronomical payrolls treg <- rstudent(reg) n <- length(treg) p <- reg$coefficients df <- n - p - 1 alpha <- 0.05 #no bonferroni correction for outliers crit <- qt(1 - alpha/2,df) treg[abs(treg) > crit] #no outliers are found #with bonferroni correction crit <- qt(1 - (alpha/2)/n,df) treg[abs(treg) > crit] #no outliers are found #comparison of outlier tests pvals <- pt(-abs(treg),df)*2 padjb <- p.adjust(pvals, method = "bonferroni") padjf <- p.adjust(pvals, method = "fdr") cbind(pvals,padjb,padjf) 

When I click Compile Notebook, this is the result:

  |...................... | 33% ordinary text without R code |........................................... | 67% label: unnamed-chunk-1 processing file: payroll.spin.Rmd Quitting from lines 9-90 (payroll.spin.Rmd) Error in contrib.url(repos, "source") : trying to use CRAN without setting a mirror Calls: <Anonymous> ... withVisible -> eval -> eval -> install.packages -> contrib.url 

I looked at other questions on how to fix this, but to no avail. I made corrections on the command line, but to no avail. Can someone tell me what I am doing wrong? Thank you.

Answer 1

Line

 install.packages("lmtest") 

- the problem is here. As the error message hints

 Error in contrib.url(repos, "source") : trying to use CRAN without setting a mirror 

you are expected to provide a repo link for the package. So, changing it to (for example):

 install.packages("lmtest", repos = "http://cran.us.r-project.org") 

gotta do the trick. But, as Mr. Flick and Ben Bolkers noted in their comments, this should probably be done when the package is not yet installed.

Answer 2

I had the same issue with publishing Knit HTML, I changed the beginning of the file like this:

 --- title: "dialectic" author: "micah smith" date: "3/4/2017" output: html_document --- ```{r setup, include=FALSE} chooseCRANmirror(graphics=FALSE, ind=1) knitr::opts_chunk$set(echo = TRUE) 

chooseCRANmirror(graphics=FALSE, ind=1) was the line that fixed it

Answer 3

 chooseCRANmirror(graphics=FALSE, ind=1) knitr::opts_chunk$set(echo = TRUE) 

Write this at the beginning of your snippet if you have already installed the package.

Answer 4

If you have already run the install.packages ("___") script, then you can try to set this code button to eval = FALSE when you try to link the tag file?