?name does not compile html in rmarkdown using knitr

[dhjones1]

install.packages("car", repos = "http://cran.us.r-project.org", type = "source")
library("car")
data(Quartet)
names(Quartet)
help(Quartet)
?Quartet
sessionInfo()

RESULTS:

"## [1] "x" "y1" "y2" "y3" "x4" "y4"
"##

"##
"##

Quartet

R Documentation

"##
"##

Four Regression Datasets

"##
"##

Description

ETC.

R version 3.3.2 (2016-10-31)

Platform: x86_64-w64-mingw32/x64 (64-bit)

Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:

[1] LC_COLLATE=English_United States.1252

[2] LC_CTYPE=English_United States.1252

[3] LC_MONETARY=English_United States.1252

[4] LC_NUMERIC=C

[5] LC_TIME=English_United States.1252

attached base packages:

[1] stats graphics grDevices utils datasets methods base

other attached packages:

[1] robustbase_0.92-6 quantreg_5.29 SparseM_1.7 MASS_7.3-45

[5] car_2.1-3 faraway_1.0.7 printr_0.0.6 knitr_1.14

loaded via a namespace (and not attached):

[1] Rcpp_0.12.5 magrittr_1.5 splines_3.3.2

[4] lattice_0.20-34 minqa_1.2.4 stringr_1.0.0

[7] tools_3.3.2 parallel_3.3.2 nnet_7.3-12

[10] pbkrtest_0.4-6 grid_3.3.2 nlme_3.1-128

[13] mgcv_1.8-15 MatrixModels_0.4-1 htmltools_0.3.5

[16] yaml_2.1.13 lme4_1.1-12 assertthat_0.1

[19] digest_0.6.9 tibble_1.1 Matrix_1.2-7.1

[22] nloptr_1.0.4 formatR_1.4 evaluate_0.10

[25] rmarkdown_1.1 stringi_1.1.1 DEoptimR_1.0-6"

[dhjones1]

Must use results = "asis" in the chunk options.

[yihui]

It seems you didn't read the issue guidelines but just deleted them when you opened this issue: it is not correctly formatted, and it is not a reproducible example (e.g. you used printr but it was not reflected in the R Markdown source).

[dhjones1]

Thank you very much for your reply.

Douglas H. Jones, PhD
Professor
Management Science and Information Systems
Director of MBA in Analytics and Information Systems (AIM)
Rutgers Business School
Please use this email in all correspondences: douglas.h.jones@gmail.com
http://www.linkedin.com/in/douglashjones
http://twitter.com/dhjones1

On Wed, Nov 2, 2016 at 11:48 PM, Yihui Xie notifications@github.com wrote:

It seems you didn't read the issue guidelines but just deleted them when
you open this issue: it is not correctly formatted, and it is not a
reproducible example (e.g. you used printr but it was not reflected in
the R Markdown source).

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[dhjones1]

My problem is that printr does not render the html code of help pages for
me anymore. I have fixed the problem by including
knitr::opts_chunk$set(results = "asis") in a chunk at the beginning.

Douglas H. Jones, PhD
Professor
Management Science and Information Systems
Director of MBA in Analytics and Information Systems (AIM)
Rutgers Business School
Please use this email in all correspondences: douglas.h.jones@gmail.com
http://www.linkedin.com/in/douglashjones
http://twitter.com/dhjones1

On Thu, Nov 3, 2016 at 12:27 AM, Douglas Jones douglas.h.jones@gmail.com
wrote:

Thank you very much for your reply.

Douglas H. Jones, PhD
Professor
Management Science and Information Systems
Director of MBA in Analytics and Information Systems (AIM)
Rutgers Business School
Please use this email in all correspondences: douglas.h.jones@gmail.com
http://www.linkedin.com/in/douglashjones
http://twitter.com/dhjones1

On Wed, Nov 2, 2016 at 11:48 PM, Yihui Xie notifications@github.com
wrote:

It seems you didn't read the issue guidelines but just deleted them when
you open this issue: it is not correctly formatted, and it is not a
reproducible example (e.g. you used printr but it was not reflected in
the R Markdown source).

—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
#1314 (comment), or mute
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.

[dhjones1]

Here is my sessionInfo()

sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C

[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] car_2.1-3 faraway_1.0.7

loaded via a namespace (and not attached):
[1] Rcpp_0.12.5 knitr_1.14 magrittr_1.5 splines_3.3.2

[5] MASS_7.3-45 lattice_0.20-34 minqa_1.2.4 stringr_1.0.0

[9] tools_3.3.2 nnet_7.3-12 pbkrtest_0.4-6
parallel_3.3.2
[13] grid_3.3.2 nlme_3.1-128 mgcv_1.8-15 quantreg_5.29

[17] MatrixModels_0.4-1 htmltools_0.3.5 yaml_2.1.13 lme4_1.1-12

[21] assertthat_0.1 digest_0.6.9 tibble_1.1
Matrix_1.2-7.1
[25] nloptr_1.0.4 rsconnect_0.4.1.4 evaluate_0.10 rmarkdown_1.1

[29] stringi_1.1.1 SparseM_1.7

Douglas H. Jones, PhD
Professor
Management Science and Information Systems
Director of MBA in Analytics and Information Systems (AIM)
Rutgers Business School
Please use this email in all correspondences: douglas.h.jones@gmail.com
http://www.linkedin.com/in/douglashjones
http://twitter.com/dhjones1

On Thu, Nov 3, 2016 at 1:59 AM, Douglas Jones douglas.h.jones@gmail.com
wrote:

My problem is that printr does not render the html code of help pages for
me anymore. I have fixed the problem by including
knitr::opts_chunk$set(results = "asis") in a chunk at the beginning.

Douglas H. Jones, PhD
Professor
Management Science and Information Systems
Director of MBA in Analytics and Information Systems (AIM)
Rutgers Business School
Please use this email in all correspondences: douglas.h.jones@gmail.com
http://www.linkedin.com/in/douglashjones
http://twitter.com/dhjones1

On Thu, Nov 3, 2016 at 12:27 AM, Douglas Jones douglas.h.jones@gmail.com
wrote:

Thank you very much for your reply.

Douglas H. Jones, PhD
Professor
Management Science and Information Systems
Director of MBA in Analytics and Information Systems (AIM)
Rutgers Business School
Please use this email in all correspondences: douglas.h.jones@gmail.com
http://www.linkedin.com/in/douglashjones
http://twitter.com/dhjones1

On Wed, Nov 2, 2016 at 11:48 PM, Yihui Xie notifications@github.com
wrote:

It seems you didn't read the issue guidelines but just deleted them when
you open this issue: it is not correctly formatted, and it is not a
reproducible example (e.g. you used printr but it was not reflected
in the R Markdown source).

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You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
#1314 (comment), or mute
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[yihui]

If you think you found an issue, please prove it is real by a minimal reproducible example. When you open a Github issue, you are expected to read the instructions listed in the issue template. Since you didn't provide such an example, I have to take time to show it is not real. Here is my minimal example that works fine:

---
title: "Hello World"
output: html_document
---

```{r}
library(printr)
```

```{r}
?c
```

[dhjones1]

---

title: "More Remedies for Error Problems"
author: "Dr DH Jones"
date: "r Sys.Date()"
output:
rmarkdown::html_vignette:
fig_caption: yes
toc: true
toc_depth: 2
vignette: >
%\VignetteIndexEntry{More Remedies for Error Problems}
%\VignetteEngine{knitr::rmarkdown}

%\VignetteEncoding{UTF-8}

install.packages("rmarkdown", repos = "https://cloud.r-project.org/", type
= "source")

include=FALSE, eval=TRUE}

# knitr options

install.packages("knitr", repos = "http://cran.us.r-project.org", type =
"source")
library(knitr)
knitr::opts_chunk$set(message=FALSE, warning=FALSE, include=TRUE, echo =
TRUE, fig.height=6, fig.width=7, tidy=TRUE, results='hold')
knitr::opts_knit$set(progress = FALSE, verbose = FALSE, message = FALSE)

# The "printr" package renders most all the table output in a nice format

install.packages('printr',type = 'source', repos = c('http://yihui.name/xran',
'http://cran.rstudio.com') )
library("printr")

R Libraries

install.packages("ggplot2", repos = "http://cran.us.r-project.org", type =
"source")
install.packages("GGally", repos = "http://cran.us.r-project.org", type =
"source")
install.packages("car", repos = "http://cran.us.r-project.org", type =
"source")
install.packages("scatterplot3d", repos = "http://cran.us.r-project.org",type
= "source")
install.packages("rgl", repos = "http://cran.us.r-project.org", type =
"source")
install.packages("faraway", repos = "http://cran.us.r-project.org", type =
"source")

include=FALSE, cache=TRUE}
install.packages("MASS", repos = "http://cran.us.r-project.org", type =
"source")
install.packages("quantreg", repos = "http://cran.us.r-project.org", type =
"source")
install.packages("faraway", repos = "http://cran.us.r-project.org", type =
"source")
install.packages("robustbase", repos = "http://cran.us.r-project.org", type
= "source")

include=TRUE, cache=F}
library("faraway")
library("car")
library("rgl")
library("MASS")
library("quantreg")
library("robustbase")

Remedy for correlated errors: Generalized Least Squares

• When errors are not independent or have non-zero correlation, OLS is the
  wrong type of analysis.
• Generalized Least Squares (GLS) accounts for dependent errors.
• The errors have to obey special rules, but these cover a wide array of
  circumstances.
• Valid inferences still require that errors are normally distributed.
• Let us demonstrate on the longley data.

library(faraway)
data("longley")
help(longley)

sessionInfo()

Douglas H. Jones, PhD
Professor
Management Science and Information Systems
Director of MBA in Analytics and Information Systems (AIM)
Rutgers Business School
Please use this email in all correspondences: douglas.h.jones@gmail.com
http://www.linkedin.com/in/douglashjones
http://twitter.com/dhjones1

On Thu, Nov 3, 2016 at 2:11 AM, Yihui Xie notifications@github.com wrote:

If you think you found an issue, please prove it is real by a minimal
reproducible example. When you open a Github issue, you are expected to
read the instructions listed in the issue template. Since you didn't
provide such an example, I have to take time to show it is not real. Here
is my minimal example that works fine:

---

title: "Hello World"

output: html_document

library(printr)

?c

[image: image]
https://cloud.githubusercontent.com/assets/163582/19957173/50af3f34-a162-11e6-90d5-953a0a0a7640.png

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[dhjones1]

The compiled file is attached:
printr_problem.pdf

[yihui]

Could you actually read the first two paragraphs of this page first? https://github.com/yihui/knitr/blob/master/.github/CONTRIBUTING.md

[dhjones1]

I did and I resubmitted my report earlier today.

Best,

Doug

Douglas H. Jones, PhD
Professor
Management Science and Information Systems
Director of MBA in Analytics and Information Systems (AIM)
Rutgers Business School
Please use this email in all correspondences: douglas.h.jones@gmail.com
http://www.linkedin.com/in/douglashjones
http://twitter.com/dhjones1

On Thu, Nov 3, 2016 at 12:26 PM, Yihui Xie notifications@github.com wrote:

Could you actually read the first two paragraphs of this page first?
https://github.com/yihui/knitr/blob/master/.github/CONTRIBUTING.md

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