In knitr, no output from pander in for loop

Question

Using knitr in RStudio, pander does not produce any (or correct) html output when in a for loop. Here is a minimal case, as an Rmd input file.

---
title: "Untitled"
output: html_document
---

Testing why pander doesn't work in for loop

```{r global_options, include=FALSE}
knitr::opts_chunk$set(fig.width=7, fig.height=5, echo=FALSE, warning=FALSE,
  message=FALSE)

```

```{r}
library(pander)

r <- 1:10
print("pander at top level")   
pander(summary(r))    # works

print("pander in for loop")
for (i in 1:2) pander(summary(r))    #does not work (nothing in output)
for (i in 1:2) print(pander(summary(r)))    #does not work  (code in output)
for (i in 1:2) print(summary(r))    # works

```

The result is the same for other (more interesting) "summary" objects, e.g. a summary of an lm fit. The same behavior was observed for pander 0.5.2 from CRAN, and also 0.5.3 loaded from github.

RStudio v 0.99.467.

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.4 (Yosemite)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] pander_0.5.3

loaded via a namespace (and not attached):
 [1] minqa_1.2.4     MASS_7.3-40     Matrix_1.2-0    htmltools_0.2.6 tools_3.2.0    
 [6] yaml_2.1.13     Rcpp_0.11.6     rmarkdown_0.7   splines_3.2.0   nlme_3.1-120   
[11] grid_3.2.0      digest_0.6.8    nloptr_1.0.4    lme4_1.1-7      lattice_0.20-31

Gilchrist

Answer 1

@daroczig answered in the comments :

1. change knitr chunk option results to asis, either at the global level knitr::opts_chunk$set(results="asis") or at the chunk level ```{r,results="asis"}
2. disable panderOption knitr.auto.asis : panderOptions('knitr.auto.asis', FALSE)

Cf. this issue

---
title: "Untitled"
output: html_document
---

Testing **when** pander doesn't work in for loop

```{r global_options, include=FALSE}
knitr::opts_chunk$set(fig.width=7, fig.height=5, echo=TRUE, warning=FALSE,
  message=FALSE)

```

```{r,results="asis"}
library(pander)
panderOptions('knitr.auto.asis', FALSE)

r <- 1:10

for (i in 1:2) pander(summary(r))

```

Valencia

Neither print or cat is needed: pander already prints to stdout (using cat internally). Related question and comment: #31491917 – Chrissie

@Chrissie could you turn that to an answer so we can point to it? I'll delete my answer – Valencia

daroczig, thanks for the pointer to the related issue. But I'm confused, because in my minimal example, just pander(..) without cat or print did not produce any visible output. – Gilchrist

@EliotSmith actually, it does if you add results="asis" and specify panderOptions('knitr.auto.asis', FALSE) between library(pander) and pander() – Valencia

pander prints to stdout, AS LONG as the document is not knitted. For more information see github.com/Rapporter/pander/issues/142 – Melda