I have a big problem since a long time and I could not find any solution. Daily, I waste a lot of time because of it.
I use knitr_1.29 to generate HTML reports (R version 4.0.0, R Studio 1.3.959). Sometimes the output of one or several chunks is not printed whitout any reason.
I mainly meet this problem with the "pheatmap" and "kable" functions.
An example: I have very similar chunks (same options, same kind of output) in my Rmd file and... some outputs are printed, some others not ! Or I will execute knitr on the same .RMD file twice: the first time, the output will be printed, the second one, it will not. This happens even if I changed nothing in my .Rmd file.
I have this problem when I use "render" or when I "knitr" directly the document...
Thank you very much for your help... I'm desesperate...
EDIT : a sort of example... But actually, with this kind of simple file, I will not meet any problem. The problem seems to occur with long and complicated files...
---
title: "Title"
subtitle: 'Subtitle'
author: "me"
date: "`r format(Sys.time(), '%d %B, %Y')`"
output:
html_document:
toc: true
toc_depth: 4
toc_float: true
code_folding: hide
theme: flatly
highlight: tango
---
<style type="text/css">
body{ /* Normal */
font-size: 16px;
}
td { /* Table */
font-size: 14px;
}
h1.title {
font-size: 60px;
color: Tomato;
}
h1 { /* Header 1 */
font-size: 28px;
color: SteelBlue;
}
h2 { /* Header 2 */
font-size: 22px;
color: SteelBlue;
}
h3 { /* Header 3 */
font-size: 18px;
color: SteelBlue;
}
code.r{ /* Code block */
font-size: 12px;
}
pre { /* Code block - determines code spacing between lines */
font-size: 14px;
}
</style>
```{r global_options,message=FALSE,results="hide"}
knitr::opts_chunk$set(fig.align="center",eval.after="fig.cap",
fig.width=12,fig.height=5,
warning=FALSE,
results="asis",
message=FALSE)
```
```{r setup, results="hide",fig.keep="none"}
library(DESeq2)
library(edgeR)
library(ade4)
library(factoextra)
library(kableExtra)
library(RColorBrewer)
library(vsn)
library(ggVennDiagram)
library(wesanderson)
library(DescTools)
library(pheatmap)
library(WGCNA)
library(readxl)
library(gage)
library(sva)
library(gageData)
library(AnnotationDbi)
library(org.Hs.eg.db)
library(SummarizedExperiment)
library(ggrepel)
library(openxlsx)
library(ggrastr)
library(viridis)
```
This chunk will print nothing
```{r,fig.height=7}
matrix1 = matrix(rnorm(200), 20, 10)
pheatmap(matrix1, color=inferno(100))
```
This chunk will print something
```{r heatmap C2 in C1 TEST,fig.height=10}
matrix2 = matrix(rnorm(200), 20, 10)
pheatmap(matrix2, color=inferno(100))
```
This chunk will print nothing
```{r model 1}
t<-sample(1:2,1)
if(t==1) {
df<-data.frame(replicate(3,sample(0:1,5,rep=TRUE)))
kable(df) %>%kable_styling("striped")
}
```
This chunk will print a table.
```{r model 2}
if(t==1) {
df<-data.frame(replicate(3,sample(0:1,5,rep=TRUE)))
kable(df) %>%kable_styling("striped")
}
```
