I'm running R-markdown with command lines:
Rscript -e "rmarkdown::render('BRS_totalRNA.Rmd',output_file='BRS_totalRNA.html')"
my code worked fine until the last step, which is to generate the html file.
my code is like that:
---
title: "BRS"
author: "Jieqiong Dai"
date: "May 1, 2019"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r}
#calculate BRAS-RAS scoring
library(DESeq2)
#reads in total RNA reads count data
rna <- read.csv("/data/daij/project/Chernobyl_phase123/phase1234/corrected_read_count/totalRNA/phase1234_totalRNA_reads_count_ready.csv",header=T,row.names=1)
head(rna)
ncol(rna)
nrow(rna)
#read in sample table
sample <- read.csv("/data/daij/project/Chernobyl_phase123/phase1234/corrected_read_count/totalRNA/tumorVSnormal/phase1234_totalRNA_sample_table_inuse.csv",header=T,row.names=1)
head(sample)
nrow(sample)
ncol(sample)
...
BRS3 <- TB3-TR3
BRS3 <- matrix(BRS3,ncol=1, byrow=T)
colnames(BRS3) <- c("BRS")
rownames(BRS3) <- colnames(top100c_vst_tu)
write.csv(BRS3,"tumor_BRS_totalRNA_183_40.csv")
save.image("totalRNA_BRS.Rdata")
```
## Including Plots
You can also embed plots, for example:
```{r, echo=TRUE}
```
All the output data files were generated and the "totalRNA_BRS.Rdata" was successfully saved.
the error message is :
output file: BRS_totalRNA.knit.md
Error in file(con, "w") : cannot open the connection
Calls: ... pandoc_html_extras_args -> as_tmpfile -> write_utf8 -> writeLines -> file
In addition: Warning message:
In file(con, "w") :
cannot open file '/tmp/RtmpB2YFLy/rmarkdown-str9c2b4aaf8416.html': No such file or directory
Execution halted
I am using R/3.5.2.
Does any body have an idea about that?
Thanks!