suppressed export of the pdf report from rna-seq_analysis.R because i…

…t creates dependency to latex which create bug under conda
SnakeChunks · Aug 18, 2018 · 69c0017 · 69c0017
1 parent ec28597
commit 69c0017
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/scripts/RSnakeChunks/R/rna-seq_analysis.R b/scripts/RSnakeChunks/R/rna-seq_analysis.R
@@ -1315,7 +1315,7 @@ knitr::opts_chunk$set(
   writeLines(text = report.text, con = report.socket)
   close(report.socket)
   rmarkdown::render(rmd.report, output_format = "html_document")
-  rmarkdown::render(rmd.report, output_format = "pdf_document")
+#  rmarkdown::render(rmd.report, output_format = "pdf_document")
   rmarkdown::render(rmd.report, output_format = "word_document")
 
 
@@ -1325,7 +1325,7 @@ knitr::opts_chunk$set(
   message("Index of input/output files\t", index.file)
   message("Report in Rmd format\t", rmd.report)
   message("Report in HTML format\t", sub(pattern = '.Rmd', replacement  = ".html", x = rmd.report))
-  message("Report in pdf format\t", sub(pattern = '.Rmd', replacement  = ".pdf", x = rmd.report))
+#  message("Report in pdf format\t", sub(pattern = '.Rmd', replacement  = ".pdf", x = rmd.report))
   message("Report in Word format\t", sub(pattern = '.Rmd', replacement  = ".docx", x = rmd.report))
   message("Job done")
 

diff --git a/scripts/snakefiles/envs/rnaseq_deg.yaml b/scripts/snakefiles/envs/rnaseq_deg.yaml
@@ -20,4 +20,6 @@ dependencies:
   - r-devtools=1.13.5
   - r-ascii=2.1
   - r-codetools=0.2_15
+#  - pandoc=2.2.2
+#  - r-tinytex=0.6
 ...