datautils issueshttps://git.mpi-cbg.de/bioinfo/datautils/-/issues2019-03-12T13:35:44Zhttps://git.mpi-cbg.de/bioinfo/datautils/-/issues/1update documentation for rendr2019-03-12T13:35:44Zhersemanupdate documentation for rendr- provided link in the installation section is no longer valid (`https://git.mpi-cbg.de/bioinfo/datautils/tree/master/tools/rendr`)- provided link in the installation section is no longer valid (`https://git.mpi-cbg.de/bioinfo/datautils/tree/master/tools/rendr`)hersemanhersemanhttps://git.mpi-cbg.de/bioinfo/datautils/-/issues/2rend.R: add script version control2020-04-16T07:26:40Zhersemanrend.R: add script version control- save a script copy to results folder
- in case of re-running the analysis, check for differences between the current and the previous script version and allow the user to choose whether to overwrite the previous data or not- save a script copy to results folder
- in case of re-running the analysis, check for differences between the current and the previous script version and allow the user to choose whether to overwrite the previous data or nothersemanhersemanhttps://git.mpi-cbg.de/bioinfo/datautils/-/issues/3script version control does not work in the function rendr_snippet()2019-04-24T15:02:50Zhersemanscript version control does not work in the function rendr_snippet()- when running `rendr_snippet()` for the second time on a slightly changed script, the process stops without allowing input whether to over-write the existing data or not- when running `rendr_snippet()` for the second time on a slightly changed script, the process stops without allowing input whether to over-write the existing data or nothersemanhersemanhttps://git.mpi-cbg.de/bioinfo/datautils/-/issues/5Bug: rend.R creates two yaml headers in pandoc 2.92020-11-19T13:48:45ZdomingueBug: rend.R creates two yaml headers in pandoc 2.9I noticed that when creating reports the resulting html would sometimes contain an extra header (see images in Reprex). This behaviour depended on the environment in which `rend.R` was called (conda env dge_BioC3.8 vs vanilla bash in fal...I noticed that when creating reports the resulting html would sometimes contain an extra header (see images in Reprex). This behaviour depended on the environment in which `rend.R` was called (conda env dge_BioC3.8 vs vanilla bash in falcon vs local bash), but not on the package versions of `rmarkdown` or `knitr`.
Ultimately I traced this behaviour to the pandoc version in use. This is a bug created in `pandoc` v2.9 and as long as we use v2.5 the reports are generated as expected. This might need to be investagated further if we we ever need to upgrade pandoc, but not critical for the time being.
# Reprex
### pandoc 2.5
```bash
conda create -n pandoc_2.5 --yes -c conda-forge pandoc=2.5
conda activate pandoc_2.5
# conda install
rend.R -e test_header.R
```
Output file has the expected header:
![pandoc_2.5](/uploads/468ae83e0c91ee1309f178fc6e24be57/pandoc_2.5.png)
### pandoc 2.9
```R
conda create -n pandoc_2.9.2 --yes -c conda-forge pandoc=2.9.2
conda activate pandoc_2.9.2
# conda install
rend.R -e test_header.R
```
Output report has two separated headers:
![pandoc_2.9](/uploads/8dc4ac0eff0fdaa4f0fc35648b2d4575/pandoc_2.9.png)
---
test_header.R:
```bash
#!/usr/bin/env Rscript
#' # Differential Expression Analysis
#'
#' Contents
#'
#' - [Data Preparation](#data-preparation)
#' - [Quality Control](#quality-control)
#' - [Size Factors](#size-factors)
#' - [Global Dispersion Model](#global-dispersion-model)
#' - [PCA and Clustering](#pca-and-clustering)
#' - [Differential Expression Test](#differential-expression-test)
#' - [MA and Volcano plots](#ma-and-volcano-plots)
#' - [Count Outlier Analysis](#count-outlier-analysis)
#' - [Hits Summary](#hits-summary)
#' - [Exported Data](#exported-data)
#'
# to rebuild toc do knitr::spin("featcounts_deseq_mf.R", FALSE)
#' Created by: `r system("whoami", intern=T)`
#'
#' Created at: `r format(Sys.Date(), format="%B %d %Y")`
plot(1:10)
```dominguedominguehttps://git.mpi-cbg.de/bioinfo/datautils/-/issues/6rend.R: report --help if no input parameters are provided2020-06-26T08:31:45Zhersemanrend.R: report --help if no input parameters are providedDue to the script version control (#2) the help function is shown quite late for both argparser and docopt setups and for docopt it also doesn't contain the optional arguments.Due to the script version control (#2) the help function is shown quite late for both argparser and docopt setups and for docopt it also doesn't contain the optional arguments.hersemanhersemanhttps://git.mpi-cbg.de/bioinfo/datautils/-/issues/7no html file exported when using rendr_snippet2020-06-26T08:53:44Zhersemanno html file exported when using rendr_snippet**Issue**: `rendr_snippet` does not longer produce HTML reports. Most likely this bug occurred due to the new help settings (#6) as we show the help and quit if no further input parameters are given. Thus the same issue would also occur ...**Issue**: `rendr_snippet` does not longer produce HTML reports. Most likely this bug occurred due to the new help settings (#6) as we show the help and quit if no further input parameters are given. Thus the same issue would also occur with any R script which doesn't need further required or optional input parameters.hersemanherseman