# R docker issue
**URL:** https://community.seqera.io/t/r-docker-issue/2357
**Category:** Ask for help
**Created:** [September 11, 2025, 5:31am UTC](https://community.seqera.io/t/r-docker-issue/2357 "2025-09-11T05:31:41Z")
**Posts on this page:** 4
**Page:** 1
### Author:  [@holly\_123789](https://community.seqera.io/u/holly_123789)
#### Post date: [September 11, 2025, 5:31am UTC](https://community.seqera.io/t/r-docker-issue/2357/1 "2025-09-11T05:31:42Z")
Hello! I’m trying to run an R script via a docker container using a very simple nextflow process, but keep coming up against this error:
I think there’s an issue with how the folders are mounted into the container, as I can run the docker interactively within the nextflow work dir and it runs correctly.
Any help would be amazing!
**Error:**
_Command executed:_
_Rscript /app/R\_extraction.R --base\_dir processed\_audio --window 40 --output\_dir ._
_Command exit status:
1_
_Command output:
(empty)_
_Command error:
Error: unexpected input in “”
Execution halted_
\*Work dir:
/mnt/c/holly/nextflowdev/work/94/5dd9c5805bb0a91f17177e8cc00ed4
-
**this is my main.nf:**
#!/usr/bin/env nextflow
nextflow.enable.dsl=2
params.input = ‘/mnt/c/holly/nextflowdev/test\_files’
params.outdir = ‘/mnt/c/holly/nextflowdev/processed\_audio’
workflow {
```
// wrap folder as a single path object
input_ch = Channel.of(file(params.input))
preproc_ch = PREPROCESS_AUDIO(input_ch)
EXTRACT_R_FEATURES(preproc_ch)
```
}
process PREPROCESS\_AUDIO {
```
container 'speak_proj/audio-preprocessing:latest'
publishDir "${params.outdir}", mode: 'copy'
input:
path audio_files
output:
path "processed_audio"
script:
"""
mkdir -p processed_audio
python3 /app/py_preprocessing.py --input ${audio_files} --outdir processed_audio
"""
```
}
process EXTRACT\_R\_FEATURES {
```
container 'speak_proj/r-extraction:latest'
publishDir "${params.outdir}/R_features", mode: 'copy'
input:
path processed_audio
output:
path "R_extracted_features.csv"
path "extracted_features.Rdata"
path "features"
script:
"""
Rscript /app/R_extraction.R --base_dir ${processed_audio} --window 40 --output_dir .
"""
```
}
---
### Author:  [@mahesh.binzerpanchal](https://community.seqera.io/u/mahesh.binzerpanchal)
#### Post date: [September 11, 2025, 9:19am UTC](https://community.seqera.io/t/r-docker-issue/2357/2 "2025-09-11T09:19:07Z")
I think the issue is that the `/app/` directory is not mounted within your container.
In terms of best practices though, scripts should be put in a `bin/` folder in the root of your workflow. They should be made executable, and have the shebang directive at the top that tells the executor which interpreter to use.
```groovy
script:
"""
mkdir -p processed_audio
py_preprocessing.py --input ${audio_files} --outdir processed_audio
"""
```
where `py_preprocessing.py` looks like:
```python
#! /usr/bin/env python
...
rest of python script
```
and similarly with your R process
```r
#! /usr/bin/env Rscript
...
rest of R script
```
and call it
```groovy
script:
"""
R_extraction.R \\
--base_dir ${processed_audio} \\
--window 40 \\
--output_dir .
"""
```
---
### Author:  [@holly\_123789](https://community.seqera.io/u/holly_123789)
#### Post date: [September 12, 2025, 1:05am UTC](https://community.seqera.io/t/r-docker-issue/2357/3 "2025-09-12T01:05:39Z")
> [@mahesh.binzerpanchal](#):
>
> I think the issue is that the `/app/` directory is not mounted within your container.
>
> In terms of best practices though, scripts should be put in a `bin/` folder in the root of your workflow. They should be made executable, and have the shebang directive at the top that tells the executor which interpreter to use.
Thank you!
I changed the scripts to pull from /bin, and they have the shebang now.
I keep getting the same error in the R docker, although I tried a similar process with a python script and that one worked ok:
// ----------------------
// R feature extraction
// ----------------------
process EXTRACT\_R\_FEATURES {
```
container 'speak_proj/r-extraction:latest'
input:
path processed_audio
output:
path "R_extracted_features.csv"
path "extracted_features.Rdata"
path "features"
script:
"""
Rscript ${params.r_extraction} --base_dir ${processed_audio} --window 40 --output_dir .
"""
```
}
executor \> local (1)
[1a/2d03d4] PREPROCESS\_AUDIO (1) [100%] 1 of 1, cached: 1 ✔
[91/b6596e] EXTRACT\_PY\_FEATURES (1) [100%] 1 of 1, cached: 1 ✔
[47/940634] EXTRACT\_R\_FEATURES (1) [0%] 0 of 1 ✘
ERROR ~ Error executing process \> ‘EXTRACT\_R\_FEATURES (1)’
Caused by:
Process `EXTRACT_R_FEATURES (1)` terminated with an error exit status (1)
Command executed:
Rscript /mnt/c/holly/nextflowdev/bin/R\_extraction.R --base\_dir processed\_audio --window 40 --output\_dir .
Command exit status:
1
Command output:
(empty)
Command error:
Error: unexpected input in “”
Execution halted
Work dir:
/mnt/c/holly/nextflowdev/work/47/940634116c43fb576d614bb380b9e4
Container:
speak\_proj/r-extraction:latest
Tip: you can try to figure out what’s wrong by changing to the process work dir and showing the script file named `.command.sh`
– Check ‘.nextflow.log’ file for details
The script works fine in docker when i mount it explicitly, but the py script works natively in nextflow following the same method: // ----------------------
// Python feature extraction
// ----------------------
process EXTRACT\_PY\_FEATURES {
```
publishDir "${params.outdir}/python_features", mode: 'copy'
input:
path processed_audio
output:
path "features"
script:
"""
python3 ${params.py_extraction} --input_dir ${processed_audio} --output_dir features
"""
```
}
---
### Author:  [@mahesh.binzerpanchal](https://community.seqera.io/u/mahesh.binzerpanchal)
#### Post date: [September 12, 2025, 7:07am UTC](https://community.seqera.io/t/r-docker-issue/2357/4 "2025-09-12T07:07:43Z")
The underlying issue is still the same. The directories aren’t mounted to docker container with the `-v` option so they’re not visible when you run the nextflow process. The directory which isn’t mounted in this case is `/mnt` now.
```auto
Rscript /mnt/c/holly/nextflowdev/bin/R_extraction.R
```
This is also because you’re passing the script name as a parameter. This isn’t portable as you’re discovering.
One shouldn’t use `params` inside processes generally ( the notable exception is with `publishDir` but that will be replaced in future ). `params` and such should be passed into the process call, and then accessed within the `process` from the `input:` variables.
```auto
workflow {
CUSTOM_PROCESS( params.my_file )
}
...
process CUSTOM_PROCESS {
input:
path some_file
...
}
```
However for scripts which are in the `bin/` folder of your workflow, you would simply call them as a command in the script:
```auto
Rscript /mnt/c/holly/nextflowdev/bin/R_extraction.R
```
should simply be ( no `params` ):
```auto
R_extraction.R
```
and have executable permission (`chmod a+x bin/R_extraction.R`).
The underlying concept is that all files a process uses should be “staged” (symlinked or copied) into the working directory, and scripts are found by extending the `PATH` env variable by adding the `bin/` directory to it before running the process.
I hope that clarifies things a bit more.
The nextflow training material goes into more depth if you’re interested: [Working with Files - training.nextflow.io](https://training.nextflow.io/latest/side_quests/working_with_files/)