Dear moderators,
We found in log file of express lane submission that:
/usr/bin/env: 'Rscript\r': No such file or directory
However, in our r-code, the first line is:
#!/usr/bin/env Rscript
.
.
.
I guess, in our r-code, there would be something wrong, e.g.:
"#!/usr/bin/env Rscript" could not be correct for the finding of directory in Docker?
submission name: syn10720241
submission ID: 9634057
No prediction file generated, please check your log file: https://www.synapse.org/#!Synapse:syn10722255
Any suggestion will be highly appreciated.
thank you and best regards,
Bruce
Created by Wei-Quan Fang deleapoli Dear Bruce,
Your prediction file has "NA" values for both submissions. The columns `predictionscore` and `highriskflag` need to be populated with values.
Best,
Tom Dear Tom,
Thank you very much for your correction, we can load the Rscript to execute code.
However, our submission encountered another error in the end; as the following message shown
"There can't be any empty predictionscore values"
submission name: syn10757601
submission ID: 9634523
or
submission name: syn10758460
submission ID: 9634535
If any suggestion, it will be highly appreciated, thanks again.
Best regards,
Bruce Dear Bruce,
Apologies for the inconvenience. The example is actually incorrect and I just updated it.
It should be:
```
...
RUN apt-get update && apt-get install -y r-base
## Install dependencies
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite("plyr")'
...
```
I just ran this on my machine and I was able to create a Rscript with `#!/usr/bin/env Rscript` and was able to execute it.
Best,
Tom Dear Tom,
Thank you for the fast reply. In the Dockerfile, we just followed the example
.
.
.
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite("plyr")'
RUN echo "r <- getOption('repos'); r['CRAN'] <- 'http://cran.us.r-project.org'; options(repos = r);" > ~/.Rprofile
RUN Rscript -e "install.packages('data.table')"
.
.
.
So I guess this "incorrect installing" problem should not occur.
Best regards,
Bruce Dear Bruce,
Sorry for your troubles. How did you install R in your docker file? If you don't have Rscript installed, then this error would definitely occur. An easy way to check is to go into your docker container by doing this:
`docker run -ti docker.synapse.org/....`
While in that environment, you can do:
`Rscript` to see if the command exists. Hope that helps.
Best,
Tom
Drop files to upload
ERROR message No such file "Rscript" page is loading…