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epiforecasts / covid-rt-estimates

National and subnational estimates of the time-varying reproduction number for Covid-19
https://epiforecasts.io/covid/
MIT License
34 stars 17 forks source link

Docker image does not work as described by README #189

Open cslatteryjbc opened 3 years ago

cslatteryjbc commented 3 years ago

Docker image fails when following README instructions. Replicated the error on Mac and an AWS Sagemaker instance.

sudo docker run -d --user rstudio --name covidrtestimates covidrtestimates /bin/bash bin/update-estimates.sh

It looks like the rstudio user does not have correct permissions.

rm: cannot remove 'last-update/update-complete': No such file or directory
Run for all regional locations2021-03-01 14:17:18 INFO Processing dataset for united-kingdom
2021-03-01 14:17:18 WARN simpleWarning in file(file, ifelse(append, "a", "w")): cannot open file 'info.log': Permission denied

2021-03-01 14:17:18 WARN simpleWarning in file(file, ifelse(append, "a", "w")): cannot open file 'info.log': Permission denied

2021-03-01 14:17:18 WARN simpleWarning in file(file, ifelse(append, "a", "w")): cannot open file 'info.log': Permission denied

2021-03-01 14:17:18 ERROR Error in file(file, ifelse(append, "a", "w")): cannot open the connection

Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: <Anonymous> ... flog.error -> .log_level -> appender -> cat -> file
In addition: Warning messages:
1: In file(file, ifelse(append, "a", "w")) :
  cannot open file 'info.log': Permission denied
2: In file(file, ifelse(append, "a", "w")) :
  cannot open file 'info.log': Permission denied
Execution halted
touch: cannot touch 'last-update/update-complete': Permission denied
cslatteryjbc commented 3 years ago

It appears to run ok without the --user flag and arg.