Error running Achilles on MIMIC IV: "no lines available in input"

Implementers
1

I’m following the Getting Started with Achilles Guide with the MIMIC-IV demo data. However, I get the following error from Achilles.achilles:

Connecting using PostgreSQL driver
Error in read.table(file = file, header = header, sep = sep, quote = quote,    :
  no lines available in input
Calls: achilles -> getAnalysisDetails -> read.csv -> read.table
In addition: Warning message:
In file(file, "rt") :
  file("") only supports open = "w+" and open = "w+b": using the former
Execution halted

I couldn’t find another example of this error, but searching for the warning brings up some related issues on the Achilles GitHub. Is there an issue in building the database that is likely to cause this error?

2

I get the same error after running ETLSyntheaBuilder on the COVID-19 10K CSV dataset.

3

The immediate cause of the error is one of the calls to the R function system.files inside the the Achilles source, which was returning a blank string. The package directory Achilles/csv/ needs to contain some CSV files. If these files are absent or blank, the issue will occur. I’ll try to find out why these files weren’t present in my local installation.