sed error while generating concepts

[yypark24]

Prerequisites

• [X ] Put an X between the brackets on this line if you have done all of the following:
  • Checked the online documentation: https://mimic.physionet.org/about/mimic/
  • Checked that your issue isn't already addressed: https://github.com/MIT-LCP/mimic-code/issues?utf8=%E2%9C%93&q=

Description

The postgres database is built and running fine. Then I tried the following two lines: psql -f postgres-functions.sql -d mimic bash postgres_make_concepts.sh

I get many of the following error messages repeatedly (the only table that doesn't produce this error and actually gets created at the end is the diagnosis table). sed: 1: "s/DATETIME_DIFF((.+?), ...": RE error: repetition-operator operand invalid sed: 1: "s/`physionet-data.(mimi ...": RE error: repetition-operator operand invalid

I could not find related issues either open or closed - thanks!

[alistairewj]

What version of sed do you use? I think I use GNU sed and if I recall BSD sed has different quirks..

[yypark24]

I didn't know but it seems that Mac uses BSD sed (i don't know the difference between the two)

[JackieMium]

I didn't know but it seems that Mac uses BSD sed (i don't know the difference between the two)

Try install GNU version of sed and set it as default. It's quite easy, just Google it.

[jpetot]

On macos run: brew info gnu-sed export PATH="/usr/local/opt/gnu-sed/libexec/gnubin:$PATH"

then which sed should return /usr/local/opt/gnu-sed/libexec/gnubin/sed

also, sed should return

Usage: sed [OPTION]... {script-only-if-no-other-script} [input-file]...
...
...
GNU sed home page: <https://www.gnu.org/software/sed/>.
General help using GNU software: <https://www.gnu.org/gethelp/>. 

After this, you can execute bash postgres_make_concepts.sh