serratus-bio / tantalus

R Data Exploration for Serratus
https://github.com/ababaian/serratus
GNU General Public License v3.0
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Problem to generate the connection to the DB #9

Closed anachshon closed 2 years ago

anachshon commented 2 years ago

Hi,

I managed to install on our Linux cluster the tantalus package and the RPostgreSQL packages, but did not manage to pass the line

con <- DBI::Connect( ...

from the readme file. The error I am getting is shown below. This is the case for both R versions 3.6.0 and 4.1.0.

Also on my mac laptop, R version 4.1.0 I am getting (different) error on the same line.

Thanks, aharon.

caught segfault address 0xffffffff, cause 'memory not mapped'

Traceback: 1: postgresqlNewConnection(drv, ...) 2: DBI::dbConnect(drv, user = "public_reader", password = "serratus", host = "serratus-aurora-20210310.cluster-ro-ccz9y6yshbls.us-east-1.rds.amazonaws.com", port = 5432, dbname = "summary") 3: DBI::dbConnect(drv, user = "public_reader", password = "serratus", host = "serratus-aurora-20210310.cluster-ro-ccz9y6yshbls.us-east-1.rds.amazonaws.com", port = 5432, dbname = "summary")

Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace

ababaian commented 2 years ago

I really don't know why it would segfault, but make sure the script has the most recent version of the login credentials as shown on this page.

anachshon commented 2 years ago

I just came back to this page to write that the problem was solved after using the right hostname and saw your response :-)

Thanks a lot for the very prompt response.

It will be nice also in the readme here (in the example code) to include the link to the updated details.

It is great / encouraging to know that someone is responding on the other side :-)

Thanks.

ababaian commented 2 years ago

@fransilvion can you update README/script plz

fransilvion commented 2 years ago

Done

eul2021 commented 2 years ago

Hi, I've tantalus installed on a cluster server Rstudio, but cannot establish connection. The session restarts with "Error: Error occurred during transmission". Thank you for any hints on how to debug this.

con <- DBI::dbConnect(drv,