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Patient level prediction Package no connection


(Sebastiaan Remmers) #1

Hi all,

I developed a Targeted and Outcome cohort using Atlas. I followed the instructions to customize the R-package but I receive every time an error while I can successfully build the package. For example, in the CodeToRun.R function I receive an error that there is no file called “setting.csv” if I want the argument createShiny = T in the function execute. If I leave createShiny = F and follow the instructions in the readme.md file I receive the error that the connection (org.postgresql.util.PSQLException) failed. However, I can access the database with my credentials in Jupyter Notebook.

I feel like I am missing something and I hope someone can help me.

Thank you in advance!

Sebastiaan

BTW, this is specified in my logs.txt

2021-03-02 10:16:08 [Main thread] INFO ERSPCdiagnosisdeath execute Creating cohorts
2021-03-02 10:16:08 [Main thread] FATAL rJava .jcheck Error in rJava::.jcall(jdbcDriver, “Ljava/sql/Connection;”, “connect”, : org.postgresql.util.PSQLException: The connection attempt failed.
2021-03-02 10:19:41 [Main thread] WARN utils read.table cannot open file ‘./ERSPCdiagnosisdeathResults/settings.csv’: No such file or directory
2021-03-02 10:19:41 [Main thread] WARN utils read.table cannot open file ‘./ERSPCdiagnosisdeathResults/settings.csv’: No such file or directory
2021-03-02 10:19:41 [Main thread] FATAL utils read.table Error in file(file, “rt”) : cannot open the connection
2021-03-02 10:19:41 [Main thread] FATAL utils read.table Error in file(file, “rt”) : cannot open the connection
2021-03-02 10:21:45 [Main thread] INFO ERSPCdiagnosisdeath execute Creating cohorts
2021-03-02 10:21:45 [Main thread] INFO ERSPCdiagnosisdeath execute Creating cohorts
2021-03-02 10:21:45 [Main thread] INFO ERSPCdiagnosisdeath execute Creating cohorts
2021-03-02 10:21:45 [Main thread] FATAL rJava .jcheck Error in rJava::.jcall(jdbcDriver, “Ljava/sql/Connection;”, “connect”, : org.postgresql.util.PSQLException: The connection attempt failed.
2021-03-02 10:21:45 [Main thread] FATAL rJava .jcheck Error in rJava::.jcall(jdbcDriver, “Ljava/sql/Connection;”, “connect”, : org.postgresql.util.PSQLException: The connection attempt failed.
2021-03-02 10:21:45 [Main thread] FATAL rJava .jcheck Error in rJava::.jcall(jdbcDriver, “Ljava/sql/Connection;”, “connect”, : org.postgresql.util.PSQLException: The connection attempt failed.

(Chungsoo Kim) #2

Hi, It seems to be because the shiny data folder is not created. Would you like to change the populateShinyApp.R code as shown below and rebuild it?

image

And - do you get an error when running the “PatientLevelPrediction::viewMultiplePlp(outputFolder)” code with createShiny = F? It can show the model results with this function whether or not doing the createShiny function.


(Sebastiaan Remmers) #3

Hi,

Thank you for your fast reply! Unfortunately, this does not work properly.
If I do createShiny = T, the error is that there is no write permission for directory.
If I do cheateShiny = F, the error is “Error in checkPlpInput(result) : Incorrect class for input result”

I am running the package on my own computer, so rights and permissions shouldn’t be an issue.

I hope you have another possibility to solve this issue.

Attached is the log,

2021-03-02 13:27:48 [Main thread] FATAL ERSPCdiagnosisdeath populateShinyApp Error in file.path(outputDirectory, “data”) : object ‘outputDirectory’ not found
2021-03-02 13:45:01 [Main thread] WARN utils download.file cannot open URL ‘https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/PACKAGES.rds’: HTTP status was ‘404 Not Found’
2021-03-02 13:45:01 [Main thread] WARN utils download.file cannot open URL ‘https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/PACKAGES.rds’: HTTP status was ‘404 Not Found’

(Jreps) #4

I think the issue is using a relative path rather than absolute (e.g., ‘./myfolder’) - make the path absolute and I think it will work


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