IncidencePrevalence Export Issue

[JordiRodeiroSJD]

Hi,

I am encountering an error in the Incidence-Prevalence section.

As noted in the image of the error trace, a function called in the code cannot be found.

Could you please provide me with assistance?

Thanks,
Jordi Rodeiro

[tiozab]

@JordiRodeiroSJD can you let me know which version of Incidence Prevalence you are using, and your database management system? Thank you.

@edward-burn any idea what is going on that all of a sudden functions cannot be found? same as the other issue #68 in Codelistgenerator?

[JordiRodeiroSJD]

I am using a SQLServer Database and the Incidence Prevalence version is 0.7.4.

[tiozab]

Thanks @JordiRodeiroSJD please use the renv.lock file and make sure it works properly :-)

[JordiRodeiroSJD]

When trying to use the renv.lock, an error pops up.

Error: Error installing package 'curl':
Error in download.file(url, basename(url), quiet = TRUE) :
cannot open URL 'https://github.com/r-windows/bundles/releases/download/curl-8.3.0/curl-8.3.0-ucrt-x86_64.tar.xz'

I understand that is not from your code, but it unables me from using the renv.lock provided.

[tiozab]

@JordiRodeiroSJD just found this on stackoverflow.
https://stackoverflow.com/questions/35931342/r-cannot-access-urls-for-package-installation

try running this command before the renv activation?
options(repos="https://CRAN.R-project.org")
however, there is one package that comes from OHDSI (circeR 1.3.1)

otherwise please install the correct versions of the following packages separately:

"Package": "PatientProfiles",
"Version": "0.4.0",

 "Package": "CDMConnector",
  "Version": "1.2.1",

"Package": "IncidencePrevalence",
  "Version": "0.6.0",

"Package": "DrugUtilisation",
"Version": "0.4.1",

  "Package": "dbplyr",
  "Version": "2.4.0",

"Package": "CodelistGenerator",
"Version": "2.1.1",

  "Package": "MASS",
  "Version": "7.3-60",

  "Package": "curl",
  "Version": "5.1.0",

from ohdsi:
"CirceR": {
"Package": "CirceR",
"Version": "1.3.1",
"Source": "GitHub",
"RemoteType": "github",
"RemoteHost": "api.github.com",
"RemoteRepo": "CirceR",
"RemoteUsername": "ohdsi",

Until here are the relevant ones.

and you can look up the other versions for these packages, however I dont think their version matters:
library("devtools")
library("odbc")
library("RPostgres")
library("DBI")
library("dplyr")

library("here")
library("log4r")
library("zip")

library("tidyr")
library("ggplot2")
library("Capr")
library("testthat")

[JordiRodeiroSJD]

I managed to use the renv.lock by deleting some of the included packages and it works. Thanks!

[tiozab]

@JordiRodeiroSJD which packages did you delete? this would be good to know in case another DP faces similar problems. thanks!

[JordiRodeiroSJD]

I deleted packages V8, curl, gert, httpuv, openssl, and rJava from the renv.lock, and I used the versions that I had already installed locally without the renv. The versions I used are 4.3.3 (V8), 5.1.0 (curl), 2.0.1 (gert), 1.6.15 (httpuv), 2.1.1 (openssl), and 1.0.11 (rJava).