Problem with DUS step

[JavierGorri]

Dear Theresa,

We have a problem when we try to run the R code of tha DUS step. Can you help us with it?

This is the trace:

rlang::last_trace()
<error/rlang_error>
Error in dplyr::collect():
! Failed to collect lazy table.
Caused by error:
! nanodbc/nanodbc.cpp:3108: 07009: [Microsoft][SQL Server Native Client 11.0]Invalid Descriptor Index

---

Backtrace:
▆

1. ├─base::source("C:/Users/D229463/Desktop/Scripts_R/MegaStudy-Fase2/MegaStudy-main/DUS Code/CodeToRun.R")
2. │ ├─base::withVisible(eval(ei, envir))
3. │ └─base::eval(ei, envir)
4. │ └─base::eval(ei, envir)
5. ├─base::source(here("DUS.R")) at MegaStudy-main/DUS Code/CodeToRun.R:47:1
6. │ ├─base::withVisible(eval(ei, envir))
7. │ └─base::eval(ei, envir)
8. │ └─base::eval(ei, envir)
9. ├─base::source(here("individual_indications.R")) at MegaStudy-main/DUS Code/DUS.R:45:1
10. │ ├─base::withVisible(eval(ei, envir))
11. │ └─base::eval(ei, envir)
12. │ └─base::eval(ei, envir)
13. ├─CodelistGenerator::getCandidateCodes(...) at MegaStudy-main/DUS Code/individual_indications.R:3:1
14. │ └─base::lapply(...)
15. │ └─CodelistGenerator (local) FUN(X[[i]], ...)
16. │ └─CodelistGenerator:::runSearch(...)
17. │ └─CodelistGenerator:::getMatches(words = tidyWords(keywords), conceptDf = workingConcept)
18. │ └─workingConcepts %>% dplyr::collect()
19. ├─dplyr::collect(.)
20. └─omopgenerics:::collect.cdm_table(.)
21. ├─dplyr::collect(removeClass(x, "cdm_table"))
22. └─dbplyr:::collect.tbl_sql(removeClass(x, "cdm_table"))
    Run rlang::last_trace(drop = FALSE) to see 6 hidden frames.

We find this.

These are the libraries a picture from the Console.

Kind regards,

[tiozab]

@JavierGorri, thanks I see you have sql_server, did you successfully run the renv for the DUS code?
packageVersion("CodelistGenerator")

In the outputfolder, as a default we call it "storage", there should be a log file, can you post this?
Did you do any changes in the code files?

[JavierGorri]

@tiozab
We attach the txt and csv files that we can find
snapshot_Bardena.csv
BARDENA_log.txt
This is the code to run
CodeToRun.txt

We have done this change in the code file

[tiozab]

@JavierGorri Thanks. It seems you cannot generate the indication concepts.
can you give me the package versions please by running these three lines and telling my what the output is?
packageVersion("CodelistGenerator")
packageVersion("omopgenerics")
packageVersion("CDMConnector")

with regards to the changes you made to the code in line 36/37, what happens if you do not outcomment these lines?

[JavierGorri]

@tiozab.
This tha package version

This is what happens:

[JavierGorri]

There is a problem with the second image in the Github. I send it also here (just in case) ***@***.*** De: Theresa Burkard ***@***.***> Enviado el: jueves, 9 de mayo de 2024 9:38 Para: oxford-pharmacoepi/MegaStudy ***@***.***> CC: Gorricho Mendívil, Javier (Serv. Centrales) ***@***.***>; Mention ***@***.***> Asunto: Re: [oxford-pharmacoepi/MegaStudy] Problem with DUS step (Issue #52) @JavierGorri<https://github.com/JavierGorri> Thanks. It seems you cannot generate the indication concepts. can you give me the package versions please by running these three lines and telling my what the output is? packageVersion("CodelistGenerator") packageVersion("omopgenerics") packageVersion("CDMConnector") with regards to the changes you made to the code in line 36/37, what happens if you do not outcomment these lines? — Reply to this email directly, view it on GitHub<#52 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AQLHROYEPXRXI3JVGDF3ZOTZBMRWNAVCNFSM6AAAAABHMKOMI2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMBSGEZDGOJVGY>. You are receiving this because you were mentioned.Message ID: ***@***.******@***.***>>

[tiozab]

Thanks @JavierGorri it seems like the use of renv has not worked, the renv.lock has CodelistGenerator 2.2.2 for example.
Please try again with renv::activate() and renv::restore()

let's not worry right now about the table names (i.e. use your outcommented versions). but first, have the correct package versions :-)

[JavierGorri]

@tiozab
We have done it, This is the Error on a png


When we see the renv.lock file it's yet on 2.2.3 version of the CodelistGenerator

Here we attach the documents of snapshot &logs:
BARDENA_log.txt
snapshot_Bardena.csv

[tiozab]

the codelistgenerator should be 2.2.2 :-)
can you pull again from the repository?

[JavierGorri]

@tiozab We have begun to change to the correct package versions (some of then we had more recent ones). We have aproblem with the CirceR that we can not install.

When we try to install from the file we have this faile:

Can you help us with this?

[tiozab]

@JavierGorri you can use the circeR from CRAN (has been recently put on CRAN)
install.packages("CirceR")
hope that fixes it

[JavierGorri]

Bad luck. We have this problem.

[tiozab]

https://cran.r-project.org/web//packages/CirceR/index.html
the package imports rJAVA package which seems to cause the problem.
Maybe by installing that yourselves before you can avoid the problem?
install.packages("rJava")

[JavierGorri]

We have this error

install.packages("rJava")
The following package(s) will be installed:

• rJava [1.0-11]
  These packages will be installed into "C:/Users/d229463/Desktop/EHDEN/MegaStudy-main/DUS Code/renv/library/windows/R-4.4/x86_64-w64-mingw32".

Do you want to proceed? [Y/n]: y

Installing packages --------------------------------------------------------

• Installing rJava ... OK [linked from cache]
  Successfully installed 1 package in 23 milliseconds.

library("rJava")
Error: package or namespace load failed for ‘rJava’:
.onLoad falló en loadNamespace() para 'rJava', detalles:
llamada: inDL(x, as.logical(local), as.logical(now), ...)
error: no es posible cargar el objeto compartido 'C:/Users/d229463/AppData/Local/R/cache/R/renv/cache/v5/windows/R-4.4/x86_64-w64-mingw32/rJava/1.0-11/524167e771b81342f8dd7a891ed3afa8/rJava/libs/x64/rJava.dll':
LoadLibrary failure: %1 no es una aplicación Win32 válida.

[JavierGorri]

@tiozab.
Hello, Theresa.

Do you have any Idea abouyt what we can do. We are really desperate.

Kind regards

[tiozab]

@janblom just gave this advice to another data partner concerning rJava / JAVA problems
• the version of java in terms of 32/64 bits should match your R version. You can check your R version by typing the command version in Rstudio. The second output line starting with "arch" should indicate whether it's 32 or 64. The screenshot below if not from a Windows environment, so it might not match what you see exactly, but there should be a clear 32/64 indication on the "arch" line. The java version you use should match that.

• The error mentioning "JAVA_HOME" indicates that the rJava package is not able to locate java in (any of) its default location(s). You can set the environment variable JAVA_HOME to point to the java installation directory, for example, if java is installed in C:\Program Files\Eclipse Adoptium\jdk-17.0.10.7-hotspot (with java.exe located here: C:\Program Files\Eclipse Adoptium\jdk-17.0.10.7-hotspot\bin\java.exe, you can set the environment variable like this (in Rstudio):
Sys.setenv(JAVA_HOME = "C:\Program Files\Eclipse Adoptium\jdk-17.0.10.7-hotspot")
Please change the directory to what applies in your environment,
Note that this only sets the environment variable in your current R/Rstudio session, you would need to repeat that every time you start R/Rstudio. It is usually better to set this permanently for the (Windows) user. I cannot provide you details on how to do that in your environment, if you do not know how to do that it is best to consult a local system support/admin person.