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)

@JavierGorrihttps://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 GitHubhttps://github.com/oxford-pharmacoepi/MegaStudy/issues/52#issuecomment-2102123956, or unsubscribehttps://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.

[janblom]

Hi @JavierGorri,

did you manage to resolve this yet? If not, I think it does make sense to verify that both your R/Rstudio environment and Java installation match in terms of their binary compatibility, i.e. both should be either 32-bits, or 64-bits. If you need help verifying this, please let me know.

Best regards, Jan Blom

[JavierGorri]

Thanks Jan,

We are trying to verify this. we keep in touch

De: janblom @.> Enviado el: lunes, 27 de mayo de 2024 14:47 Para: oxford-pharmacoepi/MegaStudy @.> CC: Gorricho Mendívil, Javier (Serv. Centrales) @.>; Mention @.> Asunto: Re: [oxford-pharmacoepi/MegaStudy] Problem with DUS step (Issue #52)

Hi @JavierGorrihttps://github.com/JavierGorri,

did you manage to resolve this yet? If not, I think it does make sense to verify that both your R/Rstudio environment and Java installation match in terms of their binary compatibility, i.e. both should be either 32-bits, or 64-bits. If you need help verifying this, please let me know.

Best regards, Jan Blom

— Reply to this email directly, view it on GitHubhttps://github.com/oxford-pharmacoepi/MegaStudy/issues/52#issuecomment-2133411719, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AQLHRO6UUFXAYWSP5F54JEDZEMTL5AVCNFSM6AAAAABHMKOMI2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMZTGQYTCNZRHE. You are receiving this because you were mentioned.Message ID: @.**@.>>

[JavierGorri]

Hello Jan,

We have installed r.java and the old version of the libraries (as Theresa has told us). We have run the DUS code and we have the same error.

We attach the txts.

Can you help with this?

Kind regards.

Javier Gorricho Servicio Navarro de Salud - Osasunbidea (SNS-O) Correo: @.**@.> @.*** [logo-bardena]

De: Gorricho Mendívil, Javier (Serv. Centrales) Enviado el: lunes, 27 de mayo de 2024 14:50 Para: 'oxford-pharmacoepi/MegaStudy' @.>; oxford-pharmacoepi/MegaStudy @.> CC: Mention @.>; Fernández Benedicto,Fernando (Hiberus, DGTD Servicio de Tecnologías de Salud) @.>; Almirantearena Legaz, Maite (Serv. Centrales) @.>; Ballesteros Dominguez, Asier (Navarrabiomed) @.>; Padilla López, Esther (TRACASA, DGTD Servicio de Tecnologías de @.>; Ballaz Echegoyen, Jerónimo (TRACASA, DGTD Servicio de Tecnologías de Salud) @.> Asunto: RE: [oxford-pharmacoepi/MegaStudy] Problem with DUS step (Issue #52)

Thanks Jan,

We are trying to verify this. we keep in touch

De: janblom @.**@.>> Enviado el: lunes, 27 de mayo de 2024 14:47 Para: oxford-pharmacoepi/MegaStudy @.**@.>> CC: Gorricho Mendívil, Javier (Serv. Centrales) @.**@.>>; Mention @.**@.>> Asunto: Re: [oxford-pharmacoepi/MegaStudy] Problem with DUS step (Issue #52)

Hi @JavierGorrihttps://github.com/JavierGorri,

did you manage to resolve this yet? If not, I think it does make sense to verify that both your R/Rstudio environment and Java installation match in terms of their binary compatibility, i.e. both should be either 32-bits, or 64-bits. If you need help verifying this, please let me know.

Best regards, Jan Blom

— Reply to this email directly, view it on GitHubhttps://github.com/oxford-pharmacoepi/MegaStudy/issues/52#issuecomment-2133411719, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AQLHRO6UUFXAYWSP5F54JEDZEMTL5AVCNFSM6AAAAABHMKOMI2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMZTGQYTCNZRHE. You are receiving this because you were mentioned.Message ID: @.**@.>>

Error in cdm_from_con() at CDMConnector/R/cdm.R:184:3: ! CDM database tables should be either all upppercase or all lowercase! Run rlang::last_trace() to see where the error occurred.

trace(cdm_from_con, edit = TRUE) Tracing function "cdm_from_con" in package "CDMConnector" [1] "cdm_from_con" source("C:/Users/d229463/Desktop/Scripts R/Ultima version con DUS/MegaStudy-main/DUS Code/CodeToRun.R") condition domain: Limiting to domains of interest condition: Getting concepts to include Error in dplyr::collect() at omopgenerics/R/classCdmTable.R:150:3: ! Failed to collect lazy table. Caused by error: ! nanodbc/nanodbc.cpp:3110: 07009: [Microsoft][SQL Server Native Client 11.0]Invalid Descriptor Index Run rlang::last_trace() to see where the error occurred. Aviso: In dbClearResult(res) : Result already cleared

rlang::last_trace() <error/rlang_error> Error in dplyr::collect() at omopgenerics/R/classCdmTable.R:150:3: ! Failed to collect lazy table. Caused by error: ! nanodbc/nanodbc.cpp:3110: 07009: [Microsoft][SQL Server Native Client 11.0]Invalid Descriptor Index

Backtrace: ▆

1. ├─base::source("C:/Users/d229463/Desktop/Scripts R/Ultima version con DUS/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:78:1
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:1:1
14. │ └─base::lapply(...) at CodelistGenerator/R/getCandidateCodes.R:129:3
15. │ └─CodelistGenerator (local) FUN(X[[i]], ...)
16. │ └─CodelistGenerator:::runSearch(...) at CodelistGenerator/R/getCandidateCodes.R:130:5
17. │ └─CodelistGenerator:::getMatches(words = tidyWords(keywords), conceptDf = workingConcept) at CodelistGenerator/R/runSearch.R:133:3
18. │ └─workingConcepts %>% dplyr::collect() at CodelistGenerator/R/runSearch.R:489:5
19. ├─dplyr::collect(.)
20. └─omopgenerics:::collect.cdm_table(.)
21. ├─dplyr::collect(removeClass(x, "cdm_table")) at omopgenerics/R/classCdmTable.R:150:3
22. └─dbplyr:::collect.tbl_sql(removeClass(x, "cdm_table")) Run rlang::last_trace(drop = FALSE) to see 6 hidden frames.

packageVersion("odbc") [1] ‘1.3.5’ packageVersion("odbc") [1] ‘1.3.5’ packageVersion("RPostgres") [1] ‘1.4.7’ packageVersion("DBI") [1] ‘1.2.1’ packageVersion("dplyr") [1] ‘1.1.4’ packageVersion("dbplyr") [1] ‘2.4.0’ packageVersion("CirceR") [1] ‘1.3.3’ packageVersion("CDMConnector") [1] ‘1.3.0’ packageVersion("here") [1] ‘1.0.1’ packageVersion("log4r") [1] ‘0.4.3’ packageVersion("zip") [1] ‘2.3.1’ packageVersion("IncidencePrevalence") [1] ‘0.7.0’ packageVersion("tidyr") [1] ‘1.3.1’ packageVersion("ggplot2") [1] ‘3.4.3’ packageVersion("CodelistGenerator") [1] ‘2.2.2’ packageVersion("lubridate") [1] ‘1.9.3’ packageVersion("glue") [1] ‘1.7.0’ packageVersion("DrugUtilisation") [1] ‘0.5.0’ packageVersion("PatientProfiles") [1] ‘0.6.1’ packageVersion("omopgenerics") [1] ‘0.2.1’ packageVersion("stringr") [1] ‘1.5.1’ packageVersion("testthat") [1] ‘3.2.1’

[tiozab]

@JavierGorri omopgenerics should be 0.0.2

[JavierGorri]

Thanks, Teheresa, we try again

De: Theresa Burkard @.> Enviado el: miércoles, 29 de mayo de 2024 11:01 Para: oxford-pharmacoepi/MegaStudy @.> CC: Gorricho Mendívil, Javier (Serv. Centrales) @.>; Mention @.> Asunto: Re: [oxford-pharmacoepi/MegaStudy] Problem with DUS step (Issue #52)

@JavierGorrihttps://github.com/JavierGorri omopgenerics should be 0.0.2

— Reply to this email directly, view it on GitHubhttps://github.com/oxford-pharmacoepi/MegaStudy/issues/52#issuecomment-2136906468, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AQLHRO6CR2QLKRJLIUJXU2DZEWKOFAVCNFSM6AAAAABHMKOMI2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMZWHEYDMNBWHA. You are receiving this because you were mentioned.Message ID: @.**@.>>

[JavierGorri]

Thanks, Theresa.

We have change it to omopgenerics 0.0.2, we find now the error that we attach.

De: Theresa Burkard @.> Enviado el: miércoles, 29 de mayo de 2024 11:01 Para: oxford-pharmacoepi/MegaStudy @.> CC: Gorricho Mendívil, Javier (Serv. Centrales) @.>; Mention @.> Asunto: Re: [oxford-pharmacoepi/MegaStudy] Problem with DUS step (Issue #52)

@JavierGorrihttps://github.com/JavierGorri omopgenerics should be 0.0.2

— Reply to this email directly, view it on GitHubhttps://github.com/oxford-pharmacoepi/MegaStudy/issues/52#issuecomment-2136906468, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AQLHRO6CR2QLKRJLIUJXU2DZEWKOFAVCNFSM6AAAAABHMKOMI2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMZWHEYDMNBWHA. You are receiving this because you were mentioned.Message ID: @.**@.>>

packageVersion("odbc") [1] ‘1.3.5’ packageVersion("RPostgres") [1] ‘1.4.7’ packageVersion("DBI") [1] ‘1.2.1’ packageVersion("dplyr") [1] ‘1.1.4’ packageVersion("dbplyr") [1] ‘2.4.0’ packageVersion("CirceR") [1] ‘1.3.3’ packageVersion("CDMConnector") [1] ‘1.3.0’ packageVersion("here") [1] ‘1.0.1’ packageVersion("log4r") [1] ‘0.4.3’ packageVersion("zip") [1] ‘2.3.0’ packageVersion("IncidencePrevalence") [1] ‘0.7.0’ packageVersion("tidyr") [1] ‘1.3.1’ packageVersion("ggplot2") [1] ‘3.4.3’ packageVersion("CodelistGenerator") [1] ‘2.2.2’ packageVersion("lubridate") [1] ‘1.9.3’ packageVersion("glue") [1] ‘1.7.0’ packageVersion("DrugUtilisation") [1] ‘0.5.0’ packageVersion("PatientProfiles") [1] ‘0.6.1’ packageVersion("omopgenerics") [1] ‘0.0.2’ packageVersion("stringr") [1] ‘1.5.1’ packageVersion("testthat") [1] ‘3.2.1’ source("C:/Users/d229463/Desktop/Scripts R/Ultima version con DUS/MegaStudy-main/DUS Code/CodeToRun.R") Error in cdm_from_con() at CDMConnector/R/cdm.R:184:3: ! CDM database tables should be either all upppercase or all lowercase!

Run rlang::last_trace() to see where the error occurred.

rlang::last_trace() <error/rlang_error> Error in cdm_from_con() at CDMConnector/R/cdm.R:184:3: ! CDM database tables should be either all upppercase or all lowercase!

Backtrace: ▆

1. ├─base::source("C:/Users/d229463/Desktop/Scripts R/Ultima version con DUS/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:78:1
6. │ ├─base::withVisible(eval(ei, envir))
7. │ └─base::eval(ei, envir)
8. │ └─base::eval(ei, envir)
9. └─CDMConnector::cdmFromCon(...) at MegaStudy-main/DUS Code/DUS.R:17:1
10. └─CDMConnector::cdm_from_con(...) at CDMConnector/R/cdm.R:184:3 Run rlang::last_trace(drop = FALSE) to see 1 hidden frame.

[tiozab]

do you want to try again to comment it out like you did before?

[JavierGorri]

This is what we see

@.***

De: Theresa Burkard @.> Enviado el: miércoles, 29 de mayo de 2024 11:55 Para: oxford-pharmacoepi/MegaStudy @.> CC: Gorricho Mendívil, Javier (Serv. Centrales) @.>; Mention @.> Asunto: Re: [oxford-pharmacoepi/MegaStudy] Problem with DUS step (Issue #52)

do you want to try again to comment it out like you did before? image.png (view on web)https://github.com/oxford-pharmacoepi/MegaStudy/assets/94674809/296ed46b-1f26-4238-bb45-38b36384f2c5

— Reply to this email directly, view it on GitHubhttps://github.com/oxford-pharmacoepi/MegaStudy/issues/52#issuecomment-2137015244, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AQLHROZMFPPFUHQGJI6VA3DZEWQXPAVCNFSM6AAAAABHMKOMI2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMZXGAYTKMRUGQ. You are receiving this because you were mentioned.Message ID: @.**@.>>

[tiozab]

@JavierGorri I am sorry, I cannot see anything, can you send a screen shot and separately the log.txt from the storage folder? sorry that this is taking so long.

[JavierGorri]

This is the screen shot.

Thanks

@.***

De: Theresa Burkard @.> Enviado el: lunes, 3 de junio de 2024 17:21 Para: oxford-pharmacoepi/MegaStudy @.> CC: Gorricho Mendívil, Javier (Serv. Centrales) @.>; Mention @.> Asunto: Re: [oxford-pharmacoepi/MegaStudy] Problem with DUS step (Issue #52)

@JavierGorrihttps://github.com/JavierGorri I am sorry, I cannot see anything, can you send a screen shot and separately the log.txt from the storage folder? sorry that this is taking so long.

— Reply to this email directly, view it on GitHubhttps://github.com/oxford-pharmacoepi/MegaStudy/issues/52#issuecomment-2145493525, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AQLHRO3PJYETR3ZOITKU2KTZFSCVDAVCNFSM6AAAAABHMKOMI2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNBVGQ4TGNJSGU. You are receiving this because you were mentioned.Message ID: @.**@.>>

Error in cdm_from_con() at CDMConnector/R/cdm.R:184:3: ! CDM database tables should be either all upppercase or all lowercase! Run rlang::last_trace() to see where the error occurred.

trace(cdm_from_con, edit = TRUE) Tracing function "cdm_from_con" in package "CDMConnector" [1] "cdm_from_con" source("C:/Users/d229463/Desktop/Scripts R/Ultima version con DUS/MegaStudy-main/DUS Code/CodeToRun.R") condition domain: Limiting to domains of interest condition: Getting concepts to include Error in dplyr::collect() at omopgenerics/R/classCdmTable.R:150:3: ! Failed to collect lazy table. Caused by error: ! nanodbc/nanodbc.cpp:3110: 07009: [Microsoft][SQL Server Native Client 11.0]Invalid Descriptor Index Run rlang::last_trace() to see where the error occurred. Aviso: In dbClearResult(res) : Result already cleared

rlang::last_trace() <error/rlang_error> Error in dplyr::collect() at omopgenerics/R/classCdmTable.R:150:3: ! Failed to collect lazy table. Caused by error: ! nanodbc/nanodbc.cpp:3110: 07009: [Microsoft][SQL Server Native Client 11.0]Invalid Descriptor Index

Backtrace: ▆

1. ├─base::source("C:/Users/d229463/Desktop/Scripts R/Ultima version con DUS/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:78:1
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:1:1
14. │ └─base::lapply(...) at CodelistGenerator/R/getCandidateCodes.R:129:3
15. │ └─CodelistGenerator (local) FUN(X[[i]], ...)
16. │ └─CodelistGenerator:::runSearch(...) at CodelistGenerator/R/getCandidateCodes.R:130:5
17. │ └─CodelistGenerator:::getMatches(words = tidyWords(keywords), conceptDf = workingConcept) at CodelistGenerator/R/runSearch.R:133:3
18. │ └─workingConcepts %>% dplyr::collect() at CodelistGenerator/R/runSearch.R:489:5
19. ├─dplyr::collect(.)
20. └─omopgenerics:::collect.cdm_table(.)
21. ├─dplyr::collect(removeClass(x, "cdm_table")) at omopgenerics/R/classCdmTable.R:150:3
22. └─dbplyr:::collect.tbl_sql(removeClass(x, "cdm_table")) Run rlang::last_trace(drop = FALSE) to see 6 hidden frames.

packageVersion("odbc") [1] ‘1.3.5’ packageVersion("odbc") [1] ‘1.3.5’ packageVersion("RPostgres") [1] ‘1.4.7’ packageVersion("DBI") [1] ‘1.2.1’ packageVersion("dplyr") [1] ‘1.1.4’ packageVersion("dbplyr") [1] ‘2.4.0’ packageVersion("CirceR") [1] ‘1.3.3’ packageVersion("CDMConnector") [1] ‘1.3.0’ packageVersion("here") [1] ‘1.0.1’ packageVersion("log4r") [1] ‘0.4.3’ packageVersion("zip") [1] ‘2.3.1’ packageVersion("IncidencePrevalence") [1] ‘0.7.0’ packageVersion("tidyr") [1] ‘1.3.1’ packageVersion("ggplot2") [1] ‘3.4.3’ packageVersion("CodelistGenerator") [1] ‘2.2.2’ packageVersion("lubridate") [1] ‘1.9.3’ packageVersion("glue") [1] ‘1.7.0’ packageVersion("DrugUtilisation") [1] ‘0.5.0’ packageVersion("PatientProfiles") [1] ‘0.6.1’ packageVersion("omopgenerics") [1] ‘0.2.1’ packageVersion("stringr") [1] ‘1.5.1’ packageVersion("testthat") [1] ‘3.2.1’

[tiozab]

@JavierGorri I am not sure what the problem is, we can have a call this afternoon or monday afternoon

[JavierGorri]

Hello Theresa,

Our timetable is from 08:00 to 15:00 CET. We are a bit overworked these days.

Is it possible for you to have a meeting on this timetable on Thursday or Friday?

Kind regards

De: Theresa Burkard @.> Enviado el: viernes, 7 de junio de 2024 15:59 Para: oxford-pharmacoepi/MegaStudy @.> CC: Gorricho Mendívil, Javier (Serv. Centrales) @.>; Mention @.> Asunto: Re: [oxford-pharmacoepi/MegaStudy] Problem with DUS step (Issue #52)

@JavierGorrihttps://github.com/JavierGorri I am not sure what the problem is, we can have a call this afternoon or monday afternoon

— Reply to this email directly, view it on GitHubhttps://github.com/oxford-pharmacoepi/MegaStudy/issues/52#issuecomment-2154904942, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AQLHROZ7XHQH63VH6MWD4JLZGG4CRAVCNFSM6AAAAABHMKOMI2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNJUHEYDIOJUGI. You are receiving this because you were mentioned.Message ID: @.**@.>>

[tiozab]

@JavierGorri I am not available thursday friday this week, however available again from 24/25th of June

[JavierGorri]

@Theresa, we are available on Monday or Thursday (24/25th of June) from 10:00 to 15:00

De: Theresa Burkard @.**@.>> Enviado el: lunes, 10 de junio de 2024 10:49 Para: oxford-pharmacoepi/MegaStudy @.**@.>> CC: Gorricho Mendívil, Javier (Serv. Centrales) @.**@.>>; Mention @.**@.>> Asunto: Re: [oxford-pharmacoepi/MegaStudy] Problem with DUS step (Issue #52)

@JavierGorrihttps://github.com/JavierGorri I am not available thursday friday this week, however available again from 24/25th of June

— Reply to this email directly, view it on GitHubhttps://github.com/oxford-pharmacoepi/MegaStudy/issues/52#issuecomment-2157738805, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AQLHROYWKWM7PFFEY54FQQLZGVR7HAVCNFSM6AAAAABHMKOMI2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNJXG4ZTQOBQGU. You are receiving this because you were mentioned.Message ID: @.**@.>>

[tiozab]

@JavierGorri is it possible for you to change all table names and column names to lower case? do you not have your table names in lower case already because you have duplicates e.g. "Person" and "person"? The problem that we see may be that the newer CDM Connector version does not allow your work around any more.

However, you can still try in the mean time a newer version that I wrote for some data partners who had problems with the DUS step (that could be fixed by newer package versions). However, as usual the correct use of the renv is very important. DUS_1point4.zip

If you can have answers to these questions and a run of the newer version ready for our discussion on monday that will speed things up hopefully :-)

[JavierGorri]

De: Theresa Burkard @.> Enviado el: martes, 18 de junio de 2024 18:39 Para: oxford-pharmacoepi/MegaStudy @.> CC: Gorricho Mendívil, Javier (Serv. Centrales) @.>; Mention @.> Asunto: Re: [oxford-pharmacoepi/MegaStudy] Problem with DUS step (Issue #52)

@JavierGorrihttps://github.com/JavierGorri is it possible for you to change all table names and column names to lower case? do you not have your table names in lower case already because you have duplicates e.g. "Person" and "person"? The problem that we see may be that the newer CDM Connector version does not allow your work around any more.

However, you can still try in the mean time a newer version that I wrote for some data partners who had problems with the DUS step (that could be fixed by newer package versions). However, as usual the correct use of the renv is very important. DUS_1point4.ziphttps://github.com/user-attachments/files/15889788/DUS_1point4.zip

If you can have answers to these questions and a run of the newer version ready for our discussion on monday that will speed things up hopefully :-)

— Reply to this email directly, view it on GitHubhttps://github.com/oxford-pharmacoepi/MegaStudy/issues/52#issuecomment-2176531054, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AQLHRO2IUWFYOQHODIGPDDLZIBPATAVCNFSM6AAAAABHMKOMI2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNZWGUZTCMBVGQ. You are receiving this because you were mentioned.Message ID: @.**@.>>

[tiozab]

@JavierGorri I am sorry I seem not to be able to see your response since your last two comments, but only the communication that I wrote, can you have a look in github.com, at what it looks like, so you may be able to understand my problem with viewing your answer? That would facilitate our communication better :-)

[JavierGorri]

@Theresa. It is not posible for us to change all tables and columns. We use sql server and is not case sensitive and so Person and person are the same objet.

We are grateful for the new package version. We are working with it, trying to find the exit of this tunnel

De: Theresa Burkard @.> Enviado el: jueves, 20 de junio de 2024 9:45 Para: oxford-pharmacoepi/MegaStudy @.> CC: Gorricho Mendívil, Javier (Serv. Centrales) @.>; Mention @.> Asunto: Re: [oxford-pharmacoepi/MegaStudy] Problem with DUS step (Issue #52)

@JavierGorrihttps://github.com/JavierGorri I am sorry I seem not to be able to see your response since your last two comments, but only the communication that I wrote, can you have a look in github.com, at what it looks like, so you may be able to understand my problem with viewing your answer? That would facilitate our communication better :-)

— Reply to this email directly, view it on GitHubhttps://github.com/oxford-pharmacoepi/MegaStudy/issues/52#issuecomment-2180030510, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AQLHRO66H36L4DZ3MEPX4ULZIKCBDAVCNFSM6AAAAABHMKOMI2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOBQGAZTANJRGA. You are receiving this because you were mentioned.Message ID: @.**@.>>

[tiozab]

@JavierGorri thanks for the call. I think it would make sense to add the github names of Fernando and Asier, so they can be part of the conversation :-)

[JavierGorri]

Yes, a great Idea. How can I do it?

These are their emails fernando.fernandez.benedicto@navarra.es and asier.ballesteros.dominguez@navarra.es

[tiozab]

@D229463 @AsierBall

I keep you posted about the CDM requirements.

[JavierGorri]

Thanks

[tiozab]

@JavierGorri @D229463 I just spoke with @edward-burn and he confirmed that all omop tables have to have lower case names and column names. Furthermore, it needs to contain all columns listed in the https://ohdsi.github.io/CommonDataModel/index.html 5.3 or 5.4. The order of the columns does not matter and there can be your own additional columns within the omop tables. Thanks for re-naming your data accordingly :-)

[JavierGorri]

@tiozab Many many Thanks. We are working on it. Great help.

[tiozab]

https://ehden.sharepoint.com/:w:/r/sites/EHDENMEGA/Gedeelde%20documenten/General/Short%20descriptions%20of%20each%20database.docx?d=w3b7774a809374c4c84b226395c6e1660&csf=1&web=1&e=Vi3Kxh may I ask you to add your database description please (the document is in EHDEN Teams) thanks :-) @JavierGorri

[JavierGorri]

I have done it.

Thanks for everything

De: Theresa Burkard @.> Enviado el: viernes, 28 de junio de 2024 10:22 Para: oxford-pharmacoepi/MegaStudy @.> CC: Gorricho Mendívil, Javier (Serv. Centrales) @.>; Mention @.> Asunto: Re: [oxford-pharmacoepi/MegaStudy] Problem with DUS step (Issue #52)

https://ehden.sharepoint.com/:w:/r/sites/EHDENMEGA/Gedeelde%20documenten/General/Short%20descriptions%20of%20each%20database.docx?d=w3b7774a809374c4c84b226395c6e1660&csf=1&web=1&e=Vi3Kxh may I ask you to add your database description please (the document is in EHDEN Teams) thanks :-) @JavierGorrihttps://github.com/JavierGorri

— Reply to this email directly, view it on GitHubhttps://github.com/oxford-pharmacoepi/MegaStudy/issues/52#issuecomment-2196390635, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AQLHRO5HY53TELOO37GCOP3ZJUMI3AVCNFSM6AAAAABHMKOMI2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOJWGM4TANRTGU. You are receiving this because you were mentioned.Message ID: @.**@.>>

[JavierGorri]

We have change the column names and we have change the driver to ‘ODBC Driver 17 for SQL Server’ (we had used ‘SQL Server Native Client 11.0’) and we can run part of the code. Thanks for helping us.

[tiozab]

I close this so we can continue on the new issue.