Last updated on 2023-12-08 19:51:21 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.12.3 | 18.45 | 342.52 | 360.97 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.12.3 | 15.07 | 258.81 | 273.88 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.12.3 | 445.31 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.12.3 | 255.85 | ERROR | |||
| r-devel-windows-x86_64 | 0.12.3 | 19.00 | 287.00 | 306.00 | ERROR | |
| r-patched-linux-x86_64 | 0.12.3 | 22.30 | 333.80 | 356.10 | ERROR | |
| r-release-linux-x86_64 | 0.12.3 | 10.87 | 325.50 | 336.37 | ERROR | |
| r-release-macos-arm64 | 0.12.3 | 153.00 | OK | |||
| r-release-macos-x86_64 | 0.12.3 | 349.00 | OK | |||
| r-release-windows-x86_64 | 0.12.3 | 23.00 | 364.00 | 387.00 | ERROR | |
| r-oldrel-macos-arm64 | 0.12.3 | 154.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.12.3 | 184.00 | OK | |||
| r-oldrel-windows-x86_64 | 0.12.3 | 25.00 | 328.00 | 353.00 | ERROR |
Version: 0.12.3
Check: examples
Result: ERROR
Running examples in ‘admiral-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create_query_data
> ### Title: Creates a queries dataset as input dataset to the
> ### 'dataset_queries' argument in 'derive_vars_query()'
> ### Aliases: create_query_data
> ### Keywords: create_aux
>
> ### ** Examples
>
> library(tibble)
> library(dplyr, warn.conflicts = FALSE)
> library(pharmaversesdtm)
> library(admiral)
>
> # creating a query dataset for a customized query
> cqterms <- tribble(
+ ~TERMNAME, ~TERMID,
+ "APPLICATION SITE ERYTHEMA", 10003041L,
+ "APPLICATION SITE PRURITUS", 10003053L
+ ) %>%
+ mutate(SRCVAR = "AEDECOD")
>
> cq <- query(
+ prefix = "CQ01",
+ name = "Application Site Issues",
+ definition = cqterms
+ )
>
> create_query_data(queries = list(cq))
# A tibble: 2 × 5
TERMNAME TERMID SRCVAR PREFIX GRPNAME
<chr> <int> <chr> <chr> <chr>
1 APPLICATION SITE ERYTHEMA 10003041 AEDECOD CQ01 Application Site Issues
2 APPLICATION SITE PRURITUS 10003053 AEDECOD CQ01 Application Site Issues
>
> # create a query dataset for SMQs
> pregsmq <- query(
+ prefix = "SMQ02",
+ id = auto,
+ definition = basket_select(
+ name = "Pregnancy and neonatal topics (SMQ)",
+ scope = "NARROW",
+ type = "smq"
+ )
+ )
>
> bilismq <- query(
+ prefix = "SMQ04",
+ definition = basket_select(
+ id = 20000121L,
+ scope = "BROAD",
+ type = "smq"
+ )
+ )
>
> # The get_terms function from pharmaversesdtm is used for this example.
> # In a real application a company-specific function must be used.
> create_query_data(
+ queries = list(pregsmq, bilismq),
+ get_terms_fun = pharmaversesdtm:::get_terms,
+ version = "20.1"
+ )
Error in `assert_terms()`:
! Variable `TERMNAME` or `TERMID` is required.
None of them is in object returned by calling get_terms_fun(basket_select = basket_select(name = "Pregnancy and neonatal topics (SMQ)", id = NULL, scope = "NARROW", type = "smq"), version = "20.1", keep_id = TRUE).
Provided variables: `TERMCHAR`, `SRCVAR`, `GRPNAME` and `GRPID`
Backtrace:
▆
1. └─admiral::create_query_data(...)
2. └─admiral:::get_terms_from_db(...)
3. └─admiral::assert_terms(...)
4. └─rlang::abort(...)
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.12.3
Check: data for non-ASCII characters
Result: NOTE
Note: found 12 marked UTF-8 strings
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.12.3
Check: examples
Result: ERROR
Running examples in ‘admiral-Ex.R’ failed
The error most likely occurred in:
> ### Name: create_query_data
> ### Title: Creates a queries dataset as input dataset to the
> ### 'dataset_queries' argument in 'derive_vars_query()'
> ### Aliases: create_query_data
> ### Keywords: create_aux
>
> ### ** Examples
>
> library(tibble)
> library(dplyr, warn.conflicts = FALSE)
> library(pharmaversesdtm)
> library(admiral)
>
> # creating a query dataset for a customized query
> cqterms <- tribble(
+ ~TERMNAME, ~TERMID,
+ "APPLICATION SITE ERYTHEMA", 10003041L,
+ "APPLICATION SITE PRURITUS", 10003053L
+ ) %>%
+ mutate(SRCVAR = "AEDECOD")
>
> cq <- query(
+ prefix = "CQ01",
+ name = "Application Site Issues",
+ definition = cqterms
+ )
>
> create_query_data(queries = list(cq))
# A tibble: 2 × 5
TERMNAME TERMID SRCVAR PREFIX GRPNAME
<chr> <int> <chr> <chr> <chr>
1 APPLICATION SITE ERYTHEMA 10003041 AEDECOD CQ01 Application Site Issues
2 APPLICATION SITE PRURITUS 10003053 AEDECOD CQ01 Application Site Issues
>
> # create a query dataset for SMQs
> pregsmq <- query(
+ prefix = "SMQ02",
+ id = auto,
+ definition = basket_select(
+ name = "Pregnancy and neonatal topics (SMQ)",
+ scope = "NARROW",
+ type = "smq"
+ )
+ )
>
> bilismq <- query(
+ prefix = "SMQ04",
+ definition = basket_select(
+ id = 20000121L,
+ scope = "BROAD",
+ type = "smq"
+ )
+ )
>
> # The get_terms function from pharmaversesdtm is used for this example.
> # In a real application a company-specific function must be used.
> create_query_data(
+ queries = list(pregsmq, bilismq),
+ get_terms_fun = pharmaversesdtm:::get_terms,
+ version = "20.1"
+ )
Error in `assert_terms()`:
! Variable `TERMNAME` or `TERMID` is required.
None of them is in object returned by calling get_terms_fun(basket_select = basket_select(name = "Pregnancy and neonatal topics (SMQ)", id = NULL, scope = "NARROW", type = "smq"), version = "20.1", keep_id = TRUE).
Provided variables: `TERMCHAR`, `SRCVAR`, `GRPNAME` and `GRPID`
Backtrace:
▆
1. └─admiral::create_query_data(...)
2. └─admiral:::get_terms_from_db(...)
3. └─admiral::assert_terms(...)
4. └─rlang::abort(...)
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64