Run revdepcheck::cloud_details(, "Andromeda")
for more info
checking examples ... ERROR ``` Running examples in ‘Andromeda-Ex.R’ failed The error most likely occurred in:
Name: groupApply
Title: Apply a function to groups of data in an Andromeda table
Aliases: groupApply
** Examples
andr <- andromeda(cars = cars) ... 12. │ │ └─rlang::is_character(x) 13. │ └─dbplyr::translate_sql_(op$order_by, con = con) 14. │ └─base::lapply(...) 15. │ └─dbplyr (local) FUN(X[[i]], ...) 16. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con) 17. │ └─rlang::eval_tidy(x, mask) 18. └─rlang::sym 19. └─cli::cli_abort(...) 20. └─rlang::abort(...) Execution halted ```
checking tests ... ERROR ``` Running ‘testthat.R’ Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > test_check("Andromeda") Loading required package: Andromeda Loading required package: dplyr
Attaching package: 'dplyr'
... 21. │ └─dbplyr (local) FUN(X[[i]], ...) 22. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con) 23. │ └─rlang::eval_tidy(x, mask) 24. └─rlang::sym 25. └─cli::cli_abort(...) 26. └─rlang::abort(...)
[ FAIL 2 | WARN 0 | SKIP 1 | PASS 95 ] Error: Test failures Execution halted ```
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘UsingAndromeda.Rmd’ using rmarkdown
Quitting from lines 175-184 [unnamed-chunk-17] (UsingAndromeda.Rmd) Error: processing vignette 'UsingAndromeda.Rmd' failed with diagnostics: No known SQL translation --- failed re-building ‘UsingAndromeda.Rmd’
SUMMARY: processing the following file failed: ‘UsingAndromeda.Rmd’
Error: Vignette re-building failed. Execution halted ```
checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: ... --- re-building ‘UsingAndromeda.Rmd’ using rmarkdown A new version of TeX Live has been released. If you need to install or update any LaTeX packages, you have to upgrade TinyTeX with tinytex::reinstall_tinytex(repository = "illinois").
tlmgr: Local TeX Live (2023) is older than remote repository (2024). Cross release updates are only supported with update-tlmgr-latest(.sh/.exe) --update See https://tug.org/texlive/upgrade.html for details. Warning in system2("tlmgr", args, ...) : ...
Error: processing vignette 'UsingAndromeda.Rmd' failed with diagnostics: LaTeX failed to compile /tmp/workdir/Andromeda/old/Andromeda.Rcheck/vign_test/Andromeda/vignettes/UsingAndromeda.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See UsingAndromeda.log for more info. --- failed re-building ‘UsingAndromeda.Rmd’
SUMMARY: processing the following file failed: ‘UsingAndromeda.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdepcheck::cloud_details(, "CDMConnector")
for more info
checking tests ... ERROR
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
...
In addition: Warning messages:
1: Connection is garbage-collected, use dbDisconnect() to avoid this.
2: Connection is garbage-collected, use dbDisconnect() to avoid this.
3: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
4: Connection is garbage-collected, use dbDisconnect() to avoid this.
5: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
6: Connection is garbage-collected, use dbDisconnect() to avoid this.
7: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
8: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
Execution halted
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘a01_getting-started.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB
Warning: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this. --- finished re-building ‘a01_getting-started.Rmd’
... No known SQL translation --- failed re-building ‘a06_using_cdm_attributes.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this. Warning: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this. SUMMARY: processing the following file failed: ‘a06_using_cdm_attributes.Rmd’
Error: Vignette re-building failed. Execution halted ```
Packages which this enhances but not available for checking:
'arrow', 'CirceR', 'Capr'
Run revdepcheck::cloud_details(, "CohortSurvival")
for more info
checking tests ... ERROR ``` Running ‘testthat.R’ Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files ...
[ FAIL 2 | WARN 4 | SKIP 42 | PASS 0 ] Error: Test failures Execution halted ```
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘a01_Single_event_of_interest.Rmd’ using rmarkdown
Quitting from lines 47-53 [unnamed-chunk-5] (a01_Single_event_of_interest.Rmd) Error: processing vignette 'a01_Single_event_of_interest.Rmd' failed with diagnostics: No known SQL translation --- failed re-building ‘a01_Single_event_of_interest.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this. ... No known SQL translation --- failed re-building ‘a02_Competing_risk_survival.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this. Warning: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this. SUMMARY: processing the following files failed: ‘a01_Single_event_of_interest.Rmd’ ‘a02_Competing_risk_survival.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdepcheck::cloud_details(, "diseasystore")
for more info
checking tests ... ERROR ``` Running ‘spelling.R’ Running ‘testthat.R’ Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html ...
[ FAIL 4 | WARN 1 | SKIP 6 | PASS 310 ] Error: Test failures Execution halted ```
Run revdepcheck::cloud_details(, "DrugUtilisation")
for more info
checking tests ... ERROR ``` Running ‘testthat.R’ Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files ... Backtrace: ▆
[ FAIL 8 | WARN 36 | SKIP 19 | PASS 139 ] Error: Test failures Execution halted ```
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘a01_introCreateCohort.Rmd’ using rmarkdown
Quitting from lines 116-122 [unnamed-chunk-6] (a01_introCreateCohort.Rmd) Error: processing vignette 'a01_introCreateCohort.Rmd' failed with diagnostics: No known SQL translation --- failed re-building ‘a01_introCreateCohort.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this. Warning: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this. ... --- finished re-building ‘routePatternDose.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this. Warning: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this. SUMMARY: processing the following files failed: ‘a01_introCreateCohort.Rmd’ ‘a03_addIndications-example.Rmd’ ‘a06_treatmentSummary.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdepcheck::cloud_details(, "IncidencePrevalence")
for more info
checking tests ... ERROR ``` Running ‘testthat.R’ Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(IncidencePrevalence) > > test_check("IncidencePrevalence") Starting 2 test processes [ FAIL 18 | WARN 0 | SKIP 72 | PASS 122 ]
... 24. │ └─dbplyr (local) FUN(X[[i]], ...) 25. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con) 26. │ └─rlang::eval_tidy(x, mask) 27. └─CDMConnector::dateadd 28. └─cli::cli_abort(...) 29. └─rlang::abort(...)
[ FAIL 18 | WARN 0 | SKIP 72 | PASS 122 ] Error: Test failures Execution halted ```
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘a01_Introduction_to_IncidencePrevalence.Rmd’ using rmarkdown
Quitting from lines 73-81 [unnamed-chunk-6] (a01_Introduction_to_IncidencePrevalence.Rmd) Error: processing vignette 'a01_Introduction_to_IncidencePrevalence.Rmd' failed with diagnostics: No known SQL translation --- failed re-building ‘a01_Introduction_to_IncidencePrevalence.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this. Warning: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this. ... Warning: Connection is garbage-collected, use dbDisconnect() to avoid this. Warning: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this. SUMMARY: processing the following files failed: ‘a01_Introduction_to_IncidencePrevalence.Rmd’ ‘a02_Creating_denominator_populations.Rmd’ ‘a03_Creating_target_denominator_populations.Rmd’ ‘a04_Calculating_prevalence.Rmd’ ‘a05_Calculating_incidence.Rmd’
Error: Vignette re-building failed. Execution halted ```
Run revdepcheck::cloud_details(, "PatientProfiles")
for more info
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘addCohortIntersections.Rmd’ using rmarkdown
Quitting from lines 71-81 [unnamed-chunk-4] (addCohortIntersections.Rmd) Error: processing vignette 'addCohortIntersections.Rmd' failed with diagnostics: No known SQL translation --- failed re-building ‘addCohortIntersections.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this. ... No known SQL translation --- failed re-building ‘addPatientCharacteristics.rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this. Warning: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this. SUMMARY: processing the following files failed: ‘addCohortIntersections.Rmd’ ‘addPatientCharacteristics.rmd’
Error: Vignette re-building failed. Execution halted ```
checking tests ... ERROR ``` Running ‘spelling.R’ Running ‘testthat.R’ Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html ...
[ FAIL 65 | WARN 21 | SKIP 1 | PASS 200 ] Error: Test failures Execution halted ```
Run revdepcheck::cloud_details(, "SCDB")
for more info
checking examples ... ERROR ``` Running examples in ‘SCDB-Ex.R’ failed The error most likely occurred in:
Name: get_schema
Title: Get the current schema of a database-related objects
Aliases: get_schema
** Examples
conn <- get_connection(drv = RSQLite::SQLite()) ...
dplyr::copy_to(conn, mtcars, name = "mtcars")
get_schema(conn) [1] "temp" get_schema(get_table(conn, id("mtcars", conn = conn))) Error in unclass(dbplyr::remote_table(.x))$schema : $ operator is invalid for atomic vectors Calls: get_schema -> get_schema.tbl_dbi Execution halted ```
checking tests ... ERROR
``
Running ‘spelling.R’
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
...
temporary = temporary, unique_indexes = unique_indexes, indexes = indexes,
analyze = analyze, in_transaction = in_transaction, ...)
: Can't copy data to table SCDB_log_patch
.
Caused by error in dplyr::db_write_table()
:
! Can't write table table SCDB_log_patch
.
Caused by error:
! Table SCDB_log_patch
exists in database, and both overwrite and append are FALSE
[ FAIL 4 | WARN 1 | SKIP 0 | PASS 294 ] Error: Test failures Execution halted ```
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘basic-principles.Rmd’ using rmarkdown
Quitting from lines 76-82 [example_1] (basic-principles.Rmd) Error: processing vignette 'basic-principles.Rmd' failed with diagnostics: error in evaluating the argument 'name' in selecting a method for function 'dbRemoveTable': invalid 'envir' argument of type 'character' --- failed re-building ‘basic-principles.Rmd’
Error in purrr::map_chr()
:
ℹ In index: 2.
...
19. └─cli::cli_abort(...)
20. └─rlang::abort(...)
--- re-building ‘slowly-changing-dimension.Rmd’ using rmarkdown
--- finished re-building ‘slowly-changing-dimension.Rmd’
SUMMARY: processing the following file failed: ‘basic-principles.Rmd’
Error: Vignette re-building failed. Execution halted ```
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