revdep/problems.md

In hadley/dbplyr: A 'dplyr' Back End for Databases

Andromeda

• Version: 0.6.5
• GitHub: https://github.com/OHDSI/Andromeda
• Source code: https://github.com/cran/Andromeda
• Date/Publication: 2024-01-22 15:32:47 UTC
• Number of recursive dependencies: 74

Run revdepcheck::cloud_details(, "Andromeda") for more info

Newly broken

• 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 ```

Newly fixed

• 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 ```

CDMConnector

• Version: 1.3.0
• GitHub: https://github.com/darwin-eu/CDMConnector
• Source code: https://github.com/cran/CDMConnector
• Date/Publication: 2024-02-05 14:20:13 UTC
• Number of recursive dependencies: 147

Run revdepcheck::cloud_details(, "CDMConnector") for more info

Newly broken

• 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 ```

In both

• checking package dependencies ... NOTE Packages which this enhances but not available for checking: 'arrow', 'CirceR', 'Capr'

CohortSurvival

• Version: 0.3.0
• GitHub: NA
• Source code: https://github.com/cran/CohortSurvival
• Date/Publication: 2024-02-08 09:50:02 UTC
• Number of recursive dependencies: 114

Run revdepcheck::cloud_details(, "CohortSurvival") for more info

Newly broken

• 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 ...

  1. │ └─dbplyr (local) FUN(X[[i]], ...)
  2. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
  3. │ └─rlang::eval_tidy(x, mask)
  4. └─CDMConnector::datediff
  5. └─cli::cli_abort(...)
  6. └─rlang::abort(...)

  [ 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 ```

diseasystore

• Version: 0.1.1
• GitHub: https://github.com/ssi-dk/diseasystore
• Source code: https://github.com/cran/diseasystore
• Date/Publication: 2024-01-18 13:40:02 UTC
• Number of recursive dependencies: 161

Run revdepcheck::cloud_details(, "diseasystore") for more info

Newly broken

• 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 ...

  1. │ │ └─methods::initialize(value, ...)
  2. │ └─RSQLite:::result_create(conn@ptr, statement)
  3. └─base::.handleSimpleError(...)
  4. └─dbplyr (local) h(simpleError(msg, call))
  5. └─cli::cli_abort(msg, parent = cnd, call = call, .envir = env)
  6. └─rlang::abort(...)

  [ FAIL 4 | WARN 1 | SKIP 6 | PASS 310 ] Error: Test failures Execution halted ```

DrugUtilisation

• Version: 0.5.2
• GitHub: NA
• Source code: https://github.com/cran/DrugUtilisation
• Date/Publication: 2024-03-06 01:00:29 UTC
• Number of recursive dependencies: 144

Run revdepcheck::cloud_details(, "DrugUtilisation") for more info

Newly broken

• 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: ▆

  1. ├─testthat::expect_true(inherits(x, "summarised_result")) at test-summariseTreatment.R:11:3
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
  4. └─base::inherits(x, "summarised_result")

  [ 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 ```

IncidencePrevalence

• Version: 0.7.1
• GitHub: NA
• Source code: https://github.com/cran/IncidencePrevalence
• Date/Publication: 2024-02-22 23:00:11 UTC
• Number of recursive dependencies: 133

Run revdepcheck::cloud_details(, "IncidencePrevalence") for more info

Newly broken

• 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 ```

PatientProfiles

• Version: 0.6.2
• GitHub: NA
• Source code: https://github.com/cran/PatientProfiles
• Date/Publication: 2024-03-05 18:50:03 UTC
• Number of recursive dependencies: 156

Run revdepcheck::cloud_details(, "PatientProfiles") for more info

Newly broken

• 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 ```

In both

• 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 ...

  1. │ └─dbplyr (local) FUN(X[[i]], ...)
  2. │ ├─dbplyr::escape(eval_tidy(x, mask), con = con)
  3. │ └─rlang::eval_tidy(x, mask)
  4. └─CDMConnector::datediff
  5. └─cli::cli_abort(...)
  6. └─rlang::abort(...)

  [ FAIL 65 | WARN 21 | SKIP 1 | PASS 200 ] Error: Test failures Execution halted ```

SCDB

• Version: 0.3
• GitHub: https://github.com/ssi-dk/SCDB
• Source code: https://github.com/cran/SCDB
• Date/Publication: 2024-01-13 01:10:02 UTC
• Number of recursive dependencies: 127

Run revdepcheck::cloud_details(, "SCDB") for more info

Newly broken

• 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 ```

hadley/dbplyr documentation built on May 4, 2024, 2:10 a.m.