CRAN Package Check Results for Package OhdsiReportGenerator

Last updated on 2025-05-07 20:49:51 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.1 5.96 97.61 103.57 OK
r-devel-linux-x86_64-debian-gcc 1.0.1 4.07 68.85 72.92 ERROR
r-devel-linux-x86_64-fedora-clang 1.1.0 379.20 OK
r-devel-linux-x86_64-fedora-gcc 1.1.0 378.34 OK
r-devel-windows-x86_64 1.0.1 9.00 118.00 127.00 OK
r-patched-linux-x86_64 1.0.1 7.32 89.98 97.30 ERROR
r-release-linux-x86_64 1.0.1 5.70 91.88 97.58 OK
r-release-macos-arm64 1.1.0 36.00 ERROR
r-release-macos-x86_64 1.1.0 79.00 ERROR
r-release-windows-x86_64 1.0.1 9.00 121.00 130.00 OK
r-oldrel-macos-arm64 1.1.0 47.00 ERROR
r-oldrel-macos-x86_64 1.1.0 100.00 ERROR
r-oldrel-windows-x86_64 1.0.1 10.00 150.00 160.00 OK

Check Details

Version: 1.0.1
Check: tests
Result: ERROR Running ‘testthat.R’ [20s/19s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > test_check("OhdsiReportGenerator") Loading required package: OhdsiReportGenerator Connecting using SQLite driver <1b>[31m processing file: assure_study_presentation_multiple.qmd <1b>[39m<1b>[31moutput file: assure_study_presentation_multiple.knit.md <1b>[39mClosing database connection <1b>[1mpandoc <1b>[22m to: revealjs output-file: assure_study_presentation_multiple.html standalone: true self-contained: true wrap: none default-image-extension: png html-math-method: method: mathjax url: >- https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.9/MathJax.js?config=TeX-AMS_HTML-full slide-level: 2 variables: {} <1b>[1mmetadata<1b>[22m link-citations: true width: 1050 height: 700 margin: 0.1 center: false navigationMode: linear controlsLayout: edges controlsTutorial: false hash: true history: true hashOneBasedIndex: false fragmentInURL: false transition: none backgroundTransition: none pdfSeparateFragments: false lang: en auto-stretch: true title: Signal Evaluation Report scrollable: true theme: - default - presentation_style.scss logo: img/logo.png title-slide-attributes: data-background-color: '#EB1700' footer: ASSURE Standardized report slideNumber: true showSlideNumber: all menu: side: left numbers: true Error running filter /opt/quarto/share/filters/main.lua: /opt/quarto/share/filters/main.lua:21750: attempt to index a nil value (field 'tabs') stack traceback: /opt/quarto/share/filters/main.lua:935: in function </opt/quarto/share/filters/main.lua:934> (...tail calls...) /opt/quarto/share/filters/main.lua:1152: in function </opt/quarto/share/filters/main.lua:1147> (...tail calls...) /opt/quarto/share/filters/main.lua:2943: in function </opt/quarto/share/filters/main.lua:2937> (...tail calls...) ...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:34: in upvalue 'run_filter_function' ...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:223: in function <...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:202> (...tail calls...) [C]: in function 'pandoc.List.map' ...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:125: in upvalue 'recurse' ...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:222: in local 'jogger' ...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:98: in upvalue 'recurse' ...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:222: in function <...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:202> (...tail calls...) ... (skipping 2 levels) ...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:98: in upvalue 'recurse' ...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:222: in function <...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:202> (...tail calls...) [C]: in function 'pandoc.List.map' ...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:125: in upvalue 'recurse' ...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:222: in local 'jogger' ...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:171: in upvalue 'recurse' ...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:222: in function <...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:202> (...tail calls...) /opt/quarto/share/filters/main.lua:572: in function </opt/quarto/share/filters/main.lua:550> (...tail calls...) /opt/quarto/share/filters/main.lua:1318: in local 'callback' /opt/quarto/share/filters/main.lua:1336: in upvalue 'run_emulated_filter_chain' /opt/quarto/share/filters/main.lua:1372: in function </opt/quarto/share/filters/main.lua:1369> [ FAIL 1 | WARN 1 | SKIP 2 | PASS 385 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • empty test (1): 'test-Helpers.R:89:1' • skip prediction report due to odd linux error (1): 'test-PredictionReport.R:5:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-Generate.R:10:3'): generatePresentationMultiple ──────────────── Error in `quarto::quarto_render(input = file.path(intermediateDir, "presentation", "assure_study_presentation_multiple.qmd"), execute_params = list(server = server, username = username, password = password, dbms = dbms, resultsSchema = resultsSchema, targetId = targetId, targetName = targetName, cmSubsetId = cmSubsetId, sccsSubsetId = sccsSubsetId, indicationName = indicationName, outcomeIds = outcomeIds, outcomeNames = outcomeNames, comparatorIds = comparatorIds, comparatorNames = comparatorNames, covariateIds = covariateIds, title = title, lead = lead, date = date, details = details, evaluationText = evaluationText))`: ✖ Error running quarto cli. Caused by error: ! System command 'quarto' failed Backtrace: ▆ 1. └─OhdsiReportGenerator::generatePresentationMultiple(...) at test-Generate.R:10:3 2. └─quarto::quarto_render(...) 3. └─quarto:::quarto_run(args, echo = TRUE, quarto_bin = quarto_bin) 4. └─base::tryCatch(...) 5. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 6. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 7. └─value[[3L]](cond) 8. └─cli::cli_abort(msg, call = .call, parent = e) 9. └─rlang::abort(...) [ FAIL 1 | WARN 1 | SKIP 2 | PASS 385 ] Error: Test failures Execution halted Closing database connection Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.0.1
Check: tests
Result: ERROR Running ‘testthat.R’ [28s/31s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > test_check("OhdsiReportGenerator") Loading required package: OhdsiReportGenerator Connecting using SQLite driver <1b>[31m processing file: assure_study_presentation_multiple.qmd <1b>[39m<1b>[31moutput file: assure_study_presentation_multiple.knit.md <1b>[39mClosing database connection <1b>[1mpandoc <1b>[22m to: revealjs output-file: assure_study_presentation_multiple.html standalone: true self-contained: true wrap: none default-image-extension: png html-math-method: method: mathjax url: >- https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.9/MathJax.js?config=TeX-AMS_HTML-full slide-level: 2 variables: {} <1b>[1mmetadata<1b>[22m link-citations: true width: 1050 height: 700 margin: 0.1 center: false navigationMode: linear controlsLayout: edges controlsTutorial: false hash: true history: true hashOneBasedIndex: false fragmentInURL: false transition: none backgroundTransition: none pdfSeparateFragments: false lang: en auto-stretch: true title: Signal Evaluation Report scrollable: true theme: - default - presentation_style.scss logo: img/logo.png title-slide-attributes: data-background-color: '#EB1700' footer: ASSURE Standardized report slideNumber: true showSlideNumber: all menu: side: left numbers: true Error running filter /opt/quarto/share/filters/main.lua: /opt/quarto/share/filters/main.lua:21750: attempt to index a nil value (field 'tabs') stack traceback: /opt/quarto/share/filters/main.lua:935: in function </opt/quarto/share/filters/main.lua:934> (...tail calls...) /opt/quarto/share/filters/main.lua:1152: in function </opt/quarto/share/filters/main.lua:1147> (...tail calls...) /opt/quarto/share/filters/main.lua:2943: in function </opt/quarto/share/filters/main.lua:2937> (...tail calls...) ...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:34: in upvalue 'run_filter_function' ...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:223: in function <...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:202> (...tail calls...) [C]: in function 'pandoc.List.map' ...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:125: in upvalue 'recurse' ...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:222: in local 'jogger' ...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:98: in upvalue 'recurse' ...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:222: in function <...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:202> (...tail calls...) ... (skipping 2 levels) ...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:98: in upvalue 'recurse' ...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:222: in function <...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:202> (...tail calls...) [C]: in function 'pandoc.List.map' ...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:125: in upvalue 'recurse' ...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:222: in local 'jogger' ...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:171: in upvalue 'recurse' ...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:222: in function <...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:202> (...tail calls...) /opt/quarto/share/filters/main.lua:572: in function </opt/quarto/share/filters/main.lua:550> (...tail calls...) /opt/quarto/share/filters/main.lua:1318: in local 'callback' /opt/quarto/share/filters/main.lua:1336: in upvalue 'run_emulated_filter_chain' /opt/quarto/share/filters/main.lua:1372: in function </opt/quarto/share/filters/main.lua:1369> [ FAIL 1 | WARN 1 | SKIP 2 | PASS 385 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • empty test (1): 'test-Helpers.R:89:1' • skip prediction report due to odd linux error (1): 'test-PredictionReport.R:5:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-Generate.R:10:3'): generatePresentationMultiple ──────────────── Error in `quarto::quarto_render(input = file.path(intermediateDir, "presentation", "assure_study_presentation_multiple.qmd"), execute_params = list(server = server, username = username, password = password, dbms = dbms, resultsSchema = resultsSchema, targetId = targetId, targetName = targetName, cmSubsetId = cmSubsetId, sccsSubsetId = sccsSubsetId, indicationName = indicationName, outcomeIds = outcomeIds, outcomeNames = outcomeNames, comparatorIds = comparatorIds, comparatorNames = comparatorNames, covariateIds = covariateIds, title = title, lead = lead, date = date, details = details, evaluationText = evaluationText))`: ✖ Error running quarto cli. Caused by error: ! System command 'quarto' failed Backtrace: ▆ 1. └─OhdsiReportGenerator::generatePresentationMultiple(...) at test-Generate.R:10:3 2. └─quarto::quarto_render(...) 3. └─quarto:::quarto_run(args, echo = TRUE, quarto_bin = quarto_bin) 4. └─base::tryCatch(...) 5. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 6. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 7. └─value[[3L]](cond) 8. └─cli::cli_abort(msg, call = .call, parent = e) 9. └─rlang::abort(...) [ FAIL 1 | WARN 1 | SKIP 2 | PASS 385 ] Error: Test failures Execution halted Closing database connection Flavor: r-patched-linux-x86_64

Version: 1.1.0
Check: tests
Result: ERROR Running ‘testthat.R’ [5s/4s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > test_check("OhdsiReportGenerator") Loading required package: OhdsiReportGenerator Connecting using SQLite driver [ FAIL 3 | WARN 2 | SKIP 2 | PASS 417 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • empty test (1): 'test-Helpers.R:89:1' • skip prediction report due to odd linux error (1): 'test-PredictionReport.R:5:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-Backwards.R:11:3'): generatePresentationMultiple old works ───── Error in `find_quarto()`: Quarto command-line tools path not found! Please make sure you have installed and added Quarto to your PATH or set the QUARTO_PATH environment variable. Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test-Backwards.R:11:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─OhdsiReportGenerator::generatePresentationMultiple(...) 7. └─OhdsiReportGenerator::generatePresentation(...) 8. └─quarto::quarto_render(...) 9. └─quarto:::find_quarto() 10. └─cli::cli_abort(quarto_not_found_msg) 11. └─rlang::abort(...) ── Error ('test-Generate.R:10:3'): generatePresentation ──────────────────────── Error in `find_quarto()`: Quarto command-line tools path not found! Please make sure you have installed and added Quarto to your PATH or set the QUARTO_PATH environment variable. Backtrace: ▆ 1. └─OhdsiReportGenerator::generatePresentation(...) at test-Generate.R:10:3 2. └─quarto::quarto_render(...) 3. └─quarto:::find_quarto() 4. └─cli::cli_abort(quarto_not_found_msg) 5. └─rlang::abort(...) ── Error ('test-Generate.R:61:3'): generateFullReport ────────────────────────── Error in `find_quarto()`: Quarto command-line tools path not found! Please make sure you have installed and added Quarto to your PATH or set the QUARTO_PATH environment variable. Backtrace: ▆ 1. └─OhdsiReportGenerator::generateFullReport(...) at test-Generate.R:61:3 2. └─quarto::quarto_render(...) 3. └─quarto:::find_quarto() 4. └─cli::cli_abort(quarto_not_found_msg) 5. └─rlang::abort(...) [ FAIL 3 | WARN 2 | SKIP 2 | PASS 417 ] Error: Test failures Execution halted Closing database connection Flavor: r-release-macos-arm64

Version: 1.1.0
Check: tests
Result: ERROR Running ‘testthat.R’ [10s/9s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > test_check("OhdsiReportGenerator") Loading required package: OhdsiReportGenerator Connecting using SQLite driver [ FAIL 3 | WARN 2 | SKIP 2 | PASS 417 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • empty test (1): 'test-Helpers.R:89:1' • skip prediction report due to odd linux error (1): 'test-PredictionReport.R:5:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-Backwards.R:11:3'): generatePresentationMultiple old works ───── Error in `find_quarto()`: Quarto command-line tools path not found! Please make sure you have installed and added Quarto to your PATH or set the QUARTO_PATH environment variable. Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test-Backwards.R:11:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─OhdsiReportGenerator::generatePresentationMultiple(...) 7. └─OhdsiReportGenerator::generatePresentation(...) 8. └─quarto::quarto_render(...) 9. └─quarto:::find_quarto() 10. └─cli::cli_abort(quarto_not_found_msg) 11. └─rlang::abort(...) ── Error ('test-Generate.R:10:3'): generatePresentation ──────────────────────── Error in `find_quarto()`: Quarto command-line tools path not found! Please make sure you have installed and added Quarto to your PATH or set the QUARTO_PATH environment variable. Backtrace: ▆ 1. └─OhdsiReportGenerator::generatePresentation(...) at test-Generate.R:10:3 2. └─quarto::quarto_render(...) 3. └─quarto:::find_quarto() 4. └─cli::cli_abort(quarto_not_found_msg) 5. └─rlang::abort(...) ── Error ('test-Generate.R:61:3'): generateFullReport ────────────────────────── Error in `find_quarto()`: Quarto command-line tools path not found! Please make sure you have installed and added Quarto to your PATH or set the QUARTO_PATH environment variable. Backtrace: ▆ 1. └─OhdsiReportGenerator::generateFullReport(...) at test-Generate.R:61:3 2. └─quarto::quarto_render(...) 3. └─quarto:::find_quarto() 4. └─cli::cli_abort(quarto_not_found_msg) 5. └─rlang::abort(...) [ FAIL 3 | WARN 2 | SKIP 2 | PASS 417 ] Error: Test failures Execution halted Closing database connection Flavor: r-release-macos-x86_64

Version: 1.1.0
Check: tests
Result: ERROR Running ‘testthat.R’ [6s/4s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > test_check("OhdsiReportGenerator") Loading required package: OhdsiReportGenerator Connecting using SQLite driver [ FAIL 3 | WARN 2 | SKIP 2 | PASS 417 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • empty test (1): 'test-Helpers.R:89:1' • skip prediction report due to odd linux error (1): 'test-PredictionReport.R:5:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-Backwards.R:11:3'): generatePresentationMultiple old works ───── Error in `find_quarto()`: Quarto command-line tools path not found! Please make sure you have installed and added Quarto to your PATH or set the QUARTO_PATH environment variable. Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test-Backwards.R:11:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─OhdsiReportGenerator::generatePresentationMultiple(...) 7. └─OhdsiReportGenerator::generatePresentation(...) 8. └─quarto::quarto_render(...) 9. └─quarto:::find_quarto() 10. └─cli::cli_abort(quarto_not_found_msg) 11. └─rlang::abort(...) ── Error ('test-Generate.R:10:3'): generatePresentation ──────────────────────── Error in `find_quarto()`: Quarto command-line tools path not found! Please make sure you have installed and added Quarto to your PATH or set the QUARTO_PATH environment variable. Backtrace: ▆ 1. └─OhdsiReportGenerator::generatePresentation(...) at test-Generate.R:10:3 2. └─quarto::quarto_render(...) 3. └─quarto:::find_quarto() 4. └─cli::cli_abort(quarto_not_found_msg) 5. └─rlang::abort(...) ── Error ('test-Generate.R:61:3'): generateFullReport ────────────────────────── Error in `find_quarto()`: Quarto command-line tools path not found! Please make sure you have installed and added Quarto to your PATH or set the QUARTO_PATH environment variable. Backtrace: ▆ 1. └─OhdsiReportGenerator::generateFullReport(...) at test-Generate.R:61:3 2. └─quarto::quarto_render(...) 3. └─quarto:::find_quarto() 4. └─cli::cli_abort(quarto_not_found_msg) 5. └─rlang::abort(...) [ FAIL 3 | WARN 2 | SKIP 2 | PASS 417 ] Error: Test failures Execution halted Closing database connection Flavor: r-oldrel-macos-arm64

Version: 1.1.0
Check: tests
Result: ERROR Running ‘testthat.R’ [10s/12s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > test_check("OhdsiReportGenerator") Loading required package: OhdsiReportGenerator Connecting using SQLite driver [ FAIL 3 | WARN 2 | SKIP 2 | PASS 417 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • empty test (1): 'test-Helpers.R:89:1' • skip prediction report due to odd linux error (1): 'test-PredictionReport.R:5:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-Backwards.R:11:3'): generatePresentationMultiple old works ───── Error in `find_quarto()`: Quarto command-line tools path not found! Please make sure you have installed and added Quarto to your PATH or set the QUARTO_PATH environment variable. Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test-Backwards.R:11:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─OhdsiReportGenerator::generatePresentationMultiple(...) 7. └─OhdsiReportGenerator::generatePresentation(...) 8. └─quarto::quarto_render(...) 9. └─quarto:::find_quarto() 10. └─cli::cli_abort(quarto_not_found_msg) 11. └─rlang::abort(...) ── Error ('test-Generate.R:10:3'): generatePresentation ──────────────────────── Error in `find_quarto()`: Quarto command-line tools path not found! Please make sure you have installed and added Quarto to your PATH or set the QUARTO_PATH environment variable. Backtrace: ▆ 1. └─OhdsiReportGenerator::generatePresentation(...) at test-Generate.R:10:3 2. └─quarto::quarto_render(...) 3. └─quarto:::find_quarto() 4. └─cli::cli_abort(quarto_not_found_msg) 5. └─rlang::abort(...) ── Error ('test-Generate.R:61:3'): generateFullReport ────────────────────────── Error in `find_quarto()`: Quarto command-line tools path not found! Please make sure you have installed and added Quarto to your PATH or set the QUARTO_PATH environment variable. Backtrace: ▆ 1. └─OhdsiReportGenerator::generateFullReport(...) at test-Generate.R:61:3 2. └─quarto::quarto_render(...) 3. └─quarto:::find_quarto() 4. └─cli::cli_abort(quarto_not_found_msg) 5. └─rlang::abort(...) [ FAIL 3 | WARN 2 | SKIP 2 | PASS 417 ] Error: Test failures Execution halted Closing database connection Flavor: r-oldrel-macos-x86_64

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.