Last updated on 2025-03-22 08:53:15 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.3 | 6.20 | 77.18 | 83.38 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.4 | 4.17 | 54.06 | 58.23 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.4 | 147.07 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.4 | 139.82 | OK | |||
| r-devel-macos-arm64 | 1.0.4 | 43.00 | OK | |||
| r-devel-macos-x86_64 | 1.0.4 | 75.00 | OK | |||
| r-devel-windows-x86_64 | 1.0.3 | 8.00 | 98.00 | 106.00 | ERROR | |
| r-patched-linux-x86_64 | 1.0.4 | 5.39 | 72.48 | 77.87 | OK | |
| r-release-linux-x86_64 | 1.0.3 | 4.39 | 70.79 | 75.18 | OK | |
| r-release-macos-arm64 | 1.0.4 | 50.00 | OK | |||
| r-release-macos-x86_64 | 1.0.4 | 81.00 | OK | |||
| r-release-windows-x86_64 | 1.0.4 | 10.00 | 89.00 | 99.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.4 | 43.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.0.4 | 81.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.0.4 | 10.00 | 105.00 | 115.00 | OK |
Version: 1.0.3
Check: examples
Result: ERROR
Running examples in 'eudract-Ex.R' failed
The error most likely occurred in:
> ### Name: clintrials_gov_convert
> ### Title: applies a conversion using xslt from a simple xml file to a
> ### ClinicalTrials.gov compatible file, and checks against the schema
> ### Aliases: clintrials_gov_convert
>
> ### ** Examples
>
> safety_statistics <- safety_summary(safety,
+ exposed=c("Experimental"=60,"Control"=67))
> simple <- tempfile(fileext = ".xml")
> eudract <- tempfile(fileext = ".xml")
> ct <- tempfile(fileext = ".xml")
> simple_safety_xml(safety_statistics, simple)
'D:\temp\2025_03_17_01_26_54_17999\RtmpYzOjMq\fileffb81cad5.xml' is created or modified
Warning in simple_safety_xml(safety_statistics, simple) :
local complex type: The content model is not determinist.Element 'TABLE': No matching global declaration available for the validation root.
> eudract_convert(input=simple,
+ output=eudract)
Error in eudract_convert(input = simple, output = eudract) :
local complex type: The content model is not determinist.Element 'TABLE': No matching global declaration available for the validation root.
Execution halted
Flavor: r-devel-windows-x86_64
Version: 1.0.3
Check: tests
Result: ERROR
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(eudract)
>
> test_check("eudract")
[ FAIL 6 | WARN 9 | SKIP 8 | PASS 73 ]
══ Skipped tests (8) ═══════════════════════════════════════════════════════════
• Need to have the userid/password as environment variables (3):
'test_basic.R:324:61', 'test_basic.R:343:61', 'test_errors.R:191:71'
• On CRAN (5): 'test_dotplot.R:38:3', 'test_dotplot.R:53:3',
'test_dotplot.R:82:3', 'test_dotplot.R:119:1', 'test_dotplot.R:129:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_basic.R:283:3'): convert to eudract ────────────────────────────
Error in `eudract_convert(input = file.path(path, "simple.xml"), output = file.path(path,
"table_eudract.xml"))`: local complex type: The content model is not determinist.Element 'TABLE': No matching global declaration available for the validation root.
Backtrace:
▆
1. └─eudract::eudract_convert(...) at test_basic.R:283:3
── Error ('test_basic.R:294:4'): convert to ClinicalTrials.Gov ─────────────────
Error in `clintrials_gov_convert(input = file.path(path, "simple.xml"),
original = file.path(original_path, "1234.xml"), output = file.path(path,
"table_ct.xml"))`: safety data is invalid
local complex type: The content model is not determinist.Element 'TABLE': No matching global declaration available for the validation root.
Backtrace:
▆
1. └─eudract::clintrials_gov_convert(...) at test_basic.R:294:4
── Error ('test_errors.R:18:13'): no aes ───────────────────────────────────────
Error in `eudract_convert(file.path(tempdir(), "test_simple.xml"), file.path(tempdir(),
"test_output.xml"))`: local complex type: The content model is not determinist.Element 'TABLE': No matching global declaration available for the validation root.
Backtrace:
▆
1. ├─testthat::expect_true(...) at test_errors.R:18:13
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─eudract::eudract_convert(...)
── Error ('test_errors.R:31:13'): no saes ──────────────────────────────────────
Error in `eudract_convert(file.path(tempdir(), "test_simple.xml"), file.path(tempdir(),
"test_output.xml"))`: local complex type: The content model is not determinist.Element 'TABLE': No matching global declaration available for the validation root.
Backtrace:
▆
1. ├─testthat::expect_true(...) at test_errors.R:31:13
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─eudract::eudract_convert(...)
── Error ('test_errors.R:54:13'): empty group ──────────────────────────────────
Error in `eudract_convert(file.path(tempdir(), "/test_simple.xml"), file.path(tempdir(),
"/test_output.xml"))`: local complex type: The content model is not determinist.Element 'TABLE': No matching global declaration available for the validation root.
Backtrace:
▆
1. ├─testthat::expect_true(...) at test_errors.R:54:13
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─eudract::eudract_convert(...)
── Failure ('test_errors.R:242:3'): invalid ct inputs ──────────────────────────
`clintrials_gov_convert(...)` threw an error with unexpected message.
Expected match: "original study file is invalid"
Actual message: "safety data is invalid\nlocal complex type: The content model is not determinist.Element 'TABLE': No matching global declaration available for the validation root."
Backtrace:
▆
1. ├─testthat::expect_error(...) at test_errors.R:242:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─eudract::clintrials_gov_convert(...)
[ FAIL 6 | WARN 9 | SKIP 8 | PASS 73 ]
Deleting unused snapshots:
• dotplot/dotplot-ref-rr.svg
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64
Version: 1.0.3
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'eudract.Rmd' using rmarkdown
Quitting from eudract.Rmd:70-82 [xml]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `eudract_convert()`:
! local complex type: The content model is not determinist.Element 'TABLE': No matching global declaration available for the validation root.
---
Backtrace:
▆
1. └─eudract::eudract_convert(input = simple, output = eudract_upload_file)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'eudract.Rmd' failed with diagnostics:
local complex type: The content model is not determinist.Element 'TABLE': No matching global declaration available for the validation root.
--- failed re-building 'eudract.Rmd'
--- re-building 'standard_reporting.Rmd' using rmarkdown
--- finished re-building 'standard_reporting.Rmd'
SUMMARY: processing the following file failed:
'eudract.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-windows-x86_64