Last updated on 2025-02-16 10:50:45 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.3 | 5.97 | 77.75 | 83.72 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.3 | 3.25 | 55.53 | 58.78 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.3 | 125.32 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.3 | 133.28 | ERROR | |||
| r-devel-macos-arm64 | 1.0.3 | 47.00 | OK | |||
| r-devel-macos-x86_64 | 1.0.3 | 92.00 | OK | |||
| r-devel-windows-x86_64 | 1.0.3 | 8.00 | 93.00 | 101.00 | OK | |
| r-patched-linux-x86_64 | 1.0.3 | 5.34 | 71.13 | 76.47 | OK | |
| r-release-linux-x86_64 | 1.0.3 | 5.79 | 71.23 | 77.02 | OK | |
| r-release-macos-arm64 | 1.0.3 | 51.00 | OK | |||
| r-release-macos-x86_64 | 1.0.3 | 118.00 | OK | |||
| r-release-windows-x86_64 | 1.0.3 | 8.00 | 86.00 | 94.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.3 | 48.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.0.3 | 127.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.0.3 | 11.00 | 96.00 | 107.00 | 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)
'/tmp/Rtmpgjcgwv/working_dir/RtmpNOrnd4/file265eea7c35258d.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-linux-x86_64-fedora-clang
Version: 1.0.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [23s/56s]
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-linux-x86_64-fedora-clang
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 lines 71-82 [xml] (eudract.Rmd)
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
** Processing: /data/gannet/ripley/R/packages/tests-clang/eudract.Rcheck/vign_test/eudract/vignettes/standard_reporting_files/figure-html/dotplot_sae-1.png
768x768 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 26100 bytes
Input file size = 26214 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20573
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20573
Output IDAT size = 20573 bytes (5527 bytes decrease)
Output file size = 20651 bytes (5563 bytes = 21.22% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/eudract.Rcheck/vign_test/eudract/vignettes/standard_reporting_files/figure-html/dotplot_ae-1.png
768x768 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 26313 bytes
Input file size = 26427 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20499
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20499
Output IDAT size = 20499 bytes (5814 bytes decrease)
Output file size = 20577 bytes (5850 bytes = 22.14% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/eudract.Rcheck/vign_test/eudract/vignettes/standard_reporting_files/figure-html/dotplot_edit-1.png
768x768 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 28575 bytes
Input file size = 28689 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22074
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22074
Output IDAT size = 22074 bytes (6501 bytes decrease)
Output file size = 22152 bytes (6537 bytes = 22.79% decrease)
--- finished re-building ‘standard_reporting.Rmd’
SUMMARY: processing the following file failed:
‘eudract.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
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)
'/tmp/RtmpP3QHpe/working_dir/RtmpDCbSsK/file12923572f1754c.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-linux-x86_64-fedora-gcc
Version: 1.0.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [21s/42s]
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-linux-x86_64-fedora-gcc
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 lines 71-82 [xml] (eudract.Rmd)
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
** Processing: /data/gannet/ripley/R/packages/tests-devel/eudract.Rcheck/vign_test/eudract/vignettes/standard_reporting_files/figure-html/dotplot_sae-1.png
768x768 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 26100 bytes
Input file size = 26214 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20573
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20573
Output IDAT size = 20573 bytes (5527 bytes decrease)
Output file size = 20651 bytes (5563 bytes = 21.22% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/eudract.Rcheck/vign_test/eudract/vignettes/standard_reporting_files/figure-html/dotplot_ae-1.png
768x768 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 26313 bytes
Input file size = 26427 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20499
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20499
Output IDAT size = 20499 bytes (5814 bytes decrease)
Output file size = 20577 bytes (5850 bytes = 22.14% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/eudract.Rcheck/vign_test/eudract/vignettes/standard_reporting_files/figure-html/dotplot_edit-1.png
768x768 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 28575 bytes
Input file size = 28689 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22074
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22074
Output IDAT size = 22074 bytes (6501 bytes decrease)
Output file size = 22152 bytes (6537 bytes = 22.79% decrease)
--- finished re-building ‘standard_reporting.Rmd’
SUMMARY: processing the following file failed:
‘eudract.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
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.