* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/eudract.Rcheck’
* using R Under development (unstable) (2025-02-28 r87848)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    clang version 20.1.0-rc3
    flang version 20.1.0-rc3
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘eudract/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘eudract’ version ‘1.0.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘eudract’ can be installed ... [10s/13s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/eudract-00install.html' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [13s/19s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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/RtmpBmyhhM/working_dir/Rtmp7pcBzy/file1294de617d18f2.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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [21s/29s] ERROR
  Running ‘testthat.R’ [21s/28s]
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:
      â–†
   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:
      â–†
   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:
      â–†
   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:
      â–†
   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:
      â–†
   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:
      â–†
   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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [18s/26s] 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

* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 3 ERRORs