• using R Under development (unstable) (2025-02-19 r87749)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 20.1.0-rc2     flang version 20.1.0-rc2
• 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 ... [9s/16s] OK See the install log 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 ... [14s/24s] 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/RtmpxG0XVM/working_dir/Rtmpa1gPHw/file2fa6b63ee5e3aa.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 ... [22s/36s] ERROR   Running ‘testthat.R’ [22s/35s] 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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [19s/29s] 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