CRAN noSuggests error: The package "xml2" is required to run run_cpp_tests()

* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/fastcpd.Rcheck’
* using R Under development (unstable) (2024-03-28 r86224)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-13 (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘fastcpd/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘fastcpd’ version ‘0.12.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: ‘gfpop’
* 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 ‘fastcpd’ can be installed ... [244s/84s] OK
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
* 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 ... [20s/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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [143s/170s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [583s/317s]
 [583s/318s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fastcpd)
  > 
  > test_check("fastcpd")
  Starting 2 test processes
  [ FAIL 2 | WARN 0 | SKIP 10 | PASS 72 ]

  ══ Skipped tests (10) ══════════════════════════════════════════════════════════
  • Skip due to time limit on CRAN. (1): 'test-vignettes-comparison-pelt.R:4:1'
  • These tests are intended to be run manually. (1): 'test-experiments.R:1:1'
  • gridExtra cannot be loaded (1): 'test-examples-data-transcriptome.R:4:5'
  • lubridate cannot be loaded (1): 'test-examples-data-uk_seatbelts.R:4:5'
  • matrixStats cannot be loaded (1):
    'test-examples-data-well_log-quantile.R:4:5'
  • mockthat cannot be loaded (1): 'test-fastcpd-class.R:3:5'
  • mvtnorm cannot be loaded (4): 'test-examples-fastcpd_1.R:4:5',
    'test-examples-fastcpd_2.R:4:5', 'test-examples-fastcpd_3.R:4:5',
    'test-examples-fastcpd_4.R:4:5'

  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-cpp.R:1:1'): (code run outside of `test_that()`) ───────────────
  <rlib_error_package_not_found/rlang_error/error/condition>
  Error in `run_cpp_tests("fastcpd")`: The package "xml2" is required to run run_cpp_tests()
  Backtrace:
      ▆
   1. └─testthat::run_cpp_tests("fastcpd") at test-cpp.R:1:1
   2.   └─rlang::check_installed("xml2", "to run run_cpp_tests()")
  ── Error ('test-coverage.R:7:5'): vanilla_percentage ───────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'mvtnorm'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-coverage.R:7:5
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)

  [ FAIL 2 | WARN 0 | SKIP 10 | PASS 72 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [9s/20s] 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: 1 ERROR, 1 NOTE
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/fastcpd.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 12:08.55, 1035.31 + 46.04
doccstat / fastcpd

CRAN noSuggests error: The package "xml2" is required to run run_cpp_tests() #11
