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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:hierinf.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings hierinf_1.27.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/hierinf.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hierinf/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘hierinf’ version ‘1.27.0’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘hierinf’ can be installed ... OK
* 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 ... NOTE
Problems with news in ‘NEWS.md’:
No news entries found.
* 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 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  compute_r2.Rd: NagelkerkeR2
  multisplit.Rd: glmnet
  test_hierarchy.Rd: glmnet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
simGWAS             111.059  0.072 112.054
test_hierarchy       24.234  0.024  24.325
test_only_hierarchy  24.024  0.000  24.084
compute_r2           15.233  0.080  15.463
print.hierT          13.250  0.000  13.425
cluster_var           9.542  0.015   9.583
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  res.S$res.hierarchy$p.value[1] not equal to expected_result$p.value[1].
  1/1 mismatches
  [1] 1.83e-16 - 8.18e-30 == 1.83e-16
  ── Failure ('test-test_only_hierarchy.R:1554:3'): test_only_hierarchy: check return object for two data sets with binary response ──
  res.S$res.hierarchy$p.value[2] not equal to expected_result$p.value[2].
  1/1 mismatches
  [1] 8.18e-30 - 1.83e-16 == -1.83e-16
  ── Failure ('test-test_only_hierarchy.R:1556:3'): test_only_hierarchy: check return object for two data sets with binary response ──
  res.S$res.hierarchy$significant.cluster not equal to expected_result$significant.cluster.
  Component 1: 1 string mismatch
  Component 2: 1 string mismatch
  
  [ FAIL 6 | WARN 0 | SKIP 12 | PASS 139 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/hierinf.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD INSTALL hierinf
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘hierinf’ ...
** this is package ‘hierinf’ version ‘1.27.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (hierinf)

R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # All tests are in the folder testthat
> require("testthat")
Loading required package: testthat
> test_check("hierinf")
Loading required package: hierinf
[ FAIL 6 | WARN 0 | SKIP 12 | PASS 139 ]

══ Skipped tests (12) ══════════════════════════════════════════════════════════
• On Bioconductor (12): 'test-cluster_var.R:182:3', 'test-multisplit.R:92:3',
  'test-test_hierarchy.R:352:3', 'test-test_hierarchy.R:461:3',
  'test-test_hierarchy.R:575:3', 'test-test_only_hierarchy.R:460:3',
  'test-test_only_hierarchy.R:570:3', 'test-test_only_hierarchy.R:684:3',
  'test-test_only_hierarchy.R:892:3', 'test-test_only_hierarchy.R:1271:3',
  'test-test_only_hierarchy.R:1563:3', 'test-test_only_hierarchy.R:1701:3'

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-test_only_hierarchy.R:1530:3'): test_only_hierarchy: check return object for two data sets with binary response ──
res.T$res.hierarchy$p.value[1] not equal to expected_result$p.value[1].
1/1 mismatches
[1] 9.02e-10 - 1.11e-16 == 9.02e-10
── Failure ('test-test_only_hierarchy.R:1532:3'): test_only_hierarchy: check return object for two data sets with binary response ──
res.T$res.hierarchy$p.value[2] not equal to expected_result$p.value[2].
1/1 mismatches
[1] 1.11e-16 - 9.02e-10 == -9.02e-10
── Failure ('test-test_only_hierarchy.R:1534:3'): test_only_hierarchy: check return object for two data sets with binary response ──
res.T$res.hierarchy$significant.cluster not equal to expected_result$significant.cluster.
Component 1: 1 string mismatch
Component 2: 1 string mismatch
── Failure ('test-test_only_hierarchy.R:1552:3'): test_only_hierarchy: check return object for two data sets with binary response ──
res.S$res.hierarchy$p.value[1] not equal to expected_result$p.value[1].
1/1 mismatches
[1] 1.83e-16 - 8.18e-30 == 1.83e-16
── Failure ('test-test_only_hierarchy.R:1554:3'): test_only_hierarchy: check return object for two data sets with binary response ──
res.S$res.hierarchy$p.value[2] not equal to expected_result$p.value[2].
1/1 mismatches
[1] 8.18e-30 - 1.83e-16 == -1.83e-16
── Failure ('test-test_only_hierarchy.R:1556:3'): test_only_hierarchy: check return object for two data sets with binary response ──
res.S$res.hierarchy$significant.cluster not equal to expected_result$significant.cluster.
Component 1: 1 string mismatch
Component 2: 1 string mismatch

[ FAIL 6 | WARN 0 | SKIP 12 | PASS 139 ]
Error: Test failures
Execution halted