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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:idr2d.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings idr2d_1.25.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/idr2d.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘idr2d/DESCRIPTION’ ... OK
* this is package ‘idr2d’ version ‘1.25.0’
* 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 ‘idr2d’ 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 ... 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 whether startup messages can be suppressed ... 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 ... 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 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
estimate_idr         9.401  0.079   9.504
estimate_idr2d       9.368  0.052   9.440
draw_hic_contact_map 5.870  0.128   6.011
* 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:
    9. │   │ └─testthat::capture_output_lines(code, print, width = width)
   10. │   │   └─testthat:::eval_with_output(code, print = print, width = width)
   11. │   │     ├─withr::with_output_sink(path, withVisible(code))
   12. │   │     │ └─base::force(code)
   13. │   │     └─base::withVisible(code)
   14. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   15. └─idr2d::parse_juicer_matrix("wrong/path", use_python = NULL, use_virtualenv = NULL)
   16.   └─reticulate::import("straw")
   17.     └─reticulate:::ensure_python_initialized(required_module = module)
   18.       └─reticulate:::initialize_python()
   19.         └─reticulate (local) python_not_found("Installation of Python not found, Python bindings not loaded.")
  
  [ FAIL 1 | WARN 6 | SKIP 0 | PASS 131 ]
  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
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/idr2d.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL idr2d
###
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘idr2d’ ...
** this is package ‘idr2d’ version ‘1.25.0’
** using staged installation
** R
** data
** 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 (idr2d)

R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
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.

> library(testthat)
> library(idr2d)
> 
> test_check("idr2d")
Error in python_config_impl(python) : 
  Error running '/home/biocbuild/.cache/R/reticulate/uv/cache/builds-v0/.tmpw7lOcw/bin/python': No such file.
[ FAIL 1 | WARN 6 | SKIP 0 | PASS 131 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-hic.R:36:5'): parse_juicer_matrix ────────────────────────────
`expect_output(...)` threw an error with unexpected message.
Expected match: "No module named|Specified version of python"
Actual message: "Installation of Python not found, Python bindings not loaded.\nSee the Python \"Order of Discovery\" here: https://rstudio.github.io/reticulate/articles/versions.html#order-of-discovery."
Backtrace:
     ▆
  1. ├─testthat::expect_error(...) at test-hic.R:36:5
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─testthat::expect_output(...)
  7. │ └─testthat:::quasi_capture(...)
  8. │   ├─testthat (local) .capture(...)
  9. │   │ └─testthat::capture_output_lines(code, print, width = width)
 10. │   │   └─testthat:::eval_with_output(code, print = print, width = width)
 11. │   │     ├─withr::with_output_sink(path, withVisible(code))
 12. │   │     │ └─base::force(code)
 13. │   │     └─base::withVisible(code)
 14. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
 15. └─idr2d::parse_juicer_matrix("wrong/path", use_python = NULL, use_virtualenv = NULL)
 16.   └─reticulate::import("straw")
 17.     └─reticulate:::ensure_python_initialized(required_module = module)
 18.       └─reticulate:::initialize_python()
 19.         └─reticulate (local) python_not_found("Installation of Python not found, Python bindings not loaded.")

[ FAIL 1 | WARN 6 | SKIP 0 | PASS 131 ]
Error: Test failures
Execution halted