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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:idr2d.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings idr2d_1.19.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/idr2d.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'idr2d/DESCRIPTION' ... OK
* this is package 'idr2d' version '1.19.0'
* 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 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 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         8.21   1.09    9.88
estimate_idr2d       7.88   1.19    9.61
draw_hic_contact_map 4.58   0.55    5.13
* 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 1 | 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
  'F:/biocbuild/bbs-3.20-bioc/meat/idr2d.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL idr2d
###
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* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'idr2d' ...
** 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 version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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")
[ FAIL 1 | WARN 1 | 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.\nPlease create a default virtual environment with `reticulate::virtualenv_create('r-reticulate')`."
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 1 | SKIP 0 | PASS 131 ]
Error: Test failures
Execution halted