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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:basilisk.utils.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings basilisk.utils_1.21.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/basilisk.utils.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘basilisk.utils/DESCRIPTION’ ... OK
* this is package ‘basilisk.utils’ version ‘1.21.2’
* 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 ‘basilisk.utils’ 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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:
   1. └─basilisk.utils::configureEnvironments(ext) at test-configureEnvironments.R:45:5
   2.   ├─base::do.call(.create_environment, cur.args)
   3.   └─basilisk.utils (local) `<fn>`(...)
  ── Error ('test-createEnvironment.R:4:1'): (code run outside of `test_that()`) ──
  Error in `.create_environment(env.loc, conda = conda, packages = packages, 
      channels = channels, override.channels = override.channels, 
      extra = extra)`: failed to create conda environment at '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp5jlh5T/filedb844938c8f8/test_env/1.0.0' (returned 1)
  Backtrace:
      ▆
   1. └─basilisk.utils::createEnvironment(...) at test-createEnvironment.R:4:1
   2.   └─basilisk.utils:::.create_environment(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 13 ]
  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
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/basilisk.utils.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL basilisk.utils
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘basilisk.utils’ ...
** this is package ‘basilisk.utils’ version ‘1.21.2’
** using staged installation
** R
** 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 (basilisk.utils)

R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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(basilisk.utils)

Attaching package: 'basilisk.utils'

The following object is masked from 'package:utils':

    find

> test_check("basilisk.utils")
Retrieving notices: ...working... Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=5)")': /conda-forge/notices.json

Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=5)")': /conda-forge/notices.json

Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=5)")': /conda-forge/notices.json

ERROR conda.notices.fetch:get_channel_notice_response(72): Request error <HTTPSConnectionPool(host='conda.anaconda.org', port=443): Max retries exceeded with url: /conda-forge/notices.json (Caused by ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=5)"))> for channel: conda-forge url: https://conda.anaconda.org/conda-forge/notices.json
done
Channels:
 - conda-forge
Platform: osx-arm64
Collecting package metadata (repodata.json): ...working... Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/noarch/repodata.json.zst

Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/osx-arm64/repodata.json.zst

Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/osx-arm64/repodata.json.zst

Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/noarch/repodata.json.zst

Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/noarch/repodata.json.zst

Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/osx-arm64/repodata.json.zst

failed

CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://conda.anaconda.org/conda-forge/osx-arm64/repodata.json>
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.
'https//conda.anaconda.org/conda-forge/osx-arm64'


Channels:
 - conda-forge
Platform: osx-arm64
Collecting package metadata (repodata.json): ...working... Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/noarch/repodata.json.zst

Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/osx-arm64/repodata.json.zst

Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/osx-arm64/repodata.json.zst

Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/noarch/repodata.json.zst

Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/osx-arm64/repodata.json.zst

Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/noarch/repodata.json.zst

failed

CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://conda.anaconda.org/conda-forge/osx-arm64/repodata.json>
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.
'https//conda.anaconda.org/conda-forge/osx-arm64'


[ FAIL 2 | WARN 0 | SKIP 0 | PASS 13 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-configureEnvironments.R:45:5'): configureEnvironments works as expected ──
Error in `(function (env.loc, conda, packages, channels, override.channels, 
    extra) 
{
    success <- FALSE
    on.exit(if (!success) unlink2(env.loc), add = TRUE, after = FALSE)
    if (is.null(conda)) {
        conda <- find()
    }
    more.args <- character(0)
    for (ch in channels) {
        more.args <- c(more.args, "-c", ch)
    }
    if (override.channels) {
        more.args <- c(more.args, "--override-channels")
    }
    status <- system2(conda, c("create", "--prefix", env.loc, 
        "--yes", packages, more.args, extra))
    if (status != 0L) {
        stop(sprintf("failed to create conda environment at '%s' (returned %i)", 
            env.loc, status))
    }
    success <- TRUE
})(env.loc = "/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp5jlh5T/filedb845d7bb134/foo/biocconda/more-test-env", 
    packages = "pandas", conda = NULL, channels = "conda-forge", 
    override.channels = TRUE, extra = "--quiet")`: failed to create conda environment at '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp5jlh5T/filedb845d7bb134/foo/biocconda/more-test-env' (returned 1)
Backtrace:
    ▆
 1. └─basilisk.utils::configureEnvironments(ext) at test-configureEnvironments.R:45:5
 2.   ├─base::do.call(.create_environment, cur.args)
 3.   └─basilisk.utils (local) `<fn>`(...)
── Error ('test-createEnvironment.R:4:1'): (code run outside of `test_that()`) ──
Error in `.create_environment(env.loc, conda = conda, packages = packages, 
    channels = channels, override.channels = override.channels, 
    extra = extra)`: failed to create conda environment at '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp5jlh5T/filedb844938c8f8/test_env/1.0.0' (returned 1)
Backtrace:
    ▆
 1. └─basilisk.utils::createEnvironment(...) at test-createEnvironment.R:4:1
 2.   └─basilisk.utils:::.create_environment(...)

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 13 ]
Error: Test failures
Execution halted