##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:basilisk.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings basilisk_1.19.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/basilisk.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘basilisk/DESCRIPTION’ ... OK
* this is package ‘basilisk’ version ‘1.19.3’
* 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 ... NOTE
Found the following hidden files and directories:
  inst/example/.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘basilisk’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/basilisk.Rcheck/00install.out’ for details.
* 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 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:
  basiliskStart.Rd: activateEnvironment, getExternalDir
  listPackages.Rd: installConda
  useBasiliskEnv.Rd: activateEnvironment
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 line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘basilisk-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: basiliskStart
> ### Title: Start and stop 'basilisk'-related processes
> ### Aliases: basiliskStart basiliskStop basiliskRun
> 
> ### ** Examples
> 
> if (.Platform$OS.type != "windows") {
+  ## Don't show: 
+ basilisk.utils::installConda()
+ ## End(Don't show)
+ 
+  # Creating an environment (note, this is not necessary
+  # when supplying a BasiliskEnvironment to basiliskStart):
+  tmploc <- file.path(tempdir(), "my_package_A")
+  if (!file.exists(tmploc)) {
+      setupBasiliskEnv(tmploc, c('pandas=2.2.3'))
+  }
+ 
+  # Pulling out the pandas version, as a demonstration:
+  cl <- basiliskStart(tmploc, testload="pandas")
+  basiliskRun(proc=cl, function() { 
+      X <- reticulate::import("pandas"); X$`__version__` 
+  })
+  basiliskStop(cl)
+ 
+  # This happily co-exists with our other environment:
+  tmploc2 <- file.path(tempdir(), "my_package_B")
+  if (!file.exists(tmploc2)) {
+      setupBasiliskEnv(tmploc2, c('pandas=2.2.2'))
+  }
+  
+  cl2 <- basiliskStart(tmploc2, testload="pandas")
+  basiliskRun(proc=cl2, function() { 
+      X <- reticulate::import("pandas"); X$`__version__` 
+  })
+  basiliskStop(cl2)
+ 
+  # Persistence of variables is possible within a Start/Stop pair.
+  cl <- basiliskStart(tmploc)
+  basiliskRun(proc=cl, function(store) {
+      store$snake.in.my.shoes <- 1
+      invisible(NULL)
+  }, persist=TRUE)
+  basiliskRun(proc=cl, function(store) {
+      return(store$snake.in.my.shoes)
+  }, persist=TRUE)
+  basiliskStop(cl)
+ }
Warning in check_forbidden_install("Python packages") :
  cannot install Python packages during R CMD check
Warning in check_forbidden_install("Conda Environments") :
  cannot install Conda Environments during R CMD check
+ /home/rapidbuild/.cache/R/basilisk/1.19.3/0/bin/conda create --yes --prefix /tmp/Rtmp6r1d0x/my_package_A 'python=3.12.8' --quiet -c conda-forge --override-channels
Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): ...working... failed

NoSpaceLeftError: No space left on devices.

Error: Error creating conda environment '/tmp/Rtmp6r1d0x/my_package_A' [exit code 1]
Execution halted
* 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:
   3.     └─reticulate::conda_install(...)
   4.       └─reticulate::conda_create(...)
   5.         └─reticulate:::stopf(fmt, envname, result, call. = FALSE)
  ── Error ('test-start.R:15:1'): (code run outside of `test_that()`) ────────────
  Error: Error creating conda environment '/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/basilisk.Rcheck/tests/testthat/install-test-client/my_package_A' [exit code 1]
  Backtrace:
      ▆
   1. └─basilisk::setupBasiliskEnv(tA, c(test.pandas, test.pandas.deps)) at test-start.R:15:1
   2.   └─reticulate::conda_install(...)
   3.     └─reticulate::conda_create(...)
   4.       └─reticulate:::stopf(fmt, envname, result, call. = FALSE)
  
  [ FAIL 9 | WARN 4 | SKIP 0 | PASS 14 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘motivation.Rmd’ using rmarkdown
Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): ...working... failed

NoSpaceLeftError: No space left on devices.


Quitting from motivation.Rmd:279-284 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error creating conda environment '/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/basilisk.Rcheck/vign_test/basilisk/vignettes/basilisk-vignette-test/1.19.3' [exit code 1]
---
Backtrace:
    ▆
 1. └─basilisk::createLocalBasiliskEnv(...)
 2.   └─basilisk::setupBasiliskEnv(envpath, ...)
 3.     └─reticulate::conda_install(...)
 4.       └─reticulate::conda_create(...)
 5.         └─reticulate:::stopf(fmt, envname, result, call. = FALSE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'motivation.Rmd' failed with diagnostics:
Error creating conda environment '/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/basilisk.Rcheck/vign_test/basilisk/vignettes/basilisk-vignette-test/1.19.3' [exit code 1]
--- failed re-building ‘motivation.Rmd’

SUMMARY: processing the following file failed:
  ‘motivation.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs, 3 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/basilisk.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL basilisk
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘basilisk’ ...
** this is package ‘basilisk’ version ‘1.19.3’
** using non-staged installation via StagedInstall field
** 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
* DONE (basilisk)

R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(basilisk)
Loading required package: reticulate
> if (.Platform$OS.type != "windows") test_check("basilisk")
Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): ...working... failed

NoSpaceLeftError: No space left on devices.

Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): ...working... failed

NoSpaceLeftError: No space left on devices.

Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): ...working... failed

NoSpaceLeftError: No space left on devices.

Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): ...working... failed

NoSpaceLeftError: No space left on devices.

Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): ...working... failed

NoSpaceLeftError: No space left on devices.

trying URL 'https://github.com/conda-forge/miniforge/releases/download/24.11.3-0/Miniforge3-24.11.3-0-Linux-x86_64.sh'
Content type 'application/octet-stream' length 77993651 bytes (74.4 MB)
=====
downloaded 8.2 MB

trying URL 'https://github.com/conda-forge/miniforge/releases/download/24.11.3-0/Miniforge3-24.11.3-0-Linux-x86_64.sh'
Content type 'application/octet-stream' length 77993651 bytes (74.4 MB)
=====
downloaded 8.2 MB

Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): ...working... failed

NoSpaceLeftError: No space left on devices.

Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): ...working... failed

NoSpaceLeftError: No space left on devices.

[ FAIL 9 | WARN 4 | SKIP 0 | PASS 14 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-install.R:16:5'): setupBasiliskEnv obtains the correct version of the packages ──
Error: Error creating conda environment '/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo' [exit code 1]
Backtrace:
    ▆
 1. └─basilisk::setupBasiliskEnv(target, c(test.pandas, test.pandas.deps)) at test-install.R:16:5
 2.   └─reticulate::conda_install(...)
 3.     └─reticulate::conda_create(...)
 4.       └─reticulate:::stopf(fmt, envname, result, call. = FALSE)
── Error ('test-install.R:38:5'): setupBasiliskEnv will install Python 2.7 if requested ──
Error: Error creating conda environment '/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo' [exit code 1]
Backtrace:
    ▆
 1. └─basilisk::setupBasiliskEnv(target, "python=2.7") at test-install.R:38:5
 2.   └─reticulate::conda_install(...)
 3.     └─reticulate::conda_create(...)
 4.       └─reticulate:::stopf(fmt, envname, result, call. = FALSE)
── Error ('test-install.R:49:5'): setupBasiliskEnv works with PyPi-hosted packages ──
Error: Error creating conda environment '/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo' [exit code 1]
Backtrace:
    ▆
 1. └─basilisk::setupBasiliskEnv(target, old.pandas.deps, pip = old.pandas) at test-install.R:49:5
 2.   └─reticulate::conda_install(...)
 3.     └─reticulate::conda_create(...)
 4.       └─reticulate:::stopf(fmt, envname, result, call. = FALSE)
── Error ('test-install.R:58:5'): setupBasiliskEnv works with local packages ───
Error: Error creating conda environment '/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo' [exit code 1]
Backtrace:
    ▆
 1. └─basilisk::setupBasiliskEnv(...) at test-install.R:58:5
 2.   └─reticulate::conda_install(...)
 3.     └─reticulate::conda_create(...)
 4.       └─reticulate:::stopf(fmt, envname, result, call. = FALSE)
── Failure ('test-install.R:65:5'): setupBasiliskEnv destroys directory on error ──
`setupBasiliskEnv(target, package = "WHHEEEEEEEEEEEEEEEEEE==0.0.1")` threw an error with unexpected message.
Expected match: "failed to install"
Actual message: "Error creating conda environment '/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo' [exit code 1]"
Backtrace:
    ▆
 1. ├─testthat::expect_error(...) at test-install.R:65:5
 2. │ └─testthat:::quasi_capture(...)
 3. │   ├─testthat (local) .capture(...)
 4. │   │ └─base::withCallingHandlers(...)
 5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
 6. └─basilisk::setupBasiliskEnv(target, package = "WHHEEEEEEEEEEEEEEEEEE==0.0.1")
 7.   └─reticulate::conda_install(...)
 8.     └─reticulate::conda_create(...)
 9.       └─reticulate:::stopf(fmt, envname, result, call. = FALSE)
── Error ('test-lazy.R:19:5'): lazy conda installation works as expected ───────
Error in `download.file(url, fname, mode = "wb")`: download from 'https://github.com/conda-forge/miniforge/releases/download/24.11.3-0/Miniforge3-24.11.3-0-Linux-x86_64.sh' failed
Backtrace:
    ▆
 1. ├─testthat::expect_true(basilisk.utils::installConda()) at test-lazy.R:19:5
 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─basilisk.utils::installConda()
 5.   └─basilisk.utils:::.expedient_download(file.path(base_url, inst_file))
 6.     └─base::tryCatch(...)
 7.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 8.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.           └─value[[3L]](cond)
── Error ('test-lazy.R:40:5'): obtainEnvironmentPath works as expected ─────────
Error in `download.file(url, fname, mode = "wb")`: download from 'https://github.com/conda-forge/miniforge/releases/download/24.11.3-0/Miniforge3-24.11.3-0-Linux-x86_64.sh' failed
Backtrace:
    ▆
 1. └─basilisk::obtainEnvironmentPath(env) at test-lazy.R:40:5
 2.   └─basilisk.utils::installConda()
 3.     └─basilisk.utils:::.expedient_download(file.path(base_url, inst_file))
 4.       └─base::tryCatch(...)
 5.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 6.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 7.             └─value[[3L]](cond)
── Error ('test-local.R:7:5'): createLocalBasiliskEnv obtains the correct version of the packages ──
Error: Error creating conda environment '/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/basilisk.Rcheck/tests/testthat/install-test-client/locality/1.19.3' [exit code 1]
Backtrace:
    ▆
 1. └─basilisk::createLocalBasiliskEnv(...) at test-local.R:7:5
 2.   └─basilisk::setupBasiliskEnv(envpath, ...)
 3.     └─reticulate::conda_install(...)
 4.       └─reticulate::conda_create(...)
 5.         └─reticulate:::stopf(fmt, envname, result, call. = FALSE)
── Error ('test-start.R:15:1'): (code run outside of `test_that()`) ────────────
Error: Error creating conda environment '/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/basilisk.Rcheck/tests/testthat/install-test-client/my_package_A' [exit code 1]
Backtrace:
    ▆
 1. └─basilisk::setupBasiliskEnv(tA, c(test.pandas, test.pandas.deps)) at test-start.R:15:1
 2.   └─reticulate::conda_install(...)
 3.     └─reticulate::conda_create(...)
 4.       └─reticulate:::stopf(fmt, envname, result, call. = FALSE)

[ FAIL 9 | WARN 4 | SKIP 0 | PASS 14 ]
Error: Test failures
Execution halted