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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:basilisk.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings basilisk_1.13.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/basilisk.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘basilisk/DESCRIPTION’ ... OK
* this is package ‘basilisk’ version ‘1.13.3’
* 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 ‘/home/biocbuild/bbs-3.18-bioc/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 R 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 ... WARNING
'library' or 'require' call not declared from: ‘reticulate’
'library' or 'require' call to ‘reticulate’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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 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
> 
> ## Don't show: 
> basilisk.utils::installConda()
[1] FALSE
> ## 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=1.4.3'))
+ }
Warning in check_forbidden_install("Python packages") :
  cannot install Python packages during R CMD check
+ '/home/biocbuild/.cache/R/basilisk/1.13.3/0/bin/conda' 'create' '--yes' '--prefix' '/home/biocbuild/tmp/RtmpRWYezO/my_package_A' 'python=3.10.12' '--quiet' '-c' 'conda-forge'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/biocbuild/tmp/RtmpRWYezO/my_package_A

  added / updated specs:
    - python=3.10.12


The following NEW packages will be INSTALLED:

  _openmp_mutex      conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu 
  bzip2              conda-forge/linux-aarch64::bzip2-1.0.8-hf897c2e_4 
  ca-certificates    conda-forge/linux-aarch64::ca-certificates-2023.7.22-hcefe29a_0 
  ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.40-h2d8c526_0 
  libffi             conda-forge/linux-aarch64::libffi-3.4.2-h3557bc0_5 
  libgcc-ng          conda-forge/linux-aarch64::libgcc-ng-13.1.0-h2b4548d_0 
  libgomp            conda-forge/linux-aarch64::libgomp-13.1.0-h2b4548d_0 
  libnsl             conda-forge/linux-aarch64::libnsl-2.0.0-hf897c2e_0 
  libsqlite          conda-forge/linux-aarch64::libsqlite-3.42.0-h194ca79_0 
  libuuid            conda-forge/linux-aarch64::libuuid-2.38.1-hb4cce97_0 
  libzlib            conda-forge/linux-aarch64::libzlib-1.2.13-h31becfc_5 
  ncurses            conda-forge/linux-aarch64::ncurses-6.4-h2e1726e_0 
  openssl            conda-forge/linux-aarch64::openssl-3.1.2-h31becfc_0 
  pip                conda-forge/noarch::pip-23.2.1-pyhd8ed1ab_0 
  python             conda-forge/linux-aarch64::python-3.10.12-hbbe8eec_0_cpython 
  readline           conda-forge/linux-aarch64::readline-8.2-h8fc344f_1 
  setuptools         conda-forge/noarch::setuptools-68.0.0-pyhd8ed1ab_0 
  tk                 conda-forge/linux-aarch64::tk-8.6.12-hd8af866_0 
  tzdata             conda-forge/noarch::tzdata-2023c-h71feb2d_0 
  wheel              conda-forge/noarch::wheel-0.41.1-pyhd8ed1ab_0 
  xz                 conda-forge/linux-aarch64::xz-5.2.6-h9cdd2b7_0 


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ '/home/biocbuild/.cache/R/basilisk/1.13.3/0/bin/conda' 'install' '--yes' '--prefix' '/home/biocbuild/tmp/RtmpRWYezO/my_package_A' 'python=3.10.12'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 23.5.0
  latest version: 23.7.2

Please update conda by running

    $ conda update -n base -c defaults conda

Or to minimize the number of packages updated during conda update use

     conda install conda=23.7.2



## Package Plan ##

  environment location: /home/biocbuild/tmp/RtmpRWYezO/my_package_A

  added / updated specs:
    - python=3.10.12


The following packages will be SUPERSEDED by a higher-priority channel:

  ca-certificates    conda-forge::ca-certificates-2023.7.2~ --> pkgs/main::ca-certificates-2023.05.30-hd43f75c_0 



Downloading and Extracting Packages

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ '/home/biocbuild/.cache/R/basilisk/1.13.3/0/bin/conda' 'install' '--yes' '--prefix' '/home/biocbuild/tmp/RtmpRWYezO/my_package_A' '-c' 'conda-forge' 'python=3.10.12' 'pandas=1.4.3'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... Error: one or more Python packages failed to install [error code 9]
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:
   2.   └─basilisk::setupBasiliskEnv(...)
   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: one or more Python packages failed to install [error code 9]
  Backtrace:
      ▆
   1. └─basilisk::setupBasiliskEnv(tA, c(test.pandas, test.pandas.deps)) at test-start.R:15:0
   2.   └─reticulate::conda_install(...)
   3.     └─reticulate:::stopf(fmt, result)
  
  [ FAIL 3 | WARN 0 | SKIP 1 | PASS 31 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘motivation.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/basilisk.Rcheck/00check.log’
for details.