##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:zellkonverter.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings zellkonverter_1.11.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/zellkonverter.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 ‘zellkonverter/DESCRIPTION’ ... OK
* this is package ‘zellkonverter’ version ‘1.11.2’
* 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 ‘zellkonverter’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/biocbuild/bbs-3.18-bioc/meat/zellkonverter.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 ... 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 line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
AnnData-Conversion 30.352  2.926  43.748
writeH5AD          10.855  0.855  19.411
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Error ('test-write.R:40:5'): writeH5AD works as expected with version 0.7.6 ──
  Error: one or more Python packages failed to install [error code 1]
  Backtrace:
      ▆
   1. └─zellkonverter::writeH5AD(sce, temp, version = "0.7.6") at test-write.R:40:4
   2.   └─basilisk::basiliskRun(...)
   3.     └─basilisk::basiliskStart(env, fork = fork, shared = shared, testload = testload)
   4.       └─basilisk::obtainEnvironmentPath(env)
   5.         └─basilisk::setupBasiliskEnv(...)
   6.           └─reticulate::conda_install(...)
   7.             └─reticulate:::stopf(fmt, result)
  
  [ FAIL 2 | WARN 24 | SKIP 3 | PASS 107 ]
  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 ...
  ‘zellkonverter.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/zellkonverter.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL zellkonverter
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘zellkonverter’ ...
** using non-staged installation via StagedInstall field
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (zellkonverter)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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.

> if (requireNamespace("spelling", quietly = TRUE)) {
+     spelling::spell_check_test(
+         vignettes = TRUE,
+         error = FALSE,
+         skip_on_cran = TRUE
+     )
+ }
NULL
> 
> proc.time()
   user  system elapsed 
  0.206   0.021   0.215 

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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(zellkonverter)
Registered S3 methods overwritten by 'zellkonverter':
  method                                             from      
  py_to_r.numpy.ndarray                              reticulate
  py_to_r.pandas.core.arrays.categorical.Categorical reticulate
> 
> test_check("zellkonverter")
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... unsuccessful attempt using repodata from current_repodata.json, retrying with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/biocbuild/.cache/R/basilisk/1.13.3/zellkonverter/1.11.2/zellkonverterAnnDataEnv-0.7.6

  added / updated specs:
    - python=3.7.10


The following NEW packages will be INSTALLED:

  _openmp_mutex      conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu 
  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-13.2.0-hf8544c7_2 
  libgomp            conda-forge/linux-aarch64::libgomp-13.2.0-hf8544c7_2 
  libnsl             conda-forge/linux-aarch64::libnsl-2.0.0-h31becfc_1 
  libsqlite          conda-forge/linux-aarch64::libsqlite-3.43.0-h194ca79_0 
  libstdcxx-ng       conda-forge/linux-aarch64::libstdcxx-ng-13.2.0-h9a76618_2 
  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-3.1.3-h31becfc_0 
  pip                conda-forge/noarch::pip-23.2.1-pyhd8ed1ab_0 
  python             conda-forge/linux-aarch64::python-3.7.10-h47f6e27_104_cpython 
  readline           conda-forge/linux-aarch64::readline-8.2-h8fc344f_1 
  setuptools         conda-forge/noarch::setuptools-68.2.2-pyhd8ed1ab_0 
  sqlite             conda-forge/linux-aarch64::sqlite-3.43.0-h3b3482f_0 
  tk                 conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0 
  wheel              conda-forge/noarch::wheel-0.41.2-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
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: 23.7.4

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=23.7.4



## Package Plan ##

  environment location: /home/biocbuild/.cache/R/basilisk/1.13.3/zellkonverter/1.11.2/zellkonverterAnnDataEnv-0.7.6

  added / updated specs:
    - python=3.7.10


The following packages will be UPDATED:

  ca-certificates    conda-forge::ca-certificates-2023.7.2~ --> pkgs/main::ca-certificates-2023.08.22-hd43f75c_0 

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

  openssl             conda-forge::openssl-3.1.3-h31becfc_0 --> pkgs/main::openssl-3.0.11-h2f4d8fa_2 



Downloading and Extracting Packages

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
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... unsuccessful initial attempt using frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  - anndata=0.7.6

Current channels:

  - https://conda.anaconda.org/conda-forge/linux-aarch64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://repo.anaconda.com/pkgs/main/linux-aarch64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/linux-aarch64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.


Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... unsuccessful attempt using repodata from current_repodata.json, retrying with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/biocbuild/.cache/R/basilisk/1.13.3/zellkonverter/1.11.2/zellkonverterAnnDataEnv-0.7.6

  added / updated specs:
    - python=3.7.10


The following NEW packages will be INSTALLED:

  _openmp_mutex      conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu 
  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-13.2.0-hf8544c7_2 
  libgomp            conda-forge/linux-aarch64::libgomp-13.2.0-hf8544c7_2 
  libnsl             conda-forge/linux-aarch64::libnsl-2.0.0-h31becfc_1 
  libsqlite          conda-forge/linux-aarch64::libsqlite-3.43.0-h194ca79_0 
  libstdcxx-ng       conda-forge/linux-aarch64::libstdcxx-ng-13.2.0-h9a76618_2 
  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-3.1.3-h31becfc_0 
  pip                conda-forge/noarch::pip-23.2.1-pyhd8ed1ab_0 
  python             conda-forge/linux-aarch64::python-3.7.10-h47f6e27_104_cpython 
  readline           conda-forge/linux-aarch64::readline-8.2-h8fc344f_1 
  setuptools         conda-forge/noarch::setuptools-68.2.2-pyhd8ed1ab_0 
  sqlite             conda-forge/linux-aarch64::sqlite-3.43.0-h3b3482f_0 
  tk                 conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0 
  wheel              conda-forge/noarch::wheel-0.41.2-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
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: 23.7.4

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=23.7.4



## Package Plan ##

  environment location: /home/biocbuild/.cache/R/basilisk/1.13.3/zellkonverter/1.11.2/zellkonverterAnnDataEnv-0.7.6

  added / updated specs:
    - python=3.7.10


The following packages will be UPDATED:

  ca-certificates    conda-forge::ca-certificates-2023.7.2~ --> pkgs/main::ca-certificates-2023.08.22-hd43f75c_0 

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

  openssl             conda-forge::openssl-3.1.3-h31becfc_0 --> pkgs/main::openssl-3.0.11-h2f4d8fa_2 



Downloading and Extracting Packages

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
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... unsuccessful initial attempt using frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  - anndata=0.7.6

Current channels:

  - https://conda.anaconda.org/conda-forge/linux-aarch64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://repo.anaconda.com/pkgs/main/linux-aarch64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/linux-aarch64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.


[ FAIL 2 | WARN 24 | SKIP 3 | PASS 107 ]

══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On CRAN (3): 'test-read.R:131:5', 'test-zzz-anndata.R:6:5',
  'test-zzz-anndata.R:55:5'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-read.R:15:5'): Reading H5AD works with version 0.7.6 ───────────
Error: one or more Python packages failed to install [error code 1]
Backtrace:
    ▆
 1. └─zellkonverter::readH5AD(file, version = "0.7.6") at test-read.R:15:4
 2.   └─basilisk::basiliskRun(...)
 3.     └─basilisk::basiliskStart(env, fork = fork, shared = shared, testload = testload)
 4.       └─basilisk::obtainEnvironmentPath(env)
 5.         └─basilisk::setupBasiliskEnv(...)
 6.           └─reticulate::conda_install(...)
 7.             └─reticulate:::stopf(fmt, result)
── Error ('test-write.R:40:5'): writeH5AD works as expected with version 0.7.6 ──
Error: one or more Python packages failed to install [error code 1]
Backtrace:
    ▆
 1. └─zellkonverter::writeH5AD(sce, temp, version = "0.7.6") at test-write.R:40:4
 2.   └─basilisk::basiliskRun(...)
 3.     └─basilisk::basiliskStart(env, fork = fork, shared = shared, testload = testload)
 4.       └─basilisk::obtainEnvironmentPath(env)
 5.         └─basilisk::setupBasiliskEnv(...)
 6.           └─reticulate::conda_install(...)
 7.             └─reticulate:::stopf(fmt, result)

[ FAIL 2 | WARN 24 | SKIP 3 | PASS 107 ]
Error: Test failures
Execution halted