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This page was generated on 2023-05-31 05:44:46 -0000 (Wed, 31 May 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4219
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for zellkonverter on kunpeng1


To the developers/maintainers of the zellkonverter package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/zellkonverter.git to reflect on this report. See Troubleshooting Build Report for more information.

- Use the following Renviron settings to reproduce errors and warnings.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 2192/2197HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
zellkonverter 1.11.1  (landing page)
Luke Zappia
Snapshot Date: 2023-05-29 10:19:22 -0000 (Mon, 29 May 2023)
git_url: https://git.bioconductor.org/packages/zellkonverter
git_branch: devel
git_last_commit: b56718d
git_last_commit_date: 2023-05-23 09:39:20 -0000 (Tue, 23 May 2023)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    ERROR  

Summary

Package: zellkonverter
Version: 1.11.1
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:zellkonverter.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings zellkonverter_1.11.1.tar.gz
StartedAt: 2023-05-30 22:39:39 -0000 (Tue, 30 May 2023)
EndedAt: 2023-05-30 22:54:21 -0000 (Tue, 30 May 2023)
EllapsedTime: 882.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: zellkonverter.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:zellkonverter.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings zellkonverter_1.11.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/zellkonverter.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘zellkonverter/DESCRIPTION’ ... OK
* this is package ‘zellkonverter’ version ‘1.11.1’
* 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 38.344  5.024  53.284
writeH5AD          15.491  2.380  25.280
* 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.

Installation output

zellkonverter.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL zellkonverter
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/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)

Tests output

zellkonverter.Rcheck/tests/spelling.Rout


R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
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 
  0.195   0.034   0.213

zellkonverter.Rcheck/tests/testthat.Rout.fail


R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
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... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/biocbuild/.cache/R/basilisk/1.13.0/zellkonverter/1.11.1/zellkonverterAnnDataEnv-0.7.6

  added / updated specs:
    - python=3.7.10


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    openssl-3.1.1              |       h31becfc_0         2.5 MB  conda-forge
    ------------------------------------------------------------
                                           Total:         2.5 MB

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-2023.5.7-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-12.2.0-h607ecd0_19
  libgomp            conda-forge/linux-aarch64::libgomp-12.2.0-h607ecd0_19
  libnsl             conda-forge/linux-aarch64::libnsl-2.0.0-hf897c2e_0
  libsqlite          conda-forge/linux-aarch64::libsqlite-3.42.0-h194ca79_0
  libstdcxx-ng       conda-forge/linux-aarch64::libstdcxx-ng-12.2.0-hc13a102_19
  libzlib            conda-forge/linux-aarch64::libzlib-1.2.13-h4e544f5_4
  ncurses            conda-forge/linux-aarch64::ncurses-6.3-headf329_1
  openssl            conda-forge/linux-aarch64::openssl-3.1.1-h31becfc_0
  pip                conda-forge/noarch::pip-23.1.2-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-67.7.2-pyhd8ed1ab_0
  sqlite             conda-forge/linux-aarch64::sqlite-3.42.0-h3b3482f_0
  tk                 conda-forge/linux-aarch64::tk-8.6.12-hd8af866_0
  wheel              conda-forge/noarch::wheel-0.40.0-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

## Package Plan ##

  environment location: /home/biocbuild/.cache/R/basilisk/1.13.0/zellkonverter/1.11.1/zellkonverterAnnDataEnv-0.7.6

  added / updated specs:
    - python=3.7.10


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

  ca-certificates    conda-forge::ca-certificates-2023.5.7~ --> pkgs/main::ca-certificates-2023.01.10-hd43f75c_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 23.5.0

Please update conda by running

    $ conda update -n base -c defaults conda


Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed with initial 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... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/biocbuild/.cache/R/basilisk/1.13.0/zellkonverter/1.11.1/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-2023.5.7-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-12.2.0-h607ecd0_19
  libgomp            conda-forge/linux-aarch64::libgomp-12.2.0-h607ecd0_19
  libnsl             conda-forge/linux-aarch64::libnsl-2.0.0-hf897c2e_0
  libsqlite          conda-forge/linux-aarch64::libsqlite-3.42.0-h194ca79_0
  libstdcxx-ng       conda-forge/linux-aarch64::libstdcxx-ng-12.2.0-hc13a102_19
  libzlib            conda-forge/linux-aarch64::libzlib-1.2.13-h4e544f5_4
  ncurses            conda-forge/linux-aarch64::ncurses-6.3-headf329_1
  openssl            conda-forge/linux-aarch64::openssl-3.1.1-h31becfc_0
  pip                conda-forge/noarch::pip-23.1.2-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-67.7.2-pyhd8ed1ab_0
  sqlite             conda-forge/linux-aarch64::sqlite-3.42.0-h3b3482f_0
  tk                 conda-forge/linux-aarch64::tk-8.6.12-hd8af866_0
  wheel              conda-forge/noarch::wheel-0.40.0-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

## Package Plan ##

  environment location: /home/biocbuild/.cache/R/basilisk/1.13.0/zellkonverter/1.11.1/zellkonverterAnnDataEnv-0.7.6

  added / updated specs:
    - python=3.7.10


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

  ca-certificates    conda-forge::ca-certificates-2023.5.7~ --> pkgs/main::ca-certificates-2023.01.10-hd43f75c_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 23.5.0

Please update conda by running

    $ conda update -n base -c defaults conda


Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed with initial 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 ═══════════════════════════════════════════════════════════════
• On CRAN (3)

══ 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

Example timings

zellkonverter.Rcheck/zellkonverter-Ex.timings

nameusersystemelapsed
AnnData-Conversion38.344 5.02453.284
AnnData-Environment0.0220.0000.022
readH5AD1.7710.1161.895
setZellkonverterVerbose0.0180.0000.018
writeH5AD15.491 2.38025.280