Back to Long Tests report for BioC 3.19

This page was generated on 2024-06-22 23:55 -0400 (Sat, 22 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4506
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

Package 33/33HostnameOS / ArchCHECK
zellkonverter 1.14.1  (landing page)
Luke Zappia
Snapshot Date: 2024-06-22 09:55 -0400 (Sat, 22 Jun 2024)
git_url: https://git.bioconductor.org/packages/zellkonverter
git_branch: RELEASE_3_19
git_last_commit: c90c58a
git_last_commit_date: 2024-06-21 04:52:52 -0400 (Fri, 21 Jun 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK  
palomino3Windows Server 2022 Datacenter / x64  ERROR  
merida1macOS 12.7.4 Monterey / x86_64  OK  

CHECK results for zellkonverter on nebbiolo1

To the developers/maintainers of the zellkonverter package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: zellkonverter
Version: 1.14.1
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no zellkonverter_1.14.1.tar.gz
StartedAt: 2024-06-22 16:31:42 -0400 (Sat, 22 Jun 2024)
EndedAt: 2024-06-22 16:56:17 -0400 (Sat, 22 Jun 2024)
EllapsedTime: 1475.1 seconds
RetCode: 0
Status:   OK  
CheckDir: zellkonverter.Rcheck
Warnings: 0

Tests output

zellkonverter.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 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(zellkonverter)
Registered S3 method overwritten by 'zellkonverter':
  method                                             from      
  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: /var/cache/basilisk/1.17.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.6

  added / updated specs:
    - python=3.12.2


The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
  bzip2              conda-forge/linux-64::bzip2-1.0.8-hd590300_5
  ca-certificates    conda-forge/linux-64::ca-certificates-2024.6.2-hbcca054_0
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.40-hf3520f5_7
  libexpat           conda-forge/linux-64::libexpat-2.6.2-h59595ed_0
  libffi             conda-forge/linux-64::libffi-3.4.2-h7f98852_5
  libgcc-ng          conda-forge/linux-64::libgcc-ng-13.2.0-h77fa898_11
  libgomp            conda-forge/linux-64::libgomp-13.2.0-h77fa898_11
  libnsl             conda-forge/linux-64::libnsl-2.0.1-hd590300_0
  libsqlite          conda-forge/linux-64::libsqlite-3.46.0-hde9e2c9_0
  libuuid            conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0
  libxcrypt          conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1
  libzlib            conda-forge/linux-64::libzlib-1.3.1-h4ab18f5_1
  ncurses            conda-forge/linux-64::ncurses-6.5-h59595ed_0
  openssl            conda-forge/linux-64::openssl-3.3.1-h4ab18f5_0
  pip                conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
  python             conda-forge/linux-64::python-3.12.2-hab00c5b_0_cpython
  readline           conda-forge/linux-64::readline-8.2-h8228510_1
  setuptools         conda-forge/noarch::setuptools-70.1.0-pyhd8ed1ab_0
  tk                 conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101
  tzdata             conda-forge/noarch::tzdata-2024a-h0c530f3_0
  wheel              conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
  xz                 conda-forge/linux-64::xz-5.2.6-h166bdaf_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: 4.12.0
  latest version: 24.5.0

Please update conda by running

    $ conda update -n base -c defaults conda



# All requested packages already installed.

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... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 24.5.0

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /var/cache/basilisk/1.17.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.6

  added / updated specs:
    - anndata=0.10.6
    - h5py=3.10.0
    - hdf5=1.14.3
    - natsort=8.4.0
    - numpy=1.26.4
    - packaging=24.0
    - pandas=2.2.1
    - python[version='3.12.2.*,3.12.2.*']
    - scipy=1.12.0


The following NEW packages will be INSTALLED:

  anndata            conda-forge/noarch::anndata-0.10.6-pyhd8ed1ab_0
  array-api-compat   conda-forge/noarch::array-api-compat-1.7.1-pyhd8ed1ab_0
  c-ares             conda-forge/linux-64::c-ares-1.28.1-hd590300_0
  cached-property    conda-forge/noarch::cached-property-1.5.2-hd8ed1ab_1
  cached_property    conda-forge/noarch::cached_property-1.5.2-pyha770c72_1
  exceptiongroup     conda-forge/noarch::exceptiongroup-1.2.0-pyhd8ed1ab_2
  h5py               conda-forge/linux-64::h5py-3.10.0-nompi_py312h1b477d7_101
  hdf5               conda-forge/linux-64::hdf5-1.14.3-nompi_hdf9ad27_105
  keyutils           conda-forge/linux-64::keyutils-1.6.1-h166bdaf_0
  krb5               conda-forge/linux-64::krb5-1.21.2-h659d440_0
  libaec             conda-forge/linux-64::libaec-1.1.3-h59595ed_0
  libblas            conda-forge/linux-64::libblas-3.9.0-22_linux64_openblas
  libcblas           conda-forge/linux-64::libcblas-3.9.0-22_linux64_openblas
  libcurl            conda-forge/linux-64::libcurl-8.8.0-hca28451_0
  libedit            conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2
  libev              conda-forge/linux-64::libev-4.33-hd590300_2
  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-13.2.0-h69a702a_11
  libgfortran5       conda-forge/linux-64::libgfortran5-13.2.0-h3d2ce59_11
  liblapack          conda-forge/linux-64::liblapack-3.9.0-22_linux64_openblas
  libnghttp2         conda-forge/linux-64::libnghttp2-1.58.0-h47da74e_1
  libopenblas        conda-forge/linux-64::libopenblas-0.3.27-pthreads_h413a1c8_0
  libssh2            conda-forge/linux-64::libssh2-1.11.0-h0841786_0
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-13.2.0-hc0a3c3a_11
  natsort            conda-forge/noarch::natsort-8.4.0-pyhd8ed1ab_0
  numpy              conda-forge/linux-64::numpy-1.26.4-py312heda63a1_0
  packaging          conda-forge/noarch::packaging-24.0-pyhd8ed1ab_0
  pandas             conda-forge/linux-64::pandas-2.2.1-py312hfb8ada1_0
  python-dateutil    conda-forge/noarch::python-dateutil-2.9.0-pyhd8ed1ab_0
  python-tzdata      conda-forge/noarch::python-tzdata-2024.1-pyhd8ed1ab_0
  python_abi         conda-forge/linux-64::python_abi-3.12-4_cp312
  pytz               conda-forge/noarch::pytz-2024.1-pyhd8ed1ab_0
  scipy              conda-forge/linux-64::scipy-1.12.0-py312heda63a1_2
  six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
  zstd               conda-forge/linux-64::zstd-1.5.6-ha6fb4c9_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
/var/cache/basilisk/1.17.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
/var/cache/basilisk/1.17.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
/var/cache/basilisk/1.17.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
/var/cache/basilisk/1.17.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
/var/cache/basilisk/1.17.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
/var/cache/basilisk/1.17.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
/var/cache/basilisk/1.17.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
/var/cache/basilisk/1.17.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
/var/cache/basilisk/1.17.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:1818: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.
  utils.warn_names_duplicates("obs")
/var/cache/basilisk/1.17.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:1818: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.
  utils.warn_names_duplicates("obs")
/var/cache/basilisk/1.17.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
/var/cache/basilisk/1.17.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:1818: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.
  utils.warn_names_duplicates("obs")
/var/cache/basilisk/1.17.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:1818: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.
  utils.warn_names_duplicates("obs")
/var/cache/basilisk/1.17.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 199 ]
> 
> proc.time()
    user   system  elapsed 
 918.035  325.441 1351.906

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no zellkonverter_1.14.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc-longtests/meat/zellkonverter.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘zellkonverter/DESCRIPTION’ ... OK
* this is package ‘zellkonverter’ version ‘1.14.1’
* 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-3.19-bioc-longtests/meat/zellkonverter.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package 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 ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* 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’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc-longtests/meat/zellkonverter.Rcheck/00check.log’
for details.

Installation output

zellkonverter.Rcheck/00install.out

* 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)