Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-25 17:44 -0400 (Tue, 25 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4760
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4494
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4508
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
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 2295/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
zellkonverter 1.14.1  (landing page)
Luke Zappia
Snapshot Date: 2024-06-23 14:00 -0400 (Sun, 23 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    OK    OK  YES
palomino3Windows Server 2022 Datacenter / x64  OK    OK    TIMEOUT    OK  
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    TIMEOUT    OK  
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  YES

CHECK results for zellkonverter on kjohnson1

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.
- 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:zellkonverter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings zellkonverter_1.14.1.tar.gz
StartedAt: 2024-06-25 13:18:03 -0400 (Tue, 25 Jun 2024)
EndedAt: 2024-06-25 13:42:17 -0400 (Tue, 25 Jun 2024)
EllapsedTime: 1454.0 seconds
RetCode: 0
Status:   OK  
CheckDir: zellkonverter.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:zellkonverter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings zellkonverter_1.14.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/zellkonverter.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 ‘/Users/biocbuild/bbs-3.19-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 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 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 28.706  3.055  32.793
writeH5AD           4.671  0.565   5.277
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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

Installation output

zellkonverter.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL zellkonverter
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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 
  0.219   0.062   0.271

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: aarch64-apple-darwin20

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: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.2

  added / updated specs:
    - python=3.11.5


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    setuptools-70.1.1          |     pyhd8ed1ab_0         485 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         485 KB

The following NEW packages will be INSTALLED:

  bzip2              conda-forge/osx-arm64::bzip2-1.0.8-h93a5062_5
  ca-certificates    conda-forge/osx-arm64::ca-certificates-2024.6.2-hf0a4a13_0
  libexpat           conda-forge/osx-arm64::libexpat-2.6.2-hebf3989_0
  libffi             conda-forge/osx-arm64::libffi-3.4.2-h3422bc3_5
  libsqlite          conda-forge/osx-arm64::libsqlite-3.46.0-hfb93653_0
  libzlib            conda-forge/osx-arm64::libzlib-1.3.1-hfb2fe0b_1
  ncurses            conda-forge/osx-arm64::ncurses-6.5-hb89a1cb_0
  openssl            conda-forge/osx-arm64::openssl-3.3.1-hfb2fe0b_0
  pip                conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
  python             conda-forge/osx-arm64::python-3.11.5-h47c9636_0_cpython
  readline           conda-forge/osx-arm64::readline-8.2-h92ec313_1
  setuptools         conda-forge/noarch::setuptools-70.1.1-pyhd8ed1ab_0
  tk                 conda-forge/osx-arm64::tk-8.6.13-h5083fa2_1
  tzdata             conda-forge/noarch::tzdata-2024a-h0c530f3_0
  wheel              conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
  xz                 conda-forge/osx-arm64::xz-5.2.6-h57fd34a_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: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.2

  added / updated specs:
    - anndata=0.10.2
    - h5py=3.10.0
    - hdf5=1.14.2
    - natsort=8.4.0
    - numpy=1.26.0
    - packaging=23.2
    - pandas=2.1.1
    - python[version='3.11.5.*,3.11.5.*']
    - scipy=1.11.3


The following NEW packages will be INSTALLED:

  anndata            conda-forge/noarch::anndata-0.10.2-pyhd8ed1ab_0
  array-api-compat   conda-forge/noarch::array-api-compat-1.7.1-pyhd8ed1ab_0
  c-ares             conda-forge/osx-arm64::c-ares-1.28.1-h93a5062_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/osx-arm64::h5py-3.10.0-nompi_py311h393cb7e_100
  hdf5               conda-forge/osx-arm64::hdf5-1.14.2-nompi_h3aba7b3_100
  krb5               conda-forge/osx-arm64::krb5-1.21.2-h92f50d5_0
  libaec             conda-forge/osx-arm64::libaec-1.1.3-hebf3989_0
  libblas            conda-forge/osx-arm64::libblas-3.9.0-20_osxarm64_openblas
  libcblas           conda-forge/osx-arm64::libcblas-3.9.0-20_osxarm64_openblas
  libcurl            conda-forge/osx-arm64::libcurl-8.8.0-h7b6f9a7_0
  libcxx             conda-forge/osx-arm64::libcxx-17.0.6-he7857fb_1
  libedit            conda-forge/osx-arm64::libedit-3.1.20191231-hc8eb9b7_2
  libev              conda-forge/osx-arm64::libev-4.33-h93a5062_2
  libgfortran        conda-forge/osx-arm64::libgfortran-5.0.0-13_2_0_hd922786_3
  libgfortran5       conda-forge/osx-arm64::libgfortran5-13.2.0-hf226fd6_3
  liblapack          conda-forge/osx-arm64::liblapack-3.9.0-20_osxarm64_openblas
  libnghttp2         conda-forge/osx-arm64::libnghttp2-1.58.0-ha4dd798_1
  libopenblas        conda-forge/osx-arm64::libopenblas-0.3.25-openmp_h6c19121_0
  libssh2            conda-forge/osx-arm64::libssh2-1.11.0-h7a5bd25_0
  llvm-openmp        conda-forge/osx-arm64::llvm-openmp-18.1.8-hde57baf_0
  natsort            conda-forge/noarch::natsort-8.4.0-pyhd8ed1ab_0
  numpy              conda-forge/osx-arm64::numpy-1.26.0-py311hb8f3215_0
  packaging          conda-forge/noarch::packaging-23.2-pyhd8ed1ab_0
  pandas             conda-forge/osx-arm64::pandas-2.1.1-py311h9e438b8_1
  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/osx-arm64::python_abi-3.11-4_cp311
  pytz               conda-forge/noarch::pytz-2024.1-pyhd8ed1ab_0
  scipy              conda-forge/osx-arm64::scipy-1.11.3-py311h93d07a4_1
  six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
  zstd               conda-forge/osx-arm64::zstd-1.5.6-hb46c0d2_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
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: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.9.2

  added / updated specs:
    - python=3.11.5


The following NEW packages will be INSTALLED:

  bzip2              conda-forge/osx-arm64::bzip2-1.0.8-h93a5062_5
  ca-certificates    conda-forge/osx-arm64::ca-certificates-2024.6.2-hf0a4a13_0
  libexpat           conda-forge/osx-arm64::libexpat-2.6.2-hebf3989_0
  libffi             conda-forge/osx-arm64::libffi-3.4.2-h3422bc3_5
  libsqlite          conda-forge/osx-arm64::libsqlite-3.46.0-hfb93653_0
  libzlib            conda-forge/osx-arm64::libzlib-1.3.1-hfb2fe0b_1
  ncurses            conda-forge/osx-arm64::ncurses-6.5-hb89a1cb_0
  openssl            conda-forge/osx-arm64::openssl-3.3.1-hfb2fe0b_0
  pip                conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
  python             conda-forge/osx-arm64::python-3.11.5-h47c9636_0_cpython
  readline           conda-forge/osx-arm64::readline-8.2-h92ec313_1
  setuptools         conda-forge/noarch::setuptools-70.1.1-pyhd8ed1ab_0
  tk                 conda-forge/osx-arm64::tk-8.6.13-h5083fa2_1
  tzdata             conda-forge/noarch::tzdata-2024a-h0c530f3_0
  wheel              conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
  xz                 conda-forge/osx-arm64::xz-5.2.6-h57fd34a_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: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.9.2

  added / updated specs:
    - anndata=0.9.2
    - h5py=3.9.0
    - hdf5=1.14.2
    - natsort=8.4.0
    - numpy=1.26.0
    - packaging=23.2
    - pandas=2.1.1
    - python[version='3.11.5.*,3.11.5.*']
    - scipy=1.11.3


The following NEW packages will be INSTALLED:

  anndata            conda-forge/noarch::anndata-0.9.2-pyhd8ed1ab_0
  c-ares             conda-forge/osx-arm64::c-ares-1.28.1-h93a5062_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
  h5py               conda-forge/osx-arm64::h5py-3.9.0-nompi_py311h4794d1a_103
  hdf5               conda-forge/osx-arm64::hdf5-1.14.2-nompi_h3aba7b3_100
  krb5               conda-forge/osx-arm64::krb5-1.21.2-h92f50d5_0
  libaec             conda-forge/osx-arm64::libaec-1.1.3-hebf3989_0
  libblas            conda-forge/osx-arm64::libblas-3.9.0-20_osxarm64_openblas
  libcblas           conda-forge/osx-arm64::libcblas-3.9.0-20_osxarm64_openblas
  libcurl            conda-forge/osx-arm64::libcurl-8.8.0-h7b6f9a7_0
  libcxx             conda-forge/osx-arm64::libcxx-17.0.6-he7857fb_1
  libedit            conda-forge/osx-arm64::libedit-3.1.20191231-hc8eb9b7_2
  libev              conda-forge/osx-arm64::libev-4.33-h93a5062_2
  libgfortran        conda-forge/osx-arm64::libgfortran-5.0.0-13_2_0_hd922786_3
  libgfortran5       conda-forge/osx-arm64::libgfortran5-13.2.0-hf226fd6_3
  liblapack          conda-forge/osx-arm64::liblapack-3.9.0-20_osxarm64_openblas
  libnghttp2         conda-forge/osx-arm64::libnghttp2-1.58.0-ha4dd798_1
  libopenblas        conda-forge/osx-arm64::libopenblas-0.3.25-openmp_h6c19121_0
  libssh2            conda-forge/osx-arm64::libssh2-1.11.0-h7a5bd25_0
  llvm-openmp        conda-forge/osx-arm64::llvm-openmp-18.1.8-hde57baf_0
  natsort            conda-forge/noarch::natsort-8.4.0-pyhd8ed1ab_0
  numpy              conda-forge/osx-arm64::numpy-1.26.0-py311hb8f3215_0
  packaging          conda-forge/noarch::packaging-23.2-pyhd8ed1ab_0
  pandas             conda-forge/osx-arm64::pandas-2.1.1-py311h9e438b8_1
  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/osx-arm64::python_abi-3.11-4_cp311
  pytz               conda-forge/noarch::pytz-2024.1-pyhd8ed1ab_0
  scipy              conda-forge/osx-arm64::scipy-1.11.3-py311h93d07a4_1
  six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
  zstd               conda-forge/osx-arm64::zstd-1.5.6-hb46c0d2_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
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: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.8.0

  added / updated specs:
    - python=3.8.13


The following NEW packages will be INSTALLED:

  bzip2              conda-forge/osx-arm64::bzip2-1.0.8-h93a5062_5
  ca-certificates    conda-forge/osx-arm64::ca-certificates-2024.6.2-hf0a4a13_0
  libffi             conda-forge/osx-arm64::libffi-3.4.2-h3422bc3_5
  libsqlite          conda-forge/osx-arm64::libsqlite-3.46.0-hfb93653_0
  libzlib            conda-forge/osx-arm64::libzlib-1.3.1-hfb2fe0b_1
  ncurses            conda-forge/osx-arm64::ncurses-6.5-hb89a1cb_0
  openssl            conda-forge/osx-arm64::openssl-3.3.1-hfb2fe0b_0
  pip                conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
  python             conda-forge/osx-arm64::python-3.8.13-hd3575e6_0_cpython
  readline           conda-forge/osx-arm64::readline-8.2-h92ec313_1
  setuptools         conda-forge/noarch::setuptools-70.1.1-pyhd8ed1ab_0
  sqlite             conda-forge/osx-arm64::sqlite-3.46.0-h5838104_0
  tk                 conda-forge/osx-arm64::tk-8.6.13-h5083fa2_1
  wheel              conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
  xz                 conda-forge/osx-arm64::xz-5.2.6-h57fd34a_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: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.8.0

  added / updated specs:
    - anndata=0.8.0
    - h5py=3.6.0
    - hdf5=1.12.1
    - natsort=8.1.0
    - numpy=1.22.3
    - packaging=21.3
    - pandas=1.4.2
    - python[version='3.8.13.*,3.8.13.*']
    - scipy=1.7.3
    - sqlite=3.38.2


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    importlib-metadata-7.2.1   |     pyha770c72_0          27 KB  conda-forge
    importlib_metadata-7.2.1   |       hd8ed1ab_0           9 KB  conda-forge
    ------------------------------------------------------------
                                           Total:          36 KB

The following NEW packages will be INSTALLED:

  anndata            conda-forge/noarch::anndata-0.8.0-pyhd8ed1ab_1
  c-ares             conda-forge/osx-arm64::c-ares-1.28.1-h93a5062_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
  h5py               conda-forge/osx-arm64::h5py-3.6.0-nompi_py38hacf61ce_100
  hdf5               conda-forge/osx-arm64::hdf5-1.12.1-nompi_hd9dbc9e_104
  importlib-metadata conda-forge/noarch::importlib-metadata-7.2.1-pyha770c72_0
  importlib_metadata conda-forge/noarch::importlib_metadata-7.2.1-hd8ed1ab_0
  krb5               conda-forge/osx-arm64::krb5-1.21.2-h92f50d5_0
  libblas            conda-forge/osx-arm64::libblas-3.9.0-20_osxarm64_openblas
  libcblas           conda-forge/osx-arm64::libcblas-3.9.0-20_osxarm64_openblas
  libcurl            conda-forge/osx-arm64::libcurl-8.8.0-h7b6f9a7_0
  libcxx             conda-forge/osx-arm64::libcxx-17.0.6-he7857fb_1
  libedit            conda-forge/osx-arm64::libedit-3.1.20191231-hc8eb9b7_2
  libev              conda-forge/osx-arm64::libev-4.33-h93a5062_2
  libgfortran        conda-forge/osx-arm64::libgfortran-5.0.0-13_2_0_hd922786_3
  libgfortran5       conda-forge/osx-arm64::libgfortran5-13.2.0-hf226fd6_3
  liblapack          conda-forge/osx-arm64::liblapack-3.9.0-20_osxarm64_openblas
  libnghttp2         conda-forge/osx-arm64::libnghttp2-1.58.0-ha4dd798_1
  libopenblas        conda-forge/osx-arm64::libopenblas-0.3.25-openmp_h6c19121_0
  libssh2            conda-forge/osx-arm64::libssh2-1.11.0-h7a5bd25_0
  llvm-openmp        conda-forge/osx-arm64::llvm-openmp-18.1.8-hde57baf_0
  natsort            conda-forge/noarch::natsort-8.1.0-pyhd8ed1ab_0
  numpy              conda-forge/osx-arm64::numpy-1.22.3-py38h4084d66_2
  packaging          conda-forge/noarch::packaging-21.3-pyhd8ed1ab_0
  pandas             conda-forge/osx-arm64::pandas-1.4.2-py38h6724fcd_2
  pyparsing          conda-forge/noarch::pyparsing-3.1.2-pyhd8ed1ab_0
  python-dateutil    conda-forge/noarch::python-dateutil-2.9.0-pyhd8ed1ab_0
  python_abi         conda-forge/osx-arm64::python_abi-3.8-4_cp38
  pytz               conda-forge/noarch::pytz-2024.1-pyhd8ed1ab_0
  scipy              conda-forge/osx-arm64::scipy-1.7.3-py38h7b4f323_1
  six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
  typing_extensions  conda-forge/noarch::typing_extensions-4.12.2-pyha770c72_0
  zipp               conda-forge/noarch::zipp-3.19.2-pyhd8ed1ab_0
  zlib               conda-forge/osx-arm64::zlib-1.2.13-hfb2fe0b_6
  zstd               conda-forge/osx-arm64::zstd-1.5.6-hb46c0d2_0

The following packages will be DOWNGRADED:

  libzlib                                  1.3.1-hfb2fe0b_1 --> 1.2.13-hfb2fe0b_6
  sqlite                                  3.46.0-h5838104_0 --> 3.38.2-h7e3ccbd_0



Downloading and Extracting Packages

importlib-metadata-7 | 27 KB     |            |   0% 
importlib-metadata-7 | 27 KB     | ########## | 100% 
importlib-metadata-7 | 27 KB     | ########## | 100% 

importlib_metadata-7 | 9 KB      |            |   0% 
importlib_metadata-7 | 9 KB      | ########## | 100% 
importlib_metadata-7 | 9 KB      | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/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(
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/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(
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.2/lib/python3.11/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/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(
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/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(
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/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(
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/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(
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/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(
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/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(
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/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(
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/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(
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/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(
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/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(
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/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(
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/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(
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/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(
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/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 26 | SKIP 5 | PASS 143 ]

══ Skipped tests (5) ═══════════════════════════════════════════════════════════
• On CRAN (3): 'test-read.R:178:5', 'test-zzz-anndata.R:6:5',
  'test-zzz-anndata.R:54:5'
• On Mac aarch64 (2): 'test-read.R:60:5', 'test-write.R:133:5'

[ FAIL 0 | WARN 26 | SKIP 5 | PASS 143 ]
> 
> proc.time()
    user   system  elapsed 
 907.713   92.105 1235.718

Example timings

zellkonverter.Rcheck/zellkonverter-Ex.timings

nameusersystemelapsed
AnnData-Conversion28.706 3.05532.793
AnnData-Environment0.0050.0030.008
readH5AD1.0450.0751.128
setZellkonverterVerbose0.0000.0000.001
writeH5AD4.6710.5655.277