Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGHIJKLMNOPQRSTUVWXY[Z]

This page was generated on 2024-06-11 14:44 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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 1.14.0  (landing page)
Luke Zappia
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/zellkonverter
git_branch: RELEASE_3_19
git_last_commit: 9254458
git_last_commit_date: 2024-04-30 11:26:15 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    ERROR    OK  

CHECK results for zellkonverter on kjohnson3

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: 1.14.0
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_1.14.0.tar.gz
StartedAt: 2024-06-11 09:48:33 -0400 (Tue, 11 Jun 2024)
EndedAt: 2024-06-11 10:02:31 -0400 (Tue, 11 Jun 2024)
EllapsedTime: 837.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: zellkonverter.Rcheck
Warnings: NA

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_1.14.0.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 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘zellkonverter/DESCRIPTION’ ... OK
* this is package ‘zellkonverter’ version ‘1.14.0’
* 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 33.706  3.247  53.083
writeH5AD           5.781  0.479   8.856
* 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: Error creating conda environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/zellkonverter/1.14.0/zellkonverterAnnDataEnv-0.7.6' [exit code 1]
  Backtrace:
      ▆
   1. └─zellkonverter::writeH5AD(sce, temp, version = "0.7.6") at test-write.R:133:5
   2.   └─basilisk::basiliskRun(...)
   3.     └─basilisk::basiliskStart(...)
   4.       └─basilisk::obtainEnvironmentPath(env)
   5.         └─basilisk::setupBasiliskEnv(...)
   6.           └─reticulate::conda_install(...)
   7.             └─reticulate::conda_create(...)
   8.               └─reticulate:::stopf(fmt, envname, result, call. = FALSE)
  
  [ FAIL 2 | WARN 29 | SKIP 3 | PASS 134 ]
  Error: Test failures
  Execution halted
* 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 ERROR, 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 
  0.198   0.086   0.468

zellkonverter.Rcheck/tests/testthat.Rout.fail


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... failed

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

  - python=3.7.10

Current channels:

  - https://conda.anaconda.org/conda-forge/osx-arm64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://repo.anaconda.com/pkgs/main/osx-arm64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/osx-arm64
  - 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.


/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/zellkonverter/1.14.0/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/1.14.0/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/1.14.0/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(
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... failed

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

  - python=3.7.10

Current channels:

  - https://conda.anaconda.org/conda-forge/osx-arm64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://repo.anaconda.com/pkgs/main/osx-arm64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/osx-arm64
  - 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.


/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/zellkonverter/1.14.0/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/1.14.0/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/1.14.0/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/1.14.0/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/1.14.0/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/1.14.0/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/1.14.0/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/1.14.0/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/1.14.0/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/1.14.0/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/1.14.0/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/1.14.0/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/1.14.0/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/1.14.0/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 2 | WARN 29 | SKIP 3 | PASS 134 ]

══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On CRAN (3): 'test-read.R:155:5', 'test-zzz-anndata.R:6:5',
  'test-zzz-anndata.R:54:5'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-read.R:39:5'): Reading H5AD works with version 0.7.6 ───────────
Error: Error creating conda environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/zellkonverter/1.14.0/zellkonverterAnnDataEnv-0.7.6' [exit code 1]
Backtrace:
    ▆
 1. └─zellkonverter::readH5AD(file, version = "0.7.6") at test-read.R:39:5
 2.   └─basilisk::basiliskRun(...)
 3.     └─basilisk::basiliskStart(...)
 4.       └─basilisk::obtainEnvironmentPath(env)
 5.         └─basilisk::setupBasiliskEnv(...)
 6.           └─reticulate::conda_install(...)
 7.             └─reticulate::conda_create(...)
 8.               └─reticulate:::stopf(fmt, envname, result, call. = FALSE)
── Error ('test-write.R:133:5'): writeH5AD works as expected with version 0.7.6 ──
Error: Error creating conda environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/zellkonverter/1.14.0/zellkonverterAnnDataEnv-0.7.6' [exit code 1]
Backtrace:
    ▆
 1. └─zellkonverter::writeH5AD(sce, temp, version = "0.7.6") at test-write.R:133:5
 2.   └─basilisk::basiliskRun(...)
 3.     └─basilisk::basiliskStart(...)
 4.       └─basilisk::obtainEnvironmentPath(env)
 5.         └─basilisk::setupBasiliskEnv(...)
 6.           └─reticulate::conda_install(...)
 7.             └─reticulate::conda_create(...)
 8.               └─reticulate:::stopf(fmt, envname, result, call. = FALSE)

[ FAIL 2 | WARN 29 | SKIP 3 | PASS 134 ]
Error: Test failures
Execution halted

Example timings

zellkonverter.Rcheck/zellkonverter-Ex.timings

nameusersystemelapsed
AnnData-Conversion33.706 3.24753.083
AnnData-Environment0.0050.0020.007
readH5AD1.1460.0981.740
setZellkonverterVerbose0.0010.0000.001
writeH5AD5.7810.4798.856