Back to Long Tests report for BioC 3.18

This page was generated on 2024-04-13 23:55:02 -0400 (Sat, 13 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4675
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4413
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4436
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 30/30HostnameOS / ArchCHECK
zellkonverter 1.12.1  (landing page)
Luke Zappia
Snapshot Date: 2024-04-13 09:55:01 -0400 (Sat, 13 Apr 2024)
git_url: https://git.bioconductor.org/packages/zellkonverter
git_branch: RELEASE_3_18
git_last_commit: 4cb6fc2
git_last_commit_date: 2023-11-13 04:55:04 -0400 (Mon, 13 Nov 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK  
palomino4Windows Server 2022 Datacenter / x64  ERROR  
merida1macOS 12.7.1 Monterey / x86_64  ERROR  

CHECK results for zellkonverter on merida1


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: 1.12.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no zellkonverter_1.12.1.tar.gz
StartedAt: 2024-04-13 16:22:37 -0400 (Sat, 13 Apr 2024)
EndedAt: 2024-04-13 16:32:42 -0400 (Sat, 13 Apr 2024)
EllapsedTime: 604.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: zellkonverter.Rcheck
Warnings: NA

Tests output

zellkonverter.Rcheck/tests/testthat.Rout.fail


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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")
/private/var/cache/basilisk/1.14.3/zellkonverter/1.12.1/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(
/private/var/cache/basilisk/1.14.3/zellkonverter/1.12.1/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(
/private/var/cache/basilisk/1.14.3/zellkonverter/1.12.1/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(
/private/var/cache/basilisk/1.14.3/zellkonverter/1.12.1/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(
/private/var/cache/basilisk/1.14.3/zellkonverter/1.12.1/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(
/private/var/cache/basilisk/1.14.3/zellkonverter/1.12.1/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(
/private/var/cache/basilisk/1.14.3/zellkonverter/1.12.1/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(
/private/var/cache/basilisk/1.14.3/zellkonverter/1.12.1/zellkonverterAnnDataEnv-0.10.2/lib/python3.11/site-packages/anndata/_core/anndata.py:1898: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.
  utils.warn_names_duplicates("obs")
/private/var/cache/basilisk/1.14.3/zellkonverter/1.12.1/zellkonverterAnnDataEnv-0.10.2/lib/python3.11/site-packages/anndata/_core/anndata.py:1898: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.
  utils.warn_names_duplicates("obs")
/private/var/cache/basilisk/1.14.3/zellkonverter/1.12.1/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(
/private/var/cache/basilisk/1.14.3/zellkonverter/1.12.1/zellkonverterAnnDataEnv-0.10.2/lib/python3.11/site-packages/anndata/_core/anndata.py:1898: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.
  utils.warn_names_duplicates("obs")
/private/var/cache/basilisk/1.14.3/zellkonverter/1.12.1/zellkonverterAnnDataEnv-0.10.2/lib/python3.11/site-packages/anndata/_core/anndata.py:1898: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.
  utils.warn_names_duplicates("obs")
/private/var/cache/basilisk/1.14.3/zellkonverter/1.12.1/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(
[ FAIL 1 | WARN 3 | SKIP 0 | PASS 179 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-gtex_8tissues.R:6:1'): (code run outside of `test_that()`) ─────
Error in `bfcrpath(cache, "https://storage.googleapis.com/gtex_analysis_v9/snrna_seq_data/GTEx_8_tissues_snRNAseq_atlas_071421.public_obs.h5ad")`: not all 'rnames' found or unique.
Backtrace:
    ▆
 1. ├─BiocFileCache::bfcrpath(cache, "https://storage.googleapis.com/gtex_analysis_v9/snrna_seq_data/GTEx_8_tissues_snRNAseq_atlas_071421.public_obs.h5ad") at test-gtex_8tissues.R:6:1
 2. └─BiocFileCache::bfcrpath(cache, "https://storage.googleapis.com/gtex_analysis_v9/snrna_seq_data/GTEx_8_tissues_snRNAseq_atlas_071421.public_obs.h5ad")

[ FAIL 1 | WARN 3 | SKIP 0 | PASS 179 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no zellkonverter_1.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-longtests/meat/zellkonverter.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* 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 ‘1.12.1’
* 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-3.18-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 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 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’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  /private/var/cache/basilisk/1.14.3/zellkonverter/1.12.1/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(
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 179 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-gtex_8tissues.R:6:1'): (code run outside of `test_that()`) ─────
  Error in `bfcrpath(cache, "https://storage.googleapis.com/gtex_analysis_v9/snrna_seq_data/GTEx_8_tissues_snRNAseq_atlas_071421.public_obs.h5ad")`: not all 'rnames' found or unique.
  Backtrace:
      ▆
   1. ├─BiocFileCache::bfcrpath(cache, "https://storage.googleapis.com/gtex_analysis_v9/snrna_seq_data/GTEx_8_tissues_snRNAseq_atlas_071421.public_obs.h5ad") at test-gtex_8tissues.R:6:1
   2. └─BiocFileCache::bfcrpath(cache, "https://storage.googleapis.com/gtex_analysis_v9/snrna_seq_data/GTEx_8_tissues_snRNAseq_atlas_071421.public_obs.h5ad")
  
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 179 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.18-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)