Back to Long Tests report for BioC 3.17

This page was generated on 2023-10-14 21:30:02 -0400 (Sat, 14 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 31/31HostnameOS / ArchCHECK
zellkonverter 1.10.1  (landing page)
Luke Zappia
Snapshot Date: 2023-10-14 09:55:02 -0400 (Sat, 14 Oct 2023)
git_url: https://git.bioconductor.org/packages/zellkonverter
git_branch: RELEASE_3_17
git_last_commit: d918d30
git_last_commit_date: 2023-05-23 05:34:59 -0400 (Tue, 23 May 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK  
palomino3Windows Server 2022 Datacenter / x64  ERROR  
merida1macOS 12.6.4 Monterey / x86_64  OK  

CHECK results for zellkonverter on palomino3


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: 1.10.1
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no zellkonverter_1.10.1.tar.gz
StartedAt: 2023-10-14 11:28:16 -0400 (Sat, 14 Oct 2023)
EndedAt: 2023-10-14 12:00:15 -0400 (Sat, 14 Oct 2023)
EllapsedTime: 1918.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: zellkonverter.Rcheck
Warnings: NA

Tests output

zellkonverter.Rcheck/tests/testthat.Rout.fail


R version 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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")
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\112~1.1\ZELLKO~1\110~1.1\ZELLKO~1.0\lib\site-packages\anndata\_core\anndata.py:1828: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.
  utils.warn_names_duplicates("obs")
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\112~1.1\ZELLKO~1\110~1.1\ZELLKO~1.0\lib\site-packages\anndata\_core\anndata.py:1828: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.
  utils.warn_names_duplicates("obs")
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\112~1.1\ZELLKO~1\110~1.1\ZELLKO~1.0\lib\site-packages\anndata\_core\anndata.py:1828: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.
  utils.warn_names_duplicates("obs")
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\112~1.1\ZELLKO~1\110~1.1\ZELLKO~1.0\lib\site-packages\anndata\_core\anndata.py:1828: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.
  utils.warn_names_duplicates("obs")
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 178 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-gtex_8tissues.R:53:10'): Reading H5AD works ────────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'colnames': INTEGER() can only be applied to a 'integer', not a 'double'
Backtrace:
     ▆
  1. ├─testthat::expect_warning(...) at test-gtex_8tissues.R:52:4
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─zellkonverter::readH5AD(file) at test-gtex_8tissues.R:53:9
  7. │ └─basilisk::basiliskRun(...)
  8. │   └─zellkonverter (local) fun(...)
  9. │     └─zellkonverter::AnnData2SCE(...)
 10. │       ├─zellkonverter:::.convert_anndata_df(...)
 11. │       │ └─BiocGenerics::colnames(adata_df)
 12. │       ├─reticulate::py_to_r(adata$obs)
 13. │       └─reticulate:::py_to_r.pandas.core.frame.DataFrame(adata$obs)
 14. │         └─reticulate:::py_convert_pandas_df(x)
 15. └─base::.handleSimpleError(...)
 16.   └─base (local) h(simpleError(msg, call))
── Error ('test-gtex_8tissues.R:59:1'): (code run outside of `test_that()`) ────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'colnames': INTEGER() can only be applied to a 'integer', not a 'double'
Backtrace:
     ▆
  1. ├─base::suppressWarnings(readH5AD(file)) at test-gtex_8tissues.R:59:0
  2. │ └─base::withCallingHandlers(...)
  3. ├─zellkonverter::readH5AD(file)
  4. │ └─basilisk::basiliskRun(...)
  5. │   └─zellkonverter (local) fun(...)
  6. │     └─zellkonverter::AnnData2SCE(...)
  7. │       ├─zellkonverter:::.convert_anndata_df(...)
  8. │       │ └─BiocGenerics::colnames(adata_df)
  9. │       ├─reticulate::py_to_r(adata$obs)
 10. │       └─reticulate:::py_to_r.pandas.core.frame.DataFrame(adata$obs)
 11. │         └─reticulate:::py_convert_pandas_df(x)
 12. └─base::.handleSimpleError(...)
 13.   └─base (local) h(simpleError(msg, call))
── Failure ('test-scvi_citeseq.R:45:5'): Round trip is as expected ─────────────
SummarizedExperiment::colData(sce) not identical to SummarizedExperiment::colData(expected).
Objects equal but not identical
Backtrace:
    ▆
 1. └─zellkonverter:::expectSCE(out, sce) at test-scvi_citeseq.R:45:4
 2.   └─testthat::expect_identical(...)

[ FAIL 3 | WARN 0 | SKIP 0 | PASS 178 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no zellkonverter_1.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-longtests/meat/zellkonverter.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 '1.10.1'
* 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 whether package 'zellkonverter' can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See 'F:/biocbuild/bbs-3.17-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:
   10. │       └─reticulate:::py_to_r.pandas.core.frame.DataFrame(adata$obs)
   11. │         └─reticulate:::py_convert_pandas_df(x)
   12. └─base::.handleSimpleError(...)
   13.   └─base (local) h(simpleError(msg, call))
  ── Failure ('test-scvi_citeseq.R:45:5'): Round trip is as expected ─────────────
  SummarizedExperiment::colData(sce) not identical to SummarizedExperiment::colData(expected).
  Objects equal but not identical
  Backtrace:
      ▆
   1. └─zellkonverter:::expectSCE(out, sce) at test-scvi_citeseq.R:45:4
   2.   └─testthat::expect_identical(...)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 178 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 1 NOTE
See
  'F:/biocbuild/bbs-3.17-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)