Multiple platform build/check report for BioC 3.21 - BUILD results for spatialDE on palomino7

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"	4783
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"	4552
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4581
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4533
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4463
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*

BUILD results for spatialDE on palomino7

To the developers/maintainers of the spatialDE package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/spatialDE.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: spatialDE

Version: 1.13.0

Command: chmod a+r spatialDE -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data spatialDE

StartedAt: 2025-03-26 22:14:14 -0400 (Wed, 26 Mar 2025)

EndedAt: 2025-03-26 22:15:03 -0400 (Wed, 26 Mar 2025)

EllapsedTime: 49.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   chmod a+r spatialDE -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data spatialDE
###
##############################################################################
##############################################################################


* checking for file 'spatialDE/DESCRIPTION' ... OK
* preparing 'spatialDE':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'spatialDE.Rmd' using rmarkdown

EnvironmentLocationNotFound: Not a conda environment: C:\Users\biocbuild\.basilisk\1.19.3\spatialDE\1.13.0\env


Quitting from spatialDE.Rmd:122-125 [stabilize]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.activate_condaenv()`:
! object 'listener' not found
---
Backtrace:
    ▆
 1. └─spatialDE::stabilize(Rep11_MOB_0)
 2.   └─basilisk::basiliskStart(spatialDE_env, testload = "scipy.optimize")
 3.     └─basilisk::useBasiliskEnv(envpath, full.activation)
 4.       └─basilisk.utils::activateEnvironment(envpath, full.activation = full.activation)
 5.         └─basilisk.utils:::.activate_condaenv(output, envpath, loc)
 6.           └─base::unserialize(listener)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'spatialDE.Rmd' failed with diagnostics:
object 'listener' not found
--- failed re-building 'spatialDE.Rmd'

SUMMARY: processing the following file failed:
  'spatialDE.Rmd'

Error: Vignette re-building failed.
Execution halted