Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2025-03-14 11:41 -0400 (Fri, 14 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4781
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4537
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4567
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4519
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4451
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 2028/2309HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
spatialDE 1.13.0  (landing page)
Gabriele Sales
Snapshot Date: 2025-03-13 13:40 -0400 (Thu, 13 Mar 2025)
git_url: https://git.bioconductor.org/packages/spatialDE
git_branch: devel
git_last_commit: 03b4e0e
git_last_commit_date: 2024-10-29 11:03:13 -0400 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    ERROR  skipped
palomino7Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.1 Ventura / arm64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped

BUILD results for spatialDE on nebbiolo1

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: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data spatialDE
StartedAt: 2025-03-13 19:12:08 -0400 (Thu, 13 Mar 2025)
EndedAt: 2025-03-13 19:13:19 -0400 (Thu, 13 Mar 2025)
EllapsedTime: 71.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R 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
Retrieving notices: ...working... done
Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/biocbuild/.cache/R/basilisk/1.19.1/spatialDE/1.13.0/env

  added / updated specs:
    - python=3.12.8


The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge 
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-2_gnu 
  bzip2              conda-forge/linux-64::bzip2-1.0.8-h4bc722e_7 
  ca-certificates    conda-forge/linux-64::ca-certificates-2025.1.31-hbcca054_0 
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.43-h712a8e2_4 
  libexpat           conda-forge/linux-64::libexpat-2.6.4-h5888daf_0 
  libffi             conda-forge/linux-64::libffi-3.4.6-h2dba641_0 
  libgcc             conda-forge/linux-64::libgcc-14.2.0-h767d61c_2 
  libgcc-ng          conda-forge/linux-64::libgcc-ng-14.2.0-h69a702a_2 
  libgomp            conda-forge/linux-64::libgomp-14.2.0-h767d61c_2 
  liblzma            conda-forge/linux-64::liblzma-5.6.4-hb9d3cd8_0 
  libnsl             conda-forge/linux-64::libnsl-2.0.1-hd590300_0 
  libsqlite          conda-forge/linux-64::libsqlite-3.49.1-hee588c1_1 
  libuuid            conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0 
  libxcrypt          conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1 
  libzlib            conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2 
  ncurses            conda-forge/linux-64::ncurses-6.5-h2d0b736_3 
  openssl            conda-forge/linux-64::openssl-3.4.1-h7b32b05_0 
  pip                conda-forge/noarch::pip-25.0.1-pyh8b19718_0 
  python             conda-forge/linux-64::python-3.12.8-h9e4cc4f_1_cpython 
  readline           conda-forge/linux-64::readline-8.2-h8c095d6_2 
  setuptools         conda-forge/noarch::setuptools-75.8.2-pyhff2d567_0 
  tk                 conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101 
  tzdata             conda-forge/noarch::tzdata-2025a-h78e105d_0 
  wheel              conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1 


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
    current version: 24.11.3
    latest version: 25.1.1

Please update conda by running

    $ conda update -n base -c conda-forge conda



# All requested packages already installed.

Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed

LibMambaUnsatisfiableError: Encountered problems while solving:
  - package scipy-1.9.3-py38h8ce737c_0 requires python_abi 3.8.* *_cp38, but none of the providers can be installed

Could not solve for environment specs
The following packages are incompatible
├─ python 3.12.8**  is installable and it requires
│  └─ python_abi 3.12.* *_cp312, which can be installed;
└─ scipy 1.9.3**  is not installable because there are no viable options
   ├─ scipy 1.9.3 would require
   │  └─ python_abi 3.8.* *_cp38, which conflicts with any installable versions previously reported;
   ├─ scipy 1.9.3 would require
   │  └─ python_abi 3.10.* *_cp310, which conflicts with any installable versions previously reported;
   ├─ scipy 1.9.3 would require
   │  └─ python_abi 3.11.* *_cp311, which conflicts with any installable versions previously reported;
   └─ scipy 1.9.3 would require
      └─ python_abi 3.9.* *_cp39, which conflicts with any installable versions previously reported.


Quitting from lines 123-125 [stabilize] (spatialDE.Rmd)
Error: processing vignette 'spatialDE.Rmd' failed with diagnostics:
one or more Python packages failed to install [error code 1]
--- failed re-building ‘spatialDE.Rmd’

SUMMARY: processing the following file failed:
  ‘spatialDE.Rmd’

Error: Vignette re-building failed.
Execution halted