| Back to Build/check report for BioC 3.23: simplified long |
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This page was generated on 2025-11-05 11:32 -0500 (Wed, 05 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4818 |
| 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 1581/2323 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Pirat 1.5.0 (landing page) Lucas Etourneau
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
|
To the developers/maintainers of the Pirat package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Pirat.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. |
| Package: Pirat |
| Version: 1.5.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data Pirat |
| StartedAt: 2025-11-04 19:12:29 -0500 (Tue, 04 Nov 2025) |
| EndedAt: 2025-11-04 19:17:16 -0500 (Tue, 04 Nov 2025) |
| EllapsedTime: 287.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data Pirat
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* checking for file ‘Pirat/DESCRIPTION’ ... OK
* preparing ‘Pirat’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘Pirat.Rmd’ using rmarkdown
Requirement already satisfied: pip in /var/cache/basilisk/1.23.0/Pirat/1.5.0/envPirat/lib/python3.10/site-packages (23.0.1)
Collecting pip
Using cached pip-25.3-py3-none-any.whl (1.8 MB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Requirement already satisfied: setuptools in /var/cache/basilisk/1.23.0/Pirat/1.5.0/envPirat/lib/python3.10/site-packages (79.0.1)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: setuptools
Found existing installation: setuptools 79.0.1
Uninstalling setuptools-79.0.1:
Successfully uninstalled setuptools-79.0.1
Attempting uninstall: pip
Found existing installation: pip 23.0.1
Uninstalling pip-23.0.1:
Successfully uninstalled pip-23.0.1
Successfully installed pip-25.3 setuptools-80.9.0 wheel-0.45.1
WARNING: There was an error checking the latest version of pip.
Collecting torch==1.13.1
Using cached torch-1.13.1-cp310-cp310-manylinux1_x86_64.whl.metadata (24 kB)
Collecting numpy==1.21
Downloading numpy-1.21.0.zip (10.3 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.3/10.3 MB 8.5 MB/s 0:00:01
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Collecting typing-extensions (from torch==1.13.1)
Using cached typing_extensions-4.15.0-py3-none-any.whl.metadata (3.3 kB)
Collecting nvidia-cuda-runtime-cu11==11.7.99 (from torch==1.13.1)
Using cached nvidia_cuda_runtime_cu11-11.7.99-py3-none-manylinux1_x86_64.whl.metadata (1.6 kB)
Collecting nvidia-cudnn-cu11==8.5.0.96 (from torch==1.13.1)
Using cached nvidia_cudnn_cu11-8.5.0.96-2-py3-none-manylinux1_x86_64.whl.metadata (1.6 kB)
Collecting nvidia-cublas-cu11==11.10.3.66 (from torch==1.13.1)
Using cached nvidia_cublas_cu11-11.10.3.66-py3-none-manylinux1_x86_64.whl.metadata (1.6 kB)
Collecting nvidia-cuda-nvrtc-cu11==11.7.99 (from torch==1.13.1)
Using cached nvidia_cuda_nvrtc_cu11-11.7.99-2-py3-none-manylinux1_x86_64.whl.metadata (1.5 kB)
Requirement already satisfied: setuptools in /var/cache/basilisk/1.23.0/Pirat/1.5.0/envPirat/lib/python3.10/site-packages (from nvidia-cublas-cu11==11.10.3.66->torch==1.13.1) (80.9.0)
Requirement already satisfied: wheel in /var/cache/basilisk/1.23.0/Pirat/1.5.0/envPirat/lib/python3.10/site-packages (from nvidia-cublas-cu11==11.10.3.66->torch==1.13.1) (0.45.1)
Using cached torch-1.13.1-cp310-cp310-manylinux1_x86_64.whl (887.5 MB)
Using cached nvidia_cublas_cu11-11.10.3.66-py3-none-manylinux1_x86_64.whl (317.1 MB)
Using cached nvidia_cuda_nvrtc_cu11-11.7.99-2-py3-none-manylinux1_x86_64.whl (21.0 MB)
Using cached nvidia_cuda_runtime_cu11-11.7.99-py3-none-manylinux1_x86_64.whl (849 kB)
Using cached nvidia_cudnn_cu11-8.5.0.96-2-py3-none-manylinux1_x86_64.whl (557.1 MB)
Using cached typing_extensions-4.15.0-py3-none-any.whl (44 kB)
Building wheels for collected packages: numpy
Building wheel for numpy (pyproject.toml): started
Building wheel for numpy (pyproject.toml): still running...
Building wheel for numpy (pyproject.toml): still running...
Building wheel for numpy (pyproject.toml): finished with status 'done'
Created wheel for numpy: filename=numpy-1.21.0-cp310-cp310-linux_x86_64.whl size=15618383 sha256=ab60e40a3381c6cad8c59b88ea8ff985f5a485b0162e4a923a5ad2008a805694
Stored in directory: /home/biocbuild/.cache/pip/wheels/05/61/d1/ccc2cd557b39e127ad98a392d9558f3c5dda28764b7f54b2f5
Successfully built numpy
Installing collected packages: typing-extensions, nvidia-cuda-runtime-cu11, nvidia-cuda-nvrtc-cu11, nvidia-cublas-cu11, numpy, nvidia-cudnn-cu11, torch
Successfully installed numpy-1.21.0 nvidia-cublas-cu11-11.10.3.66 nvidia-cuda-nvrtc-cu11-11.7.99 nvidia-cuda-runtime-cu11-11.7.99 nvidia-cudnn-cu11-8.5.0.96 torch-1.13.1 typing-extensions-4.15.0
Processing /tmp/RtmpeOX49g/Rinst118a9423a00278/Pirat/myModules
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Building wheels for collected packages: PyPirat
Building wheel for PyPirat (pyproject.toml): started
Building wheel for PyPirat (pyproject.toml): finished with status 'done'
Created wheel for PyPirat: filename=pypirat-0.1-py3-none-any.whl size=16332 sha256=9d15fe13ef208191652e20115b64fabbd1b46186fee679757f8991d778da0737
Stored in directory: /tmp/pip-ephem-wheel-cache-5_7qia4g/wheels/0b/a1/d9/9d338bd6f6712ae78910b8b26b0bfab8f43453125d7d85d8fe
Successfully built PyPirat
Installing collected packages: PyPirat
Successfully installed PyPirat-0.1
Quitting from Pirat.Rmd:90-92 [impute]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `py_module_import()`:
! ModuleNotFoundError: No module named 'PyPirat.lbfgs'
Run `reticulate::py_last_error()` for details.
---
Backtrace:
▆
1. └─Pirat::my_pipeline_llkimpute(subbouyssie)
2. └─basilisk::basiliskRun(...)
3. └─Pirat (local) fun(...)
4. └─Pirat::pipeline_llkimpute(arg1, ...)
5. └─reticulate::import("PyPirat", delay_load = TRUE)
6. └─reticulate:::py_module_import(module, convert = convert)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Pirat.Rmd' failed with diagnostics:
ModuleNotFoundError: No module named 'PyPirat.lbfgs'
Run `reticulate::py_last_error()` for details.
--- failed re-building ‘Pirat.Rmd’
SUMMARY: processing the following file failed:
‘Pirat.Rmd’
Error: Vignette re-building failed.
Execution halted