Samuel Wieczorek
| Snapshot Date: 2025-03-03 13:00 -0500 (Mon, 03 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/Pirat |
| git_branch: RELEASE_3_20 |
| git_last_commit: c6858d1 |
| git_last_commit_date: 2025-03-03 06:28:00 -0500 (Mon, 03 Mar 2025) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-03-06 12:05 -0500 (Thu, 06 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4769 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4504 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4527 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4480 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4416 |
| 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 1558/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Pirat 1.0.3 (landing page) Samuel Wieczorek
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: 1.0.3 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 Pirat |
| StartedAt: 2025-03-03 18:34:56 -0500 (Mon, 03 Mar 2025) |
| EndedAt: 2025-03-03 18:39:52 -0500 (Mon, 03 Mar 2025) |
| EllapsedTime: 296.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 Pirat
###
##############################################################################
##############################################################################
* checking for file ‘Pirat/DESCRIPTION’ ... OK
* preparing ‘Pirat’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Pirat.Rmd’ using rmarkdown
Channels:
- pytorch
- torch
- 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/1.18.0/Pirat/1.0.3/envPirat
added / updated specs:
- python=3.9.5
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
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
libffi conda-forge/linux-64::libffi-3.3-h58526e2_2
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
liblzma-devel conda-forge/linux-64::liblzma-devel-5.6.4-hb9d3cd8_0
libsqlite conda-forge/linux-64::libsqlite-3.46.0-hde9e2c9_0
libstdcxx conda-forge/linux-64::libstdcxx-14.2.0-h8f9b012_2
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-14.2.0-h4852527_2
libzlib conda-forge/linux-64::libzlib-1.2.13-h4ab18f5_6
ncurses conda-forge/linux-64::ncurses-6.5-h2d0b736_3
openssl conda-forge/linux-64::openssl-1.1.1w-hd590300_0
pip conda-forge/noarch::pip-25.0.1-pyh8b19718_0
python conda-forge/linux-64::python-3.9.5-h49503c6_0_cpython
readline conda-forge/linux-64::readline-8.2-h8c095d6_2
setuptools conda-forge/noarch::setuptools-75.8.2-pyhff2d567_0
sqlite conda-forge/linux-64::sqlite-3.46.0-h6d4b2fc_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
xz conda-forge/linux-64::xz-5.6.4-hbcc6ac9_0
xz-gpl-tools conda-forge/linux-64::xz-gpl-tools-5.6.4-hbcc6ac9_0
xz-tools conda-forge/linux-64::xz-tools-5.6.4-hb9d3cd8_0
zlib conda-forge/linux-64::zlib-1.2.13-h4ab18f5_6
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
- pytorch
- torch
- 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: 24.3.0
latest version: 25.1.1
Please update conda by running
$ conda update -n base -c conda-forge conda
# All requested packages already installed.
Channels:
- pytorch
- torch
- 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: 24.3.0
latest version: 25.1.1
Please update conda by running
$ conda update -n base -c conda-forge conda
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.18.0/Pirat/1.0.3/envPirat
added / updated specs:
- numpy=1.20.2
- python[version='3.9.5.*,3.9.5.*']
- pytorch=1.10.0
The following packages will be downloaded:
package | build
---------------------------|-----------------
blas-2.131 | mkl 16 KB conda-forge
blas-devel-3.9.0 | 31_hcf00494_mkl 16 KB conda-forge
cudatoolkit-11.3.1 | hb98b00a_13 603.5 MB conda-forge
libblas-3.9.0 | 31_hfdb39a5_mkl 17 KB conda-forge
libcblas-3.9.0 | 31_h372d94f_mkl 16 KB conda-forge
libiconv-1.18 | h4ce23a2_1 696 KB conda-forge
liblapack-3.9.0 | 31_hc41d3b0_mkl 16 KB conda-forge
liblapacke-3.9.0 | 31_hbc6e62b_mkl 16 KB conda-forge
libuv-1.50.0 | hb9d3cd8_0 870 KB conda-forge
mkl-2024.2.2 | ha957f24_16 118.9 MB conda-forge
mkl-devel-2024.2.2 | ha770c72_16 35 KB conda-forge
mkl-include-2024.2.2 | ha957f24_16 700 KB conda-forge
pytorch-1.10.0 |py3.9_cuda11.3_cudnn8.2.0_0 1.21 GB pytorch
pytorch-mutex-1.0 | cuda 3 KB pytorch
------------------------------------------------------------
Total: 1.92 GB
The following NEW packages will be INSTALLED:
blas conda-forge/linux-64::blas-2.131-mkl
blas-devel conda-forge/linux-64::blas-devel-3.9.0-31_hcf00494_mkl
cudatoolkit conda-forge/linux-64::cudatoolkit-11.3.1-hb98b00a_13
icu conda-forge/linux-64::icu-73.2-h59595ed_0
libblas conda-forge/linux-64::libblas-3.9.0-31_hfdb39a5_mkl
libcblas conda-forge/linux-64::libcblas-3.9.0-31_h372d94f_mkl
libhwloc conda-forge/linux-64::libhwloc-2.11.2-default_he43201b_1000
libiconv conda-forge/linux-64::libiconv-1.18-h4ce23a2_1
liblapack conda-forge/linux-64::liblapack-3.9.0-31_hc41d3b0_mkl
liblapacke conda-forge/linux-64::liblapacke-3.9.0-31_hbc6e62b_mkl
libuv conda-forge/linux-64::libuv-1.50.0-hb9d3cd8_0
libxml2 conda-forge/linux-64::libxml2-2.12.7-hc051c1a_1
llvm-openmp conda-forge/linux-64::llvm-openmp-19.1.7-h024ca30_0
mkl conda-forge/linux-64::mkl-2024.2.2-ha957f24_16
mkl-devel conda-forge/linux-64::mkl-devel-2024.2.2-ha770c72_16
mkl-include conda-forge/linux-64::mkl-include-2024.2.2-ha957f24_16
numpy conda-forge/linux-64::numpy-1.20.2-py39hdbf815f_0
python_abi conda-forge/linux-64::python_abi-3.9-5_cp39
pytorch pytorch/linux-64::pytorch-1.10.0-py3.9_cuda11.3_cudnn8.2.0_0
pytorch-mutex pytorch/noarch::pytorch-mutex-1.0-cuda
tbb conda-forge/linux-64::tbb-2021.13.0-hceb3a55_1
typing_extensions conda-forge/noarch::typing_extensions-4.12.2-pyha770c72_1
The following packages will be DOWNGRADED:
_openmp_mutex 4.5-2_gnu --> 4.5-2_kmp_llvm
Downloading and Extracting Packages: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... By downloading and using the CUDA Toolkit conda packages, you accept the terms and conditions of the CUDA End User License Agreement (EULA): https://docs.nvidia.com/cuda/eula/index.html
done
Processing /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpbUV60M/Rinst3afab110926f92/Pirat/myModules
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Building wheels for collected packages: PyPirat
Building wheel for PyPirat (setup.py): started
Building wheel for PyPirat (setup.py): finished with status 'done'
Created wheel for PyPirat: filename=pypirat-0.1-py3-none-any.whl size=16155 sha256=d475aedd0af8739392c53377e42b886b2686facb08e4b0d320ffa3c40c7c9e9d
Stored in directory: /home/biocbuild/bbs-3.20-bioc/tmpdir/pip-ephem-wheel-cache-jlrte1p8/wheels/ae/e4/6c/a22e0ea257c4487c17caa0918b436c1d298421bc39608b669f
Successfully built PyPirat
Installing collected packages: PyPirat
Successfully installed PyPirat-0.1
Quitting from lines 91-92 [impute] (Pirat.Rmd)
Error: processing vignette 'Pirat.Rmd' failed with diagnostics:
ImportError: /home/biocbuild/.cache/R/basilisk/1.18.0/Pirat/1.0.3/envPirat/lib/python3.9/site-packages/torch/lib/libtorch_cpu.so: undefined symbol: iJIT_NotifyEvent
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