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 12:09 -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: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data Pirat |
| StartedAt: 2025-03-03 21:11:40 -0500 (Mon, 03 Mar 2025) |
| EndedAt: 2025-03-03 21:18:35 -0500 (Mon, 03 Mar 2025) |
| EllapsedTime: 414.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data Pirat
###
##############################################################################
##############################################################################
* checking for file ‘Pirat/DESCRIPTION’ ... OK
* preparing ‘Pirat’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...sh: line 1: 57246 Killed: 9 '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/Rtmpa8ht9x/xshelld56796deabe' 2>&1
ERROR
--- re-building ‘Pirat.Rmd’ using rmarkdown
Channels:
- pytorch
- torch
- conda-forge
Platform: osx-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.18.0/Pirat/1.0.3/envPirat
added / updated specs:
- python=3.9.5
The following NEW packages will be INSTALLED:
ca-certificates conda-forge/osx-64::ca-certificates-2025.1.31-h8857fd0_0
libcxx conda-forge/osx-64::libcxx-19.1.7-hf95d169_0
libffi conda-forge/osx-64::libffi-3.3-h046ec9c_2
liblzma conda-forge/osx-64::liblzma-5.6.4-hd471939_0
liblzma-devel conda-forge/osx-64::liblzma-devel-5.6.4-hd471939_0
libsqlite conda-forge/osx-64::libsqlite-3.46.0-h1b8f9f3_0
libzlib conda-forge/osx-64::libzlib-1.2.13-h87427d6_6
ncurses conda-forge/osx-64::ncurses-6.5-h0622a9a_3
openssl conda-forge/osx-64::openssl-1.1.1w-h8a1eda9_0
pip conda-forge/noarch::pip-25.0.1-pyh8b19718_0
python conda-forge/osx-64::python-3.9.5-hd187cdc_0_cpython
readline conda-forge/osx-64::readline-8.2-h7cca4af_2
setuptools conda-forge/noarch::setuptools-75.8.2-pyhff2d567_0
sqlite conda-forge/osx-64::sqlite-3.46.0-h28673e1_0
tk conda-forge/osx-64::tk-8.6.13-h1abcd95_1
tzdata conda-forge/noarch::tzdata-2025a-h78e105d_0
wheel conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1
xz conda-forge/osx-64::xz-5.6.4-h357f2ed_0
xz-gpl-tools conda-forge/osx-64::xz-gpl-tools-5.6.4-h357f2ed_0
xz-tools conda-forge/osx-64::xz-tools-5.6.4-hd471939_0
zlib conda-forge/osx-64::zlib-1.2.13-h87427d6_6
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
- pytorch
- torch
- conda-forge
Platform: osx-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: osx-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: /Users/biocbuild/Library/Caches/org.R-project.R/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-2.120 | mkl 14 KB conda-forge
blas-devel-3.9.0 | 20_osx64_mkl 14 KB conda-forge
libblas-3.9.0 | 20_osx64_mkl 15 KB conda-forge
libcblas-3.9.0 | 20_osx64_mkl 14 KB conda-forge
libiconv-1.18 | h4b5e92a_1 653 KB conda-forge
liblapack-3.9.0 | 20_osx64_mkl 14 KB conda-forge
liblapacke-3.9.0 | 20_osx64_mkl 14 KB conda-forge
libuv-1.50.0 | h4cb831e_0 410 KB conda-forge
mkl-2023.2.0 | h54c2260_50500 114.0 MB conda-forge
mkl-devel-2023.2.0 | h694c41f_50500 29 KB conda-forge
mkl-include-2023.2.0 | h6bab518_50500 575 KB conda-forge
pytorch-1.10.0 | py3.9_0 98.0 MB pytorch
------------------------------------------------------------
Total: 213.7 MB
The following NEW packages will be INSTALLED:
blas conda-forge/osx-64::blas-2.120-mkl
blas-devel conda-forge/osx-64::blas-devel-3.9.0-20_osx64_mkl
icu conda-forge/osx-64::icu-73.2-hf5e326d_0
libblas conda-forge/osx-64::libblas-3.9.0-20_osx64_mkl
libcblas conda-forge/osx-64::libcblas-3.9.0-20_osx64_mkl
libgfortran conda-forge/osx-64::libgfortran-5.0.0-13_2_0_h97931a8_3
libgfortran5 conda-forge/osx-64::libgfortran5-13.2.0-h2873a65_3
libhwloc conda-forge/osx-64::libhwloc-2.11.2-default_hb6fbd3b_1000
libiconv conda-forge/osx-64::libiconv-1.18-h4b5e92a_1
liblapack conda-forge/osx-64::liblapack-3.9.0-20_osx64_mkl
liblapacke conda-forge/osx-64::liblapacke-3.9.0-20_osx64_mkl
libuv conda-forge/osx-64::libuv-1.50.0-h4cb831e_0
libxml2 conda-forge/osx-64::libxml2-2.12.7-h3e169fe_1
llvm-openmp conda-forge/osx-64::llvm-openmp-19.1.7-ha54dae1_0
mkl conda-forge/osx-64::mkl-2023.2.0-h54c2260_50500
mkl-devel conda-forge/osx-64::mkl-devel-2023.2.0-h694c41f_50500
mkl-include conda-forge/osx-64::mkl-include-2023.2.0-h6bab518_50500
numpy conda-forge/osx-64::numpy-1.20.2-py39h7eed0ac_0
python_abi conda-forge/osx-64::python_abi-3.9-5_cp39
pytorch pytorch/osx-64::pytorch-1.10.0-py3.9_0
tbb conda-forge/osx-64::tbb-2021.13.0-hb890de9_1
typing_extensions conda-forge/noarch::typing_extensions-4.12.2-pyha770c72_1
Downloading and Extracting Packages: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Processing /private/tmp/Rtmpa8ht9x/Rinstd567344a388b/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=aff247112b714a590901cd746fe36f4735958f319fe292d0da18ddea544b36d8
Stored in directory: /private/tmp/pip-ephem-wheel-cache-kg2ui_28/wheels/5b/e7/39/d3006c4b14e07b06c91c2a7b7675ed5470ba11f8230a68a92a
Successfully built PyPirat
Installing collected packages: PyPirat
Successfully installed PyPirat-0.1