Aaron Lun
| Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/basilisk |
| git_branch: RELEASE_3_20 |
| git_last_commit: 31887d4 |
| git_last_commit_date: 2024-10-29 10:43:26 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-04-02 19:35 -0400 (Wed, 02 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4764 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4495 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4522 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4449 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4426 |
| 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 139/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| basilisk 1.18.0 (landing page) Aaron Lun
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | TIMEOUT | OK | |||||||||
| 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 basilisk package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/basilisk.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: basilisk |
| Version: 1.18.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data basilisk |
| StartedAt: 2025-03-31 21:32:11 -0000 (Mon, 31 Mar 2025) |
| EndedAt: 2025-03-31 21:35:52 -0000 (Mon, 31 Mar 2025) |
| EllapsedTime: 221.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data basilisk
###
##############################################################################
##############################################################################
* checking for file ‘basilisk/DESCRIPTION’ ... OK
* preparing ‘basilisk’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘motivation.Rmd’ using rmarkdown
Retrieving notices: ...working... done
Channels:
- conda-forge
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/tmp/RtmpbZxIj0/Rbuild7ca0a62574a33/basilisk/vignettes/basilisk-vignette-test/1.18.0
added / updated specs:
- python=3.10.14
The following packages will be downloaded:
package | build
---------------------------|-----------------
libffi-3.4.6 | he21f813_1 55 KB conda-forge
------------------------------------------------------------
Total: 55 KB
The following NEW packages will be INSTALLED:
_openmp_mutex conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-aarch64::bzip2-1.0.8-h68df207_7
ca-certificates conda-forge/linux-aarch64::ca-certificates-2025.1.31-hcefe29a_0
ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.43-h80caac9_4
libffi conda-forge/linux-aarch64::libffi-3.4.6-he21f813_1
libgcc conda-forge/linux-aarch64::libgcc-14.2.0-he277a41_2
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-14.2.0-he9431aa_2
libgomp conda-forge/linux-aarch64::libgomp-14.2.0-he277a41_2
liblzma conda-forge/linux-aarch64::liblzma-5.6.4-h86ecc28_0
liblzma-devel conda-forge/linux-aarch64::liblzma-devel-5.6.4-h86ecc28_0
libnsl conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0
libsqlite conda-forge/linux-aarch64::libsqlite-3.49.1-h5eb1b54_2
libuuid conda-forge/linux-aarch64::libuuid-2.38.1-hb4cce97_0
libxcrypt conda-forge/linux-aarch64::libxcrypt-4.4.36-h31becfc_1
libzlib conda-forge/linux-aarch64::libzlib-1.3.1-h86ecc28_2
ncurses conda-forge/linux-aarch64::ncurses-6.5-ha32ae93_3
openssl conda-forge/linux-aarch64::openssl-3.4.1-hd08dc88_0
pip conda-forge/noarch::pip-25.0.1-pyh8b19718_0
python conda-forge/linux-aarch64::python-3.10.14-hbbe8eec_0_cpython
readline conda-forge/linux-aarch64::readline-8.2-h8382b9d_2
setuptools conda-forge/noarch::setuptools-75.8.2-pyhff2d567_0
tk conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0
tzdata conda-forge/noarch::tzdata-2025b-h78e105d_0
wheel conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1
xz conda-forge/linux-aarch64::xz-5.6.4-h2dbfc1b_0
xz-gpl-tools conda-forge/linux-aarch64::xz-gpl-tools-5.6.4-h2dbfc1b_0
xz-tools conda-forge/linux-aarch64::xz-tools-5.6.4-h86ecc28_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
- conda-forge
Platform: linux-aarch64
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: 25.3.0
Please update conda by running
$ conda update -n base -c conda-forge conda
# All requested packages already installed.
Channels:
- conda-forge
Platform: linux-aarch64
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: 25.3.0
Please update conda by running
$ conda update -n base -c conda-forge conda
## Package Plan ##
environment location: /home/biocbuild/tmp/RtmpbZxIj0/Rbuild7ca0a62574a33/basilisk/vignettes/basilisk-vignette-test/1.18.0
added / updated specs:
- numpy=1.22.1
- python=3.10.14
- scikit-learn=1.1.1
The following NEW packages will be INSTALLED:
brotli-python conda-forge/linux-aarch64::brotli-python-1.1.0-py310he30c3ed_2
certifi conda-forge/noarch::certifi-2025.1.31-pyhd8ed1ab_0
cffi conda-forge/linux-aarch64::cffi-1.17.1-py310h1451162_0
charset-normalizer conda-forge/noarch::charset-normalizer-3.4.1-pyhd8ed1ab_0
h2 conda-forge/noarch::h2-4.2.0-pyhd8ed1ab_0
hpack conda-forge/noarch::hpack-4.1.0-pyhd8ed1ab_0
hyperframe conda-forge/noarch::hyperframe-6.1.0-pyhd8ed1ab_0
idna conda-forge/noarch::idna-3.10-pyhd8ed1ab_1
joblib conda-forge/noarch::joblib-1.4.2-pyhd8ed1ab_1
libblas conda-forge/linux-aarch64::libblas-3.9.0-20_linuxaarch64_openblas
libcblas conda-forge/linux-aarch64::libcblas-3.9.0-20_linuxaarch64_openblas
libgfortran conda-forge/linux-aarch64::libgfortran-14.2.0-he9431aa_2
libgfortran-ng conda-forge/linux-aarch64::libgfortran-ng-14.2.0-he9431aa_2
libgfortran5 conda-forge/linux-aarch64::libgfortran5-14.2.0-hb6113d0_2
liblapack conda-forge/linux-aarch64::liblapack-3.9.0-20_linuxaarch64_openblas
libopenblas conda-forge/linux-aarch64::libopenblas-0.3.25-pthreads_h5a5ec62_0
libstdcxx conda-forge/linux-aarch64::libstdcxx-14.2.0-h3f4de04_2
libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-14.2.0-hf1166c9_2
numpy conda-forge/linux-aarch64::numpy-1.22.1-py310ha311ffb_0
packaging conda-forge/noarch::packaging-24.2-pyhd8ed1ab_2
platformdirs conda-forge/noarch::platformdirs-4.3.7-pyh29332c3_0
pooch conda-forge/noarch::pooch-1.8.2-pyhd8ed1ab_1
pycparser conda-forge/noarch::pycparser-2.22-pyh29332c3_1
pysocks conda-forge/noarch::pysocks-1.7.1-pyha55dd90_7
python_abi conda-forge/linux-aarch64::python_abi-3.10-5_cp310
requests conda-forge/noarch::requests-2.32.3-pyhd8ed1ab_1
scikit-learn conda-forge/linux-aarch64::scikit-learn-1.1.1-py310h960e1e0_0
scipy conda-forge/linux-aarch64::scipy-1.11.2-py310h7f380f4_0
threadpoolctl conda-forge/noarch::threadpoolctl-3.6.0-pyhecae5ae_0
urllib3 conda-forge/noarch::urllib3-2.3.0-pyhd8ed1ab_0
zstandard conda-forge/linux-aarch64::zstandard-0.23.0-py310ha766c32_1
Downloading and Extracting Packages: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
- conda-forge
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/tmp/RtmpbZxIj0/Rbuild7ca0a62574a33/basilisk/vignettes/basilisk-vignette-test2
added / updated specs:
- python=3.10
The following NEW packages will be INSTALLED:
_openmp_mutex conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-aarch64::bzip2-1.0.8-h68df207_7
ca-certificates conda-forge/linux-aarch64::ca-certificates-2025.1.31-hcefe29a_0
ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.43-h80caac9_4
libffi conda-forge/linux-aarch64::libffi-3.4.6-he21f813_1
libgcc conda-forge/linux-aarch64::libgcc-14.2.0-he277a41_2
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-14.2.0-he9431aa_2
libgomp conda-forge/linux-aarch64::libgomp-14.2.0-he277a41_2
liblzma conda-forge/linux-aarch64::liblzma-5.6.4-h86ecc28_0
libnsl conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0
libsqlite conda-forge/linux-aarch64::libsqlite-3.49.1-h5eb1b54_2
libuuid conda-forge/linux-aarch64::libuuid-2.38.1-hb4cce97_0
libxcrypt conda-forge/linux-aarch64::libxcrypt-4.4.36-h31becfc_1
libzlib conda-forge/linux-aarch64::libzlib-1.3.1-h86ecc28_2
ncurses conda-forge/linux-aarch64::ncurses-6.5-ha32ae93_3
openssl conda-forge/linux-aarch64::openssl-3.4.1-hd08dc88_0
pip conda-forge/noarch::pip-25.0.1-pyh8b19718_0
python conda-forge/linux-aarch64::python-3.10.16-h57b00e1_1_cpython
readline conda-forge/linux-aarch64::readline-8.2-h8382b9d_2
setuptools conda-forge/noarch::setuptools-75.8.2-pyhff2d567_0
tk conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0
tzdata conda-forge/noarch::tzdata-2025b-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-aarch64
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: 25.3.0
Please update conda by running
$ conda update -n base -c conda-forge conda
# All requested packages already installed.
Channels:
- conda-forge
Platform: linux-aarch64
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: 25.3.0
Please update conda by running
$ conda update -n base -c conda-forge conda
## Package Plan ##
environment location: /home/biocbuild/tmp/RtmpbZxIj0/Rbuild7ca0a62574a33/basilisk/vignettes/basilisk-vignette-test2
added / updated specs:
- python=3.10
- scipy==1.9.1
The following NEW packages will be INSTALLED:
libblas conda-forge/linux-aarch64::libblas-3.9.0-20_linuxaarch64_openblas
libcblas conda-forge/linux-aarch64::libcblas-3.9.0-20_linuxaarch64_openblas
libgfortran conda-forge/linux-aarch64::libgfortran-14.2.0-he9431aa_2
libgfortran-ng conda-forge/linux-aarch64::libgfortran-ng-14.2.0-he9431aa_2
libgfortran5 conda-forge/linux-aarch64::libgfortran5-14.2.0-hb6113d0_2
liblapack conda-forge/linux-aarch64::liblapack-3.9.0-20_linuxaarch64_openblas
libopenblas conda-forge/linux-aarch64::libopenblas-0.3.25-pthreads_h5a5ec62_0
libstdcxx conda-forge/linux-aarch64::libstdcxx-14.2.0-h3f4de04_2
libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-14.2.0-hf1166c9_2
numpy conda-forge/linux-aarch64::numpy-1.26.4-py310hcbab775_0
python_abi conda-forge/linux-aarch64::python_abi-3.10-5_cp310
scipy conda-forge/linux-aarch64::scipy-1.9.1-py310hdd6f644_0
Downloading and Extracting Packages: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Quitting from motivation.Rmd:302-331 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `serverSocket()`:
! internet routines cannot be loaded
---
Backtrace:
▆
1. └─basilisk::basiliskRun(...)
2. └─basilisk::basiliskStart(...)
3. └─parallel::makePSOCKcluster(1)
4. └─base::serverSocket(port = port)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'motivation.Rmd' failed with diagnostics:
internet routines cannot be loaded
--- failed re-building ‘motivation.Rmd’
SUMMARY: processing the following file failed:
‘motivation.Rmd’
Error: Vignette re-building failed.
Execution halted