Aaron Lun
| Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023) |
| git_url: https://git.bioconductor.org/packages/basilisk |
| git_branch: RELEASE_3_18 |
| git_last_commit: 408064e |
| git_last_commit_date: 2023-10-24 11:19:25 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-11-02 11:40:26 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
| 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 132/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| basilisk 1.14.0 (landing page) Aaron Lun
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | TIMEOUT | OK | |||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.14.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD build --keep-empty-dirs --no-resave-data basilisk |
| StartedAt: 2023-11-01 22:27:18 -0000 (Wed, 01 Nov 2023) |
| EndedAt: 2023-11-01 22:30:17 -0000 (Wed, 01 Nov 2023) |
| EllapsedTime: 179.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/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
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/tmp/RtmppLLYpW/Rbuild28fc141f6222cd/basilisk/vignettes/basilisk-vignette-test/1.14.0
added / updated specs:
- python=3.9.12
The following packages will be downloaded:
package | build
---------------------------|-----------------
sqlite-3.44.0 | h3b3482f_0 1004 KB conda-forge
------------------------------------------------------------
Total: 1004 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-hf897c2e_4
ca-certificates conda-forge/linux-aarch64::ca-certificates-2023.7.22-hcefe29a_0
ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.40-h2d8c526_0
libffi conda-forge/linux-aarch64::libffi-3.4.2-h3557bc0_5
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-13.2.0-hf8544c7_2
libgomp conda-forge/linux-aarch64::libgomp-13.2.0-hf8544c7_2
libnsl conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0
libsqlite conda-forge/linux-aarch64::libsqlite-3.44.0-h194ca79_0
libuuid conda-forge/linux-aarch64::libuuid-2.38.1-hb4cce97_0
libzlib conda-forge/linux-aarch64::libzlib-1.2.13-h31becfc_5
ncurses conda-forge/linux-aarch64::ncurses-6.4-h0425590_2
openssl conda-forge/linux-aarch64::openssl-3.1.4-h31becfc_0
pip conda-forge/noarch::pip-23.3.1-pyhd8ed1ab_0
python conda-forge/linux-aarch64::python-3.9.12-h5016f1d_1_cpython
readline conda-forge/linux-aarch64::readline-8.2-h8fc344f_1
setuptools conda-forge/noarch::setuptools-68.2.2-pyhd8ed1ab_0
sqlite conda-forge/linux-aarch64::sqlite-3.44.0-h3b3482f_0
tk conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0
tzdata conda-forge/noarch::tzdata-2023c-h71feb2d_0
wheel conda-forge/noarch::wheel-0.41.3-pyhd8ed1ab_0
xz conda-forge/linux-aarch64::xz-5.2.6-h9cdd2b7_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 23.9.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/biocbuild/tmp/RtmppLLYpW/Rbuild28fc141f6222cd/basilisk/vignettes/basilisk-vignette-test/1.14.0
added / updated specs:
- python=3.9.12
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2023.7.2~ --> pkgs/main::ca-certificates-2023.08.22-hd43f75c_0
The following packages will be SUPERSEDED by a higher-priority channel:
openssl conda-forge::openssl-3.1.4-h31becfc_0 --> pkgs/main::openssl-3.0.11-h2f4d8fa_2
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 23.9.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/biocbuild/tmp/RtmppLLYpW/Rbuild28fc141f6222cd/basilisk/vignettes/basilisk-vignette-test/1.14.0
added / updated specs:
- numpy=1.22.1
- python=3.9.12
- scikit-learn=1.1.1
The following packages will be downloaded:
package | build
---------------------------|-----------------
charset-normalizer-3.3.2 | pyhd8ed1ab_0 46 KB conda-forge
------------------------------------------------------------
Total: 46 KB
The following NEW packages will be INSTALLED:
brotli-python conda-forge/linux-aarch64::brotli-python-1.1.0-py39h387a81e_1
certifi conda-forge/noarch::certifi-2023.7.22-pyhd8ed1ab_0
charset-normalizer conda-forge/noarch::charset-normalizer-3.3.2-pyhd8ed1ab_0
idna conda-forge/noarch::idna-3.4-pyhd8ed1ab_0
joblib conda-forge/noarch::joblib-1.3.2-pyhd8ed1ab_0
libblas conda-forge/linux-aarch64::libblas-3.9.0-19_linuxaarch64_openblas
libcblas conda-forge/linux-aarch64::libcblas-3.9.0-19_linuxaarch64_openblas
libgfortran-ng conda-forge/linux-aarch64::libgfortran-ng-13.2.0-he9431aa_2
libgfortran5 conda-forge/linux-aarch64::libgfortran5-13.2.0-h582850c_2
liblapack conda-forge/linux-aarch64::liblapack-3.9.0-19_linuxaarch64_openblas
libopenblas conda-forge/linux-aarch64::libopenblas-0.3.24-pthreads_h5a5ec62_0
libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-13.2.0-h9a76618_2
numpy conda-forge/linux-aarch64::numpy-1.22.1-py39h8a86e7d_0
packaging conda-forge/noarch::packaging-23.2-pyhd8ed1ab_0
platformdirs conda-forge/noarch::platformdirs-3.11.0-pyhd8ed1ab_0
pooch conda-forge/noarch::pooch-1.8.0-pyhd8ed1ab_0
pysocks conda-forge/noarch::pysocks-1.7.1-pyha2e5f31_6
python_abi conda-forge/linux-aarch64::python_abi-3.9-4_cp39
requests conda-forge/noarch::requests-2.31.0-pyhd8ed1ab_0
scikit-learn conda-forge/linux-aarch64::scikit-learn-1.1.1-py39hd7c7e1b_0
scipy conda-forge/linux-aarch64::scipy-1.11.2-py39hf88902c_0
threadpoolctl conda-forge/noarch::threadpoolctl-3.2.0-pyha21a80b_0
typing-extensions conda-forge/noarch::typing-extensions-4.8.0-hd8ed1ab_0
typing_extensions conda-forge/noarch::typing_extensions-4.8.0-pyha770c72_0
urllib3 conda-forge/noarch::urllib3-2.0.7-pyhd8ed1ab_0
The following packages will be UPDATED:
openssl pkgs/main::openssl-3.0.11-h2f4d8fa_2 --> conda-forge::openssl-3.1.4-h31becfc_0
The following packages will be SUPERSEDED by a higher-priority channel:
ca-certificates pkgs/main::ca-certificates-2023.08.22~ --> conda-forge::ca-certificates-2023.7.22-hcefe29a_0
Downloading and Extracting Packages
charset-normalizer-3 | 46 KB | | 0%
charset-normalizer-3 | 46 KB | ########## | 100%
charset-normalizer-3 | 46 KB | ########## | 100%
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
WARNING: ignoring environment value of R_HOME
Quitting from lines 280-287 [unnamed-chunk-5] (motivation.Rmd)
Error: processing vignette 'motivation.Rmd' failed with diagnostics:
one node produced an error: Package ‘reticulate’ version 1.34.0 cannot be unloaded:
Error in unloadNamespace(package) : namespace ‘reticulate’ is imported by ‘basilisk’ so cannot be unloaded
--- failed re-building ‘motivation.Rmd’
SUMMARY: processing the following file failed:
‘motivation.Rmd’
Error: Vignette re-building failed.
Execution halted