| Back to Build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-03-01 07:38:35 -0000 (Wed, 01 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
| 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 | ||||
|
To the developers/maintainers of the basilisk package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 119/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| basilisk 1.11.2 (landing page) Aaron Lun
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | ERROR | skipped | |||||||||
| Package: basilisk |
| Version: 1.11.2 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data basilisk |
| StartedAt: 2023-02-27 11:07:10 -0000 (Mon, 27 Feb 2023) |
| EndedAt: 2023-02-27 11:10:10 -0000 (Mon, 27 Feb 2023) |
| EllapsedTime: 180.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/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
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /tmp/RtmpCFB0iC/Rbuild65fce678e0ba4/basilisk/vignettes/basilisk-vignette-test/1.11.2
added / updated specs:
- python=3.8.13
The following NEW packages will be INSTALLED:
_openmp_mutex conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu
ca-certificates conda-forge/linux-aarch64::ca-certificates-2022.12.7-h4fd8a4c_0
ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.40-h2d8c526_0
libffi conda-forge/linux-aarch64::libffi-3.3-h884eca8_2
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-12.2.0-h607ecd0_19
libgomp conda-forge/linux-aarch64::libgomp-12.2.0-h607ecd0_19
libsqlite conda-forge/linux-aarch64::libsqlite-3.40.0-hf9034f9_0
libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-12.2.0-hc13a102_19
libzlib conda-forge/linux-aarch64::libzlib-1.2.13-h4e544f5_4
ncurses conda-forge/linux-aarch64::ncurses-6.3-headf329_1
openssl conda-forge/linux-aarch64::openssl-1.1.1t-hb4cce97_0
pip conda-forge/noarch::pip-23.0.1-pyhd8ed1ab_0
python pkgs/main/linux-aarch64::python-3.8.13-h6c906d0_1
readline conda-forge/linux-aarch64::readline-8.1.2-h38e3740_0
setuptools conda-forge/noarch::setuptools-67.4.0-pyhd8ed1ab_0
sqlite conda-forge/linux-aarch64::sqlite-3.40.0-h69ca7e5_0
tk conda-forge/linux-aarch64::tk-8.6.12-hd8af866_0
wheel conda-forge/noarch::wheel-0.38.4-pyhd8ed1ab_0
xz conda-forge/linux-aarch64::xz-5.2.6-h9cdd2b7_0
zlib conda-forge/linux-aarch64::zlib-1.2.13-h4e544f5_4
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /tmp/RtmpCFB0iC/Rbuild65fce678e0ba4/basilisk/vignettes/basilisk-vignette-test/1.11.2
added / updated specs:
- python=3.8.13
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2022.12.~ --> pkgs/main::ca-certificates-2023.01.10-hd43f75c_0
The following packages will be SUPERSEDED by a higher-priority channel:
openssl conda-forge::openssl-1.1.1t-hb4cce97_0 --> pkgs/main::openssl-1.1.1t-h2f4d8fa_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 23.1.0
Please update conda by running
$ conda update -n base -c defaults conda
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
## Package Plan ##
environment location: /tmp/RtmpCFB0iC/Rbuild65fce678e0ba4/basilisk/vignettes/basilisk-vignette-test/1.11.2
added / updated specs:
- numpy=1.22.1
- python=3.8.13
- scikit-learn=1.1.1
The following packages will be downloaded:
package | build
---------------------------|-----------------
scipy-1.10.1 | py38h39f6eef_0 23.1 MB conda-forge
------------------------------------------------------------
Total: 23.1 MB
The following NEW packages will be INSTALLED:
appdirs conda-forge/noarch::appdirs-1.4.4-pyh9f0ad1d_0
brotlipy conda-forge/linux-aarch64::brotlipy-0.7.0-py38hdacc76a_1005
bzip2 conda-forge/linux-aarch64::bzip2-1.0.8-hf897c2e_4
certifi conda-forge/noarch::certifi-2022.12.7-pyhd8ed1ab_0
cffi conda-forge/linux-aarch64::cffi-1.15.1-py38h6989fa8_3
charset-normalizer conda-forge/noarch::charset-normalizer-2.1.1-pyhd8ed1ab_0
cryptography conda-forge/linux-aarch64::cryptography-39.0.1-py38hd0a2be6_0
idna conda-forge/noarch::idna-3.4-pyhd8ed1ab_0
joblib conda-forge/noarch::joblib-1.2.0-pyhd8ed1ab_0
libblas conda-forge/linux-aarch64::libblas-3.9.0-16_linuxaarch64_openblas
libcblas conda-forge/linux-aarch64::libcblas-3.9.0-16_linuxaarch64_openblas
libgfortran-ng conda-forge/linux-aarch64::libgfortran-ng-12.2.0-he9431aa_19
libgfortran5 conda-forge/linux-aarch64::libgfortran5-12.2.0-hf695500_19
liblapack conda-forge/linux-aarch64::liblapack-3.9.0-16_linuxaarch64_openblas
libnsl conda-forge/linux-aarch64::libnsl-2.0.0-hf897c2e_0
libopenblas conda-forge/linux-aarch64::libopenblas-0.3.21-pthreads_h6cb6f83_3
libuuid conda-forge/linux-aarch64::libuuid-2.32.1-hf897c2e_1000
numpy conda-forge/linux-aarch64::numpy-1.22.1-py38he9a3fad_0
packaging conda-forge/noarch::packaging-23.0-pyhd8ed1ab_0
pooch conda-forge/noarch::pooch-1.6.0-pyhd8ed1ab_0
pycparser conda-forge/noarch::pycparser-2.21-pyhd8ed1ab_0
pyopenssl conda-forge/noarch::pyopenssl-23.0.0-pyhd8ed1ab_0
pysocks conda-forge/noarch::pysocks-1.7.1-pyha2e5f31_6
python_abi conda-forge/linux-aarch64::python_abi-3.8-3_cp38
requests conda-forge/noarch::requests-2.28.2-pyhd8ed1ab_0
scikit-learn conda-forge/linux-aarch64::scikit-learn-1.1.1-py38h8b84137_0
scipy conda-forge/linux-aarch64::scipy-1.10.1-py38h39f6eef_0
threadpoolctl conda-forge/noarch::threadpoolctl-3.1.0-pyh8a188c0_0
urllib3 conda-forge/noarch::urllib3-1.26.14-pyhd8ed1ab_0
The following packages will be UPDATED:
libffi 3.3-h884eca8_2 --> 3.4.2-h3557bc0_5
openssl pkgs/main::openssl-1.1.1t-h2f4d8fa_0 --> conda-forge::openssl-3.0.8-hb4cce97_0
The following packages will be SUPERSEDED by a higher-priority channel:
ca-certificates pkgs/main::ca-certificates-2023.01.10~ --> conda-forge::ca-certificates-2022.12.7-h4fd8a4c_0
python pkgs/main::python-3.8.13-h6c906d0_1 --> conda-forge::python-3.8.13-h92ab765_0_cpython
Downloading and Extracting Packages
scipy-1.10.1 | 23.1 MB | | 0%
scipy-1.10.1 | 23.1 MB | | 0%
scipy-1.10.1 | 23.1 MB | | 1%
scipy-1.10.1 | 23.1 MB | 1 | 1%
scipy-1.10.1 | 23.1 MB | 1 | 2%
scipy-1.10.1 | 23.1 MB | 2 | 2%
scipy-1.10.1 | 23.1 MB | 3 | 4%
scipy-1.10.1 | 23.1 MB | 4 | 5%
scipy-1.10.1 | 23.1 MB | 6 | 6%
scipy-1.10.1 | 23.1 MB | 8 | 9%
scipy-1.10.1 | 23.1 MB | #2 | 12%
scipy-1.10.1 | 23.1 MB | #5 | 16%
scipy-1.10.1 | 23.1 MB | #9 | 19%
scipy-1.10.1 | 23.1 MB | ##1 | 22%
scipy-1.10.1 | 23.1 MB | ##3 | 24%
scipy-1.10.1 | 23.1 MB | ##4 | 25%
scipy-1.10.1 | 23.1 MB | ##6 | 26%
scipy-1.10.1 | 23.1 MB | ##7 | 28%
scipy-1.10.1 | 23.1 MB | ##8 | 29%
scipy-1.10.1 | 23.1 MB | ### | 30%
scipy-1.10.1 | 23.1 MB | ###3 | 33%
scipy-1.10.1 | 23.1 MB | ###4 | 35%
scipy-1.10.1 | 23.1 MB | ###5 | 36%
scipy-1.10.1 | 23.1 MB | ###9 | 39%
scipy-1.10.1 | 23.1 MB | #### | 41%
scipy-1.10.1 | 23.1 MB | ####1 | 42%
scipy-1.10.1 | 23.1 MB | ####2 | 43%
scipy-1.10.1 | 23.1 MB | ####3 | 44%
scipy-1.10.1 | 23.1 MB | ####4 | 44%
scipy-1.10.1 | 23.1 MB | ####5 | 46%
scipy-1.10.1 | 23.1 MB | ####6 | 47%
scipy-1.10.1 | 23.1 MB | ####8 | 49%
scipy-1.10.1 | 23.1 MB | ##### | 50%
scipy-1.10.1 | 23.1 MB | #####1 | 51%
scipy-1.10.1 | 23.1 MB | #####2 | 53%
scipy-1.10.1 | 23.1 MB | #####4 | 54%
scipy-1.10.1 | 23.1 MB | #####6 | 56%
scipy-1.10.1 | 23.1 MB | #####7 | 57%
scipy-1.10.1 | 23.1 MB | #####7 | 58%
scipy-1.10.1 | 23.1 MB | #####8 | 58%
scipy-1.10.1 | 23.1 MB | #####8 | 59%
scipy-1.10.1 | 23.1 MB | ###### | 61%
scipy-1.10.1 | 23.1 MB | ######3 | 64%
scipy-1.10.1 | 23.1 MB | ######4 | 65%
scipy-1.10.1 | 23.1 MB | ######5 | 65%
scipy-1.10.1 | 23.1 MB | ######6 | 66%
scipy-1.10.1 | 23.1 MB | ######8 | 68%
scipy-1.10.1 | 23.1 MB | ######9 | 69%
scipy-1.10.1 | 23.1 MB | ####### | 71%
scipy-1.10.1 | 23.1 MB | #######2 | 72%
scipy-1.10.1 | 23.1 MB | #######2 | 73%
scipy-1.10.1 | 23.1 MB | #######4 | 74%
scipy-1.10.1 | 23.1 MB | #######5 | 76%
scipy-1.10.1 | 23.1 MB | #######6 | 76%
scipy-1.10.1 | 23.1 MB | #######7 | 78%
scipy-1.10.1 | 23.1 MB | #######8 | 78%
scipy-1.10.1 | 23.1 MB | #######9 | 79%
scipy-1.10.1 | 23.1 MB | #######9 | 80%
scipy-1.10.1 | 23.1 MB | ######## | 80%
scipy-1.10.1 | 23.1 MB | ######## | 81%
scipy-1.10.1 | 23.1 MB | ########1 | 81%
scipy-1.10.1 | 23.1 MB | ########5 | 86%
scipy-1.10.1 | 23.1 MB | ########7 | 87%
scipy-1.10.1 | 23.1 MB | ########8 | 89%
scipy-1.10.1 | 23.1 MB | ########9 | 90%
scipy-1.10.1 | 23.1 MB | ######### | 90%
scipy-1.10.1 | 23.1 MB | #########1 | 91%
scipy-1.10.1 | 23.1 MB | #########9 | 100%
scipy-1.10.1 | 23.1 MB | ########## | 100%
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 23.1.0
Please update conda by running
$ conda update -n base -c defaults conda
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /tmp/RtmpCFB0iC/Rbuild65fce678e0ba4/basilisk/vignettes/basilisk-vignette-test2
added / updated specs:
- python=3.8
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-2022.12.7-h4fd8a4c_0
expat conda-forge/linux-aarch64::expat-2.5.0-ha18d298_0
gdbm conda-forge/linux-aarch64::gdbm-1.18-h0a1914f_2
libffi conda-forge/linux-aarch64::libffi-3.4.2-h3557bc0_5
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-12.2.0-h607ecd0_19
libgomp conda-forge/linux-aarch64::libgomp-12.2.0-h607ecd0_19
libsqlite conda-forge/linux-aarch64::libsqlite-3.40.0-hf9034f9_0
libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-12.2.0-hc13a102_19
libzlib conda-forge/linux-aarch64::libzlib-1.2.13-h4e544f5_4
ncurses conda-forge/linux-aarch64::ncurses-6.3-headf329_1
openssl conda-forge/linux-aarch64::openssl-3.0.8-hb4cce97_0
pip conda-forge/noarch::pip-23.0.1-pyhd8ed1ab_0
pypy3.8 conda-forge/linux-aarch64::pypy3.8-7.3.11-hf9a8208_0
python conda-forge/linux-aarch64::python-3.8.16-0_73_pypy
python_abi conda-forge/linux-aarch64::python_abi-3.8-3_pypy38_pp73
readline conda-forge/linux-aarch64::readline-8.1.2-h38e3740_0
setuptools conda-forge/noarch::setuptools-67.4.0-pyhd8ed1ab_0
sqlite conda-forge/linux-aarch64::sqlite-3.40.0-h69ca7e5_0
tk conda-forge/linux-aarch64::tk-8.6.12-hd8af866_0
wheel conda-forge/noarch::wheel-0.38.4-pyhd8ed1ab_0
xz conda-forge/linux-aarch64::xz-5.2.6-h9cdd2b7_0
zlib conda-forge/linux-aarch64::zlib-1.2.13-h4e544f5_4
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /tmp/RtmpCFB0iC/Rbuild65fce678e0ba4/basilisk/vignettes/basilisk-vignette-test2
added / updated specs:
- python=3.8
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2022.12.~ --> pkgs/main::ca-certificates-2023.01.10-hd43f75c_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 23.1.0
Please update conda by running
$ conda update -n base -c defaults conda
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /tmp/RtmpCFB0iC/Rbuild65fce678e0ba4/basilisk/vignettes/basilisk-vignette-test2
added / updated specs:
- python=3.8
- scipy==1.9.1
The following NEW packages will be INSTALLED:
blas pkgs/main/linux-aarch64::blas-1.0-openblas
fftw conda-forge/linux-aarch64::fftw-3.3.10-nompi_ha1d0423_106
libblas conda-forge/linux-aarch64::libblas-3.9.0-16_linuxaarch64_openblas
libcblas conda-forge/linux-aarch64::libcblas-3.9.0-16_linuxaarch64_openblas
libgfortran-ng conda-forge/linux-aarch64::libgfortran-ng-12.2.0-he9431aa_19
libgfortran5 conda-forge/linux-aarch64::libgfortran5-12.2.0-hf695500_19
liblapack conda-forge/linux-aarch64::liblapack-3.9.0-16_linuxaarch64_openblas
libopenblas conda-forge/linux-aarch64::libopenblas-0.3.21-pthreads_h6cb6f83_3
numpy conda-forge/linux-aarch64::numpy-1.24.2-py38h87260ed_0
scipy pkgs/main/linux-aarch64::scipy-1.9.1-py38h7caaa05_0
The following packages will be SUPERSEDED by a higher-priority channel:
ca-certificates pkgs/main::ca-certificates-2023.01.10~ --> conda-forge::ca-certificates-2022.12.7-h4fd8a4c_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 23.1.0
Please update conda by running
$ conda update -n base -c defaults conda
Quitting from lines 294-313 (motivation.Rmd)
Error: processing vignette 'motivation.Rmd' failed with diagnostics:
one node produced an error: '/tmp/RtmpCFB0iC/Rbuild65fce678e0ba4/basilisk/vignettes/basilisk-vignette-test2/bin/python' was not built with a shared library.
reticulate can only bind to copies of Python built with '--enable-shared'.
--- failed re-building ‘motivation.Rmd’
SUMMARY: processing the following file failed:
‘motivation.Rmd’
Error: Vignette re-building failed.
Execution halted