Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:14:51 -0000 (Wed, 08 Feb 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" | 4164 |
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 119/2164 | 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: 2023-02-06 05:07:43 -0000 (Mon, 06 Feb 2023) |
EndedAt: 2023-02-06 05:10:43 -0000 (Mon, 06 Feb 2023) |
EllapsedTime: 179.2 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/RtmpGmbh42/Rbuild7deff1e21169e/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-1.1.1s-hb4cce97_1 pip conda-forge/noarch::pip-23.0-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-67.1.0-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/RtmpGmbh42/Rbuild7deff1e21169e/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-1.1.1s-hb4cce97_1 --> pkgs/main::openssl-1.1.1s-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/RtmpGmbh42/Rbuild7deff1e21169e/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-1.10.0 | py38h39f6eef_2 22.3 MB conda-forge ------------------------------------------------------------ Total: 22.3 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-39.0.0-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-1.10.0-py38h39f6eef_2 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-1.1.1s-h2f4d8fa_0 --> conda-forge::openssl-3.0.7-hb4cce97_2 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-1.10.0 | 22.3 MB | | 0% scipy-1.10.0 | 22.3 MB | | 0% scipy-1.10.0 | 22.3 MB | | 0% scipy-1.10.0 | 22.3 MB | | 1% scipy-1.10.0 | 22.3 MB | 1 | 1% scipy-1.10.0 | 22.3 MB | 2 | 2% scipy-1.10.0 | 22.3 MB | 2 | 3% scipy-1.10.0 | 22.3 MB | 3 | 4% scipy-1.10.0 | 22.3 MB | 5 | 6% scipy-1.10.0 | 22.3 MB | 7 | 8% scipy-1.10.0 | 22.3 MB | # | 10% scipy-1.10.0 | 22.3 MB | #3 | 13% scipy-1.10.0 | 22.3 MB | #7 | 17% scipy-1.10.0 | 22.3 MB | ## | 21% scipy-1.10.0 | 22.3 MB | ##3 | 24% scipy-1.10.0 | 22.3 MB | ##6 | 26% scipy-1.10.0 | 22.3 MB | ##7 | 28% scipy-1.10.0 | 22.3 MB | ### | 31% scipy-1.10.0 | 22.3 MB | ###2 | 33% scipy-1.10.0 | 22.3 MB | ###3 | 34% scipy-1.10.0 | 22.3 MB | ###4 | 35% scipy-1.10.0 | 22.3 MB | ###5 | 36% scipy-1.10.0 | 22.3 MB | ###6 | 36% scipy-1.10.0 | 22.3 MB | ###7 | 37% scipy-1.10.0 | 22.3 MB | ###8 | 38% scipy-1.10.0 | 22.3 MB | #### | 41% scipy-1.10.0 | 22.3 MB | ####2 | 42% scipy-1.10.0 | 22.3 MB | ####3 | 44% scipy-1.10.0 | 22.3 MB | ####4 | 45% scipy-1.10.0 | 22.3 MB | ####6 | 46% scipy-1.10.0 | 22.3 MB | ####6 | 47% scipy-1.10.0 | 22.3 MB | ####7 | 48% scipy-1.10.0 | 22.3 MB | ####8 | 49% scipy-1.10.0 | 22.3 MB | ####9 | 49% scipy-1.10.0 | 22.3 MB | ##### | 50% scipy-1.10.0 | 22.3 MB | #####1 | 51% scipy-1.10.0 | 22.3 MB | #####4 | 55% scipy-1.10.0 | 22.3 MB | #####7 | 57% scipy-1.10.0 | 22.3 MB | #####8 | 58% scipy-1.10.0 | 22.3 MB | #####9 | 60% scipy-1.10.0 | 22.3 MB | ###### | 61% scipy-1.10.0 | 22.3 MB | ######3 | 63% scipy-1.10.0 | 22.3 MB | ######4 | 65% scipy-1.10.0 | 22.3 MB | ######6 | 66% scipy-1.10.0 | 22.3 MB | ######7 | 68% scipy-1.10.0 | 22.3 MB | ######8 | 68% scipy-1.10.0 | 22.3 MB | ######8 | 69% scipy-1.10.0 | 22.3 MB | ######9 | 70% scipy-1.10.0 | 22.3 MB | ####### | 70% scipy-1.10.0 | 22.3 MB | #######1 | 72% scipy-1.10.0 | 22.3 MB | #######3 | 74% scipy-1.10.0 | 22.3 MB | #######5 | 75% scipy-1.10.0 | 22.3 MB | #######6 | 77% scipy-1.10.0 | 22.3 MB | #######9 | 80% scipy-1.10.0 | 22.3 MB | ########2 | 82% scipy-1.10.0 | 22.3 MB | ########3 | 84% scipy-1.10.0 | 22.3 MB | ########5 | 85% scipy-1.10.0 | 22.3 MB | ########6 | 86% scipy-1.10.0 | 22.3 MB | ########7 | 87% scipy-1.10.0 | 22.3 MB | ########8 | 88% scipy-1.10.0 | 22.3 MB | ######### | 91% scipy-1.10.0 | 22.3 MB | #########2 | 92% scipy-1.10.0 | 22.3 MB | #########3 | 93% scipy-1.10.0 | 22.3 MB | #########4 | 95% scipy-1.10.0 | 22.3 MB | #########5 | 95% scipy-1.10.0 | 22.3 MB | #########6 | 96% scipy-1.10.0 | 22.3 MB | #########7 | 97% scipy-1.10.0 | 22.3 MB | #########7 | 98% scipy-1.10.0 | 22.3 MB | #########8 | 98% scipy-1.10.0 | 22.3 MB | #########8 | 99% scipy-1.10.0 | 22.3 MB | #########9 | 100% scipy-1.10.0 | 22.3 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/RtmpGmbh42/Rbuild7deff1e21169e/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-3.0.7-hb4cce97_2 pip conda-forge/noarch::pip-23.0-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-67.1.0-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/RtmpGmbh42/Rbuild7deff1e21169e/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/RtmpGmbh42/Rbuild7deff1e21169e/basilisk/vignettes/basilisk-vignette-test2 added / updated specs: - python=3.8 - scipy==1.9.1 The following packages will be downloaded: package | build ---------------------------|----------------- numpy-1.24.2 | py38h87260ed_0 5.8 MB conda-forge ------------------------------------------------------------ Total: 5.8 MB 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 Downloading and Extracting Packages numpy-1.24.2 | 5.8 MB | | 0% numpy-1.24.2 | 5.8 MB | | 0% numpy-1.24.2 | 5.8 MB | 3 | 3% numpy-1.24.2 | 5.8 MB | 6 | 7% numpy-1.24.2 | 5.8 MB | 9 | 10% numpy-1.24.2 | 5.8 MB | #3 | 13% numpy-1.24.2 | 5.8 MB | #6 | 17% numpy-1.24.2 | 5.8 MB | ##2 | 22% numpy-1.24.2 | 5.8 MB | ###1 | 31% numpy-1.24.2 | 5.8 MB | ###7 | 38% numpy-1.24.2 | 5.8 MB | ####7 | 48% numpy-1.24.2 | 5.8 MB | ######3 | 63% numpy-1.24.2 | 5.8 MB | ########1 | 81% numpy-1.24.2 | 5.8 MB | #########3 | 93% numpy-1.24.2 | 5.8 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 Quitting from lines 294-313 (motivation.Rmd) Error: processing vignette 'motivation.Rmd' failed with diagnostics: one node produced an error: '/tmp/RtmpGmbh42/Rbuild7deff1e21169e/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