Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-24 09:03 -0400 (Wed, 24 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4747 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4467 |
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 134/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
basilisk 1.16.0 (landing page) Aaron Lun
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | 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 | |||||||||
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. |
Package: basilisk |
Version: 1.16.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:basilisk.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings basilisk_1.16.0.tar.gz |
StartedAt: 2024-07-21 21:53:26 -0400 (Sun, 21 Jul 2024) |
EndedAt: 2024-07-21 22:29:31 -0400 (Sun, 21 Jul 2024) |
EllapsedTime: 2165.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: basilisk.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:basilisk.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings basilisk_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘basilisk/DESCRIPTION’ ... OK * this is package ‘basilisk’ version ‘1.16.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: inst/example/.BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘basilisk’ can be installed ... NOTE Found the following notes/warnings: Non-staged installation was used See ‘/home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/00install.out’ for details. * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in shell scripts ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed basiliskStart 340.896 30.152 377.002 createLocalBasiliskEnv 117.431 10.348 130.867 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/00check.log’ for details.
basilisk.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL basilisk ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘basilisk’ ... ** using non-staged installation via StagedInstall field ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (basilisk)
basilisk.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(basilisk) Loading required package: reticulate > if (.Platform$OS.type != "windows") test_check("basilisk") 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/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo added / updated specs: - python=3.9.12 The following NEW packages will be INSTALLED: _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu bzip2 conda-forge/linux-64::bzip2-1.0.8-h4bc722e_7 ca-certificates conda-forge/linux-64::ca-certificates-2024.7.4-hbcca054_0 ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.40-hf3520f5_7 libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5 libgcc-ng conda-forge/linux-64::libgcc-ng-14.1.0-h77fa898_0 libgomp conda-forge/linux-64::libgomp-14.1.0-h77fa898_0 libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0 libsqlite conda-forge/linux-64::libsqlite-3.46.0-hde9e2c9_0 libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0 libzlib conda-forge/linux-64::libzlib-1.3.1-h4ab18f5_1 ncurses conda-forge/linux-64::ncurses-6.5-h59595ed_0 openssl conda-forge/linux-64::openssl-3.3.1-h4bc722e_2 pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 python conda-forge/linux-64::python-3.9.12-h2660328_1_cpython readline conda-forge/linux-64::readline-8.2-h8228510_1 setuptools conda-forge/noarch::setuptools-71.0.4-pyhd8ed1ab_0 sqlite conda-forge/linux-64::sqlite-3.46.0-h6d4b2fc_0 tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101 tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0 wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1 xz conda-forge/linux-64::xz-5.2.6-h166bdaf_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: 24.5.0 Please update conda by running $ conda update -n base -c defaults conda # All requested packages already installed. 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: 24.5.0 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo added / updated specs: - pandas=1.4.3 - python-dateutil=2.8.2 - python=3.9.12 - pytz=2022.2.1 The following NEW packages will be INSTALLED: libblas conda-forge/linux-64::libblas-3.9.0-22_linux64_openblas libcblas conda-forge/linux-64::libcblas-3.9.0-22_linux64_openblas libgfortran-ng conda-forge/linux-64::libgfortran-ng-14.1.0-h69a702a_0 libgfortran5 conda-forge/linux-64::libgfortran5-14.1.0-hc5f4f2c_0 liblapack conda-forge/linux-64::liblapack-3.9.0-22_linux64_openblas libopenblas conda-forge/linux-64::libopenblas-0.3.27-pthreads_hac2b453_1 libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-14.1.0-hc0a3c3a_0 numpy conda-forge/linux-64::numpy-1.26.4-py39h474f0d3_0 pandas conda-forge/linux-64::pandas-1.4.3-py39h1832856_0 python-dateutil conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0 python_abi conda-forge/linux-64::python_abi-3.9-4_cp39 pytz conda-forge/noarch::pytz-2022.2.1-pyhd8ed1ab_0 six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0 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 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/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo added / updated specs: - python=3.9.12 The following NEW packages will be INSTALLED: _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu bzip2 conda-forge/linux-64::bzip2-1.0.8-h4bc722e_7 ca-certificates conda-forge/linux-64::ca-certificates-2024.7.4-hbcca054_0 ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.40-hf3520f5_7 libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5 libgcc-ng conda-forge/linux-64::libgcc-ng-14.1.0-h77fa898_0 libgomp conda-forge/linux-64::libgomp-14.1.0-h77fa898_0 libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0 libsqlite conda-forge/linux-64::libsqlite-3.46.0-hde9e2c9_0 libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0 libzlib conda-forge/linux-64::libzlib-1.3.1-h4ab18f5_1 ncurses conda-forge/linux-64::ncurses-6.5-h59595ed_0 openssl conda-forge/linux-64::openssl-3.3.1-h4bc722e_2 pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 python conda-forge/linux-64::python-3.9.12-h2660328_1_cpython readline conda-forge/linux-64::readline-8.2-h8228510_1 setuptools conda-forge/noarch::setuptools-71.0.4-pyhd8ed1ab_0 sqlite conda-forge/linux-64::sqlite-3.46.0-h6d4b2fc_0 tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101 tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0 wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1 xz conda-forge/linux-64::xz-5.2.6-h166bdaf_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: 24.5.0 Please update conda by running $ conda update -n base -c defaults conda # All requested packages already installed. 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: 24.5.0 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo added / updated specs: - pandas=1.4.2 - python-dateutil=2.8.1 - python=3.9.12 - pytz=2022.1 The following NEW packages will be INSTALLED: libblas conda-forge/linux-64::libblas-3.9.0-22_linux64_openblas libcblas conda-forge/linux-64::libcblas-3.9.0-22_linux64_openblas libgfortran-ng conda-forge/linux-64::libgfortran-ng-14.1.0-h69a702a_0 libgfortran5 conda-forge/linux-64::libgfortran5-14.1.0-hc5f4f2c_0 liblapack conda-forge/linux-64::liblapack-3.9.0-22_linux64_openblas libopenblas conda-forge/linux-64::libopenblas-0.3.27-pthreads_hac2b453_1 libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-14.1.0-hc0a3c3a_0 numpy conda-forge/linux-64::numpy-1.26.4-py39h474f0d3_0 pandas conda-forge/linux-64::pandas-1.4.2-py39h1832856_2 python-dateutil conda-forge/noarch::python-dateutil-2.8.1-py_0 python_abi conda-forge/linux-64::python_abi-3.9-4_cp39 pytz conda-forge/noarch::pytz-2022.1-pyhd8ed1ab_0 six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0 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 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/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo added / updated specs: - python=2.7 The following NEW packages will be INSTALLED: _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu ca-certificates conda-forge/linux-64::ca-certificates-2024.7.4-hbcca054_0 certifi conda-forge/linux-64::certifi-2019.11.28-py27h8c360ce_1 ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.40-hf3520f5_7 libffi conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007 libgcc-ng conda-forge/linux-64::libgcc-ng-14.1.0-h77fa898_0 libgomp conda-forge/linux-64::libgomp-14.1.0-h77fa898_0 libsqlite conda-forge/linux-64::libsqlite-3.46.0-hde9e2c9_0 libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-14.1.0-hc0a3c3a_0 libzlib conda-forge/linux-64::libzlib-1.2.13-h4ab18f5_6 ncurses conda-forge/linux-64::ncurses-6.5-h59595ed_0 openssl conda-forge/linux-64::openssl-1.1.1w-hd590300_0 pip conda-forge/noarch::pip-20.1.1-pyh9f0ad1d_0 python conda-forge/linux-64::python-2.7.15-h5a48372_1011_cpython python_abi conda-forge/linux-64::python_abi-2.7-1_cp27mu readline conda-forge/linux-64::readline-8.2-h8228510_1 setuptools conda-forge/linux-64::setuptools-44.0.0-py27_0 sqlite conda-forge/linux-64::sqlite-3.46.0-h6d4b2fc_0 tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101 wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0 zlib conda-forge/linux-64::zlib-1.2.13-h4ab18f5_6 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: 24.5.0 Please update conda by running $ conda update -n base -c defaults conda # All requested packages already installed. 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: 24.5.0 Please update conda by running $ conda update -n base -c defaults conda # All requested packages already installed. 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/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo added / updated specs: - python=3.9.12 The following NEW packages will be INSTALLED: _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu bzip2 conda-forge/linux-64::bzip2-1.0.8-h4bc722e_7 ca-certificates conda-forge/linux-64::ca-certificates-2024.7.4-hbcca054_0 ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.40-hf3520f5_7 libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5 libgcc-ng conda-forge/linux-64::libgcc-ng-14.1.0-h77fa898_0 libgomp conda-forge/linux-64::libgomp-14.1.0-h77fa898_0 libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0 libsqlite conda-forge/linux-64::libsqlite-3.46.0-hde9e2c9_0 libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0 libzlib conda-forge/linux-64::libzlib-1.3.1-h4ab18f5_1 ncurses conda-forge/linux-64::ncurses-6.5-h59595ed_0 openssl conda-forge/linux-64::openssl-3.3.1-h4bc722e_2 pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 python conda-forge/linux-64::python-3.9.12-h2660328_1_cpython readline conda-forge/linux-64::readline-8.2-h8228510_1 setuptools conda-forge/noarch::setuptools-71.0.4-pyhd8ed1ab_0 sqlite conda-forge/linux-64::sqlite-3.46.0-h6d4b2fc_0 tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101 tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0 wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1 xz conda-forge/linux-64::xz-5.2.6-h166bdaf_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: 24.5.0 Please update conda by running $ conda update -n base -c defaults conda # All requested packages already installed. 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: 24.5.0 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo added / updated specs: - python-dateutil=2.8.1 - python=3.9.12 - pytz=2022.1 The following NEW packages will be INSTALLED: python-dateutil conda-forge/noarch::python-dateutil-2.8.1-py_0 pytz conda-forge/noarch::pytz-2022.1-pyhd8ed1ab_0 six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Collecting pandas==1.4.2 Using cached pandas-1.4.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (12 kB) Requirement already satisfied: python-dateutil>=2.8.1 in ./install-test-client/thingo/lib/python3.9/site-packages (from pandas==1.4.2) (2.8.1) Requirement already satisfied: pytz>=2020.1 in ./install-test-client/thingo/lib/python3.9/site-packages (from pandas==1.4.2) (2022.1) Collecting numpy>=1.18.5 (from pandas==1.4.2) Downloading numpy-2.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.9/60.9 kB 1.0 MB/s eta 0:00:00 Requirement already satisfied: six>=1.5 in ./install-test-client/thingo/lib/python3.9/site-packages (from python-dateutil>=2.8.1->pandas==1.4.2) (1.16.0) Using cached pandas-1.4.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.7 MB) Downloading numpy-2.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (19.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 19.5/19.5 MB 9.3 MB/s eta 0:00:00 Installing collected packages: numpy, pandas Successfully installed numpy-2.0.1 pandas-1.4.2 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/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo added / updated specs: - python=3.9.12 The following NEW packages will be INSTALLED: _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu bzip2 conda-forge/linux-64::bzip2-1.0.8-h4bc722e_7 ca-certificates conda-forge/linux-64::ca-certificates-2024.7.4-hbcca054_0 ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.40-hf3520f5_7 libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5 libgcc-ng conda-forge/linux-64::libgcc-ng-14.1.0-h77fa898_0 libgomp conda-forge/linux-64::libgomp-14.1.0-h77fa898_0 libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0 libsqlite conda-forge/linux-64::libsqlite-3.46.0-hde9e2c9_0 libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0 libzlib conda-forge/linux-64::libzlib-1.3.1-h4ab18f5_1 ncurses conda-forge/linux-64::ncurses-6.5-h59595ed_0 openssl conda-forge/linux-64::openssl-3.3.1-h4bc722e_2 pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 python conda-forge/linux-64::python-3.9.12-h2660328_1_cpython readline conda-forge/linux-64::readline-8.2-h8228510_1 setuptools conda-forge/noarch::setuptools-71.0.4-pyhd8ed1ab_0 sqlite conda-forge/linux-64::sqlite-3.46.0-h6d4b2fc_0 tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101 tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0 wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1 xz conda-forge/linux-64::xz-5.2.6-h166bdaf_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: 24.5.0 Please update conda by running $ conda update -n base -c defaults conda # All requested packages already installed. 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: 24.5.0 Please update conda by running $ conda update -n base -c defaults conda # All requested packages already installed. Processing /home/biocbuild/bbs-3.19-bioc/R/site-library/basilisk/example/inst/test_dummy Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Building wheels for collected packages: test_dummy Building wheel for test_dummy (setup.py): started Building wheel for test_dummy (setup.py): finished with status 'done' Created wheel for test_dummy: filename=test_dummy-0.1-py3-none-any.whl size=1279 sha256=27f4c3ea4fc94154d9dbbeb397df85eb3d0fe2e6203d4ca9b3deb23846599391 Stored in directory: /tmp/pip-ephem-wheel-cache-6wr8qk4g/wheels/93/5c/8f/49eb68fb0d8a5efcd98f2af153ab0d203539968f05c4cc21b7 Successfully built test_dummy Installing collected packages: test_dummy Successfully installed test_dummy-0.1 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/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo added / updated specs: - python=3.9.12 The following NEW packages will be INSTALLED: _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu bzip2 conda-forge/linux-64::bzip2-1.0.8-h4bc722e_7 ca-certificates conda-forge/linux-64::ca-certificates-2024.7.4-hbcca054_0 ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.40-hf3520f5_7 libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5 libgcc-ng conda-forge/linux-64::libgcc-ng-14.1.0-h77fa898_0 libgomp conda-forge/linux-64::libgomp-14.1.0-h77fa898_0 libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0 libsqlite conda-forge/linux-64::libsqlite-3.46.0-hde9e2c9_0 libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0 libzlib conda-forge/linux-64::libzlib-1.3.1-h4ab18f5_1 ncurses conda-forge/linux-64::ncurses-6.5-h59595ed_0 openssl conda-forge/linux-64::openssl-3.3.1-h4bc722e_2 pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 python conda-forge/linux-64::python-3.9.12-h2660328_1_cpython readline conda-forge/linux-64::readline-8.2-h8228510_1 setuptools conda-forge/noarch::setuptools-71.0.4-pyhd8ed1ab_0 sqlite conda-forge/linux-64::sqlite-3.46.0-h6d4b2fc_0 tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101 tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0 wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1 xz conda-forge/linux-64::xz-5.2.6-h166bdaf_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: 24.5.0 Please update conda by running $ conda update -n base -c defaults conda # All requested packages already installed. 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... failed with initial frozen solve. Retrying with flexible solve. PackagesNotFoundError: The following packages are not available from current channels: - whheeeeeeeeeeeeeeeeee=0.0.1 Current channels: - https://conda.anaconda.org/conda-forge/linux-64 - https://conda.anaconda.org/conda-forge/noarch - https://repo.anaconda.com/pkgs/main/linux-64 - https://repo.anaconda.com/pkgs/main/noarch - https://repo.anaconda.com/pkgs/r/linux-64 - https://repo.anaconda.com/pkgs/r/noarch To search for alternate channels that may provide the conda package you're looking for, navigate to https://anaconda.org and use the search bar at the top of the page. trying URL 'https://repo.anaconda.com/miniconda/Miniconda3-py39_4.12.0-Linux-x86_64.sh' Content type 'application/x-sh' length 76607678 bytes (73.1 MB) ================================================== downloaded 73.1 MB PREFIX=/tmp/RtmpwUyKgp/file3929b4fa45923/1.16.0/0 Unpacking payload ... 0%| | 0/40 [00:00<?, ?it/s] Extracting : charset-normalizer-2.0.4-pyhd3eb1b0_0.conda: 0%| | 0/40 [00:00<?, ?it/s] Extracting : charset-normalizer-2.0.4-pyhd3eb1b0_0.conda: 2%|▎ | 1/40 [00:00<00:15, 2.58it/s] Extracting : libffi-3.3-he6710b0_2.conda: 2%|▎ | 1/40 [00:00<00:15, 2.58it/s] Extracting : pycparser-2.21-pyhd3eb1b0_0.conda: 5%|▌ | 2/40 [00:00<00:14, 2.58it/s] Extracting : brotlipy-0.7.0-py39h27cfd23_1003.conda: 8%|▊ | 3/40 [00:00<00:14, 2.58it/s] Extracting : libstdcxx-ng-9.3.0-hd4cf53a_17.conda: 10%|█ | 4/40 [00:00<00:13, 2.58it/s] Extracting : cffi-1.15.0-py39hd667e15_1.conda: 12%|█▎ | 5/40 [00:00<00:13, 2.58it/s] Extracting : certifi-2021.10.8-py39h06a4308_2.conda: 15%|█▌ | 6/40 [00:00<00:13, 2.58it/s] Extracting : tzdata-2022a-hda174b7_0.conda: 18%|█▊ | 7/40 [00:00<00:12, 2.58it/s] Extracting : conda-package-handling-1.8.1-py39h7f8727e_0.conda: 20%|██ | 8/40 [00:00<00:12, 2.58it/s] Extracting : cryptography-36.0.0-py39h9ce1e76_0.conda: 22%|██▎ | 9/40 [00:00<00:12, 2.58it/s] Extracting : ld_impl_linux-64-2.35.1-h7274673_9.conda: 25%|██▌ | 10/40 [00:00<00:11, 2.58it/s] Extracting : pysocks-1.7.1-py39h06a4308_0.conda: 28%|██▊ | 11/40 [00:00<00:11, 2.58it/s] Extracting : idna-3.3-pyhd3eb1b0_0.conda: 30%|███ | 12/40 [00:00<00:10, 2.58it/s] Extracting : ruamel_yaml-0.15.100-py39h27cfd23_0.conda: 32%|███▎ | 13/40 [00:00<00:10, 2.58it/s] Extracting : tk-8.6.11-h1ccaba5_0.conda: 35%|███▌ | 14/40 [00:00<00:10, 2.58it/s] Extracting : colorama-0.4.4-pyhd3eb1b0_0.conda: 38%|███▊ | 15/40 [00:00<00:09, 2.58it/s] Extracting : pyopenssl-22.0.0-pyhd3eb1b0_0.conda: 40%|████ | 16/40 [00:00<00:09, 2.58it/s] Extracting : setuptools-61.2.0-py39h06a4308_0.conda: 42%|████▎ | 17/40 [00:00<00:08, 2.58it/s] Extracting : wheel-0.37.1-pyhd3eb1b0_0.conda: 45%|████▌ | 18/40 [00:00<00:08, 2.58it/s] Extracting : ncurses-6.3-h7f8727e_2.conda: 48%|████▊ | 19/40 [00:00<00:08, 2.58it/s] Extracting : requests-2.27.1-pyhd3eb1b0_0.conda: 50%|█████ | 20/40 [00:00<00:07, 2.58it/s] Extracting : pycosat-0.6.3-py39h27cfd23_0.conda: 52%|█████▎ | 21/40 [00:00<00:07, 2.58it/s] Extracting : conda-content-trust-0.1.1-pyhd3eb1b0_0.conda: 55%|█████▌ | 22/40 [00:00<00:06, 2.58it/s] Extracting : libgomp-9.3.0-h5101ec6_17.conda: 57%|█████▊ | 23/40 [00:00<00:06, 2.58it/s] Extracting : ca-certificates-2022.3.29-h06a4308_1.conda: 60%|██████ | 24/40 [00:00<00:06, 2.58it/s] Extracting : ca-certificates-2022.3.29-h06a4308_1.conda: 62%|██████▎ | 25/40 [00:00<00:00, 55.32it/s] Extracting : tqdm-4.63.0-pyhd3eb1b0_0.conda: 62%|██████▎ | 25/40 [00:00<00:00, 55.32it/s] Extracting : openssl-1.1.1n-h7f8727e_0.conda: 65%|██████▌ | 26/40 [00:00<00:00, 55.32it/s] Extracting : conda-4.12.0-py39h06a4308_0.conda: 68%|██████▊ | 27/40 [00:00<00:00, 55.32it/s] Extracting : readline-8.1.2-h7f8727e_1.conda: 70%|███████ | 28/40 [00:00<00:00, 55.32it/s] Extracting : xz-5.2.5-h7b6447c_0.conda: 72%|███████▎ | 29/40 [00:00<00:00, 55.32it/s] Extracting : _libgcc_mutex-0.1-main.conda: 75%|███████▌ | 30/40 [00:00<00:00, 55.32it/s] Extracting : zlib-1.2.12-h7f8727e_1.conda: 78%|███████▊ | 31/40 [00:00<00:00, 55.32it/s] Extracting : sqlite-3.38.2-hc218d9a_0.conda: 80%|████████ | 32/40 [00:00<00:00, 55.32it/s] Extracting : yaml-0.2.5-h7b6447c_0.conda: 82%|████████▎ | 33/40 [00:00<00:00, 55.32it/s] Extracting : yaml-0.2.5-h7b6447c_0.conda: 85%|████████▌ | 34/40 [00:00<00:00, 47.09it/s] Extracting : pip-21.2.4-py39h06a4308_0.conda: 85%|████████▌ | 34/40 [00:00<00:00, 47.09it/s] Extracting : python-3.9.12-h12debd9_0.conda: 88%|████████▊ | 35/40 [00:00<00:00, 47.09it/s] Extracting : libgcc-ng-9.3.0-h5101ec6_17.conda: 90%|█████████ | 36/40 [00:00<00:00, 47.09it/s] Extracting : urllib3-1.26.8-pyhd3eb1b0_0.conda: 92%|█████████▎| 37/40 [00:00<00:00, 47.09it/s] Extracting : six-1.16.0-pyhd3eb1b0_1.conda: 95%|█████████▌| 38/40 [00:00<00:00, 47.09it/s] Extracting : _openmp_mutex-4.5-1_gnu.tar.bz2: 98%|█████████▊| 39/40 [00:00<00:00, 47.09it/s] Collecting package metadata (current_repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /tmp/RtmpwUyKgp/file3929b4fa45923/1.16.0/0 added / updated specs: - _libgcc_mutex==0.1=main - _openmp_mutex==4.5=1_gnu - brotlipy==0.7.0=py39h27cfd23_1003 - ca-certificates==2022.3.29=h06a4308_1 - certifi==2021.10.8=py39h06a4308_2 - cffi==1.15.0=py39hd667e15_1 - charset-normalizer==2.0.4=pyhd3eb1b0_0 - colorama==0.4.4=pyhd3eb1b0_0 - conda-content-trust==0.1.1=pyhd3eb1b0_0 - conda-package-handling==1.8.1=py39h7f8727e_0 - conda==4.12.0=py39h06a4308_0 - cryptography==36.0.0=py39h9ce1e76_0 - idna==3.3=pyhd3eb1b0_0 - ld_impl_linux-64==2.35.1=h7274673_9 - libffi==3.3=he6710b0_2 - libgcc-ng==9.3.0=h5101ec6_17 - libgomp==9.3.0=h5101ec6_17 - libstdcxx-ng==9.3.0=hd4cf53a_17 - ncurses==6.3=h7f8727e_2 - openssl==1.1.1n=h7f8727e_0 - pip==21.2.4=py39h06a4308_0 - pycosat==0.6.3=py39h27cfd23_0 - pycparser==2.21=pyhd3eb1b0_0 - pyopenssl==22.0.0=pyhd3eb1b0_0 - pysocks==1.7.1=py39h06a4308_0 - python==3.9.12=h12debd9_0 - readline==8.1.2=h7f8727e_1 - requests==2.27.1=pyhd3eb1b0_0 - ruamel_yaml==0.15.100=py39h27cfd23_0 - setuptools==61.2.0=py39h06a4308_0 - six==1.16.0=pyhd3eb1b0_1 - sqlite==3.38.2=hc218d9a_0 - tk==8.6.11=h1ccaba5_0 - tqdm==4.63.0=pyhd3eb1b0_0 - tzdata==2022a=hda174b7_0 - urllib3==1.26.8=pyhd3eb1b0_0 - wheel==0.37.1=pyhd3eb1b0_0 - xz==5.2.5=h7b6447c_0 - yaml==0.2.5=h7b6447c_0 - zlib==1.2.12=h7f8727e_1 The following NEW packages will be INSTALLED: _libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main _openmp_mutex pkgs/main/linux-64::_openmp_mutex-4.5-1_gnu brotlipy pkgs/main/linux-64::brotlipy-0.7.0-py39h27cfd23_1003 ca-certificates pkgs/main/linux-64::ca-certificates-2022.3.29-h06a4308_1 certifi pkgs/main/linux-64::certifi-2021.10.8-py39h06a4308_2 cffi pkgs/main/linux-64::cffi-1.15.0-py39hd667e15_1 charset-normalizer pkgs/main/noarch::charset-normalizer-2.0.4-pyhd3eb1b0_0 colorama pkgs/main/noarch::colorama-0.4.4-pyhd3eb1b0_0 conda pkgs/main/linux-64::conda-4.12.0-py39h06a4308_0 conda-content-tru~ pkgs/main/noarch::conda-content-trust-0.1.1-pyhd3eb1b0_0 conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.8.1-py39h7f8727e_0 cryptography pkgs/main/linux-64::cryptography-36.0.0-py39h9ce1e76_0 idna pkgs/main/noarch::idna-3.3-pyhd3eb1b0_0 ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.35.1-h7274673_9 libffi pkgs/main/linux-64::libffi-3.3-he6710b0_2 libgcc-ng pkgs/main/linux-64::libgcc-ng-9.3.0-h5101ec6_17 libgomp pkgs/main/linux-64::libgomp-9.3.0-h5101ec6_17 libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-9.3.0-hd4cf53a_17 ncurses pkgs/main/linux-64::ncurses-6.3-h7f8727e_2 openssl pkgs/main/linux-64::openssl-1.1.1n-h7f8727e_0 pip pkgs/main/linux-64::pip-21.2.4-py39h06a4308_0 pycosat pkgs/main/linux-64::pycosat-0.6.3-py39h27cfd23_0 pycparser pkgs/main/noarch::pycparser-2.21-pyhd3eb1b0_0 pyopenssl pkgs/main/noarch::pyopenssl-22.0.0-pyhd3eb1b0_0 pysocks pkgs/main/linux-64::pysocks-1.7.1-py39h06a4308_0 python pkgs/main/linux-64::python-3.9.12-h12debd9_0 readline pkgs/main/linux-64::readline-8.1.2-h7f8727e_1 requests pkgs/main/noarch::requests-2.27.1-pyhd3eb1b0_0 ruamel_yaml pkgs/main/linux-64::ruamel_yaml-0.15.100-py39h27cfd23_0 setuptools pkgs/main/linux-64::setuptools-61.2.0-py39h06a4308_0 six pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_1 sqlite pkgs/main/linux-64::sqlite-3.38.2-hc218d9a_0 tk pkgs/main/linux-64::tk-8.6.11-h1ccaba5_0 tqdm pkgs/main/noarch::tqdm-4.63.0-pyhd3eb1b0_0 tzdata pkgs/main/noarch::tzdata-2022a-hda174b7_0 urllib3 pkgs/main/noarch::urllib3-1.26.8-pyhd3eb1b0_0 wheel pkgs/main/noarch::wheel-0.37.1-pyhd3eb1b0_0 xz pkgs/main/linux-64::xz-5.2.5-h7b6447c_0 yaml pkgs/main/linux-64::yaml-0.2.5-h7b6447c_0 zlib pkgs/main/linux-64::zlib-1.2.12-h7f8727e_1 Preparing transaction: ...working... done Executing transaction: ...working... done installation finished. 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: /tmp/RtmpwUyKgp/file3929b4fa45923/1.16.0/basilisk.utils/1.16.0/test added / updated specs: - python=3.9.12 The following packages will be downloaded: package | build ---------------------------|----------------- _libgcc_mutex-0.1 | conda_forge 3 KB conda-forge _openmp_mutex-4.5 | 2_gnu 23 KB conda-forge bzip2-1.0.8 | h4bc722e_7 247 KB conda-forge ca-certificates-2024.7.4 | hbcca054_0 151 KB conda-forge ld_impl_linux-64-2.40 | hf3520f5_7 691 KB conda-forge libffi-3.4.2 | h7f98852_5 57 KB conda-forge libgcc-ng-14.1.0 | h77fa898_0 822 KB conda-forge libgomp-14.1.0 | h77fa898_0 446 KB conda-forge libnsl-2.0.1 | hd590300_0 33 KB conda-forge libsqlite-3.46.0 | hde9e2c9_0 845 KB conda-forge libuuid-2.38.1 | h0b41bf4_0 33 KB conda-forge libzlib-1.3.1 | h4ab18f5_1 60 KB conda-forge ncurses-6.5 | h59595ed_0 867 KB conda-forge openssl-3.3.1 | h4bc722e_2 2.8 MB conda-forge pip-24.0 | pyhd8ed1ab_0 1.3 MB conda-forge python-3.9.12 |h2660328_1_cpython 26.6 MB conda-forge readline-8.2 | h8228510_1 275 KB conda-forge setuptools-71.0.4 | pyhd8ed1ab_0 1.4 MB conda-forge sqlite-3.46.0 | h6d4b2fc_0 840 KB conda-forge tk-8.6.13 |noxft_h4845f30_101 3.2 MB conda-forge tzdata-2024a | h0c530f3_0 117 KB conda-forge wheel-0.43.0 | pyhd8ed1ab_1 57 KB conda-forge xz-5.2.6 | h166bdaf_0 409 KB conda-forge ------------------------------------------------------------ Total: 41.1 MB The following NEW packages will be INSTALLED: _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu bzip2 conda-forge/linux-64::bzip2-1.0.8-h4bc722e_7 ca-certificates conda-forge/linux-64::ca-certificates-2024.7.4-hbcca054_0 ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.40-hf3520f5_7 libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5 libgcc-ng conda-forge/linux-64::libgcc-ng-14.1.0-h77fa898_0 libgomp conda-forge/linux-64::libgomp-14.1.0-h77fa898_0 libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0 libsqlite conda-forge/linux-64::libsqlite-3.46.0-hde9e2c9_0 libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0 libzlib conda-forge/linux-64::libzlib-1.3.1-h4ab18f5_1 ncurses conda-forge/linux-64::ncurses-6.5-h59595ed_0 openssl conda-forge/linux-64::openssl-3.3.1-h4bc722e_2 pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 python conda-forge/linux-64::python-3.9.12-h2660328_1_cpython readline conda-forge/linux-64::readline-8.2-h8228510_1 setuptools conda-forge/noarch::setuptools-71.0.4-pyhd8ed1ab_0 sqlite conda-forge/linux-64::sqlite-3.46.0-h6d4b2fc_0 tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101 tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0 wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1 xz conda-forge/linux-64::xz-5.2.6-h166bdaf_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: 24.5.0 Please update conda by running $ conda update -n base -c defaults conda # All requested packages already installed. 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: 24.5.0 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /tmp/RtmpwUyKgp/file3929b4fa45923/1.16.0/basilisk.utils/1.16.0/test added / updated specs: - pandas=1.4.3 - python=3.9.12 The following packages will be downloaded: package | build ---------------------------|----------------- libblas-3.9.0 |22_linux64_openblas 14 KB conda-forge libcblas-3.9.0 |22_linux64_openblas 14 KB conda-forge libgfortran-ng-14.1.0 | h69a702a_0 49 KB conda-forge libgfortran5-14.1.0 | hc5f4f2c_0 1.4 MB conda-forge liblapack-3.9.0 |22_linux64_openblas 14 KB conda-forge libopenblas-0.3.27 |pthreads_hac2b453_1 5.3 MB conda-forge libstdcxx-ng-14.1.0 | hc0a3c3a_0 3.7 MB conda-forge numpy-1.26.4 | py39h474f0d3_0 6.7 MB conda-forge pandas-1.4.3 | py39h1832856_0 12.5 MB conda-forge python-dateutil-2.9.0 | pyhd8ed1ab_0 218 KB conda-forge python_abi-3.9 | 4_cp39 6 KB conda-forge pytz-2024.1 | pyhd8ed1ab_0 184 KB conda-forge six-1.16.0 | pyh6c4a22f_0 14 KB conda-forge ------------------------------------------------------------ Total: 30.1 MB The following NEW packages will be INSTALLED: libblas conda-forge/linux-64::libblas-3.9.0-22_linux64_openblas libcblas conda-forge/linux-64::libcblas-3.9.0-22_linux64_openblas libgfortran-ng conda-forge/linux-64::libgfortran-ng-14.1.0-h69a702a_0 libgfortran5 conda-forge/linux-64::libgfortran5-14.1.0-hc5f4f2c_0 liblapack conda-forge/linux-64::liblapack-3.9.0-22_linux64_openblas libopenblas conda-forge/linux-64::libopenblas-0.3.27-pthreads_hac2b453_1 libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-14.1.0-hc0a3c3a_0 numpy conda-forge/linux-64::numpy-1.26.4-py39h474f0d3_0 pandas conda-forge/linux-64::pandas-1.4.3-py39h1832856_0 python-dateutil conda-forge/noarch::python-dateutil-2.9.0-pyhd8ed1ab_0 python_abi conda-forge/linux-64::python_abi-3.9-4_cp39 pytz conda-forge/noarch::pytz-2024.1-pyhd8ed1ab_0 six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0 Downloading and Extracting Packages liblapack-3.9.0 | 14 KB | | 0% liblapack-3.9.0 | 14 KB | ########## | 100% liblapack-3.9.0 | 14 KB | ########## | 100% python_abi-3.9 | 6 KB | | 0% python_abi-3.9 | 6 KB | ########## | 100% python_abi-3.9 | 6 KB | ########## | 100% pytz-2024.1 | 184 KB | | 0% pytz-2024.1 | 184 KB | ####3 | 43% pytz-2024.1 | 184 KB | ########## | 100% pytz-2024.1 | 184 KB | ########## | 100% python-dateutil-2.9. | 218 KB | | 0% python-dateutil-2.9. | 218 KB | ########## | 100% python-dateutil-2.9. | 218 KB | ########## | 100% libgfortran5-14.1.0 | 1.4 MB | | 0% libgfortran5-14.1.0 | 1.4 MB | ###4 | 35% libgfortran5-14.1.0 | 1.4 MB | ########## | 100% libgfortran5-14.1.0 | 1.4 MB | ########## | 100% libblas-3.9.0 | 14 KB | | 0% libblas-3.9.0 | 14 KB | ########## | 100% libblas-3.9.0 | 14 KB | ########## | 100% libstdcxx-ng-14.1.0 | 3.7 MB | | 0% libstdcxx-ng-14.1.0 | 3.7 MB | ##9 | 29% libstdcxx-ng-14.1.0 | 3.7 MB | #######8 | 79% libstdcxx-ng-14.1.0 | 3.7 MB | ########## | 100% numpy-1.26.4 | 6.7 MB | | 0% numpy-1.26.4 | 6.7 MB | #4 | 15% numpy-1.26.4 | 6.7 MB | ####2 | 42% numpy-1.26.4 | 6.7 MB | ######9 | 70% numpy-1.26.4 | 6.7 MB | #########7 | 97% numpy-1.26.4 | 6.7 MB | ########## | 100% six-1.16.0 | 14 KB | | 0% six-1.16.0 | 14 KB | ########## | 100% pandas-1.4.3 | 12.5 MB | | 0% pandas-1.4.3 | 12.5 MB | 8 | 9% pandas-1.4.3 | 12.5 MB | ##3 | 23% pandas-1.4.3 | 12.5 MB | ###7 | 38% pandas-1.4.3 | 12.5 MB | #####2 | 52% pandas-1.4.3 | 12.5 MB | ######6 | 67% pandas-1.4.3 | 12.5 MB | ########1 | 81% pandas-1.4.3 | 12.5 MB | #########5 | 95% pandas-1.4.3 | 12.5 MB | ########## | 100% libgfortran-ng-14.1. | 49 KB | | 0% libgfortran-ng-14.1. | 49 KB | ########## | 100% libgfortran-ng-14.1. | 49 KB | ########## | 100% libcblas-3.9.0 | 14 KB | | 0% libcblas-3.9.0 | 14 KB | ########## | 100% libcblas-3.9.0 | 14 KB | ########## | 100% libopenblas-0.3.27 | 5.3 MB | | 0% libopenblas-0.3.27 | 5.3 MB | #9 | 19% libopenblas-0.3.27 | 5.3 MB | #####4 | 54% libopenblas-0.3.27 | 5.3 MB | ########8 | 88% libopenblas-0.3.27 | 5.3 MB | ########## | 100% 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 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/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/locality/1.16.0 added / updated specs: - python=3.9.12 The following NEW packages will be INSTALLED: _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu bzip2 conda-forge/linux-64::bzip2-1.0.8-h4bc722e_7 ca-certificates conda-forge/linux-64::ca-certificates-2024.7.4-hbcca054_0 ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.40-hf3520f5_7 libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5 libgcc-ng conda-forge/linux-64::libgcc-ng-14.1.0-h77fa898_0 libgomp conda-forge/linux-64::libgomp-14.1.0-h77fa898_0 libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0 libsqlite conda-forge/linux-64::libsqlite-3.46.0-hde9e2c9_0 libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0 libzlib conda-forge/linux-64::libzlib-1.3.1-h4ab18f5_1 ncurses conda-forge/linux-64::ncurses-6.5-h59595ed_0 openssl conda-forge/linux-64::openssl-3.3.1-h4bc722e_2 pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 python conda-forge/linux-64::python-3.9.12-h2660328_1_cpython readline conda-forge/linux-64::readline-8.2-h8228510_1 setuptools conda-forge/noarch::setuptools-71.0.4-pyhd8ed1ab_0 sqlite conda-forge/linux-64::sqlite-3.46.0-h6d4b2fc_0 tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101 tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0 wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1 xz conda-forge/linux-64::xz-5.2.6-h166bdaf_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: 24.5.0 Please update conda by running $ conda update -n base -c defaults conda # All requested packages already installed. 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: 24.5.0 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/locality/1.16.0 added / updated specs: - pandas=1.4.3 - python-dateutil=2.8.2 - python=3.9.12 - pytz=2022.2.1 The following NEW packages will be INSTALLED: libblas conda-forge/linux-64::libblas-3.9.0-22_linux64_openblas libcblas conda-forge/linux-64::libcblas-3.9.0-22_linux64_openblas libgfortran-ng conda-forge/linux-64::libgfortran-ng-14.1.0-h69a702a_0 libgfortran5 conda-forge/linux-64::libgfortran5-14.1.0-hc5f4f2c_0 liblapack conda-forge/linux-64::liblapack-3.9.0-22_linux64_openblas libopenblas conda-forge/linux-64::libopenblas-0.3.27-pthreads_hac2b453_1 libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-14.1.0-hc0a3c3a_0 numpy conda-forge/linux-64::numpy-1.26.4-py39h474f0d3_0 pandas conda-forge/linux-64::pandas-1.4.3-py39h1832856_0 python-dateutil conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0 python_abi conda-forge/linux-64::python_abi-3.9-4_cp39 pytz conda-forge/noarch::pytz-2022.2.1-pyhd8ed1ab_0 six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0 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 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/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/my_package_A added / updated specs: - python=3.9.12 The following NEW packages will be INSTALLED: _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu bzip2 conda-forge/linux-64::bzip2-1.0.8-h4bc722e_7 ca-certificates conda-forge/linux-64::ca-certificates-2024.7.4-hbcca054_0 ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.40-hf3520f5_7 libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5 libgcc-ng conda-forge/linux-64::libgcc-ng-14.1.0-h77fa898_0 libgomp conda-forge/linux-64::libgomp-14.1.0-h77fa898_0 libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0 libsqlite conda-forge/linux-64::libsqlite-3.46.0-hde9e2c9_0 libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0 libzlib conda-forge/linux-64::libzlib-1.3.1-h4ab18f5_1 ncurses conda-forge/linux-64::ncurses-6.5-h59595ed_0 openssl conda-forge/linux-64::openssl-3.3.1-h4bc722e_2 pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 python conda-forge/linux-64::python-3.9.12-h2660328_1_cpython readline conda-forge/linux-64::readline-8.2-h8228510_1 setuptools conda-forge/noarch::setuptools-71.0.4-pyhd8ed1ab_0 sqlite conda-forge/linux-64::sqlite-3.46.0-h6d4b2fc_0 tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101 tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0 wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1 xz conda-forge/linux-64::xz-5.2.6-h166bdaf_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: 24.5.0 Please update conda by running $ conda update -n base -c defaults conda # All requested packages already installed. 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: 24.5.0 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/my_package_A added / updated specs: - pandas=1.4.3 - python-dateutil=2.8.2 - python=3.9.12 - pytz=2022.2.1 The following NEW packages will be INSTALLED: libblas conda-forge/linux-64::libblas-3.9.0-22_linux64_openblas libcblas conda-forge/linux-64::libcblas-3.9.0-22_linux64_openblas libgfortran-ng conda-forge/linux-64::libgfortran-ng-14.1.0-h69a702a_0 libgfortran5 conda-forge/linux-64::libgfortran5-14.1.0-hc5f4f2c_0 liblapack conda-forge/linux-64::liblapack-3.9.0-22_linux64_openblas libopenblas conda-forge/linux-64::libopenblas-0.3.27-pthreads_hac2b453_1 libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-14.1.0-hc0a3c3a_0 numpy conda-forge/linux-64::numpy-1.26.4-py39h474f0d3_0 pandas conda-forge/linux-64::pandas-1.4.3-py39h1832856_0 python-dateutil conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0 python_abi conda-forge/linux-64::python_abi-3.9-4_cp39 pytz conda-forge/noarch::pytz-2022.2.1-pyhd8ed1ab_0 six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0 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 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/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/my_package_B added / updated specs: - python=3.9.12 The following NEW packages will be INSTALLED: _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu bzip2 conda-forge/linux-64::bzip2-1.0.8-h4bc722e_7 ca-certificates conda-forge/linux-64::ca-certificates-2024.7.4-hbcca054_0 ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.40-hf3520f5_7 libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5 libgcc-ng conda-forge/linux-64::libgcc-ng-14.1.0-h77fa898_0 libgomp conda-forge/linux-64::libgomp-14.1.0-h77fa898_0 libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0 libsqlite conda-forge/linux-64::libsqlite-3.46.0-hde9e2c9_0 libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0 libzlib conda-forge/linux-64::libzlib-1.3.1-h4ab18f5_1 ncurses conda-forge/linux-64::ncurses-6.5-h59595ed_0 openssl conda-forge/linux-64::openssl-3.3.1-h4bc722e_2 pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 python conda-forge/linux-64::python-3.9.12-h2660328_1_cpython readline conda-forge/linux-64::readline-8.2-h8228510_1 setuptools conda-forge/noarch::setuptools-71.0.4-pyhd8ed1ab_0 sqlite conda-forge/linux-64::sqlite-3.46.0-h6d4b2fc_0 tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101 tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0 wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1 xz conda-forge/linux-64::xz-5.2.6-h166bdaf_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: 24.5.0 Please update conda by running $ conda update -n base -c defaults conda # All requested packages already installed. 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: 24.5.0 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/my_package_B added / updated specs: - pandas=1.4.2 - python-dateutil=2.8.1 - python=3.9.12 - pytz=2022.1 The following NEW packages will be INSTALLED: libblas conda-forge/linux-64::libblas-3.9.0-22_linux64_openblas libcblas conda-forge/linux-64::libcblas-3.9.0-22_linux64_openblas libgfortran-ng conda-forge/linux-64::libgfortran-ng-14.1.0-h69a702a_0 libgfortran5 conda-forge/linux-64::libgfortran5-14.1.0-hc5f4f2c_0 liblapack conda-forge/linux-64::liblapack-3.9.0-22_linux64_openblas libopenblas conda-forge/linux-64::libopenblas-0.3.27-pthreads_hac2b453_1 libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-14.1.0-hc0a3c3a_0 numpy conda-forge/linux-64::numpy-1.26.4-py39h474f0d3_0 pandas conda-forge/linux-64::pandas-1.4.2-py39h1832856_2 python-dateutil conda-forge/noarch::python-dateutil-2.8.1-py_0 python_abi conda-forge/linux-64::python_abi-3.9-4_cp39 pytz conda-forge/noarch::pytz-2022.1-pyhd8ed1ab_0 six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done [ FAIL 0 | WARN 0 | SKIP 0 | PASS 63 ] > > proc.time() user system elapsed 1184.258 138.982 1397.674
basilisk.Rcheck/basilisk-Ex.timings
name | user | system | elapsed | |
BasiliskEnvironment-class | 0.003 | 0.000 | 0.004 | |
PyPiLink | 0.001 | 0.000 | 0.000 | |
basiliskOptions | 0.000 | 0.000 | 0.001 | |
basiliskStart | 340.896 | 30.152 | 377.002 | |
configureBasiliskEnv | 0.001 | 0.000 | 0.001 | |
createLocalBasiliskEnv | 117.431 | 10.348 | 130.867 | |
listPackages | 0.455 | 0.074 | 0.601 | |
obtainEnvironmentPath | 0.003 | 0.004 | 0.006 | |
setupBasiliskEnv | 0.005 | 0.000 | 0.004 | |
useBasiliskEnv | 0.708 | 0.095 | 0.707 | |