Back to Multiple platform build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-10-16 11:36:50 -0400 (Mon, 16 Oct 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
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 133/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
basilisk 1.12.1 (landing page) Aaron Lun
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | TIMEOUT | OK | |||||||||
merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | TIMEOUT | OK | |||||||||
kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
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: 1.12.1 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:basilisk.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings basilisk_1.12.1.tar.gz |
StartedAt: 2023-10-15 22:47:43 -0400 (Sun, 15 Oct 2023) |
EndedAt: 2023-10-15 23:27:44 -0400 (Sun, 15 Oct 2023) |
EllapsedTime: 2401.0 seconds |
RetCode: None |
Status: TIMEOUT |
CheckDir: basilisk.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:basilisk.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings basilisk_1.12.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/basilisk.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘basilisk/DESCRIPTION’ ... OK * this is package ‘basilisk’ version ‘1.12.1’ * 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 ‘/Users/biocbuild/bbs-3.17-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 R 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 dependencies in R code ... WARNING 'library' or 'require' call not declared from: ‘reticulate’ 'library' or 'require' call to ‘reticulate’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * 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 616.336 73.999 945.088 createLocalBasiliskEnv 194.970 31.830 333.669 useBasiliskEnv 3.011 1.183 5.858 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’
basilisk.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL basilisk ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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 4.3.1 (2023-06-16) -- "Beagle Scouts" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 (64-bit) 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) > 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: /Users/biocbuild/bbs-3.17-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo added / updated specs: - python=3.8.13 The following NEW packages will be INSTALLED: bzip2 conda-forge/osx-64::bzip2-1.0.8-h0d85af4_4 ca-certificates conda-forge/osx-64::ca-certificates-2023.7.22-h8857fd0_0 libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5 libsqlite conda-forge/osx-64::libsqlite-3.43.2-h92b6c6a_0 libzlib conda-forge/osx-64::libzlib-1.2.13-h8a1eda9_5 ncurses conda-forge/osx-64::ncurses-6.4-hf0c8a7f_0 openssl conda-forge/osx-64::openssl-3.1.3-h8a1eda9_0 pip conda-forge/noarch::pip-23.3-pyhd8ed1ab_0 python conda-forge/osx-64::python-3.8.13-h66c20e1_0_cpython readline conda-forge/osx-64::readline-8.2-h9e318b2_1 setuptools conda-forge/noarch::setuptools-68.2.2-pyhd8ed1ab_0 sqlite conda-forge/osx-64::sqlite-3.43.2-h7461747_0 tk conda-forge/osx-64::tk-8.6.13-hef22860_0 wheel conda-forge/noarch::wheel-0.41.2-pyhd8ed1ab_0 xz conda-forge/osx-64::xz-5.2.6-h775f41a_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 ## Package Plan ## environment location: /Users/biocbuild/bbs-3.17-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo added / updated specs: - python=3.8.13 The following packages will be UPDATED: ca-certificates conda-forge::ca-certificates-2023.7.2~ --> pkgs/main::ca-certificates-2023.08.22-hecd8cb5_0 The following packages will be SUPERSEDED by a higher-priority channel: openssl conda-forge::openssl-3.1.3-h8a1eda9_0 --> pkgs/main::openssl-3.0.11-hca72f7f_2 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: 23.9.0 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: /Users/biocbuild/bbs-3.17-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo added / updated specs: - pandas=1.4.3 - python-dateutil=2.8.2 - python=3.8.13 - pytz=2022.2.1 The following NEW packages will be INSTALLED: libblas conda-forge/osx-64::libblas-3.9.0-18_osx64_openblas libcblas conda-forge/osx-64::libcblas-3.9.0-18_osx64_openblas libcxx conda-forge/osx-64::libcxx-16.0.6-hd57cbcb_0 libgfortran conda-forge/osx-64::libgfortran-5.0.0-13_2_0_h97931a8_1 libgfortran5 conda-forge/osx-64::libgfortran5-13.2.0-h2873a65_1 liblapack conda-forge/osx-64::liblapack-3.9.0-18_osx64_openblas libopenblas conda-forge/osx-64::libopenblas-0.3.24-openmp_h48a4ad5_0 llvm-openmp conda-forge/osx-64::llvm-openmp-17.0.2-hff08bdf_0 numpy conda-forge/osx-64::numpy-1.24.4-py38h9a4a08f_0 pandas conda-forge/osx-64::pandas-1.4.3-py38h2b30649_0 python-dateutil conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0 python_abi conda-forge/osx-64::python_abi-3.8-4_cp38 pytz conda-forge/noarch::pytz-2022.2.1-pyhd8ed1ab_0 six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0 The following packages will be UPDATED: openssl pkgs/main::openssl-3.0.11-hca72f7f_2 --> conda-forge::openssl-3.1.3-h8a1eda9_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-h8857fd0_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: 23.9.0 Please update conda by running $ conda update -n base -c defaults conda WARNING: There was an error checking the latest version of pip. 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: /Users/biocbuild/bbs-3.17-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo added / updated specs: - python=3.8.13 The following NEW packages will be INSTALLED: bzip2 conda-forge/osx-64::bzip2-1.0.8-h0d85af4_4 ca-certificates conda-forge/osx-64::ca-certificates-2023.7.22-h8857fd0_0 libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5 libsqlite conda-forge/osx-64::libsqlite-3.43.2-h92b6c6a_0 libzlib conda-forge/osx-64::libzlib-1.2.13-h8a1eda9_5 ncurses conda-forge/osx-64::ncurses-6.4-hf0c8a7f_0 openssl conda-forge/osx-64::openssl-3.1.3-h8a1eda9_0 pip conda-forge/noarch::pip-23.3-pyhd8ed1ab_0 python conda-forge/osx-64::python-3.8.13-h66c20e1_0_cpython readline conda-forge/osx-64::readline-8.2-h9e318b2_1 setuptools conda-forge/noarch::setuptools-68.2.2-pyhd8ed1ab_0 sqlite conda-forge/osx-64::sqlite-3.43.2-h7461747_0 tk conda-forge/osx-64::tk-8.6.13-hef22860_0 wheel conda-forge/noarch::wheel-0.41.2-pyhd8ed1ab_0 xz conda-forge/osx-64::xz-5.2.6-h775f41a_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 ## Package Plan ## environment location: /Users/biocbuild/bbs-3.17-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo added / updated specs: - python=3.8.13 The following packages will be UPDATED: ca-certificates conda-forge::ca-certificates-2023.7.2~ --> pkgs/main::ca-certificates-2023.08.22-hecd8cb5_0 The following packages will be SUPERSEDED by a higher-priority channel: openssl conda-forge::openssl-3.1.3-h8a1eda9_0 --> pkgs/main::openssl-3.0.11-hca72f7f_2 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: 23.9.0 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: /Users/biocbuild/bbs-3.17-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo added / updated specs: - pandas=1.4.2 - python-dateutil=2.8.1 - python=3.8.13 - pytz=2022.1 The following NEW packages will be INSTALLED: libblas conda-forge/osx-64::libblas-3.9.0-18_osx64_openblas libcblas conda-forge/osx-64::libcblas-3.9.0-18_osx64_openblas libcxx conda-forge/osx-64::libcxx-16.0.6-hd57cbcb_0 libgfortran conda-forge/osx-64::libgfortran-5.0.0-13_2_0_h97931a8_1 libgfortran5 conda-forge/osx-64::libgfortran5-13.2.0-h2873a65_1 liblapack conda-forge/osx-64::liblapack-3.9.0-18_osx64_openblas libopenblas conda-forge/osx-64::libopenblas-0.3.24-openmp_h48a4ad5_0 llvm-openmp conda-forge/osx-64::llvm-openmp-17.0.2-hff08bdf_0 numpy conda-forge/osx-64::numpy-1.24.4-py38h9a4a08f_0 pandas conda-forge/osx-64::pandas-1.4.2-py38h2b30649_2 python-dateutil conda-forge/noarch::python-dateutil-2.8.1-py_0 python_abi conda-forge/osx-64::python_abi-3.8-4_cp38 pytz conda-forge/noarch::pytz-2022.1-pyhd8ed1ab_0 six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0 The following packages will be UPDATED: openssl pkgs/main::openssl-3.0.11-hca72f7f_2 --> conda-forge::openssl-3.1.3-h8a1eda9_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-h8857fd0_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: 23.9.0 Please update conda by running $ conda update -n base -c defaults conda WARNING: There was an error checking the latest version of pip. WARNING: There was an error checking the latest version of pip. 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: /Users/biocbuild/bbs-3.17-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo added / updated specs: - python=2.7 The following NEW packages will be INSTALLED: ca-certificates conda-forge/osx-64::ca-certificates-2023.7.22-h8857fd0_0 certifi conda-forge/osx-64::certifi-2019.11.28-py27h8c360ce_1 libcxx conda-forge/osx-64::libcxx-16.0.6-hd57cbcb_0 libffi conda-forge/osx-64::libffi-3.2.1-hb1e8313_1007 libsqlite conda-forge/osx-64::libsqlite-3.43.2-h92b6c6a_0 libzlib conda-forge/osx-64::libzlib-1.2.13-h8a1eda9_5 ncurses conda-forge/osx-64::ncurses-6.4-hf0c8a7f_0 openssl conda-forge/osx-64::openssl-1.1.1w-h8a1eda9_0 pip conda-forge/noarch::pip-20.1.1-pyh9f0ad1d_0 python conda-forge/osx-64::python-2.7.15-h8e446fc_1011_cpython python_abi conda-forge/osx-64::python_abi-2.7-1_cp27m readline conda-forge/osx-64::readline-8.2-h9e318b2_1 setuptools conda-forge/osx-64::setuptools-44.0.0-py27_0 sqlite conda-forge/osx-64::sqlite-3.43.2-h7461747_0 tk conda-forge/osx-64::tk-8.6.13-hef22860_0 wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0 zlib conda-forge/osx-64::zlib-1.2.13-h8a1eda9_5 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: /Users/biocbuild/bbs-3.17-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo added / updated specs: - python=2.7 The following packages will be UPDATED: ca-certificates conda-forge::ca-certificates-2023.7.2~ --> pkgs/main::ca-certificates-2023.08.22-hecd8cb5_0 certifi conda-forge/osx-64::certifi-2019.11.2~ --> pkgs/main/noarch::certifi-2020.6.20-pyhd3eb1b0_3 openssl conda-forge::openssl-1.1.1w-h8a1eda9_0 --> pkgs/main::openssl-3.0.11-hca72f7f_2 python conda-forge::python-2.7.15-h8e446fc_1~ --> pkgs/main::python-2.7.18-hc817775_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: 23.9.0 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: /Users/biocbuild/bbs-3.17-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo added / updated specs: - python[version='2.7.*,2.7.*'] 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-h8857fd0_0 certifi pkgs/main/noarch::certifi-2020.6.20-p~ --> conda-forge/osx-64::certifi-2016.9.26-py27_0 openssl pkgs/main::openssl-3.0.11-hca72f7f_2 --> conda-forge::openssl-1.1.1w-h8a1eda9_0 python pkgs/main::python-2.7.18-hc817775_0 --> conda-forge::python-2.7.15-h8e446fc_1011_cpython 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: 23.9.0 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 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: /Users/biocbuild/bbs-3.17-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo added / updated specs: - python=3.8.13 The following NEW packages will be INSTALLED: bzip2 conda-forge/osx-64::bzip2-1.0.8-h0d85af4_4 ca-certificates conda-forge/osx-64::ca-certificates-2023.7.22-h8857fd0_0 libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5 libsqlite conda-forge/osx-64::libsqlite-3.43.2-h92b6c6a_0 libzlib conda-forge/osx-64::libzlib-1.2.13-h8a1eda9_5 ncurses conda-forge/osx-64::ncurses-6.4-hf0c8a7f_0 openssl conda-forge/osx-64::openssl-3.1.3-h8a1eda9_0 pip conda-forge/noarch::pip-23.3-pyhd8ed1ab_0 python conda-forge/osx-64::python-3.8.13-h66c20e1_0_cpython readline conda-forge/osx-64::readline-8.2-h9e318b2_1 setuptools conda-forge/noarch::setuptools-68.2.2-pyhd8ed1ab_0 sqlite conda-forge/osx-64::sqlite-3.43.2-h7461747_0 tk conda-forge/osx-64::tk-8.6.13-hef22860_0 wheel conda-forge/noarch::wheel-0.41.2-pyhd8ed1ab_0 xz conda-forge/osx-64::xz-5.2.6-h775f41a_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 ## Package Plan ## environment location: /Users/biocbuild/bbs-3.17-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo added / updated specs: - python=3.8.13 The following packages will be UPDATED: ca-certificates conda-forge::ca-certificates-2023.7.2~ --> pkgs/main::ca-certificates-2023.08.22-hecd8cb5_0 The following packages will be SUPERSEDED by a higher-priority channel: openssl conda-forge::openssl-3.1.3-h8a1eda9_0 --> pkgs/main::openssl-3.0.11-hca72f7f_2 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: 23.9.0 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: /Users/biocbuild/bbs-3.17-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo added / updated specs: - python-dateutil=2.8.1 - python=3.8.13 - 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 The following packages will be UPDATED: openssl pkgs/main::openssl-3.0.11-hca72f7f_2 --> conda-forge::openssl-3.1.3-h8a1eda9_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-h8857fd0_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: 23.9.0 Please update conda by running $ conda update -n base -c defaults conda Collecting pandas==1.4.2 Downloading pandas-1.4.2-cp38-cp38-macosx_10_9_x86_64.whl (11.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.0/11.0 MB 14.2 MB/s eta 0:00:00 Requirement already satisfied: python-dateutil>=2.8.1 in ./install-test-client/thingo/lib/python3.8/site-packages (from pandas==1.4.2) (2.8.1) Requirement already satisfied: pytz>=2020.1 in ./install-test-client/thingo/lib/python3.8/site-packages (from pandas==1.4.2) (2022.1) Collecting numpy>=1.18.5 (from pandas==1.4.2) Downloading numpy-1.24.4-cp38-cp38-macosx_10_9_x86_64.whl.metadata (5.6 kB) Requirement already satisfied: six>=1.5 in ./install-test-client/thingo/lib/python3.8/site-packages (from python-dateutil>=2.8.1->pandas==1.4.2) (1.16.0) Downloading numpy-1.24.4-cp38-cp38-macosx_10_9_x86_64.whl (19.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 19.8/19.8 MB 23.6 MB/s eta 0:00:00 Installing collected packages: numpy, pandas ERROR: Could not install packages due to an OSError: [Errno 2] No such file or directory: '/Users/biocbuild/bbs-3.17-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo/lib/python3.8/site-packages/pandas-1.4.2.dist-info/INSTALLERw3o7ew_7.tmp' WARNING: There was an error checking the latest version of pip.
basilisk.Rcheck/basilisk-Ex.timings
name | user | system | elapsed | |
BasiliskEnvironment-class | 0.006 | 0.002 | 0.009 | |
PyPiLink | 0.001 | 0.001 | 0.001 | |
basiliskOptions | 0.001 | 0.000 | 0.001 | |
basiliskStart | 616.336 | 73.999 | 945.088 | |
configureBasiliskEnv | 0.000 | 0.000 | 0.001 | |
createLocalBasiliskEnv | 194.970 | 31.830 | 333.669 | |
listPackages | 1.685 | 0.760 | 4.525 | |
obtainEnvironmentPath | 0.005 | 0.002 | 0.008 | |
setupBasiliskEnv | 0.005 | 0.002 | 0.012 | |
useBasiliskEnv | 3.011 | 1.183 | 5.858 | |