Aaron Lun
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/basilisk |
| git_branch: RELEASE_3_17 |
| git_last_commit: 374eda1 |
| git_last_commit_date: 2023-06-07 02:59:19 -0400 (Wed, 07 Jun 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
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 | |