Aaron Lun
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/basilisk |
| git_branch: RELEASE_3_19 |
| git_last_commit: 0a27ae6 |
| git_last_commit_date: 2024-04-30 11:20:50 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-11 14:41 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4522 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4468 |
| 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 | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | TIMEOUT | OK | |||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | TIMEOUT | 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: /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_1.16.0.tar.gz |
| StartedAt: 2024-06-09 18:52:04 -0400 (Sun, 09 Jun 2024) |
| EndedAt: 2024-06-09 19:32:04 -0400 (Sun, 09 Jun 2024) |
| EllapsedTime: 2400.3 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_1.16.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 ‘/Users/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 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 334.436 43.918 418.029
createLocalBasiliskEnv 113.783 20.692 155.348
* 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/4.4-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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: /Users/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:
bzip2 conda-forge/osx-64::bzip2-1.0.8-h10d778d_5
ca-certificates conda-forge/osx-64::ca-certificates-2024.6.2-h8857fd0_0
libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
libsqlite conda-forge/osx-64::libsqlite-3.45.3-h92b6c6a_0
libzlib conda-forge/osx-64::libzlib-1.3.1-h87427d6_1
ncurses conda-forge/osx-64::ncurses-6.5-h5846eda_0
openssl conda-forge/osx-64::openssl-3.3.1-h87427d6_0
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/osx-64::python-3.9.12-h1cc4136_1_cpython
readline conda-forge/osx-64::readline-8.2-h9e318b2_1
setuptools conda-forge/noarch::setuptools-70.0.0-pyhd8ed1ab_0
sqlite conda-forge/osx-64::sqlite-3.45.3-h7461747_0
tk conda-forge/osx-64::tk-8.6.13-h1abcd95_1
tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0
wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
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
==> 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: /Users/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/osx-64::libblas-3.9.0-22_osx64_openblas
libcblas conda-forge/osx-64::libcblas-3.9.0-22_osx64_openblas
libcxx conda-forge/osx-64::libcxx-17.0.6-h88467a6_0
libgfortran conda-forge/osx-64::libgfortran-5.0.0-13_2_0_h97931a8_3
libgfortran5 conda-forge/osx-64::libgfortran5-13.2.0-h2873a65_3
liblapack conda-forge/osx-64::liblapack-3.9.0-22_osx64_openblas
libopenblas conda-forge/osx-64::libopenblas-0.3.27-openmp_hfef2a42_0
llvm-openmp conda-forge/osx-64::llvm-openmp-18.1.7-h15ab845_0
numpy conda-forge/osx-64::numpy-1.26.4-py39h28c39a1_0
pandas conda-forge/osx-64::pandas-1.4.3-py39hf72b562_0
python-dateutil conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
python_abi conda-forge/osx-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: /Users/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:
bzip2 conda-forge/osx-64::bzip2-1.0.8-h10d778d_5
ca-certificates conda-forge/osx-64::ca-certificates-2024.6.2-h8857fd0_0
libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
libsqlite conda-forge/osx-64::libsqlite-3.45.3-h92b6c6a_0
libzlib conda-forge/osx-64::libzlib-1.3.1-h87427d6_1
ncurses conda-forge/osx-64::ncurses-6.5-h5846eda_0
openssl conda-forge/osx-64::openssl-3.3.1-h87427d6_0
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/osx-64::python-3.9.12-h1cc4136_1_cpython
readline conda-forge/osx-64::readline-8.2-h9e318b2_1
setuptools conda-forge/noarch::setuptools-70.0.0-pyhd8ed1ab_0
sqlite conda-forge/osx-64::sqlite-3.45.3-h7461747_0
tk conda-forge/osx-64::tk-8.6.13-h1abcd95_1
tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0
wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
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
==> 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: /Users/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/osx-64::libblas-3.9.0-22_osx64_openblas
libcblas conda-forge/osx-64::libcblas-3.9.0-22_osx64_openblas
libcxx conda-forge/osx-64::libcxx-17.0.6-h88467a6_0
libgfortran conda-forge/osx-64::libgfortran-5.0.0-13_2_0_h97931a8_3
libgfortran5 conda-forge/osx-64::libgfortran5-13.2.0-h2873a65_3
liblapack conda-forge/osx-64::liblapack-3.9.0-22_osx64_openblas
libopenblas conda-forge/osx-64::libopenblas-0.3.27-openmp_hfef2a42_0
llvm-openmp conda-forge/osx-64::llvm-openmp-18.1.7-h15ab845_0
numpy conda-forge/osx-64::numpy-1.26.4-py39h28c39a1_0
pandas conda-forge/osx-64::pandas-1.4.2-py39hf72b562_2
python-dateutil conda-forge/noarch::python-dateutil-2.8.1-py_0
python_abi conda-forge/osx-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: /Users/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:
ca-certificates conda-forge/osx-64::ca-certificates-2024.6.2-h8857fd0_0
certifi conda-forge/osx-64::certifi-2019.11.28-py27h8c360ce_1
libcxx conda-forge/osx-64::libcxx-17.0.6-h88467a6_0
libffi conda-forge/osx-64::libffi-3.2.1-hb1e8313_1007
libsqlite conda-forge/osx-64::libsqlite-3.45.3-h92b6c6a_0
libzlib conda-forge/osx-64::libzlib-1.2.13-h87427d6_6
ncurses conda-forge/osx-64::ncurses-6.5-h5846eda_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-3.45.3-h7461747_0
tk conda-forge/osx-64::tk-8.6.13-h1abcd95_1
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
zlib conda-forge/osx-64::zlib-1.2.13-h87427d6_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: /Users/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:
bzip2 conda-forge/osx-64::bzip2-1.0.8-h10d778d_5
ca-certificates conda-forge/osx-64::ca-certificates-2024.6.2-h8857fd0_0
libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
libsqlite conda-forge/osx-64::libsqlite-3.45.3-h92b6c6a_0
libzlib conda-forge/osx-64::libzlib-1.3.1-h87427d6_1
ncurses conda-forge/osx-64::ncurses-6.5-h5846eda_0
openssl conda-forge/osx-64::openssl-3.3.1-h87427d6_0
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/osx-64::python-3.9.12-h1cc4136_1_cpython
readline conda-forge/osx-64::readline-8.2-h9e318b2_1
setuptools conda-forge/noarch::setuptools-70.0.0-pyhd8ed1ab_0
sqlite conda-forge/osx-64::sqlite-3.45.3-h7461747_0
tk conda-forge/osx-64::tk-8.6.13-h1abcd95_1
tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0
wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
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
==> 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: /Users/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-macosx_10_9_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)
Using cached numpy-1.26.4-cp39-cp39-macosx_10_9_x86_64.whl.metadata (61 kB)
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-macosx_10_9_x86_64.whl (11.1 MB)
Using cached numpy-1.26.4-cp39-cp39-macosx_10_9_x86_64.whl (20.6 MB)
Installing collected packages: numpy, pandas
Successfully installed numpy-1.26.4 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: /Users/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:
bzip2 conda-forge/osx-64::bzip2-1.0.8-h10d778d_5
ca-certificates conda-forge/osx-64::ca-certificates-2024.6.2-h8857fd0_0
libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
libsqlite conda-forge/osx-64::libsqlite-3.45.3-h92b6c6a_0
libzlib conda-forge/osx-64::libzlib-1.3.1-h87427d6_1
ncurses conda-forge/osx-64::ncurses-6.5-h5846eda_0
openssl conda-forge/osx-64::openssl-3.3.1-h87427d6_0
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/osx-64::python-3.9.12-h1cc4136_1_cpython
readline conda-forge/osx-64::readline-8.2-h9e318b2_1
setuptools conda-forge/noarch::setuptools-70.0.0-pyhd8ed1ab_0
sqlite conda-forge/osx-64::sqlite-3.45.3-h7461747_0
tk conda-forge/osx-64::tk-8.6.13-h1abcd95_1
tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0
wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
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
==> 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 /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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=1281 sha256=ba368f6697c1e224fa269f8d8675931c811f7374166641eb51d61d77c9837a00
Stored in directory: /private/tmp/pip-ephem-wheel-cache-896ad7eh/wheels/06/ea/2c/64b176a5f0e0d5c54a10e7c2192ba5c12db574a01cb72ede1f
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: /Users/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:
bzip2 conda-forge/osx-64::bzip2-1.0.8-h10d778d_5
ca-certificates conda-forge/osx-64::ca-certificates-2024.6.2-h8857fd0_0
libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
libsqlite conda-forge/osx-64::libsqlite-3.45.3-h92b6c6a_0
libzlib conda-forge/osx-64::libzlib-1.3.1-h87427d6_1
ncurses conda-forge/osx-64::ncurses-6.5-h5846eda_0
openssl conda-forge/osx-64::openssl-3.3.1-h87427d6_0
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/osx-64::python-3.9.12-h1cc4136_1_cpython
readline conda-forge/osx-64::readline-8.2-h9e318b2_1
setuptools conda-forge/noarch::setuptools-70.0.0-pyhd8ed1ab_0
sqlite conda-forge/osx-64::sqlite-3.45.3-h7461747_0
tk conda-forge/osx-64::tk-8.6.13-h1abcd95_1
tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0
wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
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
==> 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/osx-64
- https://conda.anaconda.org/conda-forge/noarch
- https://repo.anaconda.com/pkgs/main/osx-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/osx-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-MacOSX-x86_64.sh'
Content type 'application/x-sh' length 58693864 bytes (56.0 MB)
==================================================
downloaded 56.0 MB
PREFIX=/tmp/Rtmp61IEbk/file72d35fa5285/1.16.0/0
Unpacking payload ...
0%| | 0/36 [00:00<?, ?it/s]
Extracting : cffi-1.15.0-py39hc55c11b_1.conda: 0%| | 0/36 [00:00<?, ?it/s]
Extracting : cffi-1.15.0-py39hc55c11b_1.conda: 3%|▎ | 1/36 [00:00<00:17, 1.99it/s]
Extracting : openssl-1.1.1n-hca72f7f_0.conda: 3%|▎ | 1/36 [00:01<00:17, 1.99it/s]
Extracting : openssl-1.1.1n-hca72f7f_0.conda: 6%|▌ | 2/36 [00:01<00:19, 1.72it/s]
Extracting : certifi-2021.10.8-py39hecd8cb5_2.conda: 6%|▌ | 2/36 [00:01<00:19, 1.72it/s]
Extracting : conda-package-handling-1.8.1-py39hca72f7f_0.conda: 8%|▊ | 3/36 [00:01<00:19, 1.72it/s]
Extracting : libffi-3.3-hb1e8313_2.conda: 11%|█ | 4/36 [00:01<00:18, 1.72it/s]
Extracting : ruamel_yaml-0.15.100-py39h9ed2024_0.conda: 14%|█▍ | 5/36 [00:01<00:17, 1.72it/s]
Extracting : requests-2.27.1-pyhd3eb1b0_0.conda: 17%|█▋ | 6/36 [00:01<00:17, 1.72it/s]
Extracting : ca-certificates-2022.3.29-hecd8cb5_1.conda: 19%|█▉ | 7/36 [00:01<00:16, 1.72it/s]
Extracting : pysocks-1.7.1-py39hecd8cb5_0.conda: 22%|██▏ | 8/36 [00:01<00:16, 1.72it/s]
Extracting : zlib-1.2.12-h4dc903c_1.conda: 25%|██▌ | 9/36 [00:01<00:15, 1.72it/s]
Extracting : six-1.16.0-pyhd3eb1b0_1.conda: 28%|██▊ | 10/36 [00:01<00:15, 1.72it/s]
Extracting : ncurses-6.3-hca72f7f_2.conda: 31%|███ | 11/36 [00:03<00:14, 1.72it/s]
Extracting : ncurses-6.3-hca72f7f_2.conda: 33%|███▎ | 12/36 [00:03<00:05, 4.37it/s]
Extracting : colorama-0.4.4-pyhd3eb1b0_0.conda: 33%|███▎ | 12/36 [00:03<00:05, 4.37it/s]
Extracting : wheel-0.37.1-pyhd3eb1b0_0.conda: 36%|███▌ | 13/36 [00:03<00:05, 4.37it/s]
Extracting : brotlipy-0.7.0-py39h9ed2024_1003.conda: 39%|███▉ | 14/36 [00:03<00:05, 4.37it/s]
Extracting : charset-normalizer-2.0.4-pyhd3eb1b0_0.conda: 42%|████▏ | 15/36 [00:03<00:04, 4.37it/s]
Extracting : tk-8.6.11-h7bc2e8c_0.conda: 44%|████▍ | 16/36 [00:03<00:04, 4.37it/s]
Extracting : pycosat-0.6.3-py39h9ed2024_0.conda: 47%|████▋ | 17/36 [00:03<00:04, 4.37it/s]
Extracting : sqlite-3.38.2-h707629a_0.conda: 50%|█████ | 18/36 [00:03<00:04, 4.37it/s]
Extracting : readline-8.1.2-hca72f7f_1.conda: 53%|█████▎ | 19/36 [00:03<00:03, 4.37it/s]
Extracting : pycparser-2.21-pyhd3eb1b0_0.conda: 56%|█████▌ | 20/36 [00:03<00:03, 4.37it/s]
Extracting : python-3.9.12-hdfd78df_0.conda: 58%|█████▊ | 21/36 [00:03<00:03, 4.37it/s]
Extracting : python-3.9.12-hdfd78df_0.conda: 61%|██████ | 22/36 [00:03<00:01, 8.89it/s]
Extracting : pyopenssl-22.0.0-pyhd3eb1b0_0.conda: 61%|██████ | 22/36 [00:03<00:01, 8.89it/s]
Extracting : pip-21.2.4-py39hecd8cb5_0.conda: 64%|██████▍ | 23/36 [00:03<00:01, 8.89it/s]
Extracting : conda-4.12.0-py39hecd8cb5_0.conda: 67%|██████▋ | 24/36 [00:03<00:01, 8.89it/s]
Extracting : conda-4.12.0-py39hecd8cb5_0.conda: 69%|██████▉ | 25/36 [00:03<00:01, 7.75it/s]
Extracting : cryptography-36.0.0-py39hf6deb26_0.conda: 69%|██████▉ | 25/36 [00:03<00:01, 7.75it/s]
Extracting : urllib3-1.26.8-pyhd3eb1b0_0.conda: 72%|███████▏ | 26/36 [00:03<00:01, 7.75it/s]
Extracting : python.app-3-py39hca72f7f_0.conda: 75%|███████▌ | 27/36 [00:03<00:01, 7.75it/s]
Extracting : conda-content-trust-0.1.1-pyhd3eb1b0_0.conda: 78%|███████▊ | 28/36 [00:03<00:01, 7.75it/s]
Extracting : idna-3.3-pyhd3eb1b0_0.conda: 81%|████████ | 29/36 [00:03<00:00, 7.75it/s]
Extracting : tzdata-2022a-hda174b7_0.conda: 83%|████████▎ | 30/36 [00:03<00:00, 7.75it/s]
Extracting : xz-5.2.5-h1de35cc_0.conda: 86%|████████▌ | 31/36 [00:03<00:00, 7.75it/s]
Extracting : libcxx-12.0.0-h2f01273_0.conda: 89%|████████▉ | 32/36 [00:03<00:00, 7.75it/s]
Extracting : yaml-0.2.5-haf1e3a3_0.conda: 92%|█████████▏| 33/36 [00:03<00:00, 7.75it/s]
Extracting : tqdm-4.63.0-pyhd3eb1b0_0.conda: 94%|█████████▍| 34/36 [00:03<00:00, 7.75it/s]
Extracting : setuptools-61.2.0-py39hecd8cb5_0.conda: 97%|█████████▋| 35/36 [00:03<00:00, 7.75it/s]
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /tmp/Rtmp61IEbk/file72d35fa5285/1.16.0/0
added / updated specs:
- brotlipy==0.7.0=py39h9ed2024_1003
- ca-certificates==2022.3.29=hecd8cb5_1
- certifi==2021.10.8=py39hecd8cb5_2
- cffi==1.15.0=py39hc55c11b_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=py39hca72f7f_0
- conda==4.12.0=py39hecd8cb5_0
- cryptography==36.0.0=py39hf6deb26_0
- idna==3.3=pyhd3eb1b0_0
- libcxx==12.0.0=h2f01273_0
- libffi==3.3=hb1e8313_2
- ncurses==6.3=hca72f7f_2
- openssl==1.1.1n=hca72f7f_0
- pip==21.2.4=py39hecd8cb5_0
- pycosat==0.6.3=py39h9ed2024_0
- pycparser==2.21=pyhd3eb1b0_0
- pyopenssl==22.0.0=pyhd3eb1b0_0
- pysocks==1.7.1=py39hecd8cb5_0
- python.app==3=py39hca72f7f_0
- python==3.9.12=hdfd78df_0
- readline==8.1.2=hca72f7f_1
- requests==2.27.1=pyhd3eb1b0_0
- ruamel_yaml==0.15.100=py39h9ed2024_0
- setuptools==61.2.0=py39hecd8cb5_0
- six==1.16.0=pyhd3eb1b0_1
- sqlite==3.38.2=h707629a_0
- tk==8.6.11=h7bc2e8c_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=h1de35cc_0
- yaml==0.2.5=haf1e3a3_0
- zlib==1.2.12=h4dc903c_1
The following NEW packages will be INSTALLED:
brotlipy pkgs/main/osx-64::brotlipy-0.7.0-py39h9ed2024_1003
ca-certificates pkgs/main/osx-64::ca-certificates-2022.3.29-hecd8cb5_1
certifi pkgs/main/osx-64::certifi-2021.10.8-py39hecd8cb5_2
cffi pkgs/main/osx-64::cffi-1.15.0-py39hc55c11b_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/osx-64::conda-4.12.0-py39hecd8cb5_0
conda-content-tru~ pkgs/main/noarch::conda-content-trust-0.1.1-pyhd3eb1b0_0
conda-package-han~ pkgs/main/osx-64::conda-package-handling-1.8.1-py39hca72f7f_0
cryptography pkgs/main/osx-64::cryptography-36.0.0-py39hf6deb26_0
idna pkgs/main/noarch::idna-3.3-pyhd3eb1b0_0
libcxx pkgs/main/osx-64::libcxx-12.0.0-h2f01273_0
libffi pkgs/main/osx-64::libffi-3.3-hb1e8313_2
ncurses pkgs/main/osx-64::ncurses-6.3-hca72f7f_2
openssl pkgs/main/osx-64::openssl-1.1.1n-hca72f7f_0
pip pkgs/main/osx-64::pip-21.2.4-py39hecd8cb5_0
pycosat pkgs/main/osx-64::pycosat-0.6.3-py39h9ed2024_0
pycparser pkgs/main/noarch::pycparser-2.21-pyhd3eb1b0_0
pyopenssl pkgs/main/noarch::pyopenssl-22.0.0-pyhd3eb1b0_0
pysocks pkgs/main/osx-64::pysocks-1.7.1-py39hecd8cb5_0
python pkgs/main/osx-64::python-3.9.12-hdfd78df_0
python.app pkgs/main/osx-64::python.app-3-py39hca72f7f_0
readline pkgs/main/osx-64::readline-8.1.2-hca72f7f_1
requests pkgs/main/noarch::requests-2.27.1-pyhd3eb1b0_0
ruamel_yaml pkgs/main/osx-64::ruamel_yaml-0.15.100-py39h9ed2024_0
setuptools pkgs/main/osx-64::setuptools-61.2.0-py39hecd8cb5_0
six pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_1
sqlite pkgs/main/osx-64::sqlite-3.38.2-h707629a_0
tk pkgs/main/osx-64::tk-8.6.11-h7bc2e8c_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/osx-64::xz-5.2.5-h1de35cc_0
yaml pkgs/main/osx-64::yaml-0.2.5-haf1e3a3_0
zlib pkgs/main/osx-64::zlib-1.2.12-h4dc903c_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: /private/tmp/Rtmp61IEbk/file72d35fa5285/1.16.0/basilisk.utils/1.16.0/test
added / updated specs:
- python=3.9.12
The following packages will be downloaded:
package | build
---------------------------|-----------------
bzip2-1.0.8 | h10d778d_5 125 KB conda-forge
ca-certificates-2024.6.2 | h8857fd0_0 152 KB conda-forge
libffi-3.4.2 | h0d85af4_5 50 KB conda-forge
libsqlite-3.45.3 | h92b6c6a_0 881 KB conda-forge
libzlib-1.3.1 | h87427d6_1 56 KB conda-forge
ncurses-6.5 | h5846eda_0 804 KB conda-forge
openssl-3.3.1 | h87427d6_0 2.4 MB conda-forge
pip-24.0 | pyhd8ed1ab_0 1.3 MB conda-forge
python-3.9.12 |h1cc4136_1_cpython 12.9 MB conda-forge
readline-8.2 | h9e318b2_1 250 KB conda-forge
setuptools-70.0.0 | pyhd8ed1ab_0 472 KB conda-forge
sqlite-3.45.3 | h7461747_0 880 KB conda-forge
tk-8.6.13 | h1abcd95_1 3.1 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 | h775f41a_0 233 KB conda-forge
------------------------------------------------------------
Total: 23.7 MB
The following NEW packages will be INSTALLED:
bzip2 conda-forge/osx-64::bzip2-1.0.8-h10d778d_5
ca-certificates conda-forge/osx-64::ca-certificates-2024.6.2-h8857fd0_0
libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
libsqlite conda-forge/osx-64::libsqlite-3.45.3-h92b6c6a_0
libzlib conda-forge/osx-64::libzlib-1.3.1-h87427d6_1
ncurses conda-forge/osx-64::ncurses-6.5-h5846eda_0
openssl conda-forge/osx-64::openssl-3.3.1-h87427d6_0
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/osx-64::python-3.9.12-h1cc4136_1_cpython
readline conda-forge/osx-64::readline-8.2-h9e318b2_1
setuptools conda-forge/noarch::setuptools-70.0.0-pyhd8ed1ab_0
sqlite conda-forge/osx-64::sqlite-3.45.3-h7461747_0
tk conda-forge/osx-64::tk-8.6.13-h1abcd95_1
tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0
wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
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
==> 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: /private/tmp/Rtmp61IEbk/file72d35fa5285/1.16.0/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_osx64_openblas 14 KB conda-forge
libcblas-3.9.0 |22_osx64_openblas 14 KB conda-forge
libcxx-17.0.6 | h88467a6_0 1.2 MB conda-forge
libgfortran-5.0.0 |13_2_0_h97931a8_3 108 KB conda-forge
libgfortran5-13.2.0 | h2873a65_3 1.5 MB conda-forge
liblapack-3.9.0 |22_osx64_openblas 14 KB conda-forge
libopenblas-0.3.27 |openmp_hfef2a42_0 5.8 MB conda-forge
llvm-openmp-18.1.7 | h15ab845_0 294 KB conda-forge
numpy-1.26.4 | py39h28c39a1_0 6.2 MB conda-forge
pandas-1.4.3 | py39hf72b562_0 11.9 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: 27.3 MB
The following NEW packages will be INSTALLED:
libblas conda-forge/osx-64::libblas-3.9.0-22_osx64_openblas
libcblas conda-forge/osx-64::libcblas-3.9.0-22_osx64_openblas
libcxx conda-forge/osx-64::libcxx-17.0.6-h88467a6_0
libgfortran conda-forge/osx-64::libgfortran-5.0.0-13_2_0_h97931a8_3
libgfortran5 conda-forge/osx-64::libgfortran5-13.2.0-h2873a65_3
liblapack conda-forge/osx-64::liblapack-3.9.0-22_osx64_openblas
libopenblas conda-forge/osx-64::libopenblas-0.3.27-openmp_hfef2a42_0
llvm-openmp conda-forge/osx-64::llvm-openmp-18.1.7-h15ab845_0
numpy conda-forge/osx-64::numpy-1.26.4-py39h28c39a1_0
pandas conda-forge/osx-64::pandas-1.4.3-py39hf72b562_0
python-dateutil conda-forge/noarch::python-dateutil-2.9.0-pyhd8ed1ab_0
python_abi conda-forge/osx-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
python_abi-3.9 | 6 KB | | 0%
python_abi-3.9 | 6 KB | ########## | 100%
python_abi-3.9 | 6 KB | ########## | 100%
libgfortran-5.0.0 | 108 KB | | 0%
libgfortran-5.0.0 | 108 KB | ########## | 100%
libgfortran-5.0.0 | 108 KB | ########## | 100%
pytz-2024.1 | 184 KB | | 0%
pytz-2024.1 | 184 KB | ########## | 100%
pytz-2024.1 | 184 KB | ########## | 100%
six-1.16.0 | 14 KB | | 0%
six-1.16.0 | 14 KB | ########## | 100%
pandas-1.4.3 | 11.9 MB | | 0%
pandas-1.4.3 | 11.9 MB | | 0%
pandas-1.4.3 | 11.9 MB | #1 | 11%
pandas-1.4.3 | 11.9 MB | ##6 | 27%
pandas-1.4.3 | 11.9 MB | ####2 | 42%
pandas-1.4.3 | 11.9 MB | #####6 | 56%
pandas-1.4.3 | 11.9 MB | #######1 | 72%
pandas-1.4.3 | 11.9 MB | ########7 | 88%
pandas-1.4.3 | 11.9 MB | ########## | 100%
libgfortran5-13.2.0 | 1.5 MB | | 0%
libgfortran5-13.2.0 | 1.5 MB | ####7 | 48%
libgfortran5-13.2.0 | 1.5 MB | ########## | 100%
libgfortran5-13.2.0 | 1.5 MB | ########## | 100%
libopenblas-0.3.27 | 5.8 MB | | 0%
libopenblas-0.3.27 | 5.8 MB | #1 | 12%
libopenblas-0.3.27 | 5.8 MB | ####1 | 42%
libopenblas-0.3.27 | 5.8 MB | #######1 | 71%
libopenblas-0.3.27 | 5.8 MB | ########## | 100%
libopenblas-0.3.27 | 5.8 MB | ########## | 100%
libcxx-17.0.6 | 1.2 MB | | 0%
libcxx-17.0.6 | 1.2 MB | #######6 | 76%
libcxx-17.0.6 | 1.2 MB | ########## | 100%
llvm-openmp-18.1.7 | 294 KB | | 0%
llvm-openmp-18.1.7 | 294 KB | ########## | 100%
llvm-openmp-18.1.7 | 294 KB | ########## | 100%
liblapack-3.9.0 | 14 KB | | 0%
liblapack-3.9.0 | 14 KB | ########## | 100%
liblapack-3.9.0 | 14 KB | ########## | 100%
libcblas-3.9.0 | 14 KB | | 0%
libcblas-3.9.0 | 14 KB | ########## | 100%
libcblas-3.9.0 | 14 KB | ########## | 100%
numpy-1.26.4 | 6.2 MB | | 0%
numpy-1.26.4 | 6.2 MB | #5 | 15%
numpy-1.26.4 | 6.2 MB | ####2 | 42%
numpy-1.26.4 | 6.2 MB | #######2 | 72%
numpy-1.26.4 | 6.2 MB | #########7 | 98%
numpy-1.26.4 | 6.2 MB | ########## | 100%
python-dateutil-2.9. | 218 KB | | 0%
python-dateutil-2.9. | 218 KB | ########## | 100%
python-dateutil-2.9. | 218 KB | ########## | 100%
libblas-3.9.0 | 14 KB | | 0%
libblas-3.9.0 | 14 KB | ########## | 100%
libblas-3.9.0 | 14 KB | ########## | 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: /Users/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:
bzip2 conda-forge/osx-64::bzip2-1.0.8-h10d778d_5
ca-certificates conda-forge/osx-64::ca-certificates-2024.6.2-h8857fd0_0
libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
libsqlite conda-forge/osx-64::libsqlite-3.45.3-h92b6c6a_0
libzlib conda-forge/osx-64::libzlib-1.3.1-h87427d6_1
ncurses conda-forge/osx-64::ncurses-6.5-h5846eda_0
openssl conda-forge/osx-64::openssl-3.3.1-h87427d6_0
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/osx-64::python-3.9.12-h1cc4136_1_cpython
readline conda-forge/osx-64::readline-8.2-h9e318b2_1
setuptools conda-forge/noarch::setuptools-70.0.0-pyhd8ed1ab_0
sqlite conda-forge/osx-64::sqlite-3.45.3-h7461747_0
tk conda-forge/osx-64::tk-8.6.13-h1abcd95_1
tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0
wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
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
==> 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: /Users/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/osx-64::libblas-3.9.0-22_osx64_openblas
libcblas conda-forge/osx-64::libcblas-3.9.0-22_osx64_openblas
libcxx conda-forge/osx-64::libcxx-17.0.6-h88467a6_0
libgfortran conda-forge/osx-64::libgfortran-5.0.0-13_2_0_h97931a8_3
libgfortran5 conda-forge/osx-64::libgfortran5-13.2.0-h2873a65_3
liblapack conda-forge/osx-64::liblapack-3.9.0-22_osx64_openblas
libopenblas conda-forge/osx-64::libopenblas-0.3.27-openmp_hfef2a42_0
llvm-openmp conda-forge/osx-64::llvm-openmp-18.1.7-h15ab845_0
numpy conda-forge/osx-64::numpy-1.26.4-py39h28c39a1_0
pandas conda-forge/osx-64::pandas-1.4.3-py39hf72b562_0
python-dateutil conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
python_abi conda-forge/osx-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: /Users/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:
bzip2 conda-forge/osx-64::bzip2-1.0.8-h10d778d_5
ca-certificates conda-forge/osx-64::ca-certificates-2024.6.2-h8857fd0_0
libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
libsqlite conda-forge/osx-64::libsqlite-3.45.3-h92b6c6a_0
libzlib conda-forge/osx-64::libzlib-1.3.1-h87427d6_1
ncurses conda-forge/osx-64::ncurses-6.5-h5846eda_0
openssl conda-forge/osx-64::openssl-3.3.1-h87427d6_0
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/osx-64::python-3.9.12-h1cc4136_1_cpython
readline conda-forge/osx-64::readline-8.2-h9e318b2_1
setuptools conda-forge/noarch::setuptools-70.0.0-pyhd8ed1ab_0
sqlite conda-forge/osx-64::sqlite-3.45.3-h7461747_0
tk conda-forge/osx-64::tk-8.6.13-h1abcd95_1
tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0
wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
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
==> 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: /Users/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/osx-64::libblas-3.9.0-22_osx64_openblas
libcblas conda-forge/osx-64::libcblas-3.9.0-22_osx64_openblas
libcxx conda-forge/osx-64::libcxx-17.0.6-h88467a6_0
libgfortran conda-forge/osx-64::libgfortran-5.0.0-13_2_0_h97931a8_3
libgfortran5 conda-forge/osx-64::libgfortran5-13.2.0-h2873a65_3
liblapack conda-forge/osx-64::liblapack-3.9.0-22_osx64_openblas
libopenblas conda-forge/osx-64::libopenblas-0.3.27-openmp_hfef2a42_0
llvm-openmp conda-forge/osx-64::llvm-openmp-18.1.7-h15ab845_0
numpy conda-forge/osx-64::numpy-1.26.4-py39h28c39a1_0
pandas conda-forge/osx-64::pandas-1.4.3-py39hf72b562_0
python-dateutil conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
python_abi conda-forge/osx-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: /Users/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:
bzip2 conda-forge/osx-64::bzip2-1.0.8-h10d778d_5
ca-certificates conda-forge/osx-64::ca-certificates-2024.6.2-h8857fd0_0
libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
libsqlite conda-forge/osx-64::libsqlite-3.45.3-h92b6c6a_0
libzlib conda-forge/osx-64::libzlib-1.3.1-h87427d6_1
ncurses conda-forge/osx-64::ncurses-6.5-h5846eda_0
openssl conda-forge/osx-64::openssl-3.3.1-h87427d6_0
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/osx-64::python-3.9.12-h1cc4136_1_cpython
readline conda-forge/osx-64::readline-8.2-h9e318b2_1
setuptools conda-forge/noarch::setuptools-70.0.0-pyhd8ed1ab_0
sqlite conda-forge/osx-64::sqlite-3.45.3-h7461747_0
tk conda-forge/osx-64::tk-8.6.13-h1abcd95_1
tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0
wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
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
==> 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: /Users/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/osx-64::libblas-3.9.0-22_osx64_openblas
libcblas conda-forge/osx-64::libcblas-3.9.0-22_osx64_openblas
libcxx conda-forge/osx-64::libcxx-17.0.6-h88467a6_0
libgfortran conda-forge/osx-64::libgfortran-5.0.0-13_2_0_h97931a8_3
libgfortran5 conda-forge/osx-64::libgfortran5-13.2.0-h2873a65_3
liblapack conda-forge/osx-64::liblapack-3.9.0-22_osx64_openblas
libopenblas conda-forge/osx-64::libopenblas-0.3.27-openmp_hfef2a42_0
llvm-openmp conda-forge/osx-64::llvm-openmp-18.1.7-h15ab845_0
numpy conda-forge/osx-64::numpy-1.26.4-py39h28c39a1_0
pandas conda-forge/osx-64::pandas-1.4.2-py39hf72b562_2
python-dateutil conda-forge/noarch::python-dateutil-2.8.1-py_0
python_abi conda-forge/osx-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 2 | WARN 0 | SKIP 0 | PASS 56 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-start.R:180:5'): basilisk uses sockets correctly ───────────────
<callr_status_error/callr_error/rlib_error_3_0/rlib_error/error/condition>
Error: ! in callr subprocess.
Caused by error in `checkForRemoteErrors(lapply(cl, recvResult))`:
! one node produced an error: Unable to locate conda environment '/Users/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/my_package_B'.
Backtrace:
▆
1. ├─testthat::expect_true(...) at test-start.R:180:5
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─callr::r(...)
5. └─callr:::get_result(output = out, options)
6. └─throw(callr_remote_error(remerr, output), parent = fix_msg(remerr[[3]]))
── Error ('test-start.R:193:5'): basilisk hits the fallback R ──────────────────
<callr_status_error/callr_error/rlib_error_3_0/rlib_error/error/condition>
Error: ! in callr subprocess.
Caused by error in `checkForRemoteErrors(lapply(cl, recvResult))`:
! one node produced an error: path[1]="install-test-client/my_package_A": No such file or directory
Backtrace:
▆
1. ├─testthat::expect_true(...) at test-start.R:193:5
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─callr::r(...)
5. └─callr:::get_result(output = out, options)
6. └─throw(callr_remote_error(remerr, output), parent = fix_msg(remerr[[3]]))
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 56 ]
Error: Test failures
Execution halted
basilisk.Rcheck/basilisk-Ex.timings
| name | user | system | elapsed | |
| BasiliskEnvironment-class | 0.004 | 0.002 | 0.008 | |
| PyPiLink | 0 | 0 | 0 | |
| basiliskOptions | 0.000 | 0.000 | 0.001 | |
| basiliskStart | 334.436 | 43.918 | 418.029 | |
| configureBasiliskEnv | 0.000 | 0.000 | 0.001 | |
| createLocalBasiliskEnv | 113.783 | 20.692 | 155.348 | |
| listPackages | 0.558 | 0.261 | 1.070 | |
| obtainEnvironmentPath | 0.004 | 0.002 | 0.006 | |
| setupBasiliskEnv | 0.004 | 0.001 | 0.006 | |
| useBasiliskEnv | 0.935 | 0.380 | 1.430 | |