Aaron Lun
| Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 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 2024-10-18 20:38 -0400 (Fri, 18 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4530 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4480 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 134/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| basilisk 1.16.0 (landing page) Aaron Lun
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | TIMEOUT | OK | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the basilisk package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/basilisk.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: basilisk |
| Version: 1.16.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:basilisk.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings basilisk_1.16.0.tar.gz |
| StartedAt: 2024-10-16 21:49:50 -0400 (Wed, 16 Oct 2024) |
| EndedAt: 2024-10-16 22:28:09 -0400 (Wed, 16 Oct 2024) |
| EllapsedTime: 2298.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: basilisk.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:basilisk.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings basilisk_1.16.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.5 LTS
* using session charset: UTF-8
* checking for file ‘basilisk/DESCRIPTION’ ... OK
* this is package ‘basilisk’ version ‘1.16.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
inst/example/.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘basilisk’ can be installed ... NOTE
Found the following notes/warnings:
Non-staged installation was used
See ‘/home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
basiliskStart 371.353 31.056 408.426
createLocalBasiliskEnv 126.194 15.929 144.994
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/00check.log’
for details.
basilisk.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL basilisk ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘basilisk’ ... ** using non-staged installation via StagedInstall field ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (basilisk)
basilisk.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(basilisk)
Loading required package: reticulate
> if (.Platform$OS.type != "windows") test_check("basilisk")
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo
added / updated specs:
- python=3.9.12
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-64::bzip2-1.0.8-h4bc722e_7
ca-certificates conda-forge/linux-64::ca-certificates-2024.8.30-hbcca054_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.43-h712a8e2_1
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc conda-forge/linux-64::libgcc-14.2.0-h77fa898_1
libgcc-ng conda-forge/linux-64::libgcc-ng-14.2.0-h69a702a_1
libgomp conda-forge/linux-64::libgomp-14.2.0-h77fa898_1
libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0
libsqlite conda-forge/linux-64::libsqlite-3.46.1-hadc24fc_0
libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0
libzlib conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2
ncurses conda-forge/linux-64::ncurses-6.5-he02047a_1
openssl conda-forge/linux-64::openssl-3.3.2-hb9d3cd8_0
pip conda-forge/noarch::pip-24.2-pyh8b19718_1
python conda-forge/linux-64::python-3.9.12-h2660328_1_cpython
readline conda-forge/linux-64::readline-8.2-h8228510_1
setuptools conda-forge/noarch::setuptools-75.1.0-pyhd8ed1ab_0
sqlite conda-forge/linux-64::sqlite-3.46.1-h9eae976_0
tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101
tzdata conda-forge/noarch::tzdata-2024b-hc8b5060_0
wheel conda-forge/noarch::wheel-0.44.0-pyhd8ed1ab_0
xz conda-forge/linux-64::xz-5.2.6-h166bdaf_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 24.9.1
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: 24.9.1
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo
added / updated specs:
- pandas=1.4.3
- python-dateutil=2.8.2
- python=3.9.12
- pytz=2022.2.1
The following NEW packages will be INSTALLED:
libblas conda-forge/linux-64::libblas-3.9.0-24_linux64_openblas
libcblas conda-forge/linux-64::libcblas-3.9.0-24_linux64_openblas
libgfortran conda-forge/linux-64::libgfortran-14.2.0-h69a702a_1
libgfortran-ng conda-forge/linux-64::libgfortran-ng-14.2.0-h69a702a_1
libgfortran5 conda-forge/linux-64::libgfortran5-14.2.0-hd5240d6_1
liblapack conda-forge/linux-64::liblapack-3.9.0-24_linux64_openblas
libopenblas conda-forge/linux-64::libopenblas-0.3.27-pthreads_hac2b453_1
libstdcxx conda-forge/linux-64::libstdcxx-14.2.0-hc0a3c3a_1
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-14.2.0-h4852527_1
numpy conda-forge/linux-64::numpy-1.26.4-py39h474f0d3_0
pandas conda-forge/linux-64::pandas-1.4.3-py39h1832856_0
python-dateutil conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
python_abi conda-forge/linux-64::python_abi-3.9-5_cp39
pytz conda-forge/noarch::pytz-2022.2.1-pyhd8ed1ab_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo
added / updated specs:
- python=3.9.12
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-64::bzip2-1.0.8-h4bc722e_7
ca-certificates conda-forge/linux-64::ca-certificates-2024.8.30-hbcca054_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.43-h712a8e2_1
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc conda-forge/linux-64::libgcc-14.2.0-h77fa898_1
libgcc-ng conda-forge/linux-64::libgcc-ng-14.2.0-h69a702a_1
libgomp conda-forge/linux-64::libgomp-14.2.0-h77fa898_1
libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0
libsqlite conda-forge/linux-64::libsqlite-3.46.1-hadc24fc_0
libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0
libzlib conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2
ncurses conda-forge/linux-64::ncurses-6.5-he02047a_1
openssl conda-forge/linux-64::openssl-3.3.2-hb9d3cd8_0
pip conda-forge/noarch::pip-24.2-pyh8b19718_1
python conda-forge/linux-64::python-3.9.12-h2660328_1_cpython
readline conda-forge/linux-64::readline-8.2-h8228510_1
setuptools conda-forge/noarch::setuptools-75.1.0-pyhd8ed1ab_0
sqlite conda-forge/linux-64::sqlite-3.46.1-h9eae976_0
tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101
tzdata conda-forge/noarch::tzdata-2024b-hc8b5060_0
wheel conda-forge/noarch::wheel-0.44.0-pyhd8ed1ab_0
xz conda-forge/linux-64::xz-5.2.6-h166bdaf_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 24.9.1
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: 24.9.1
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo
added / updated specs:
- pandas=1.4.2
- python-dateutil=2.8.1
- python=3.9.12
- pytz=2022.1
The following NEW packages will be INSTALLED:
libblas conda-forge/linux-64::libblas-3.9.0-24_linux64_openblas
libcblas conda-forge/linux-64::libcblas-3.9.0-24_linux64_openblas
libgfortran conda-forge/linux-64::libgfortran-14.2.0-h69a702a_1
libgfortran-ng conda-forge/linux-64::libgfortran-ng-14.2.0-h69a702a_1
libgfortran5 conda-forge/linux-64::libgfortran5-14.2.0-hd5240d6_1
liblapack conda-forge/linux-64::liblapack-3.9.0-24_linux64_openblas
libopenblas conda-forge/linux-64::libopenblas-0.3.27-pthreads_hac2b453_1
libstdcxx conda-forge/linux-64::libstdcxx-14.2.0-hc0a3c3a_1
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-14.2.0-h4852527_1
numpy conda-forge/linux-64::numpy-1.26.4-py39h474f0d3_0
pandas conda-forge/linux-64::pandas-1.4.2-py39h1832856_2
python-dateutil conda-forge/noarch::python-dateutil-2.8.1-py_0
python_abi conda-forge/linux-64::python_abi-3.9-5_cp39
pytz conda-forge/noarch::pytz-2022.1-pyhd8ed1ab_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo
added / updated specs:
- python=2.7
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
ca-certificates conda-forge/linux-64::ca-certificates-2024.8.30-hbcca054_0
certifi conda-forge/linux-64::certifi-2019.11.28-py27h8c360ce_1
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.43-h712a8e2_1
libffi conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007
libgcc conda-forge/linux-64::libgcc-14.2.0-h77fa898_1
libgcc-ng conda-forge/linux-64::libgcc-ng-14.2.0-h69a702a_1
libgomp conda-forge/linux-64::libgomp-14.2.0-h77fa898_1
libsqlite conda-forge/linux-64::libsqlite-3.46.0-hde9e2c9_0
libstdcxx conda-forge/linux-64::libstdcxx-14.2.0-hc0a3c3a_1
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-14.2.0-h4852527_1
libzlib conda-forge/linux-64::libzlib-1.2.13-h4ab18f5_6
ncurses conda-forge/linux-64::ncurses-6.5-he02047a_1
openssl conda-forge/linux-64::openssl-1.1.1w-hd590300_0
pip conda-forge/noarch::pip-20.1.1-pyh9f0ad1d_0
python conda-forge/linux-64::python-2.7.15-h5a48372_1011_cpython
python_abi conda-forge/linux-64::python_abi-2.7-1_cp27mu
readline conda-forge/linux-64::readline-8.2-h8228510_1
setuptools conda-forge/linux-64::setuptools-44.0.0-py27_0
sqlite conda-forge/linux-64::sqlite-3.46.0-h6d4b2fc_0
tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
zlib conda-forge/linux-64::zlib-1.2.13-h4ab18f5_6
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 24.9.1
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: 24.9.1
Please update conda by running
$ conda update -n base -c defaults conda
# All requested packages already installed.
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo
added / updated specs:
- python=3.9.12
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-64::bzip2-1.0.8-h4bc722e_7
ca-certificates conda-forge/linux-64::ca-certificates-2024.8.30-hbcca054_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.43-h712a8e2_1
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc conda-forge/linux-64::libgcc-14.2.0-h77fa898_1
libgcc-ng conda-forge/linux-64::libgcc-ng-14.2.0-h69a702a_1
libgomp conda-forge/linux-64::libgomp-14.2.0-h77fa898_1
libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0
libsqlite conda-forge/linux-64::libsqlite-3.46.1-hadc24fc_0
libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0
libzlib conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2
ncurses conda-forge/linux-64::ncurses-6.5-he02047a_1
openssl conda-forge/linux-64::openssl-3.3.2-hb9d3cd8_0
pip conda-forge/noarch::pip-24.2-pyh8b19718_1
python conda-forge/linux-64::python-3.9.12-h2660328_1_cpython
readline conda-forge/linux-64::readline-8.2-h8228510_1
setuptools conda-forge/noarch::setuptools-75.1.0-pyhd8ed1ab_0
sqlite conda-forge/linux-64::sqlite-3.46.1-h9eae976_0
tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101
tzdata conda-forge/noarch::tzdata-2024b-hc8b5060_0
wheel conda-forge/noarch::wheel-0.44.0-pyhd8ed1ab_0
xz conda-forge/linux-64::xz-5.2.6-h166bdaf_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 24.9.1
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: 24.9.1
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo
added / updated specs:
- python-dateutil=2.8.1
- python=3.9.12
- pytz=2022.1
The following NEW packages will be INSTALLED:
python-dateutil conda-forge/noarch::python-dateutil-2.8.1-py_0
pytz conda-forge/noarch::pytz-2022.1-pyhd8ed1ab_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting pandas==1.4.2
Using cached pandas-1.4.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (12 kB)
Requirement already satisfied: python-dateutil>=2.8.1 in ./install-test-client/thingo/lib/python3.9/site-packages (from pandas==1.4.2) (2.8.1)
Requirement already satisfied: pytz>=2020.1 in ./install-test-client/thingo/lib/python3.9/site-packages (from pandas==1.4.2) (2022.1)
Collecting numpy>=1.18.5 (from pandas==1.4.2)
Using cached numpy-2.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 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-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.7 MB)
Using cached numpy-2.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (19.5 MB)
Installing collected packages: numpy, pandas
Successfully installed numpy-2.0.2 pandas-1.4.2
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo
added / updated specs:
- python=3.9.12
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-64::bzip2-1.0.8-h4bc722e_7
ca-certificates conda-forge/linux-64::ca-certificates-2024.8.30-hbcca054_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.43-h712a8e2_1
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc conda-forge/linux-64::libgcc-14.2.0-h77fa898_1
libgcc-ng conda-forge/linux-64::libgcc-ng-14.2.0-h69a702a_1
libgomp conda-forge/linux-64::libgomp-14.2.0-h77fa898_1
libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0
libsqlite conda-forge/linux-64::libsqlite-3.46.1-hadc24fc_0
libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0
libzlib conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2
ncurses conda-forge/linux-64::ncurses-6.5-he02047a_1
openssl conda-forge/linux-64::openssl-3.3.2-hb9d3cd8_0
pip conda-forge/noarch::pip-24.2-pyh8b19718_1
python conda-forge/linux-64::python-3.9.12-h2660328_1_cpython
readline conda-forge/linux-64::readline-8.2-h8228510_1
setuptools conda-forge/noarch::setuptools-75.1.0-pyhd8ed1ab_0
sqlite conda-forge/linux-64::sqlite-3.46.1-h9eae976_0
tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101
tzdata conda-forge/noarch::tzdata-2024b-hc8b5060_0
wheel conda-forge/noarch::wheel-0.44.0-pyhd8ed1ab_0
xz conda-forge/linux-64::xz-5.2.6-h166bdaf_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 24.9.1
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: 24.9.1
Please update conda by running
$ conda update -n base -c defaults conda
# All requested packages already installed.
Processing /home/biocbuild/bbs-3.19-bioc/R/site-library/basilisk/example/inst/test_dummy
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Building wheels for collected packages: test_dummy
Building wheel for test_dummy (setup.py): started
Building wheel for test_dummy (setup.py): finished with status 'done'
Created wheel for test_dummy: filename=test_dummy-0.1-py3-none-any.whl size=1279 sha256=00a48658820eb5d345cac8a186296e7e4643860a4e170ef98e65e69bf5b1221e
Stored in directory: /tmp/pip-ephem-wheel-cache-4ev1ds2g/wheels/93/5c/8f/49eb68fb0d8a5efcd98f2af153ab0d203539968f05c4cc21b7
Successfully built test_dummy
Installing collected packages: test_dummy
Successfully installed test_dummy-0.1
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo
added / updated specs:
- python=3.9.12
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-64::bzip2-1.0.8-h4bc722e_7
ca-certificates conda-forge/linux-64::ca-certificates-2024.8.30-hbcca054_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.43-h712a8e2_1
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc conda-forge/linux-64::libgcc-14.2.0-h77fa898_1
libgcc-ng conda-forge/linux-64::libgcc-ng-14.2.0-h69a702a_1
libgomp conda-forge/linux-64::libgomp-14.2.0-h77fa898_1
libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0
libsqlite conda-forge/linux-64::libsqlite-3.46.1-hadc24fc_0
libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0
libzlib conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2
ncurses conda-forge/linux-64::ncurses-6.5-he02047a_1
openssl conda-forge/linux-64::openssl-3.3.2-hb9d3cd8_0
pip conda-forge/noarch::pip-24.2-pyh8b19718_1
python conda-forge/linux-64::python-3.9.12-h2660328_1_cpython
readline conda-forge/linux-64::readline-8.2-h8228510_1
setuptools conda-forge/noarch::setuptools-75.1.0-pyhd8ed1ab_0
sqlite conda-forge/linux-64::sqlite-3.46.1-h9eae976_0
tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101
tzdata conda-forge/noarch::tzdata-2024b-hc8b5060_0
wheel conda-forge/noarch::wheel-0.44.0-pyhd8ed1ab_0
xz conda-forge/linux-64::xz-5.2.6-h166bdaf_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 24.9.1
Please update conda by running
$ conda update -n base -c defaults conda
# All requested packages already installed.
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
PackagesNotFoundError: The following packages are not available from current channels:
- whheeeeeeeeeeeeeeeeee=0.0.1
Current channels:
- https://conda.anaconda.org/conda-forge/linux-64
- https://conda.anaconda.org/conda-forge/noarch
- https://repo.anaconda.com/pkgs/main/linux-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/linux-64
- https://repo.anaconda.com/pkgs/r/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
trying URL 'https://repo.anaconda.com/miniconda/Miniconda3-py39_4.12.0-Linux-x86_64.sh'
Content type 'application/x-sh' length 76607678 bytes (73.1 MB)
==================================================
downloaded 73.1 MB
PREFIX=/tmp/RtmpRVl4VB/file12bd745e24964b/1.16.0/0
Unpacking payload ...
0%| | 0/40 [00:00<?, ?it/s]
Extracting : charset-normalizer-2.0.4-pyhd3eb1b0_0.conda: 0%| | 0/40 [00:00<?, ?it/s]
Extracting : charset-normalizer-2.0.4-pyhd3eb1b0_0.conda: 2%|▎ | 1/40 [00:00<00:08, 4.83it/s]
Extracting : libffi-3.3-he6710b0_2.conda: 2%|▎ | 1/40 [00:00<00:08, 4.83it/s]
Extracting : pycparser-2.21-pyhd3eb1b0_0.conda: 5%|▌ | 2/40 [00:00<00:07, 4.83it/s]
Extracting : brotlipy-0.7.0-py39h27cfd23_1003.conda: 8%|▊ | 3/40 [00:00<00:07, 4.83it/s]
Extracting : libstdcxx-ng-9.3.0-hd4cf53a_17.conda: 10%|█ | 4/40 [00:00<00:07, 4.83it/s]
Extracting : cffi-1.15.0-py39hd667e15_1.conda: 12%|█▎ | 5/40 [00:00<00:07, 4.83it/s]
Extracting : certifi-2021.10.8-py39h06a4308_2.conda: 15%|█▌ | 6/40 [00:00<00:07, 4.83it/s]
Extracting : tzdata-2022a-hda174b7_0.conda: 18%|█▊ | 7/40 [00:00<00:06, 4.83it/s]
Extracting : conda-package-handling-1.8.1-py39h7f8727e_0.conda: 20%|██ | 8/40 [00:00<00:06, 4.83it/s]
Extracting : cryptography-36.0.0-py39h9ce1e76_0.conda: 22%|██▎ | 9/40 [00:00<00:06, 4.83it/s]
Extracting : ld_impl_linux-64-2.35.1-h7274673_9.conda: 25%|██▌ | 10/40 [00:00<00:06, 4.83it/s]
Extracting : pysocks-1.7.1-py39h06a4308_0.conda: 28%|██▊ | 11/40 [00:00<00:06, 4.83it/s]
Extracting : idna-3.3-pyhd3eb1b0_0.conda: 30%|███ | 12/40 [00:00<00:05, 4.83it/s]
Extracting : ruamel_yaml-0.15.100-py39h27cfd23_0.conda: 32%|███▎ | 13/40 [00:00<00:05, 4.83it/s]
Extracting : tk-8.6.11-h1ccaba5_0.conda: 35%|███▌ | 14/40 [00:00<00:05, 4.83it/s]
Extracting : colorama-0.4.4-pyhd3eb1b0_0.conda: 38%|███▊ | 15/40 [00:00<00:05, 4.83it/s]
Extracting : pyopenssl-22.0.0-pyhd3eb1b0_0.conda: 40%|████ | 16/40 [00:00<00:04, 4.83it/s]
Extracting : setuptools-61.2.0-py39h06a4308_0.conda: 42%|████▎ | 17/40 [00:00<00:04, 4.83it/s]
Extracting : wheel-0.37.1-pyhd3eb1b0_0.conda: 45%|████▌ | 18/40 [00:00<00:04, 4.83it/s]
Extracting : wheel-0.37.1-pyhd3eb1b0_0.conda: 48%|████▊ | 19/40 [00:00<00:00, 65.35it/s]
Extracting : ncurses-6.3-h7f8727e_2.conda: 48%|████▊ | 19/40 [00:00<00:00, 65.35it/s]
Extracting : requests-2.27.1-pyhd3eb1b0_0.conda: 50%|█████ | 20/40 [00:00<00:00, 65.35it/s]
Extracting : pycosat-0.6.3-py39h27cfd23_0.conda: 52%|█████▎ | 21/40 [00:00<00:00, 65.35it/s]
Extracting : conda-content-trust-0.1.1-pyhd3eb1b0_0.conda: 55%|█████▌ | 22/40 [00:00<00:00, 65.35it/s]
Extracting : libgomp-9.3.0-h5101ec6_17.conda: 57%|█████▊ | 23/40 [00:00<00:00, 65.35it/s]
Extracting : ca-certificates-2022.3.29-h06a4308_1.conda: 60%|██████ | 24/40 [00:00<00:00, 65.35it/s]
Extracting : tqdm-4.63.0-pyhd3eb1b0_0.conda: 62%|██████▎ | 25/40 [00:00<00:00, 65.35it/s]
Extracting : openssl-1.1.1n-h7f8727e_0.conda: 65%|██████▌ | 26/40 [00:00<00:00, 65.35it/s]
Extracting : conda-4.12.0-py39h06a4308_0.conda: 68%|██████▊ | 27/40 [00:00<00:00, 65.35it/s]
Extracting : conda-4.12.0-py39h06a4308_0.conda: 70%|███████ | 28/40 [00:00<00:00, 52.36it/s]
Extracting : readline-8.1.2-h7f8727e_1.conda: 70%|███████ | 28/40 [00:00<00:00, 52.36it/s]
Extracting : xz-5.2.5-h7b6447c_0.conda: 72%|███████▎ | 29/40 [00:00<00:00, 52.36it/s]
Extracting : _libgcc_mutex-0.1-main.conda: 75%|███████▌ | 30/40 [00:00<00:00, 52.36it/s]
Extracting : zlib-1.2.12-h7f8727e_1.conda: 78%|███████▊ | 31/40 [00:00<00:00, 52.36it/s]
Extracting : sqlite-3.38.2-hc218d9a_0.conda: 80%|████████ | 32/40 [00:00<00:00, 52.36it/s]
Extracting : yaml-0.2.5-h7b6447c_0.conda: 82%|████████▎ | 33/40 [00:00<00:00, 52.36it/s]
Extracting : pip-21.2.4-py39h06a4308_0.conda: 85%|████████▌ | 34/40 [00:00<00:00, 52.36it/s]
Extracting : python-3.9.12-h12debd9_0.conda: 88%|████████▊ | 35/40 [00:00<00:00, 52.36it/s]
Extracting : libgcc-ng-9.3.0-h5101ec6_17.conda: 90%|█████████ | 36/40 [00:00<00:00, 52.36it/s]
Extracting : urllib3-1.26.8-pyhd3eb1b0_0.conda: 92%|█████████▎| 37/40 [00:00<00:00, 52.36it/s]
Extracting : six-1.16.0-pyhd3eb1b0_1.conda: 95%|█████████▌| 38/40 [00:00<00:00, 52.36it/s]
Extracting : _openmp_mutex-4.5-1_gnu.tar.bz2: 98%|█████████▊| 39/40 [00:00<00:00, 52.36it/s]
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /tmp/RtmpRVl4VB/file12bd745e24964b/1.16.0/0
added / updated specs:
- _libgcc_mutex==0.1=main
- _openmp_mutex==4.5=1_gnu
- brotlipy==0.7.0=py39h27cfd23_1003
- ca-certificates==2022.3.29=h06a4308_1
- certifi==2021.10.8=py39h06a4308_2
- cffi==1.15.0=py39hd667e15_1
- charset-normalizer==2.0.4=pyhd3eb1b0_0
- colorama==0.4.4=pyhd3eb1b0_0
- conda-content-trust==0.1.1=pyhd3eb1b0_0
- conda-package-handling==1.8.1=py39h7f8727e_0
- conda==4.12.0=py39h06a4308_0
- cryptography==36.0.0=py39h9ce1e76_0
- idna==3.3=pyhd3eb1b0_0
- ld_impl_linux-64==2.35.1=h7274673_9
- libffi==3.3=he6710b0_2
- libgcc-ng==9.3.0=h5101ec6_17
- libgomp==9.3.0=h5101ec6_17
- libstdcxx-ng==9.3.0=hd4cf53a_17
- ncurses==6.3=h7f8727e_2
- openssl==1.1.1n=h7f8727e_0
- pip==21.2.4=py39h06a4308_0
- pycosat==0.6.3=py39h27cfd23_0
- pycparser==2.21=pyhd3eb1b0_0
- pyopenssl==22.0.0=pyhd3eb1b0_0
- pysocks==1.7.1=py39h06a4308_0
- python==3.9.12=h12debd9_0
- readline==8.1.2=h7f8727e_1
- requests==2.27.1=pyhd3eb1b0_0
- ruamel_yaml==0.15.100=py39h27cfd23_0
- setuptools==61.2.0=py39h06a4308_0
- six==1.16.0=pyhd3eb1b0_1
- sqlite==3.38.2=hc218d9a_0
- tk==8.6.11=h1ccaba5_0
- tqdm==4.63.0=pyhd3eb1b0_0
- tzdata==2022a=hda174b7_0
- urllib3==1.26.8=pyhd3eb1b0_0
- wheel==0.37.1=pyhd3eb1b0_0
- xz==5.2.5=h7b6447c_0
- yaml==0.2.5=h7b6447c_0
- zlib==1.2.12=h7f8727e_1
The following NEW packages will be INSTALLED:
_libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main
_openmp_mutex pkgs/main/linux-64::_openmp_mutex-4.5-1_gnu
brotlipy pkgs/main/linux-64::brotlipy-0.7.0-py39h27cfd23_1003
ca-certificates pkgs/main/linux-64::ca-certificates-2022.3.29-h06a4308_1
certifi pkgs/main/linux-64::certifi-2021.10.8-py39h06a4308_2
cffi pkgs/main/linux-64::cffi-1.15.0-py39hd667e15_1
charset-normalizer pkgs/main/noarch::charset-normalizer-2.0.4-pyhd3eb1b0_0
colorama pkgs/main/noarch::colorama-0.4.4-pyhd3eb1b0_0
conda pkgs/main/linux-64::conda-4.12.0-py39h06a4308_0
conda-content-tru~ pkgs/main/noarch::conda-content-trust-0.1.1-pyhd3eb1b0_0
conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.8.1-py39h7f8727e_0
cryptography pkgs/main/linux-64::cryptography-36.0.0-py39h9ce1e76_0
idna pkgs/main/noarch::idna-3.3-pyhd3eb1b0_0
ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.35.1-h7274673_9
libffi pkgs/main/linux-64::libffi-3.3-he6710b0_2
libgcc-ng pkgs/main/linux-64::libgcc-ng-9.3.0-h5101ec6_17
libgomp pkgs/main/linux-64::libgomp-9.3.0-h5101ec6_17
libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-9.3.0-hd4cf53a_17
ncurses pkgs/main/linux-64::ncurses-6.3-h7f8727e_2
openssl pkgs/main/linux-64::openssl-1.1.1n-h7f8727e_0
pip pkgs/main/linux-64::pip-21.2.4-py39h06a4308_0
pycosat pkgs/main/linux-64::pycosat-0.6.3-py39h27cfd23_0
pycparser pkgs/main/noarch::pycparser-2.21-pyhd3eb1b0_0
pyopenssl pkgs/main/noarch::pyopenssl-22.0.0-pyhd3eb1b0_0
pysocks pkgs/main/linux-64::pysocks-1.7.1-py39h06a4308_0
python pkgs/main/linux-64::python-3.9.12-h12debd9_0
readline pkgs/main/linux-64::readline-8.1.2-h7f8727e_1
requests pkgs/main/noarch::requests-2.27.1-pyhd3eb1b0_0
ruamel_yaml pkgs/main/linux-64::ruamel_yaml-0.15.100-py39h27cfd23_0
setuptools pkgs/main/linux-64::setuptools-61.2.0-py39h06a4308_0
six pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_1
sqlite pkgs/main/linux-64::sqlite-3.38.2-hc218d9a_0
tk pkgs/main/linux-64::tk-8.6.11-h1ccaba5_0
tqdm pkgs/main/noarch::tqdm-4.63.0-pyhd3eb1b0_0
tzdata pkgs/main/noarch::tzdata-2022a-hda174b7_0
urllib3 pkgs/main/noarch::urllib3-1.26.8-pyhd3eb1b0_0
wheel pkgs/main/noarch::wheel-0.37.1-pyhd3eb1b0_0
xz pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
yaml pkgs/main/linux-64::yaml-0.2.5-h7b6447c_0
zlib pkgs/main/linux-64::zlib-1.2.12-h7f8727e_1
Preparing transaction: ...working... done
Executing transaction: ...working... done
installation finished.
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /tmp/RtmpRVl4VB/file12bd745e24964b/1.16.0/basilisk.utils/1.16.0/test
added / updated specs:
- python=3.9.12
The following packages will be downloaded:
package | build
---------------------------|-----------------
_libgcc_mutex-0.1 | conda_forge 3 KB conda-forge
_openmp_mutex-4.5 | 2_gnu 23 KB conda-forge
bzip2-1.0.8 | h4bc722e_7 247 KB conda-forge
ca-certificates-2024.8.30 | hbcca054_0 155 KB conda-forge
ld_impl_linux-64-2.43 | h712a8e2_1 654 KB conda-forge
libffi-3.4.2 | h7f98852_5 57 KB conda-forge
libgcc-14.2.0 | h77fa898_1 829 KB conda-forge
libgcc-ng-14.2.0 | h69a702a_1 53 KB conda-forge
libgomp-14.2.0 | h77fa898_1 450 KB conda-forge
libnsl-2.0.1 | hd590300_0 33 KB conda-forge
libsqlite-3.46.1 | hadc24fc_0 845 KB conda-forge
libuuid-2.38.1 | h0b41bf4_0 33 KB conda-forge
libzlib-1.3.1 | hb9d3cd8_2 60 KB conda-forge
ncurses-6.5 | he02047a_1 868 KB conda-forge
openssl-3.3.2 | hb9d3cd8_0 2.8 MB conda-forge
pip-24.2 | pyh8b19718_1 1.2 MB conda-forge
python-3.9.12 |h2660328_1_cpython 26.6 MB conda-forge
readline-8.2 | h8228510_1 275 KB conda-forge
setuptools-75.1.0 | pyhd8ed1ab_0 759 KB conda-forge
sqlite-3.46.1 | h9eae976_0 839 KB conda-forge
tk-8.6.13 |noxft_h4845f30_101 3.2 MB conda-forge
tzdata-2024b | hc8b5060_0 119 KB conda-forge
wheel-0.44.0 | pyhd8ed1ab_0 57 KB conda-forge
xz-5.2.6 | h166bdaf_0 409 KB conda-forge
------------------------------------------------------------
Total: 40.3 MB
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-64::bzip2-1.0.8-h4bc722e_7
ca-certificates conda-forge/linux-64::ca-certificates-2024.8.30-hbcca054_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.43-h712a8e2_1
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc conda-forge/linux-64::libgcc-14.2.0-h77fa898_1
libgcc-ng conda-forge/linux-64::libgcc-ng-14.2.0-h69a702a_1
libgomp conda-forge/linux-64::libgomp-14.2.0-h77fa898_1
libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0
libsqlite conda-forge/linux-64::libsqlite-3.46.1-hadc24fc_0
libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0
libzlib conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2
ncurses conda-forge/linux-64::ncurses-6.5-he02047a_1
openssl conda-forge/linux-64::openssl-3.3.2-hb9d3cd8_0
pip conda-forge/noarch::pip-24.2-pyh8b19718_1
python conda-forge/linux-64::python-3.9.12-h2660328_1_cpython
readline conda-forge/linux-64::readline-8.2-h8228510_1
setuptools conda-forge/noarch::setuptools-75.1.0-pyhd8ed1ab_0
sqlite conda-forge/linux-64::sqlite-3.46.1-h9eae976_0
tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101
tzdata conda-forge/noarch::tzdata-2024b-hc8b5060_0
wheel conda-forge/noarch::wheel-0.44.0-pyhd8ed1ab_0
xz conda-forge/linux-64::xz-5.2.6-h166bdaf_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 24.9.1
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: 24.9.1
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /tmp/RtmpRVl4VB/file12bd745e24964b/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 |24_linux64_openblas 15 KB conda-forge
libcblas-3.9.0 |24_linux64_openblas 15 KB conda-forge
libgfortran-14.2.0 | h69a702a_1 53 KB conda-forge
libgfortran-ng-14.2.0 | h69a702a_1 53 KB conda-forge
libgfortran5-14.2.0 | hd5240d6_1 1.4 MB conda-forge
liblapack-3.9.0 |24_linux64_openblas 15 KB conda-forge
libopenblas-0.3.27 |pthreads_hac2b453_1 5.3 MB conda-forge
libstdcxx-14.2.0 | hc0a3c3a_1 3.7 MB conda-forge
libstdcxx-ng-14.2.0 | h4852527_1 53 KB conda-forge
numpy-1.26.4 | py39h474f0d3_0 6.7 MB conda-forge
pandas-1.4.3 | py39h1832856_0 12.5 MB conda-forge
python-dateutil-2.9.0 | pyhd8ed1ab_0 218 KB conda-forge
python_abi-3.9 | 5_cp39 6 KB conda-forge
pytz-2024.2 | pyhd8ed1ab_0 183 KB conda-forge
six-1.16.0 | pyh6c4a22f_0 14 KB conda-forge
------------------------------------------------------------
Total: 30.2 MB
The following NEW packages will be INSTALLED:
libblas conda-forge/linux-64::libblas-3.9.0-24_linux64_openblas
libcblas conda-forge/linux-64::libcblas-3.9.0-24_linux64_openblas
libgfortran conda-forge/linux-64::libgfortran-14.2.0-h69a702a_1
libgfortran-ng conda-forge/linux-64::libgfortran-ng-14.2.0-h69a702a_1
libgfortran5 conda-forge/linux-64::libgfortran5-14.2.0-hd5240d6_1
liblapack conda-forge/linux-64::liblapack-3.9.0-24_linux64_openblas
libopenblas conda-forge/linux-64::libopenblas-0.3.27-pthreads_hac2b453_1
libstdcxx conda-forge/linux-64::libstdcxx-14.2.0-hc0a3c3a_1
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-14.2.0-h4852527_1
numpy conda-forge/linux-64::numpy-1.26.4-py39h474f0d3_0
pandas conda-forge/linux-64::pandas-1.4.3-py39h1832856_0
python-dateutil conda-forge/noarch::python-dateutil-2.9.0-pyhd8ed1ab_0
python_abi conda-forge/linux-64::python_abi-3.9-5_cp39
pytz conda-forge/noarch::pytz-2024.2-pyhd8ed1ab_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
Downloading and Extracting Packages
libgfortran-14.2.0 | 53 KB | | 0%
libgfortran-14.2.0 | 53 KB | ########## | 100%
libgfortran-14.2.0 | 53 KB | ########## | 100%
pytz-2024.2 | 183 KB | | 0%
pytz-2024.2 | 183 KB | ########## | 100%
pytz-2024.2 | 183 KB | ########## | 100%
python_abi-3.9 | 6 KB | | 0%
python_abi-3.9 | 6 KB | ########## | 100%
python_abi-3.9 | 6 KB | ########## | 100%
libstdcxx-14.2.0 | 3.7 MB | | 0%
libstdcxx-14.2.0 | 3.7 MB | #########9 | 100%
libstdcxx-14.2.0 | 3.7 MB | ########## | 100%
libstdcxx-ng-14.2.0 | 53 KB | | 0%
libstdcxx-ng-14.2.0 | 53 KB | ########## | 100%
libstdcxx-ng-14.2.0 | 53 KB | ########## | 100%
libopenblas-0.3.27 | 5.3 MB | | 0%
libopenblas-0.3.27 | 5.3 MB | ########3 | 84%
libopenblas-0.3.27 | 5.3 MB | ########## | 100%
pandas-1.4.3 | 12.5 MB | | 0%
pandas-1.4.3 | 12.5 MB | ##4 | 24%
pandas-1.4.3 | 12.5 MB | #########5 | 96%
pandas-1.4.3 | 12.5 MB | ########## | 100%
python-dateutil-2.9. | 218 KB | | 0%
python-dateutil-2.9. | 218 KB | ########## | 100%
python-dateutil-2.9. | 218 KB | ########## | 100%
libgfortran-ng-14.2. | 53 KB | | 0%
libgfortran-ng-14.2. | 53 KB | ########## | 100%
libgfortran-ng-14.2. | 53 KB | ########## | 100%
six-1.16.0 | 14 KB | | 0%
six-1.16.0 | 14 KB | ########## | 100%
libgfortran5-14.2.0 | 1.4 MB | | 0%
libgfortran5-14.2.0 | 1.4 MB | ########## | 100%
libgfortran5-14.2.0 | 1.4 MB | ########## | 100%
liblapack-3.9.0 | 15 KB | | 0%
liblapack-3.9.0 | 15 KB | ########## | 100%
liblapack-3.9.0 | 15 KB | ########## | 100%
libblas-3.9.0 | 15 KB | | 0%
libblas-3.9.0 | 15 KB | ########## | 100%
libblas-3.9.0 | 15 KB | ########## | 100%
numpy-1.26.4 | 6.7 MB | | 0%
numpy-1.26.4 | 6.7 MB | #####4 | 55%
numpy-1.26.4 | 6.7 MB | ########## | 100%
libcblas-3.9.0 | 15 KB | | 0%
libcblas-3.9.0 | 15 KB | ########## | 100%
libcblas-3.9.0 | 15 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: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/locality/1.16.0
added / updated specs:
- python=3.9.12
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-64::bzip2-1.0.8-h4bc722e_7
ca-certificates conda-forge/linux-64::ca-certificates-2024.8.30-hbcca054_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.43-h712a8e2_1
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc conda-forge/linux-64::libgcc-14.2.0-h77fa898_1
libgcc-ng conda-forge/linux-64::libgcc-ng-14.2.0-h69a702a_1
libgomp conda-forge/linux-64::libgomp-14.2.0-h77fa898_1
libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0
libsqlite conda-forge/linux-64::libsqlite-3.46.1-hadc24fc_0
libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0
libzlib conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2
ncurses conda-forge/linux-64::ncurses-6.5-he02047a_1
openssl conda-forge/linux-64::openssl-3.3.2-hb9d3cd8_0
pip conda-forge/noarch::pip-24.2-pyh8b19718_1
python conda-forge/linux-64::python-3.9.12-h2660328_1_cpython
readline conda-forge/linux-64::readline-8.2-h8228510_1
setuptools conda-forge/noarch::setuptools-75.1.0-pyhd8ed1ab_0
sqlite conda-forge/linux-64::sqlite-3.46.1-h9eae976_0
tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101
tzdata conda-forge/noarch::tzdata-2024b-hc8b5060_0
wheel conda-forge/noarch::wheel-0.44.0-pyhd8ed1ab_0
xz conda-forge/linux-64::xz-5.2.6-h166bdaf_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 24.9.1
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: 24.9.1
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/locality/1.16.0
added / updated specs:
- pandas=1.4.3
- python-dateutil=2.8.2
- python=3.9.12
- pytz=2022.2.1
The following NEW packages will be INSTALLED:
libblas conda-forge/linux-64::libblas-3.9.0-24_linux64_openblas
libcblas conda-forge/linux-64::libcblas-3.9.0-24_linux64_openblas
libgfortran conda-forge/linux-64::libgfortran-14.2.0-h69a702a_1
libgfortran-ng conda-forge/linux-64::libgfortran-ng-14.2.0-h69a702a_1
libgfortran5 conda-forge/linux-64::libgfortran5-14.2.0-hd5240d6_1
liblapack conda-forge/linux-64::liblapack-3.9.0-24_linux64_openblas
libopenblas conda-forge/linux-64::libopenblas-0.3.27-pthreads_hac2b453_1
libstdcxx conda-forge/linux-64::libstdcxx-14.2.0-hc0a3c3a_1
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-14.2.0-h4852527_1
numpy conda-forge/linux-64::numpy-1.26.4-py39h474f0d3_0
pandas conda-forge/linux-64::pandas-1.4.3-py39h1832856_0
python-dateutil conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
python_abi conda-forge/linux-64::python_abi-3.9-5_cp39
pytz conda-forge/noarch::pytz-2022.2.1-pyhd8ed1ab_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/my_package_A
added / updated specs:
- python=3.9.12
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-64::bzip2-1.0.8-h4bc722e_7
ca-certificates conda-forge/linux-64::ca-certificates-2024.8.30-hbcca054_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.43-h712a8e2_1
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc conda-forge/linux-64::libgcc-14.2.0-h77fa898_1
libgcc-ng conda-forge/linux-64::libgcc-ng-14.2.0-h69a702a_1
libgomp conda-forge/linux-64::libgomp-14.2.0-h77fa898_1
libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0
libsqlite conda-forge/linux-64::libsqlite-3.46.1-hadc24fc_0
libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0
libzlib conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2
ncurses conda-forge/linux-64::ncurses-6.5-he02047a_1
openssl conda-forge/linux-64::openssl-3.3.2-hb9d3cd8_0
pip conda-forge/noarch::pip-24.2-pyh8b19718_1
python conda-forge/linux-64::python-3.9.12-h2660328_1_cpython
readline conda-forge/linux-64::readline-8.2-h8228510_1
setuptools conda-forge/noarch::setuptools-75.1.0-pyhd8ed1ab_0
sqlite conda-forge/linux-64::sqlite-3.46.1-h9eae976_0
tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101
tzdata conda-forge/noarch::tzdata-2024b-hc8b5060_0
wheel conda-forge/noarch::wheel-0.44.0-pyhd8ed1ab_0
xz conda-forge/linux-64::xz-5.2.6-h166bdaf_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 24.9.1
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: 24.9.1
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/my_package_A
added / updated specs:
- pandas=1.4.3
- python-dateutil=2.8.2
- python=3.9.12
- pytz=2022.2.1
The following NEW packages will be INSTALLED:
libblas conda-forge/linux-64::libblas-3.9.0-24_linux64_openblas
libcblas conda-forge/linux-64::libcblas-3.9.0-24_linux64_openblas
libgfortran conda-forge/linux-64::libgfortran-14.2.0-h69a702a_1
libgfortran-ng conda-forge/linux-64::libgfortran-ng-14.2.0-h69a702a_1
libgfortran5 conda-forge/linux-64::libgfortran5-14.2.0-hd5240d6_1
liblapack conda-forge/linux-64::liblapack-3.9.0-24_linux64_openblas
libopenblas conda-forge/linux-64::libopenblas-0.3.27-pthreads_hac2b453_1
libstdcxx conda-forge/linux-64::libstdcxx-14.2.0-hc0a3c3a_1
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-14.2.0-h4852527_1
numpy conda-forge/linux-64::numpy-1.26.4-py39h474f0d3_0
pandas conda-forge/linux-64::pandas-1.4.3-py39h1832856_0
python-dateutil conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
python_abi conda-forge/linux-64::python_abi-3.9-5_cp39
pytz conda-forge/noarch::pytz-2022.2.1-pyhd8ed1ab_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/my_package_B
added / updated specs:
- python=3.9.12
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-64::bzip2-1.0.8-h4bc722e_7
ca-certificates conda-forge/linux-64::ca-certificates-2024.8.30-hbcca054_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.43-h712a8e2_1
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc conda-forge/linux-64::libgcc-14.2.0-h77fa898_1
libgcc-ng conda-forge/linux-64::libgcc-ng-14.2.0-h69a702a_1
libgomp conda-forge/linux-64::libgomp-14.2.0-h77fa898_1
libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0
libsqlite conda-forge/linux-64::libsqlite-3.46.1-hadc24fc_0
libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0
libzlib conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2
ncurses conda-forge/linux-64::ncurses-6.5-he02047a_1
openssl conda-forge/linux-64::openssl-3.3.2-hb9d3cd8_0
pip conda-forge/noarch::pip-24.2-pyh8b19718_1
python conda-forge/linux-64::python-3.9.12-h2660328_1_cpython
readline conda-forge/linux-64::readline-8.2-h8228510_1
setuptools conda-forge/noarch::setuptools-75.1.0-pyhd8ed1ab_0
sqlite conda-forge/linux-64::sqlite-3.46.1-h9eae976_0
tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101
tzdata conda-forge/noarch::tzdata-2024b-hc8b5060_0
wheel conda-forge/noarch::wheel-0.44.0-pyhd8ed1ab_0
xz conda-forge/linux-64::xz-5.2.6-h166bdaf_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 24.9.1
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: 24.9.1
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/my_package_B
added / updated specs:
- pandas=1.4.2
- python-dateutil=2.8.1
- python=3.9.12
- pytz=2022.1
The following NEW packages will be INSTALLED:
libblas conda-forge/linux-64::libblas-3.9.0-24_linux64_openblas
libcblas conda-forge/linux-64::libcblas-3.9.0-24_linux64_openblas
libgfortran conda-forge/linux-64::libgfortran-14.2.0-h69a702a_1
libgfortran-ng conda-forge/linux-64::libgfortran-ng-14.2.0-h69a702a_1
libgfortran5 conda-forge/linux-64::libgfortran5-14.2.0-hd5240d6_1
liblapack conda-forge/linux-64::liblapack-3.9.0-24_linux64_openblas
libopenblas conda-forge/linux-64::libopenblas-0.3.27-pthreads_hac2b453_1
libstdcxx conda-forge/linux-64::libstdcxx-14.2.0-hc0a3c3a_1
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-14.2.0-h4852527_1
numpy conda-forge/linux-64::numpy-1.26.4-py39h474f0d3_0
pandas conda-forge/linux-64::pandas-1.4.2-py39h1832856_2
python-dateutil conda-forge/noarch::python-dateutil-2.8.1-py_0
python_abi conda-forge/linux-64::python_abi-3.9-5_cp39
pytz conda-forge/noarch::pytz-2022.1-pyhd8ed1ab_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 63 ]
>
> proc.time()
user system elapsed
1213.086 149.896 1475.273
basilisk.Rcheck/basilisk-Ex.timings
| name | user | system | elapsed | |
| BasiliskEnvironment-class | 0.004 | 0.000 | 0.003 | |
| PyPiLink | 0 | 0 | 0 | |
| basiliskOptions | 0 | 0 | 0 | |
| basiliskStart | 371.353 | 31.056 | 408.426 | |
| configureBasiliskEnv | 0 | 0 | 0 | |
| createLocalBasiliskEnv | 126.194 | 15.929 | 144.994 | |
| listPackages | 0.413 | 0.124 | 0.810 | |
| obtainEnvironmentPath | 0.002 | 0.002 | 0.004 | |
| setupBasiliskEnv | 0.004 | 0.000 | 0.004 | |
| useBasiliskEnv | 0.673 | 0.096 | 0.676 | |