Aaron Lun
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/basilisk |
| git_branch: devel |
| git_last_commit: 6d0abb9 |
| git_last_commit_date: 2024-02-17 15:55:52 -0400 (Sat, 17 Feb 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:40:20 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 134/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| basilisk 1.15.5 (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 | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: basilisk |
| Version: 1.15.5 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:basilisk.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings basilisk_1.15.5.tar.gz |
| StartedAt: 2024-03-28 03:00:11 -0000 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 03:26:00 -0000 (Thu, 28 Mar 2024) |
| EllapsedTime: 1549.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: basilisk.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:basilisk.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings basilisk_1.15.5.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘basilisk/DESCRIPTION’ ... OK
* this is package ‘basilisk’ version ‘1.15.5’
* 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 216.160 15.916 253.139
createLocalBasiliskEnv 88.637 7.571 100.533
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-lazy.R:40:5'): obtainEnvironmentPath works as expected ─────────
Error: Error creating conda environment '/home/biocbuild/tmp/RtmprbWRCJ/file339dfd2a17b8/1.15.5/basilisk.utils/1.15.1/test' [exit code 9]
Backtrace:
▆
1. └─basilisk::obtainEnvironmentPath(env) at test-lazy.R:40:5
2. └─basilisk::setupBasiliskEnv(...)
3. └─reticulate::conda_install(...)
4. └─reticulate::conda_create(...)
5. └─reticulate:::stopf(fmt, envname, result, call. = FALSE)
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 57 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/00check.log’
for details.
basilisk.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL basilisk ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/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.fail
R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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:
_openmp_mutex conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-aarch64::bzip2-1.0.8-h31becfc_5
ca-certificates conda-forge/linux-aarch64::ca-certificates-2024.2.2-hcefe29a_0
ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.40-h2d8c526_0
libffi conda-forge/linux-aarch64::libffi-3.4.2-h3557bc0_5
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-13.2.0-hf8544c7_5
libgomp conda-forge/linux-aarch64::libgomp-13.2.0-hf8544c7_5
libnsl conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0
libsqlite conda-forge/linux-aarch64::libsqlite-3.45.2-h194ca79_0
libuuid conda-forge/linux-aarch64::libuuid-2.38.1-hb4cce97_0
libzlib conda-forge/linux-aarch64::libzlib-1.2.13-h31becfc_5
ncurses conda-forge/linux-aarch64::ncurses-6.4.20240210-h0425590_0
openssl conda-forge/linux-aarch64::openssl-3.2.1-h31becfc_1
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/linux-aarch64::python-3.9.12-h5016f1d_1_cpython
readline conda-forge/linux-aarch64::readline-8.2-h8fc344f_1
setuptools conda-forge/noarch::setuptools-69.2.0-pyhd8ed1ab_0
sqlite conda-forge/linux-aarch64::sqlite-3.45.2-h3b3482f_0
tk conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0
tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0
wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
xz conda-forge/linux-aarch64::xz-5.2.6-h9cdd2b7_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: 24.3.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo
added / updated specs:
- python=3.9.12
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2024.2.2~ --> pkgs/main::ca-certificates-2024.3.11-hd43f75c_0
The following packages will be SUPERSEDED by a higher-priority channel:
openssl conda-forge::openssl-3.2.1-h31becfc_1 --> pkgs/main::openssl-3.0.13-h2f4d8fa_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 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: 24.3.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo
added / updated specs:
- pandas=1.4.3
- python-dateutil=2.8.2
- python=3.9.12
- pytz=2022.2.1
The following NEW packages will be INSTALLED:
libblas conda-forge/linux-aarch64::libblas-3.9.0-21_linuxaarch64_openblas
libcblas conda-forge/linux-aarch64::libcblas-3.9.0-21_linuxaarch64_openblas
libgfortran-ng conda-forge/linux-aarch64::libgfortran-ng-13.2.0-he9431aa_5
libgfortran5 conda-forge/linux-aarch64::libgfortran5-13.2.0-h582850c_5
liblapack conda-forge/linux-aarch64::liblapack-3.9.0-21_linuxaarch64_openblas
libopenblas conda-forge/linux-aarch64::libopenblas-0.3.26-pthreads_h5a5ec62_0
libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-13.2.0-h9a76618_5
numpy conda-forge/linux-aarch64::numpy-1.26.4-py39h91c28bb_0
pandas conda-forge/linux-aarch64::pandas-1.4.3-py39h63591b6_0
python-dateutil conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
python_abi conda-forge/linux-aarch64::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
The following packages will be UPDATED:
openssl pkgs/main::openssl-3.0.13-h2f4d8fa_0 --> conda-forge::openssl-3.2.1-h31becfc_1
The following packages will be SUPERSEDED by a higher-priority channel:
ca-certificates pkgs/main::ca-certificates-2024.3.11-~ --> conda-forge::ca-certificates-2024.2.2-hcefe29a_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:
_openmp_mutex conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-aarch64::bzip2-1.0.8-h31becfc_5
ca-certificates conda-forge/linux-aarch64::ca-certificates-2024.2.2-hcefe29a_0
ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.40-h2d8c526_0
libffi conda-forge/linux-aarch64::libffi-3.4.2-h3557bc0_5
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-13.2.0-hf8544c7_5
libgomp conda-forge/linux-aarch64::libgomp-13.2.0-hf8544c7_5
libnsl conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0
libsqlite conda-forge/linux-aarch64::libsqlite-3.45.2-h194ca79_0
libuuid conda-forge/linux-aarch64::libuuid-2.38.1-hb4cce97_0
libzlib conda-forge/linux-aarch64::libzlib-1.2.13-h31becfc_5
ncurses conda-forge/linux-aarch64::ncurses-6.4.20240210-h0425590_0
openssl conda-forge/linux-aarch64::openssl-3.2.1-h31becfc_1
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/linux-aarch64::python-3.9.12-h5016f1d_1_cpython
readline conda-forge/linux-aarch64::readline-8.2-h8fc344f_1
setuptools conda-forge/noarch::setuptools-69.2.0-pyhd8ed1ab_0
sqlite conda-forge/linux-aarch64::sqlite-3.45.2-h3b3482f_0
tk conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0
tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0
wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
xz conda-forge/linux-aarch64::xz-5.2.6-h9cdd2b7_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: 24.3.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo
added / updated specs:
- python=3.9.12
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2024.2.2~ --> pkgs/main::ca-certificates-2024.3.11-hd43f75c_0
The following packages will be SUPERSEDED by a higher-priority channel:
openssl conda-forge::openssl-3.2.1-h31becfc_1 --> pkgs/main::openssl-3.0.13-h2f4d8fa_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 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: 24.3.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo
added / updated specs:
- pandas=1.4.2
- python-dateutil=2.8.1
- python=3.9.12
- pytz=2022.1
The following NEW packages will be INSTALLED:
libblas conda-forge/linux-aarch64::libblas-3.9.0-21_linuxaarch64_openblas
libcblas conda-forge/linux-aarch64::libcblas-3.9.0-21_linuxaarch64_openblas
libgfortran-ng conda-forge/linux-aarch64::libgfortran-ng-13.2.0-he9431aa_5
libgfortran5 conda-forge/linux-aarch64::libgfortran5-13.2.0-h582850c_5
liblapack conda-forge/linux-aarch64::liblapack-3.9.0-21_linuxaarch64_openblas
libopenblas conda-forge/linux-aarch64::libopenblas-0.3.26-pthreads_h5a5ec62_0
libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-13.2.0-h9a76618_5
numpy conda-forge/linux-aarch64::numpy-1.26.4-py39h91c28bb_0
pandas conda-forge/linux-aarch64::pandas-1.4.2-py39h63591b6_2
python-dateutil conda-forge/noarch::python-dateutil-2.8.1-py_0
python_abi conda-forge/linux-aarch64::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
The following packages will be UPDATED:
openssl pkgs/main::openssl-3.0.13-h2f4d8fa_0 --> conda-forge::openssl-3.2.1-h31becfc_1
The following packages will be SUPERSEDED by a higher-priority channel:
ca-certificates pkgs/main::ca-certificates-2024.3.11-~ --> conda-forge::ca-certificates-2024.2.2-hcefe29a_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:
_openmp_mutex conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-aarch64::bzip2-1.0.8-h31becfc_5
ca-certificates conda-forge/linux-aarch64::ca-certificates-2024.2.2-hcefe29a_0
ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.40-h2d8c526_0
libffi conda-forge/linux-aarch64::libffi-3.4.2-h3557bc0_5
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-13.2.0-hf8544c7_5
libgomp conda-forge/linux-aarch64::libgomp-13.2.0-hf8544c7_5
libnsl conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0
libsqlite conda-forge/linux-aarch64::libsqlite-3.45.2-h194ca79_0
libuuid conda-forge/linux-aarch64::libuuid-2.38.1-hb4cce97_0
libzlib conda-forge/linux-aarch64::libzlib-1.2.13-h31becfc_5
ncurses conda-forge/linux-aarch64::ncurses-6.4.20240210-h0425590_0
openssl conda-forge/linux-aarch64::openssl-3.2.1-h31becfc_1
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/linux-aarch64::python-3.9.12-h5016f1d_1_cpython
readline conda-forge/linux-aarch64::readline-8.2-h8fc344f_1
setuptools conda-forge/noarch::setuptools-69.2.0-pyhd8ed1ab_0
sqlite conda-forge/linux-aarch64::sqlite-3.45.2-h3b3482f_0
tk conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0
tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0
wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
xz conda-forge/linux-aarch64::xz-5.2.6-h9cdd2b7_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: 24.3.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo
added / updated specs:
- python=3.9.12
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2024.2.2~ --> pkgs/main::ca-certificates-2024.3.11-hd43f75c_0
The following packages will be SUPERSEDED by a higher-priority channel:
openssl conda-forge::openssl-3.2.1-h31becfc_1 --> pkgs/main::openssl-3.0.13-h2f4d8fa_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: 24.3.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo
added / updated specs:
- python-dateutil=2.8.1
- python=3.9.12
- pytz=2022.1
The following NEW packages will be INSTALLED:
python-dateutil conda-forge/noarch::python-dateutil-2.8.1-py_0
pytz conda-forge/noarch::pytz-2022.1-pyhd8ed1ab_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
The following packages will be UPDATED:
openssl pkgs/main::openssl-3.0.13-h2f4d8fa_0 --> conda-forge::openssl-3.2.1-h31becfc_1
The following packages will be SUPERSEDED by a higher-priority channel:
ca-certificates pkgs/main::ca-certificates-2024.3.11-~ --> conda-forge::ca-certificates-2024.2.2-hcefe29a_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_aarch64.manylinux2014_aarch64.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>=1.19.2 (from pandas==1.4.2)
Using cached numpy-1.26.4-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (62 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_aarch64.manylinux2014_aarch64.whl (11.0 MB)
Using cached numpy-1.26.4-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (14.2 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: /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:
_openmp_mutex conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-aarch64::bzip2-1.0.8-h31becfc_5
ca-certificates conda-forge/linux-aarch64::ca-certificates-2024.2.2-hcefe29a_0
ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.40-h2d8c526_0
libffi conda-forge/linux-aarch64::libffi-3.4.2-h3557bc0_5
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-13.2.0-hf8544c7_5
libgomp conda-forge/linux-aarch64::libgomp-13.2.0-hf8544c7_5
libnsl conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0
libsqlite conda-forge/linux-aarch64::libsqlite-3.45.2-h194ca79_0
libuuid conda-forge/linux-aarch64::libuuid-2.38.1-hb4cce97_0
libzlib conda-forge/linux-aarch64::libzlib-1.2.13-h31becfc_5
ncurses conda-forge/linux-aarch64::ncurses-6.4.20240210-h0425590_0
openssl conda-forge/linux-aarch64::openssl-3.2.1-h31becfc_1
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/linux-aarch64::python-3.9.12-h5016f1d_1_cpython
readline conda-forge/linux-aarch64::readline-8.2-h8fc344f_1
setuptools conda-forge/noarch::setuptools-69.2.0-pyhd8ed1ab_0
sqlite conda-forge/linux-aarch64::sqlite-3.45.2-h3b3482f_0
tk conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0
tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0
wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
xz conda-forge/linux-aarch64::xz-5.2.6-h9cdd2b7_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: 24.3.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo
added / updated specs:
- python=3.9.12
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2024.2.2~ --> pkgs/main::ca-certificates-2024.3.11-hd43f75c_0
The following packages will be SUPERSEDED by a higher-priority channel:
openssl conda-forge::openssl-3.2.1-h31becfc_1 --> pkgs/main::openssl-3.0.13-h2f4d8fa_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: 24.3.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo
added / updated specs:
- python=3.9.12
The following packages will be UPDATED:
openssl pkgs/main::openssl-3.0.13-h2f4d8fa_0 --> conda-forge::openssl-3.2.1-h31becfc_1
The following packages will be SUPERSEDED by a higher-priority channel:
ca-certificates pkgs/main::ca-certificates-2024.3.11-~ --> conda-forge::ca-certificates-2024.2.2-hcefe29a_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Processing /home/biocbuild/R/R-4.4-devel-2024.03.20/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=1281 sha256=c880990d112bcaaa5431854914329f8f2866fa681d7954adc404c5720e7fa4df
Stored in directory: /home/biocbuild/tmp/pip-ephem-wheel-cache-tdwg4in_/wheels/be/dd/0d/efabfb9ab0605624582aef64e8d5fdc6c86f76bf89b732eb95
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:
_openmp_mutex conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-aarch64::bzip2-1.0.8-h31becfc_5
ca-certificates conda-forge/linux-aarch64::ca-certificates-2024.2.2-hcefe29a_0
ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.40-h2d8c526_0
libffi conda-forge/linux-aarch64::libffi-3.4.2-h3557bc0_5
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-13.2.0-hf8544c7_5
libgomp conda-forge/linux-aarch64::libgomp-13.2.0-hf8544c7_5
libnsl conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0
libsqlite conda-forge/linux-aarch64::libsqlite-3.45.2-h194ca79_0
libuuid conda-forge/linux-aarch64::libuuid-2.38.1-hb4cce97_0
libzlib conda-forge/linux-aarch64::libzlib-1.2.13-h31becfc_5
ncurses conda-forge/linux-aarch64::ncurses-6.4.20240210-h0425590_0
openssl conda-forge/linux-aarch64::openssl-3.2.1-h31becfc_1
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/linux-aarch64::python-3.9.12-h5016f1d_1_cpython
readline conda-forge/linux-aarch64::readline-8.2-h8fc344f_1
setuptools conda-forge/noarch::setuptools-69.2.0-pyhd8ed1ab_0
sqlite conda-forge/linux-aarch64::sqlite-3.45.2-h3b3482f_0
tk conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0
tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0
wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
xz conda-forge/linux-aarch64::xz-5.2.6-h9cdd2b7_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: 24.3.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo
added / updated specs:
- python=3.9.12
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2024.2.2~ --> pkgs/main::ca-certificates-2024.3.11-hd43f75c_0
The following packages will be SUPERSEDED by a higher-priority channel:
openssl conda-forge::openssl-3.2.1-h31becfc_1 --> pkgs/main::openssl-3.0.13-h2f4d8fa_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 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-aarch64
- https://conda.anaconda.org/conda-forge/noarch
- https://repo.anaconda.com/pkgs/main/linux-aarch64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/linux-aarch64
- 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-aarch64.sh'
Content type 'application/x-sh' length 78905633 bytes (75.3 MB)
==================================================
downloaded 75.3 MB
PREFIX=/home/biocbuild/tmp/RtmprbWRCJ/file339dfd2a17b8/1.15.5/0
Unpacking payload ...
0%| | 0/40 [00:00<?, ?it/s]
Extracting : colorama-0.4.4-pyhd3eb1b0_0.conda: 0%| | 0/40 [00:00<?, ?it/s]
Extracting : colorama-0.4.4-pyhd3eb1b0_0.conda: 2%|▎ | 1/40 [00:00<00:13, 2.96it/s]
Extracting : urllib3-1.26.8-pyhd3eb1b0_0.conda: 2%|▎ | 1/40 [00:00<00:13, 2.96it/s]
Extracting : ruamel_yaml-0.15.100-py39h2f4d8fa_0.conda: 5%|▌ | 2/40 [00:00<00:12, 2.96it/s]
Extracting : tk-8.6.11-h241ca14_0.conda: 8%|▊ | 3/40 [00:00<00:12, 2.96it/s]
Extracting : conda-4.12.0-py39hd43f75c_0.conda: 10%|█ | 4/40 [00:01<00:12, 2.96it/s]
Extracting : conda-4.12.0-py39hd43f75c_0.conda: 12%|█▎ | 5/40 [00:01<00:06, 5.07it/s]
Extracting : _libgcc_mutex-0.1-main.conda: 12%|█▎ | 5/40 [00:01<00:06, 5.07it/s]
Extracting : conda-package-handling-1.8.1-py39h2f4d8fa_0.conda: 15%|█▌ | 6/40 [00:01<00:06, 5.07it/s]
Extracting : python-3.9.12-hc137634_0.conda: 18%|█▊ | 7/40 [00:01<00:06, 5.07it/s]
Extracting : python-3.9.12-hc137634_0.conda: 20%|██ | 8/40 [00:01<00:04, 7.00it/s]
Extracting : cffi-1.15.0-py39h9a3cfec_1.conda: 20%|██ | 8/40 [00:01<00:04, 7.00it/s]
Extracting : six-1.16.0-pyhd3eb1b0_1.conda: 22%|██▎ | 9/40 [00:01<00:04, 7.00it/s]
Extracting : wheel-0.37.1-pyhd3eb1b0_0.conda: 25%|██▌ | 10/40 [00:01<00:04, 7.00it/s]
Extracting : _openmp_mutex-5.1-51_gnu.conda: 28%|██▊ | 11/40 [00:01<00:04, 7.00it/s]
Extracting : conda-content-trust-0.1.1-pyhd3eb1b0_0.conda: 30%|███ | 12/40 [00:01<00:03, 7.00it/s]
Extracting : ld_impl_linux-aarch64-2.36.1-h0ab8de2_3.conda: 32%|███▎ | 13/40 [00:01<00:03, 7.00it/s]
Extracting : idna-3.3-pyhd3eb1b0_0.conda: 35%|███▌ | 14/40 [00:01<00:03, 7.00it/s]
Extracting : certifi-2021.10.8-py39hd43f75c_2.conda: 38%|███▊ | 15/40 [00:01<00:03, 7.00it/s]
Extracting : pycosat-0.6.3-py39hfd63f10_2.conda: 40%|████ | 16/40 [00:01<00:03, 7.00it/s]
Extracting : libgcc-ng-10.2.0-h1234567_51.conda: 42%|████▎ | 17/40 [00:01<00:03, 7.00it/s]
Extracting : brotlipy-0.7.0-py39hfd63f10_1002.conda: 45%|████▌ | 18/40 [00:01<00:03, 7.00it/s]
Extracting : ca-certificates-2022.3.29-hd43f75c_1.conda: 48%|████▊ | 19/40 [00:01<00:02, 7.00it/s]
Extracting : charset-normalizer-2.0.4-pyhd3eb1b0_0.conda: 50%|█████ | 20/40 [00:01<00:02, 7.00it/s]
Extracting : zlib-1.2.12-h2f4d8fa_1.conda: 52%|█████▎ | 21/40 [00:01<00:02, 7.00it/s]
Extracting : readline-8.1.2-h2f4d8fa_1.conda: 55%|█████▌ | 22/40 [00:01<00:02, 7.00it/s]
Extracting : tqdm-4.63.0-pyhd3eb1b0_0.conda: 57%|█████▊ | 23/40 [00:01<00:02, 7.00it/s]
Extracting : cryptography-36.0.0-py39h3d58568_0.conda: 60%|██████ | 24/40 [00:01<00:02, 7.00it/s]
Extracting : xz-5.2.5-hfd63f10_1.conda: 62%|██████▎ | 25/40 [00:01<00:02, 7.00it/s]
Extracting : ncurses-6.3-h2f4d8fa_2.conda: 65%|██████▌ | 26/40 [00:01<00:01, 7.00it/s]
Extracting : openssl-1.1.1n-h2f4d8fa_0.conda: 68%|██████▊ | 27/40 [00:01<00:01, 7.00it/s]
Extracting : pip-21.2.4-py39hd43f75c_0.conda: 70%|███████ | 28/40 [00:01<00:01, 7.00it/s]
Extracting : yaml-0.2.5-hfd63f10_0.conda: 72%|███████▎ | 29/40 [00:01<00:01, 7.00it/s]
Extracting : libgomp-10.2.0-h1234567_51.conda: 75%|███████▌ | 30/40 [00:01<00:01, 7.00it/s]
Extracting : tzdata-2022a-hda174b7_0.conda: 78%|███████▊ | 31/40 [00:01<00:01, 7.00it/s]
Extracting : requests-2.27.1-pyhd3eb1b0_0.conda: 80%|████████ | 32/40 [00:01<00:01, 7.00it/s]
Extracting : libffi-3.3-h7c1a80f_2.conda: 82%|████████▎ | 33/40 [00:01<00:00, 7.00it/s]
Extracting : sqlite-3.38.2-h6632b73_0.conda: 85%|████████▌ | 34/40 [00:01<00:00, 7.00it/s]
Extracting : pyopenssl-22.0.0-pyhd3eb1b0_0.conda: 88%|████████▊ | 35/40 [00:01<00:00, 7.00it/s]
Extracting : libstdcxx-ng-10.2.0-h1234567_51.conda: 90%|█████████ | 36/40 [00:01<00:00, 7.00it/s]
Extracting : pycparser-2.21-pyhd3eb1b0_0.conda: 92%|█████████▎| 37/40 [00:01<00:00, 7.00it/s]
Extracting : pysocks-1.7.1-py39hd43f75c_0.conda: 95%|█████████▌| 38/40 [00:01<00:00, 7.00it/s]
Extracting : setuptools-61.2.0-py39hd43f75c_0.conda: 98%|█████████▊| 39/40 [00:01<00:00, 7.00it/s]
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/tmp/RtmprbWRCJ/file339dfd2a17b8/1.15.5/0
added / updated specs:
- _libgcc_mutex==0.1=main
- _openmp_mutex==5.1=51_gnu
- brotlipy==0.7.0=py39hfd63f10_1002
- ca-certificates==2022.3.29=hd43f75c_1
- certifi==2021.10.8=py39hd43f75c_2
- cffi==1.15.0=py39h9a3cfec_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=py39h2f4d8fa_0
- conda==4.12.0=py39hd43f75c_0
- cryptography==36.0.0=py39h3d58568_0
- idna==3.3=pyhd3eb1b0_0
- ld_impl_linux-aarch64==2.36.1=h0ab8de2_3
- libffi==3.3=h7c1a80f_2
- libgcc-ng==10.2.0=h1234567_51
- libgomp==10.2.0=h1234567_51
- libstdcxx-ng==10.2.0=h1234567_51
- ncurses==6.3=h2f4d8fa_2
- openssl==1.1.1n=h2f4d8fa_0
- pip==21.2.4=py39hd43f75c_0
- pycosat==0.6.3=py39hfd63f10_2
- pycparser==2.21=pyhd3eb1b0_0
- pyopenssl==22.0.0=pyhd3eb1b0_0
- pysocks==1.7.1=py39hd43f75c_0
- python==3.9.12=hc137634_0
- readline==8.1.2=h2f4d8fa_1
- requests==2.27.1=pyhd3eb1b0_0
- ruamel_yaml==0.15.100=py39h2f4d8fa_0
- setuptools==61.2.0=py39hd43f75c_0
- six==1.16.0=pyhd3eb1b0_1
- sqlite==3.38.2=h6632b73_0
- tk==8.6.11=h241ca14_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=hfd63f10_1
- yaml==0.2.5=hfd63f10_0
- zlib==1.2.12=h2f4d8fa_1
The following NEW packages will be INSTALLED:
_libgcc_mutex pkgs/main/linux-aarch64::_libgcc_mutex-0.1-main
_openmp_mutex pkgs/main/linux-aarch64::_openmp_mutex-5.1-51_gnu
brotlipy pkgs/main/linux-aarch64::brotlipy-0.7.0-py39hfd63f10_1002
ca-certificates pkgs/main/linux-aarch64::ca-certificates-2022.3.29-hd43f75c_1
certifi pkgs/main/linux-aarch64::certifi-2021.10.8-py39hd43f75c_2
cffi pkgs/main/linux-aarch64::cffi-1.15.0-py39h9a3cfec_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-aarch64::conda-4.12.0-py39hd43f75c_0
conda-content-tru~ pkgs/main/noarch::conda-content-trust-0.1.1-pyhd3eb1b0_0
conda-package-han~ pkgs/main/linux-aarch64::conda-package-handling-1.8.1-py39h2f4d8fa_0
cryptography pkgs/main/linux-aarch64::cryptography-36.0.0-py39h3d58568_0
idna pkgs/main/noarch::idna-3.3-pyhd3eb1b0_0
ld_impl_linux-aar~ pkgs/main/linux-aarch64::ld_impl_linux-aarch64-2.36.1-h0ab8de2_3
libffi pkgs/main/linux-aarch64::libffi-3.3-h7c1a80f_2
libgcc-ng pkgs/main/linux-aarch64::libgcc-ng-10.2.0-h1234567_51
libgomp pkgs/main/linux-aarch64::libgomp-10.2.0-h1234567_51
libstdcxx-ng pkgs/main/linux-aarch64::libstdcxx-ng-10.2.0-h1234567_51
ncurses pkgs/main/linux-aarch64::ncurses-6.3-h2f4d8fa_2
openssl pkgs/main/linux-aarch64::openssl-1.1.1n-h2f4d8fa_0
pip pkgs/main/linux-aarch64::pip-21.2.4-py39hd43f75c_0
pycosat pkgs/main/linux-aarch64::pycosat-0.6.3-py39hfd63f10_2
pycparser pkgs/main/noarch::pycparser-2.21-pyhd3eb1b0_0
pyopenssl pkgs/main/noarch::pyopenssl-22.0.0-pyhd3eb1b0_0
pysocks pkgs/main/linux-aarch64::pysocks-1.7.1-py39hd43f75c_0
python pkgs/main/linux-aarch64::python-3.9.12-hc137634_0
readline pkgs/main/linux-aarch64::readline-8.1.2-h2f4d8fa_1
requests pkgs/main/noarch::requests-2.27.1-pyhd3eb1b0_0
ruamel_yaml pkgs/main/linux-aarch64::ruamel_yaml-0.15.100-py39h2f4d8fa_0
setuptools pkgs/main/linux-aarch64::setuptools-61.2.0-py39hd43f75c_0
six pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_1
sqlite pkgs/main/linux-aarch64::sqlite-3.38.2-h6632b73_0
tk pkgs/main/linux-aarch64::tk-8.6.11-h241ca14_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-aarch64::xz-5.2.5-hfd63f10_1
yaml pkgs/main/linux-aarch64::yaml-0.2.5-hfd63f10_0
zlib pkgs/main/linux-aarch64::zlib-1.2.12-h2f4d8fa_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... 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/1.15.5
added / updated specs:
- python=3.9.12
The following NEW packages will be INSTALLED:
_openmp_mutex conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-aarch64::bzip2-1.0.8-h31becfc_5
ca-certificates conda-forge/linux-aarch64::ca-certificates-2024.2.2-hcefe29a_0
ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.40-h2d8c526_0
libffi conda-forge/linux-aarch64::libffi-3.4.2-h3557bc0_5
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-13.2.0-hf8544c7_5
libgomp conda-forge/linux-aarch64::libgomp-13.2.0-hf8544c7_5
libnsl conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0
libsqlite conda-forge/linux-aarch64::libsqlite-3.45.2-h194ca79_0
libuuid conda-forge/linux-aarch64::libuuid-2.38.1-hb4cce97_0
libzlib conda-forge/linux-aarch64::libzlib-1.2.13-h31becfc_5
ncurses conda-forge/linux-aarch64::ncurses-6.4.20240210-h0425590_0
openssl conda-forge/linux-aarch64::openssl-3.2.1-h31becfc_1
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/linux-aarch64::python-3.9.12-h5016f1d_1_cpython
readline conda-forge/linux-aarch64::readline-8.2-h8fc344f_1
setuptools conda-forge/noarch::setuptools-69.2.0-pyhd8ed1ab_0
sqlite conda-forge/linux-aarch64::sqlite-3.45.2-h3b3482f_0
tk conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0
tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0
wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
xz conda-forge/linux-aarch64::xz-5.2.6-h9cdd2b7_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: 24.3.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/locality/1.15.5
added / updated specs:
- python=3.9.12
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2024.2.2~ --> pkgs/main::ca-certificates-2024.3.11-hd43f75c_0
The following packages will be SUPERSEDED by a higher-priority channel:
openssl conda-forge::openssl-3.2.1-h31becfc_1 --> pkgs/main::openssl-3.0.13-h2f4d8fa_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 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: 24.3.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/locality/1.15.5
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-aarch64::libblas-3.9.0-21_linuxaarch64_openblas
libcblas conda-forge/linux-aarch64::libcblas-3.9.0-21_linuxaarch64_openblas
libgfortran-ng conda-forge/linux-aarch64::libgfortran-ng-13.2.0-he9431aa_5
libgfortran5 conda-forge/linux-aarch64::libgfortran5-13.2.0-h582850c_5
liblapack conda-forge/linux-aarch64::liblapack-3.9.0-21_linuxaarch64_openblas
libopenblas conda-forge/linux-aarch64::libopenblas-0.3.26-pthreads_h5a5ec62_0
libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-13.2.0-h9a76618_5
numpy conda-forge/linux-aarch64::numpy-1.26.4-py39h91c28bb_0
pandas conda-forge/linux-aarch64::pandas-1.4.3-py39h63591b6_0
python-dateutil conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
python_abi conda-forge/linux-aarch64::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
The following packages will be UPDATED:
openssl pkgs/main::openssl-3.0.13-h2f4d8fa_0 --> conda-forge::openssl-3.2.1-h31becfc_1
The following packages will be SUPERSEDED by a higher-priority channel:
ca-certificates pkgs/main::ca-certificates-2024.3.11-~ --> conda-forge::ca-certificates-2024.2.2-hcefe29a_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:
_openmp_mutex conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-aarch64::bzip2-1.0.8-h31becfc_5
ca-certificates conda-forge/linux-aarch64::ca-certificates-2024.2.2-hcefe29a_0
ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.40-h2d8c526_0
libffi conda-forge/linux-aarch64::libffi-3.4.2-h3557bc0_5
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-13.2.0-hf8544c7_5
libgomp conda-forge/linux-aarch64::libgomp-13.2.0-hf8544c7_5
libnsl conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0
libsqlite conda-forge/linux-aarch64::libsqlite-3.45.2-h194ca79_0
libuuid conda-forge/linux-aarch64::libuuid-2.38.1-hb4cce97_0
libzlib conda-forge/linux-aarch64::libzlib-1.2.13-h31becfc_5
ncurses conda-forge/linux-aarch64::ncurses-6.4.20240210-h0425590_0
openssl conda-forge/linux-aarch64::openssl-3.2.1-h31becfc_1
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/linux-aarch64::python-3.9.12-h5016f1d_1_cpython
readline conda-forge/linux-aarch64::readline-8.2-h8fc344f_1
setuptools conda-forge/noarch::setuptools-69.2.0-pyhd8ed1ab_0
sqlite conda-forge/linux-aarch64::sqlite-3.45.2-h3b3482f_0
tk conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0
tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0
wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
xz conda-forge/linux-aarch64::xz-5.2.6-h9cdd2b7_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: 24.3.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/my_package_A
added / updated specs:
- python=3.9.12
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2024.2.2~ --> pkgs/main::ca-certificates-2024.3.11-hd43f75c_0
The following packages will be SUPERSEDED by a higher-priority channel:
openssl conda-forge::openssl-3.2.1-h31becfc_1 --> pkgs/main::openssl-3.0.13-h2f4d8fa_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 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: 24.3.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/my_package_A
added / updated specs:
- pandas=1.4.3
- python-dateutil=2.8.2
- python=3.9.12
- pytz=2022.2.1
The following NEW packages will be INSTALLED:
libblas conda-forge/linux-aarch64::libblas-3.9.0-21_linuxaarch64_openblas
libcblas conda-forge/linux-aarch64::libcblas-3.9.0-21_linuxaarch64_openblas
libgfortran-ng conda-forge/linux-aarch64::libgfortran-ng-13.2.0-he9431aa_5
libgfortran5 conda-forge/linux-aarch64::libgfortran5-13.2.0-h582850c_5
liblapack conda-forge/linux-aarch64::liblapack-3.9.0-21_linuxaarch64_openblas
libopenblas conda-forge/linux-aarch64::libopenblas-0.3.26-pthreads_h5a5ec62_0
libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-13.2.0-h9a76618_5
numpy conda-forge/linux-aarch64::numpy-1.26.4-py39h91c28bb_0
pandas conda-forge/linux-aarch64::pandas-1.4.3-py39h63591b6_0
python-dateutil conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
python_abi conda-forge/linux-aarch64::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
The following packages will be UPDATED:
openssl pkgs/main::openssl-3.0.13-h2f4d8fa_0 --> conda-forge::openssl-3.2.1-h31becfc_1
The following packages will be SUPERSEDED by a higher-priority channel:
ca-certificates pkgs/main::ca-certificates-2024.3.11-~ --> conda-forge::ca-certificates-2024.2.2-hcefe29a_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:
_openmp_mutex conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-aarch64::bzip2-1.0.8-h31becfc_5
ca-certificates conda-forge/linux-aarch64::ca-certificates-2024.2.2-hcefe29a_0
ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.40-h2d8c526_0
libffi conda-forge/linux-aarch64::libffi-3.4.2-h3557bc0_5
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-13.2.0-hf8544c7_5
libgomp conda-forge/linux-aarch64::libgomp-13.2.0-hf8544c7_5
libnsl conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0
libsqlite conda-forge/linux-aarch64::libsqlite-3.45.2-h194ca79_0
libuuid conda-forge/linux-aarch64::libuuid-2.38.1-hb4cce97_0
libzlib conda-forge/linux-aarch64::libzlib-1.2.13-h31becfc_5
ncurses conda-forge/linux-aarch64::ncurses-6.4.20240210-h0425590_0
openssl conda-forge/linux-aarch64::openssl-3.2.1-h31becfc_1
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/linux-aarch64::python-3.9.12-h5016f1d_1_cpython
readline conda-forge/linux-aarch64::readline-8.2-h8fc344f_1
setuptools conda-forge/noarch::setuptools-69.2.0-pyhd8ed1ab_0
sqlite conda-forge/linux-aarch64::sqlite-3.45.2-h3b3482f_0
tk conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0
tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0
wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
xz conda-forge/linux-aarch64::xz-5.2.6-h9cdd2b7_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: 24.3.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/my_package_B
added / updated specs:
- python=3.9.12
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2024.2.2~ --> pkgs/main::ca-certificates-2024.3.11-hd43f75c_0
The following packages will be SUPERSEDED by a higher-priority channel:
openssl conda-forge::openssl-3.2.1-h31becfc_1 --> pkgs/main::openssl-3.0.13-h2f4d8fa_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 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: 24.3.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/my_package_B
added / updated specs:
- pandas=1.4.2
- python-dateutil=2.8.1
- python=3.9.12
- pytz=2022.1
The following NEW packages will be INSTALLED:
libblas conda-forge/linux-aarch64::libblas-3.9.0-21_linuxaarch64_openblas
libcblas conda-forge/linux-aarch64::libcblas-3.9.0-21_linuxaarch64_openblas
libgfortran-ng conda-forge/linux-aarch64::libgfortran-ng-13.2.0-he9431aa_5
libgfortran5 conda-forge/linux-aarch64::libgfortran5-13.2.0-h582850c_5
liblapack conda-forge/linux-aarch64::liblapack-3.9.0-21_linuxaarch64_openblas
libopenblas conda-forge/linux-aarch64::libopenblas-0.3.26-pthreads_h5a5ec62_0
libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-13.2.0-h9a76618_5
numpy conda-forge/linux-aarch64::numpy-1.26.4-py39h91c28bb_0
pandas conda-forge/linux-aarch64::pandas-1.4.2-py39h63591b6_2
python-dateutil conda-forge/noarch::python-dateutil-2.8.1-py_0
python_abi conda-forge/linux-aarch64::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
The following packages will be UPDATED:
openssl pkgs/main::openssl-3.0.13-h2f4d8fa_0 --> conda-forge::openssl-3.2.1-h31becfc_1
The following packages will be SUPERSEDED by a higher-priority channel:
ca-certificates pkgs/main::ca-certificates-2024.3.11-~ --> conda-forge::ca-certificates-2024.2.2-hcefe29a_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 57 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On Linux aarch64 (1): 'test-install.R:35:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-lazy.R:40:5'): obtainEnvironmentPath works as expected ─────────
Error: Error creating conda environment '/home/biocbuild/tmp/RtmprbWRCJ/file339dfd2a17b8/1.15.5/basilisk.utils/1.15.1/test' [exit code 9]
Backtrace:
▆
1. └─basilisk::obtainEnvironmentPath(env) at test-lazy.R:40:5
2. └─basilisk::setupBasiliskEnv(...)
3. └─reticulate::conda_install(...)
4. └─reticulate::conda_create(...)
5. └─reticulate:::stopf(fmt, envname, result, call. = FALSE)
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 57 ]
Error: Test failures
Execution halted
basilisk.Rcheck/basilisk-Ex.timings
| name | user | system | elapsed | |
| BasiliskEnvironment-class | 0.004 | 0.000 | 0.004 | |
| PyPiLink | 0 | 0 | 0 | |
| basiliskOptions | 0.001 | 0.000 | 0.000 | |
| basiliskStart | 216.160 | 15.916 | 253.139 | |
| configureBasiliskEnv | 0 | 0 | 0 | |
| createLocalBasiliskEnv | 88.637 | 7.571 | 100.533 | |
| listPackages | 0.506 | 0.104 | 0.875 | |
| obtainEnvironmentPath | 0.004 | 0.000 | 0.004 | |
| setupBasiliskEnv | 0.003 | 0.000 | 0.004 | |
| useBasiliskEnv | 0.889 | 0.091 | 0.897 | |