Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2023-08-10 11:39:38 -0400 (Thu, 10 Aug 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4629
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4367
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4372
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4369
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 132/2216HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
basilisk 1.13.3  (landing page)
Aaron Lun
Snapshot Date: 2023-08-09 14:05:06 -0400 (Wed, 09 Aug 2023)
git_url: https://git.bioconductor.org/packages/basilisk
git_branch: devel
git_last_commit: 54dee79
git_last_commit_date: 2023-07-11 18:33:42 -0400 (Tue, 11 Jul 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    TIMEOUT  
palomino4Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    TIMEOUT    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

CHECK results for basilisk on kunpeng2


The builds on kunpeng2 (Linux ARM64) are experimental!
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.

raw results

Summary

Package: basilisk
Version: 1.13.3
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:basilisk.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings basilisk_1.13.3.tar.gz
StartedAt: 2023-08-10 04:36:19 -0000 (Thu, 10 Aug 2023)
EndedAt: 2023-08-10 05:05:04 -0000 (Thu, 10 Aug 2023)
EllapsedTime: 1725.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: basilisk.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:basilisk.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings basilisk_1.13.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/basilisk.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* 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
* checking for file ‘basilisk/DESCRIPTION’ ... OK
* this is package ‘basilisk’ version ‘1.13.3’
* 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-3.18-bioc/meat/basilisk.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... WARNING
'library' or 'require' call not declared from: ‘reticulate’
'library' or 'require' call to ‘reticulate’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘basilisk-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: basiliskStart
> ### Title: Start and stop 'basilisk'-related processes
> ### Aliases: basiliskStart basiliskStop basiliskRun
> 
> ### ** Examples
> 
> ## Don't show: 
> basilisk.utils::installConda()
[1] FALSE
> ## End(Don't show)
> 
> # Creating an environment (note, this is not necessary
> # when supplying a BasiliskEnvironment to basiliskStart):
> tmploc <- file.path(tempdir(), "my_package_A")
> if (!file.exists(tmploc)) {
+     setupBasiliskEnv(tmploc, c('pandas=1.4.3'))
+ }
Warning in check_forbidden_install("Python packages") :
  cannot install Python packages during R CMD check
+ '/home/biocbuild/.cache/R/basilisk/1.13.3/0/bin/conda' 'create' '--yes' '--prefix' '/home/biocbuild/tmp/RtmpRWYezO/my_package_A' 'python=3.10.12' '--quiet' '-c' 'conda-forge'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/biocbuild/tmp/RtmpRWYezO/my_package_A

  added / updated specs:
    - python=3.10.12


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-hf897c2e_4 
  ca-certificates    conda-forge/linux-aarch64::ca-certificates-2023.7.22-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-13.1.0-h2b4548d_0 
  libgomp            conda-forge/linux-aarch64::libgomp-13.1.0-h2b4548d_0 
  libnsl             conda-forge/linux-aarch64::libnsl-2.0.0-hf897c2e_0 
  libsqlite          conda-forge/linux-aarch64::libsqlite-3.42.0-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-h2e1726e_0 
  openssl            conda-forge/linux-aarch64::openssl-3.1.2-h31becfc_0 
  pip                conda-forge/noarch::pip-23.2.1-pyhd8ed1ab_0 
  python             conda-forge/linux-aarch64::python-3.10.12-hbbe8eec_0_cpython 
  readline           conda-forge/linux-aarch64::readline-8.2-h8fc344f_1 
  setuptools         conda-forge/noarch::setuptools-68.0.0-pyhd8ed1ab_0 
  tk                 conda-forge/linux-aarch64::tk-8.6.12-hd8af866_0 
  tzdata             conda-forge/noarch::tzdata-2023c-h71feb2d_0 
  wheel              conda-forge/noarch::wheel-0.41.1-pyhd8ed1ab_0 
  xz                 conda-forge/linux-aarch64::xz-5.2.6-h9cdd2b7_0 


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ '/home/biocbuild/.cache/R/basilisk/1.13.3/0/bin/conda' 'install' '--yes' '--prefix' '/home/biocbuild/tmp/RtmpRWYezO/my_package_A' 'python=3.10.12'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 23.5.0
  latest version: 23.7.2

Please update conda by running

    $ conda update -n base -c defaults conda

Or to minimize the number of packages updated during conda update use

     conda install conda=23.7.2



## Package Plan ##

  environment location: /home/biocbuild/tmp/RtmpRWYezO/my_package_A

  added / updated specs:
    - python=3.10.12


The following packages will be SUPERSEDED by a higher-priority channel:

  ca-certificates    conda-forge::ca-certificates-2023.7.2~ --> pkgs/main::ca-certificates-2023.05.30-hd43f75c_0 



Downloading and Extracting Packages

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ '/home/biocbuild/.cache/R/basilisk/1.13.3/0/bin/conda' 'install' '--yes' '--prefix' '/home/biocbuild/tmp/RtmpRWYezO/my_package_A' '-c' 'conda-forge' 'python=3.10.12' 'pandas=1.4.3'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... Error: one or more Python packages failed to install [error code 9]
Execution halted
* 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:
   2.   └─basilisk::setupBasiliskEnv(...)
   3.     └─reticulate::conda_install(...)
   4.       └─reticulate::conda_create(...)
   5.         └─reticulate:::stopf(fmt, envname, result, call. = FALSE)
  ── Error ('test-start.R:15:1'): (code run outside of `test_that()`) ────────────
  Error: one or more Python packages failed to install [error code 9]
  Backtrace:
      ▆
   1. └─basilisk::setupBasiliskEnv(tA, c(test.pandas, test.pandas.deps)) at test-start.R:15:0
   2.   └─reticulate::conda_install(...)
   3.     └─reticulate:::stopf(fmt, result)
  
  [ FAIL 3 | WARN 0 | SKIP 1 | PASS 31 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘motivation.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/basilisk.Rcheck/00check.log’
for details.

Installation output

basilisk.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL basilisk
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/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)

Tests output

basilisk.Rcheck/tests/testthat.Rout.fail


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(basilisk)
> test_check("basilisk")
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/biocbuild/bbs-3.18-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - python=3.10.12


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-hf897c2e_4 
  ca-certificates    conda-forge/linux-aarch64::ca-certificates-2023.7.22-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-13.1.0-h2b4548d_0 
  libgomp            conda-forge/linux-aarch64::libgomp-13.1.0-h2b4548d_0 
  libnsl             conda-forge/linux-aarch64::libnsl-2.0.0-hf897c2e_0 
  libsqlite          conda-forge/linux-aarch64::libsqlite-3.42.0-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-h2e1726e_0 
  openssl            conda-forge/linux-aarch64::openssl-3.1.2-h31becfc_0 
  pip                conda-forge/noarch::pip-23.2.1-pyhd8ed1ab_0 
  python             conda-forge/linux-aarch64::python-3.10.12-hbbe8eec_0_cpython 
  readline           conda-forge/linux-aarch64::readline-8.2-h8fc344f_1 
  setuptools         conda-forge/noarch::setuptools-68.0.0-pyhd8ed1ab_0 
  tk                 conda-forge/linux-aarch64::tk-8.6.12-hd8af866_0 
  tzdata             conda-forge/noarch::tzdata-2023c-h71feb2d_0 
  wheel              conda-forge/noarch::wheel-0.41.1-pyhd8ed1ab_0 
  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: 23.5.0
  latest version: 23.7.2

Please update conda by running

    $ conda update -n base -c defaults conda

Or to minimize the number of packages updated during conda update use

     conda install conda=23.7.2



## Package Plan ##

  environment location: /home/biocbuild/bbs-3.18-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - python=3.10.12


The following packages will be SUPERSEDED by a higher-priority channel:

  ca-certificates    conda-forge::ca-certificates-2023.7.2~ --> pkgs/main::ca-certificates-2023.05.30-hd43f75c_0 



Downloading and Extracting Packages

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/biocbuild/bbs-3.18-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - python=3.10.12


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-hf897c2e_4 
  ca-certificates    conda-forge/linux-aarch64::ca-certificates-2023.7.22-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-13.1.0-h2b4548d_0 
  libgomp            conda-forge/linux-aarch64::libgomp-13.1.0-h2b4548d_0 
  libnsl             conda-forge/linux-aarch64::libnsl-2.0.0-hf897c2e_0 
  libsqlite          conda-forge/linux-aarch64::libsqlite-3.42.0-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-h2e1726e_0 
  openssl            conda-forge/linux-aarch64::openssl-3.1.2-h31becfc_0 
  pip                conda-forge/noarch::pip-23.2.1-pyhd8ed1ab_0 
  python             conda-forge/linux-aarch64::python-3.10.12-hbbe8eec_0_cpython 
  readline           conda-forge/linux-aarch64::readline-8.2-h8fc344f_1 
  setuptools         conda-forge/noarch::setuptools-68.0.0-pyhd8ed1ab_0 
  tk                 conda-forge/linux-aarch64::tk-8.6.12-hd8af866_0 
  tzdata             conda-forge/noarch::tzdata-2023c-h71feb2d_0 
  wheel              conda-forge/noarch::wheel-0.41.1-pyhd8ed1ab_0 
  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: 23.5.0
  latest version: 23.7.2

Please update conda by running

    $ conda update -n base -c defaults conda

Or to minimize the number of packages updated during conda update use

     conda install conda=23.7.2



## Package Plan ##

  environment location: /home/biocbuild/bbs-3.18-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - python=3.10.12


The following packages will be SUPERSEDED by a higher-priority channel:

  ca-certificates    conda-forge::ca-certificates-2023.7.2~ --> pkgs/main::ca-certificates-2023.05.30-hd43f75c_0 



Downloading and Extracting Packages

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: 23.5.0
  latest version: 23.7.2

Please update conda by running

    $ conda update -n base -c defaults conda

Or to minimize the number of packages updated during conda update use

     conda install conda=23.7.2



## Package Plan ##

  environment location: /home/biocbuild/bbs-3.18-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - python-dateutil=2.8.1
    - python=3.10.12
    - 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:

  ca-certificates    pkgs/main::ca-certificates-2023.05.30~ --> conda-forge::ca-certificates-2023.7.22-hcefe29a_0 



Downloading and Extracting Packages

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting pandas==1.4.2
  Using cached pandas-1.4.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (11.0 MB)
Requirement already satisfied: python-dateutil>=2.8.1 in ./install-test-client/thingo/lib/python3.10/site-packages (from pandas==1.4.2) (2.8.1)
Requirement already satisfied: pytz>=2020.1 in ./install-test-client/thingo/lib/python3.10/site-packages (from pandas==1.4.2) (2022.1)
Collecting numpy>=1.21.0 (from pandas==1.4.2)
  Obtaining dependency information for numpy>=1.21.0 from https://files.pythonhosted.org/packages/b1/39/3f88e2bfac1fb510c112dc0c78a1e7cad8f3a2d75e714d1484a044c56682/numpy-1.25.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata
  Using cached numpy-1.25.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (5.6 kB)
Requirement already satisfied: six>=1.5 in ./install-test-client/thingo/lib/python3.10/site-packages (from python-dateutil>=2.8.1->pandas==1.4.2) (1.16.0)
Using cached numpy-1.25.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (14.2 MB)
Installing collected packages: numpy, pandas
Successfully installed numpy-1.25.2 pandas-1.4.2
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/biocbuild/bbs-3.18-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - python=3.10.12


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-hf897c2e_4 
  ca-certificates    conda-forge/linux-aarch64::ca-certificates-2023.7.22-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-13.1.0-h2b4548d_0 
  libgomp            conda-forge/linux-aarch64::libgomp-13.1.0-h2b4548d_0 
  libnsl             conda-forge/linux-aarch64::libnsl-2.0.0-hf897c2e_0 
  libsqlite          conda-forge/linux-aarch64::libsqlite-3.42.0-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-h2e1726e_0 
  openssl            conda-forge/linux-aarch64::openssl-3.1.2-h31becfc_0 
  pip                conda-forge/noarch::pip-23.2.1-pyhd8ed1ab_0 
  python             conda-forge/linux-aarch64::python-3.10.12-hbbe8eec_0_cpython 
  readline           conda-forge/linux-aarch64::readline-8.2-h8fc344f_1 
  setuptools         conda-forge/noarch::setuptools-68.0.0-pyhd8ed1ab_0 
  tk                 conda-forge/linux-aarch64::tk-8.6.12-hd8af866_0 
  tzdata             conda-forge/noarch::tzdata-2023c-h71feb2d_0 
  wheel              conda-forge/noarch::wheel-0.41.1-pyhd8ed1ab_0 
  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: 23.5.0
  latest version: 23.7.2

Please update conda by running

    $ conda update -n base -c defaults conda

Or to minimize the number of packages updated during conda update use

     conda install conda=23.7.2



## Package Plan ##

  environment location: /home/biocbuild/bbs-3.18-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - python=3.10.12


The following packages will be SUPERSEDED by a higher-priority channel:

  ca-certificates    conda-forge::ca-certificates-2023.7.2~ --> pkgs/main::ca-certificates-2023.05.30-hd43f75c_0 



Downloading and Extracting Packages

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: 23.5.0
  latest version: 23.7.2

Please update conda by running

    $ conda update -n base -c defaults conda

Or to minimize the number of packages updated during conda update use

     conda install conda=23.7.2



## Package Plan ##

  environment location: /home/biocbuild/bbs-3.18-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - python=3.10.12


The following packages will be UPDATED:

  ca-certificates    pkgs/main::ca-certificates-2023.05.30~ --> conda-forge::ca-certificates-2023.7.22-hcefe29a_0 



Downloading and Extracting Packages

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Processing /home/biocbuild/R/R-4.3.1/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=1280 sha256=125f78840d567cf31712311fff94cefde78b57ec88acedc13d9029b044cddfca
  Stored in directory: /home/biocbuild/tmp/pip-ephem-wheel-cache-r0w9g8gk/wheels/d5/a7/8c/376089940ba393454e5b026dc128a08a02562517b63acd4d9c
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... done

## Package Plan ##

  environment location: /home/biocbuild/bbs-3.18-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - python=3.10.12


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-hf897c2e_4 
  ca-certificates    conda-forge/linux-aarch64::ca-certificates-2023.7.22-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-13.1.0-h2b4548d_0 
  libgomp            conda-forge/linux-aarch64::libgomp-13.1.0-h2b4548d_0 
  libnsl             conda-forge/linux-aarch64::libnsl-2.0.0-hf897c2e_0 
  libsqlite          conda-forge/linux-aarch64::libsqlite-3.42.0-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-h2e1726e_0 
  openssl            conda-forge/linux-aarch64::openssl-3.1.2-h31becfc_0 
  pip                conda-forge/noarch::pip-23.2.1-pyhd8ed1ab_0 
  python             conda-forge/linux-aarch64::python-3.10.12-hbbe8eec_0_cpython 
  readline           conda-forge/linux-aarch64::readline-8.2-h8fc344f_1 
  setuptools         conda-forge/noarch::setuptools-68.0.0-pyhd8ed1ab_0 
  tk                 conda-forge/linux-aarch64::tk-8.6.12-hd8af866_0 
  tzdata             conda-forge/noarch::tzdata-2023c-h71feb2d_0 
  wheel              conda-forge/noarch::wheel-0.41.1-pyhd8ed1ab_0 
  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: 23.5.0
  latest version: 23.7.2

Please update conda by running

    $ conda update -n base -c defaults conda

Or to minimize the number of packages updated during conda update use

     conda install conda=23.7.2



## Package Plan ##

  environment location: /home/biocbuild/bbs-3.18-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - python=3.10.12


The following packages will be SUPERSEDED by a higher-priority channel:

  ca-certificates    conda-forge::ca-certificates-2023.7.2~ --> pkgs/main::ca-certificates-2023.05.30-hd43f75c_0 



Downloading and Extracting Packages

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... unsuccessful initial attempt using 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-py310_23.5.0-3-Linux-aarch64.sh'
Content type 'application/x-sh' length 76492398 bytes (72.9 MB)
==================================================
downloaded 72.9 MB

PREFIX=/home/biocbuild/tmp/Rtmpge4VSy/file17f624585a74cd/1.13.3/0
Unpacking payload ...

  0%|          | 0/71 [00:00<?, ?it/s]
Extracting : jsonpointer-2.1-pyhd3eb1b0_0.conda:   0%|          | 0/71 [00:00<?, ?it/s]
Extracting : jsonpointer-2.1-pyhd3eb1b0_0.conda:   1%|▏         | 1/71 [00:00<00:13,  5.29it/s]
Extracting : pycosat-0.6.4-py310h998d150_0.conda:   1%|▏         | 1/71 [00:00<00:13,  5.29it/s]
Extracting : libssh2-1.10.0-h6ac735f_2.conda:   3%|▎         | 2/71 [00:00<00:13,  5.29it/s]    
Extracting : libssh2-1.10.0-h6ac735f_2.conda:   4%|▍         | 3/71 [00:00<00:09,  7.05it/s]
Extracting : pip-23.1.2-py310hd43f75c_0.conda:   4%|▍         | 3/71 [00:00<00:09,  7.05it/s]
Extracting : pip-23.1.2-py310hd43f75c_0.conda:   6%|▌         | 4/71 [00:00<00:17,  3.76it/s]
Extracting : certifi-2023.5.7-py310hd43f75c_0.conda:   6%|▌         | 4/71 [00:00<00:17,  3.76it/s]
Extracting : pybind11-abi-4-hd3eb1b0_1.conda:   7%|▋         | 5/71 [00:00<00:17,  3.76it/s]       
Extracting : ncurses-6.4-h419075a_0.conda:   8%|▊         | 6/71 [00:01<00:17,  3.76it/s]   
Extracting : ncurses-6.4-h419075a_0.conda:  10%|▉         | 7/71 [00:01<00:15,  4.16it/s]
Extracting : urllib3-1.26.16-py310hd43f75c_0.conda:  10%|▉         | 7/71 [00:01<00:15,  4.16it/s]
Extracting : conda-libmamba-solver-23.5.0-py310hd43f75c_0.conda:  11%|█▏        | 8/71 [00:01<00:15,  4.16it/s]
Extracting : brotlipy-0.7.0-py310h2f4d8fa_1002.conda:  13%|█▎        | 9/71 [00:01<00:14,  4.16it/s]           
Extracting : _libgcc_mutex-0.1-main.conda:  14%|█▍        | 10/71 [00:01<00:14,  4.16it/s]          
Extracting : libcurl-8.1.1-hfa2bbb0_1.conda:  15%|█▌        | 11/71 [00:01<00:14,  4.16it/s]
Extracting : libstdcxx-ng-11.2.0-h1234567_1.conda:  17%|█▋        | 12/71 [00:01<00:14,  4.16it/s]
Extracting : libmambapy-1.4.1-py310hd82f176_1.conda:  18%|█▊        | 13/71 [00:01<00:13,  4.16it/s]
Extracting : libedit-3.1.20221030-h998d150_0.conda:  20%|█▉        | 14/71 [00:01<00:13,  4.16it/s] 
Extracting : fmt-9.1.0-hb8fdbf2_0.conda:  21%|██        | 15/71 [00:01<00:13,  4.16it/s]           
Extracting : six-1.16.0-pyhd3eb1b0_1.conda:  23%|██▎       | 16/71 [00:01<00:13,  4.16it/s]
Extracting : tzdata-2023c-h04d1e81_0.conda:  24%|██▍       | 17/71 [00:01<00:12,  4.16it/s]
Extracting : pluggy-1.0.0-py310hd43f75c_1.conda:  25%|██▌       | 18/71 [00:01<00:12,  4.16it/s]
Extracting : _openmp_mutex-5.1-51_gnu.conda:  27%|██▋       | 19/71 [00:01<00:12,  4.16it/s]    
Extracting : libffi-3.4.4-h419075a_0.conda:  28%|██▊       | 20/71 [00:01<00:12,  4.16it/s] 
Extracting : cffi-1.15.1-py310h998d150_3.conda:  30%|██▉       | 21/71 [00:01<00:12,  4.16it/s]
Extracting : libxml2-2.10.3-hd6958ba_0.conda:  31%|███       | 22/71 [00:01<00:11,  4.16it/s]  
Extracting : conda-content-trust-0.1.3-py310hd43f75c_0.conda:  32%|███▏      | 23/71 [00:01<00:11,  4.16it/s]
Extracting : ruamel.yaml.clib-0.2.6-py310h998d150_1.conda:  34%|███▍      | 24/71 [00:01<00:11,  4.16it/s]   
Extracting : libuuid-1.41.5-h998d150_0.conda:  35%|███▌      | 25/71 [00:01<00:11,  4.16it/s]             
Extracting : idna-3.4-py310hd43f75c_0.conda:  37%|███▋      | 26/71 [00:01<00:10,  4.16it/s] 
Extracting : ruamel.yaml-0.17.21-py310h998d150_0.conda:  38%|███▊      | 27/71 [00:01<00:10,  4.16it/s]
Extracting : krb5-1.20.1-h2e2fba8_1.conda:  39%|███▉      | 28/71 [00:01<00:10,  4.16it/s]             
Extracting : sqlite-3.41.2-h998d150_0.conda:  41%|████      | 29/71 [00:01<00:10,  4.16it/s]
Extracting : conda-package-handling-2.1.0-py310hd43f75c_0.conda:  42%|████▏     | 30/71 [00:01<00:09,  4.16it/s]
Extracting : openssl-3.0.9-h2f4d8fa_0.conda:  44%|████▎     | 31/71 [00:01<00:09,  4.16it/s]                    
Extracting : packaging-23.0-py310hd43f75c_0.conda:  45%|████▌     | 32/71 [00:01<00:09,  4.16it/s]
Extracting : libarchive-3.6.2-h654c02d_2.conda:  46%|████▋     | 33/71 [00:01<00:09,  4.16it/s]   
Extracting : toolz-0.12.0-py310hd43f75c_0.conda:  48%|████▊     | 34/71 [00:01<00:08,  4.16it/s]
Extracting : charset-normalizer-2.0.4-pyhd3eb1b0_0.conda:  49%|████▉     | 35/71 [00:01<00:08,  4.16it/s]
Extracting : libgcc-ng-11.2.0-h1234567_1.conda:  51%|█████     | 36/71 [00:01<00:08,  4.16it/s]          
Extracting : requests-2.29.0-py310hd43f75c_0.conda:  52%|█████▏    | 37/71 [00:01<00:08,  4.16it/s]
Extracting : ca-certificates-2023.05.30-hd43f75c_0.conda:  54%|█████▎    | 38/71 [00:01<00:07,  4.16it/s]
Extracting : libev-4.33-hfd63f10_1.conda:  55%|█████▍    | 39/71 [00:01<00:07,  4.16it/s]                
Extracting : cryptography-39.0.1-py310h3d58568_2.conda:  56%|█████▋    | 40/71 [00:01<00:07,  4.16it/s]
Extracting : zlib-1.2.13-h998d150_0.conda:  58%|█████▊    | 41/71 [00:01<00:07,  4.16it/s]             
Extracting : tk-8.6.12-h241ca14_0.conda:  59%|█████▉    | 42/71 [00:01<00:06,  4.16it/s]  
Extracting : python-3.10.12-h4bb2201_0.conda:  61%|██████    | 43/71 [00:02<00:06,  4.16it/s]
Extracting : python-3.10.12-h4bb2201_0.conda:  62%|██████▏   | 44/71 [00:02<00:00, 29.74it/s]
Extracting : lz4-c-1.9.4-h419075a_0.conda:  62%|██████▏   | 44/71 [00:02<00:00, 29.74it/s]   
Extracting : conda-package-streaming-0.8.0-py310hd43f75c_0.conda:  63%|██████▎   | 45/71 [00:02<00:00, 29.74it/s]
Extracting : libnghttp2-1.52.0-hb788212_1.conda:  65%|██████▍   | 46/71 [00:02<00:00, 29.74it/s]                 
Extracting : c-ares-1.19.0-h998d150_0.conda:  66%|██████▌   | 47/71 [00:02<00:00, 29.74it/s]    
Extracting : ld_impl_linux-aarch64-2.38-h8131f2d_1.conda:  68%|██████▊   | 48/71 [00:02<00:00, 29.74it/s]
Extracting : bzip2-1.0.8-hfd63f10_2.conda:  69%|██████▉   | 49/71 [00:02<00:00, 29.74it/s]               
Extracting : zstandard-0.19.0-py310h998d150_0.conda:  70%|███████   | 50/71 [00:02<00:00, 29.74it/s]
Extracting : libgomp-11.2.0-h1234567_1.conda:  72%|███████▏  | 51/71 [00:02<00:00, 29.74it/s]       
Extracting : yaml-cpp-0.7.0-h22f4aa5_1.conda:  73%|███████▎  | 52/71 [00:02<00:00, 29.74it/s]
Extracting : boltons-23.0.0-py310hd43f75c_0.conda:  75%|███████▍  | 53/71 [00:02<00:00, 29.74it/s]
Extracting : wheel-0.38.4-py310hd43f75c_0.conda:  76%|███████▌  | 54/71 [00:02<00:00, 29.74it/s]  
Extracting : readline-8.2-h998d150_0.conda:  77%|███████▋  | 55/71 [00:02<00:00, 29.74it/s]     
Extracting : reproc-14.2.4-h22f4aa5_1.conda:  79%|███████▉  | 56/71 [00:02<00:00, 29.74it/s]
Extracting : jsonpatch-1.32-pyhd3eb1b0_0.conda:  80%|████████  | 57/71 [00:02<00:00, 29.74it/s]
Extracting : reproc-cpp-14.2.4-h22f4aa5_1.conda:  82%|████████▏ | 58/71 [00:02<00:00, 29.74it/s]
Extracting : pcre2-10.37-ha6b7f17_1.conda:  83%|████████▎ | 59/71 [00:02<00:00, 29.74it/s]      
Extracting : xz-5.4.2-h998d150_0.conda:  85%|████████▍ | 60/71 [00:02<00:00, 29.74it/s]   
Extracting : pyopenssl-23.0.0-py310hd43f75c_0.conda:  86%|████████▌ | 61/71 [00:02<00:00, 29.74it/s]
Extracting : pysocks-1.7.1-py310hd43f75c_0.conda:  87%|████████▋ | 62/71 [00:02<00:00, 29.74it/s]   
Extracting : setuptools-67.8.0-py310hd43f75c_0.conda:  89%|████████▊ | 63/71 [00:02<00:00, 29.74it/s]
Extracting : tqdm-4.65.0-py310ha5ee653_0.conda:  90%|█████████ | 64/71 [00:02<00:00, 29.74it/s]      
Extracting : zstd-1.5.5-h6a09583_0.conda:  92%|█████████▏| 65/71 [00:02<00:00, 29.74it/s]      
Extracting : icu-68.1-h22f4aa5_0.conda:  93%|█████████▎| 66/71 [00:02<00:00, 29.74it/s]  
Extracting : libmamba-1.4.1-hd82f176_1.conda:  94%|█████████▍| 67/71 [00:02<00:00, 29.74it/s]
Extracting : pycparser-2.21-pyhd3eb1b0_0.conda:  96%|█████████▌| 68/71 [00:02<00:00, 29.74it/s]
Extracting : libsolv-0.7.22-h94b7715_0.conda:  97%|█████████▋| 69/71 [00:02<00:00, 29.74it/s]  
Extracting : conda-23.5.0-py310hd43f75c_0.conda:  99%|█████████▊| 70/71 [00:02<00:00, 29.74it/s]
                                                                                                
Installing base environment...


Downloading and Extracting Packages


Downloading and Extracting Packages

Preparing transaction: ...working... done
Executing transaction: ...working... done
installation finished.
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://conda.anaconda.org/conda-forge/linux-aarch64/libsqlite-3.42.0-h194ca79_0.conda>
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.



## Package Plan ##

  environment location: /home/biocbuild/tmp/Rtmpge4VSy/file17f624585a74cd/1.13.3/basilisk.utils/1.13.2/test

  added / updated specs:
    - python=3.10.12


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    _openmp_mutex-4.5          |            2_gnu          23 KB  conda-forge
    bzip2-1.0.8                |       hf897c2e_4         396 KB  conda-forge
    ca-certificates-2023.7.22  |       hcefe29a_0         146 KB  conda-forge
    ld_impl_linux-aarch64-2.40 |       h2d8c526_0         721 KB  conda-forge
    libffi-3.4.2               |       h3557bc0_5          58 KB  conda-forge
    libgcc-ng-13.1.0           |       h2b4548d_0         446 KB  conda-forge
    libgomp-13.1.0             |       h2b4548d_0         413 KB  conda-forge
    libnsl-2.0.0               |       hf897c2e_0          31 KB  conda-forge
    libsqlite-3.42.0           |       h194ca79_0         992 KB  conda-forge
    libuuid-2.38.1             |       hb4cce97_0          35 KB  conda-forge
    libzlib-1.2.13             |       h31becfc_5          65 KB  conda-forge
    ncurses-6.4                |       h2e1726e_0         900 KB  conda-forge
    openssl-3.1.2              |       h31becfc_0         2.5 MB  conda-forge
    pip-23.2.1                 |     pyhd8ed1ab_0         1.3 MB  conda-forge
    python-3.10.12             |hbbe8eec_0_cpython        11.9 MB  conda-forge
    readline-8.2               |       h8fc344f_1         287 KB  conda-forge
    setuptools-68.0.0          |     pyhd8ed1ab_0         453 KB  conda-forge
    tk-8.6.12                  |       hd8af866_0         3.4 MB  conda-forge
    tzdata-2023c               |       h71feb2d_0         115 KB  conda-forge
    wheel-0.41.1               |     pyhd8ed1ab_0          56 KB  conda-forge
    xz-5.2.6                   |       h9cdd2b7_0         430 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        24.5 MB

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-hf897c2e_4 
  ca-certificates    conda-forge/linux-aarch64::ca-certificates-2023.7.22-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-13.1.0-h2b4548d_0 
  libgomp            conda-forge/linux-aarch64::libgomp-13.1.0-h2b4548d_0 
  libnsl             conda-forge/linux-aarch64::libnsl-2.0.0-hf897c2e_0 
  libsqlite          conda-forge/linux-aarch64::libsqlite-3.42.0-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-h2e1726e_0 
  openssl            conda-forge/linux-aarch64::openssl-3.1.2-h31becfc_0 
  pip                conda-forge/noarch::pip-23.2.1-pyhd8ed1ab_0 
  python             conda-forge/linux-aarch64::python-3.10.12-hbbe8eec_0_cpython 
  readline           conda-forge/linux-aarch64::readline-8.2-h8fc344f_1 
  setuptools         conda-forge/noarch::setuptools-68.0.0-pyhd8ed1ab_0 
  tk                 conda-forge/linux-aarch64::tk-8.6.12-hd8af866_0 
  tzdata             conda-forge/noarch::tzdata-2023c-h71feb2d_0 
  wheel              conda-forge/noarch::wheel-0.41.1-pyhd8ed1ab_0 
  xz                 conda-forge/linux-aarch64::xz-5.2.6-h9cdd2b7_0 


Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/biocbuild/bbs-3.18-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/locality/1.13.3

  added / updated specs:
    - python=3.10.12


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-hf897c2e_4 
  ca-certificates    conda-forge/linux-aarch64::ca-certificates-2023.7.22-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-13.1.0-h2b4548d_0 
  libgomp            conda-forge/linux-aarch64::libgomp-13.1.0-h2b4548d_0 
  libnsl             conda-forge/linux-aarch64::libnsl-2.0.0-hf897c2e_0 
  libsqlite          conda-forge/linux-aarch64::libsqlite-3.42.0-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-h2e1726e_0 
  openssl            conda-forge/linux-aarch64::openssl-3.1.2-h31becfc_0 
  pip                conda-forge/noarch::pip-23.2.1-pyhd8ed1ab_0 
  python             conda-forge/linux-aarch64::python-3.10.12-hbbe8eec_0_cpython 
  readline           conda-forge/linux-aarch64::readline-8.2-h8fc344f_1 
  setuptools         conda-forge/noarch::setuptools-68.0.0-pyhd8ed1ab_0 
  tk                 conda-forge/linux-aarch64::tk-8.6.12-hd8af866_0 
  tzdata             conda-forge/noarch::tzdata-2023c-h71feb2d_0 
  wheel              conda-forge/noarch::wheel-0.41.1-pyhd8ed1ab_0 
  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: 23.5.0
  latest version: 23.7.2

Please update conda by running

    $ conda update -n base -c defaults conda

Or to minimize the number of packages updated during conda update use

     conda install conda=23.7.2



## Package Plan ##

  environment location: /home/biocbuild/bbs-3.18-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/locality/1.13.3

  added / updated specs:
    - python=3.10.12


The following packages will be SUPERSEDED by a higher-priority channel:

  ca-certificates    conda-forge::ca-certificates-2023.7.2~ --> pkgs/main::ca-certificates-2023.05.30-hd43f75c_0 



Downloading and Extracting Packages

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... unsuccessful initial attempt using 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: 23.5.0
  latest version: 23.7.2

Please update conda by running

    $ conda update -n base -c defaults conda

Or to minimize the number of packages updated during conda update use

     conda install conda=23.7.2



## Package Plan ##

  environment location: /home/biocbuild/bbs-3.18-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/locality/1.13.3

  added / updated specs:
    - pandas=1.4.3
    - python-dateutil=2.8.2
    - python=3.10.12
    - pytz=2022.2.1


The following NEW packages will be INSTALLED:

  libblas            conda-forge/linux-aarch64::libblas-3.9.0-17_linuxaarch64_openblas 
  libcblas           conda-forge/linux-aarch64::libcblas-3.9.0-17_linuxaarch64_openblas 
  libgfortran-ng     conda-forge/linux-aarch64::libgfortran-ng-13.1.0-he9431aa_0 
  libgfortran5       conda-forge/linux-aarch64::libgfortran5-13.1.0-h24e4805_0 
  liblapack          conda-forge/linux-aarch64::liblapack-3.9.0-17_linuxaarch64_openblas 
  libopenblas        conda-forge/linux-aarch64::libopenblas-0.3.23-pthreads_hd703e6f_0 
  libstdcxx-ng       conda-forge/linux-aarch64::libstdcxx-ng-13.1.0-h452befe_0 
  numpy              conda-forge/linux-aarch64::numpy-1.25.2-py310h7f380f4_0 
  pandas             conda-forge/linux-aarch64::pandas-1.4.3-py310h9e1bc84_0 
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0 
  python_abi         conda-forge/linux-aarch64::python_abi-3.10-3_cp310 
  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:

  ca-certificates    pkgs/main::ca-certificates-2023.05.30~ --> conda-forge::ca-certificates-2023.7.22-hcefe29a_0 



Downloading and Extracting Packages

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/biocbuild/bbs-3.18-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/my_package_A

  added / updated specs:
    - python=3.10.12


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-hf897c2e_4 
  ca-certificates    conda-forge/linux-aarch64::ca-certificates-2023.7.22-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-13.1.0-h2b4548d_0 
  libgomp            conda-forge/linux-aarch64::libgomp-13.1.0-h2b4548d_0 
  libnsl             conda-forge/linux-aarch64::libnsl-2.0.0-hf897c2e_0 
  libsqlite          conda-forge/linux-aarch64::libsqlite-3.42.0-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-h2e1726e_0 
  openssl            conda-forge/linux-aarch64::openssl-3.1.2-h31becfc_0 
  pip                conda-forge/noarch::pip-23.2.1-pyhd8ed1ab_0 
  python             conda-forge/linux-aarch64::python-3.10.12-hbbe8eec_0_cpython 
  readline           conda-forge/linux-aarch64::readline-8.2-h8fc344f_1 
  setuptools         conda-forge/noarch::setuptools-68.0.0-pyhd8ed1ab_0 
  tk                 conda-forge/linux-aarch64::tk-8.6.12-hd8af866_0 
  tzdata             conda-forge/noarch::tzdata-2023c-h71feb2d_0 
  wheel              conda-forge/noarch::wheel-0.41.1-pyhd8ed1ab_0 
  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: 23.5.0
  latest version: 23.7.2

Please update conda by running

    $ conda update -n base -c defaults conda

Or to minimize the number of packages updated during conda update use

     conda install conda=23.7.2



## Package Plan ##

  environment location: /home/biocbuild/bbs-3.18-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/my_package_A

  added / updated specs:
    - python=3.10.12


The following packages will be SUPERSEDED by a higher-priority channel:

  ca-certificates    conda-forge::ca-certificates-2023.7.2~ --> pkgs/main::ca-certificates-2023.05.30-hd43f75c_0 



Downloading and Extracting Packages

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... [ FAIL 3 | WARN 0 | SKIP 1 | PASS 31 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On Linux aarch64 (1): 'test-install.R:35:5'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-install.R:16:5'): setupBasiliskEnv obtains the correct version of the packages ──
Error: one or more Python packages failed to install [error code 9]
Backtrace:
    ▆
 1. └─basilisk::setupBasiliskEnv(target, c(test.pandas, test.pandas.deps)) at test-install.R:16:4
 2.   └─reticulate::conda_install(...)
 3.     └─reticulate:::stopf(fmt, result)
── Error ('test-lazy.R:40:5'): obtainEnvironmentPath works as expected ─────────
Error: Error creating conda environment '/home/biocbuild/tmp/Rtmpge4VSy/file17f624585a74cd/1.13.3/basilisk.utils/1.13.2/test' [exit code 1]
Backtrace:
    ▆
 1. └─basilisk::obtainEnvironmentPath(env) at test-lazy.R:40:4
 2.   └─basilisk::setupBasiliskEnv(...)
 3.     └─reticulate::conda_install(...)
 4.       └─reticulate::conda_create(...)
 5.         └─reticulate:::stopf(fmt, envname, result, call. = FALSE)
── Error ('test-start.R:15:1'): (code run outside of `test_that()`) ────────────
Error: one or more Python packages failed to install [error code 9]
Backtrace:
    ▆
 1. └─basilisk::setupBasiliskEnv(tA, c(test.pandas, test.pandas.deps)) at test-start.R:15:0
 2.   └─reticulate::conda_install(...)
 3.     └─reticulate:::stopf(fmt, result)

[ FAIL 3 | WARN 0 | SKIP 1 | PASS 31 ]
Error: Test failures
Execution halted

Example timings

basilisk.Rcheck/basilisk-Ex.timings

nameusersystemelapsed
BasiliskEnvironment-class0.0030.0000.003
PyPiLink000
basiliskOptions000