Back to Multiple platform build/check report for BioC 3.19:   simplified   long
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-03-04 11:38:52 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 134/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
basilisk 1.15.5  (landing page)
Aaron Lun
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 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 -0500 (Sat, 17 Feb 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    TIMEOUT    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

CHECK results for basilisk on merida1


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.

raw results

Summary

Package: basilisk
Version: 1.15.5
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:basilisk.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings basilisk_1.15.5.tar.gz
StartedAt: 2024-03-02 00:23:26 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 01:03:27 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 2400.9 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: basilisk.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:basilisk.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings basilisk_1.15.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘basilisk/DESCRIPTION’ ... OK
* this is package ‘basilisk’ version ‘1.15.5’
* 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 ‘/Users/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... 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          702.963 83.424 993.601
createLocalBasiliskEnv 216.143 35.619 324.947
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’

Installation output

basilisk.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL basilisk
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘basilisk’ ...
** using non-staged installation via StagedInstall field
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (basilisk)

Tests output

basilisk.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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

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

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

> library(testthat)
> library(basilisk)
Loading required package: reticulate
> if (.Platform$OS.type != "windows") test_check("basilisk")
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /Users/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - python=3.9.12


The following NEW packages will be INSTALLED:

  bzip2              conda-forge/osx-64::bzip2-1.0.8-h10d778d_5
  ca-certificates    conda-forge/osx-64::ca-certificates-2024.2.2-h8857fd0_0
  libffi             conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
  libsqlite          conda-forge/osx-64::libsqlite-3.45.1-h92b6c6a_0
  libzlib            conda-forge/osx-64::libzlib-1.2.13-h8a1eda9_5
  ncurses            conda-forge/osx-64::ncurses-6.4-h93d8f39_2
  openssl            conda-forge/osx-64::openssl-3.2.1-hd75f5a5_0
  pip                conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
  python             conda-forge/osx-64::python-3.9.12-h1cc4136_1_cpython
  readline           conda-forge/osx-64::readline-8.2-h9e318b2_1
  setuptools         conda-forge/noarch::setuptools-69.1.1-pyhd8ed1ab_0
  sqlite             conda-forge/osx-64::sqlite-3.45.1-h7461747_0
  tk                 conda-forge/osx-64::tk-8.6.13-h1abcd95_1
  tzdata             conda-forge/noarch::tzdata-2024a-h0c530f3_0
  wheel              conda-forge/noarch::wheel-0.42.0-pyhd8ed1ab_0
  xz                 conda-forge/osx-64::xz-5.2.6-h775f41a_0


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 24.1.2

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /Users/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - python=3.9.12


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

  ca-certificates    conda-forge::ca-certificates-2024.2.2~ --> pkgs/main::ca-certificates-2023.12.12-hecd8cb5_0
  openssl             conda-forge::openssl-3.2.1-hd75f5a5_0 --> pkgs/main::openssl-3.0.13-hca72f7f_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: 24.1.2

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /Users/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - pandas=1.4.3
    - python-dateutil=2.8.2
    - python=3.9.12
    - pytz=2022.2.1


The following NEW packages will be INSTALLED:

  libblas            conda-forge/osx-64::libblas-3.9.0-21_osx64_openblas
  libcblas           conda-forge/osx-64::libcblas-3.9.0-21_osx64_openblas
  libcxx             conda-forge/osx-64::libcxx-16.0.6-hd57cbcb_0
  libgfortran        conda-forge/osx-64::libgfortran-5.0.0-13_2_0_h97931a8_3
  libgfortran5       conda-forge/osx-64::libgfortran5-13.2.0-h2873a65_3
  liblapack          conda-forge/osx-64::liblapack-3.9.0-21_osx64_openblas
  libopenblas        conda-forge/osx-64::libopenblas-0.3.26-openmp_hfef2a42_0
  llvm-openmp        conda-forge/osx-64::llvm-openmp-17.0.6-hb6ac08f_0
  numpy              conda-forge/osx-64::numpy-1.26.4-py39h28c39a1_0
  pandas             conda-forge/osx-64::pandas-1.4.3-py39hf72b562_0
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
  python_abi         conda-forge/osx-64::python_abi-3.9-4_cp39
  pytz               conda-forge/noarch::pytz-2022.2.1-pyhd8ed1ab_0
  six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0

The following packages will be UPDATED:

  ca-certificates    pkgs/main::ca-certificates-2023.12.12~ --> conda-forge::ca-certificates-2024.2.2-h8857fd0_0
  openssl              pkgs/main::openssl-3.0.13-hca72f7f_0 --> conda-forge::openssl-3.2.1-hd75f5a5_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /Users/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - python=3.9.12


The following NEW packages will be INSTALLED:

  bzip2              conda-forge/osx-64::bzip2-1.0.8-h10d778d_5
  ca-certificates    conda-forge/osx-64::ca-certificates-2024.2.2-h8857fd0_0
  libffi             conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
  libsqlite          conda-forge/osx-64::libsqlite-3.45.1-h92b6c6a_0
  libzlib            conda-forge/osx-64::libzlib-1.2.13-h8a1eda9_5
  ncurses            conda-forge/osx-64::ncurses-6.4-h93d8f39_2
  openssl            conda-forge/osx-64::openssl-3.2.1-hd75f5a5_0
  pip                conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
  python             conda-forge/osx-64::python-3.9.12-h1cc4136_1_cpython
  readline           conda-forge/osx-64::readline-8.2-h9e318b2_1
  setuptools         conda-forge/noarch::setuptools-69.1.1-pyhd8ed1ab_0
  sqlite             conda-forge/osx-64::sqlite-3.45.1-h7461747_0
  tk                 conda-forge/osx-64::tk-8.6.13-h1abcd95_1
  tzdata             conda-forge/noarch::tzdata-2024a-h0c530f3_0
  wheel              conda-forge/noarch::wheel-0.42.0-pyhd8ed1ab_0
  xz                 conda-forge/osx-64::xz-5.2.6-h775f41a_0


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 24.1.2

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /Users/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - python=3.9.12


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

  ca-certificates    conda-forge::ca-certificates-2024.2.2~ --> pkgs/main::ca-certificates-2023.12.12-hecd8cb5_0
  openssl             conda-forge::openssl-3.2.1-hd75f5a5_0 --> pkgs/main::openssl-3.0.13-hca72f7f_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: 24.1.2

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /Users/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - pandas=1.4.2
    - python-dateutil=2.8.1
    - python=3.9.12
    - pytz=2022.1


The following NEW packages will be INSTALLED:

  libblas            conda-forge/osx-64::libblas-3.9.0-21_osx64_openblas
  libcblas           conda-forge/osx-64::libcblas-3.9.0-21_osx64_openblas
  libcxx             conda-forge/osx-64::libcxx-16.0.6-hd57cbcb_0
  libgfortran        conda-forge/osx-64::libgfortran-5.0.0-13_2_0_h97931a8_3
  libgfortran5       conda-forge/osx-64::libgfortran5-13.2.0-h2873a65_3
  liblapack          conda-forge/osx-64::liblapack-3.9.0-21_osx64_openblas
  libopenblas        conda-forge/osx-64::libopenblas-0.3.26-openmp_hfef2a42_0
  llvm-openmp        conda-forge/osx-64::llvm-openmp-17.0.6-hb6ac08f_0
  numpy              conda-forge/osx-64::numpy-1.26.4-py39h28c39a1_0
  pandas             conda-forge/osx-64::pandas-1.4.2-py39hf72b562_2
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.1-py_0
  python_abi         conda-forge/osx-64::python_abi-3.9-4_cp39
  pytz               conda-forge/noarch::pytz-2022.1-pyhd8ed1ab_0
  six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0

The following packages will be UPDATED:

  ca-certificates    pkgs/main::ca-certificates-2023.12.12~ --> conda-forge::ca-certificates-2024.2.2-h8857fd0_0
  openssl              pkgs/main::openssl-3.0.13-hca72f7f_0 --> conda-forge::openssl-3.2.1-hd75f5a5_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /Users/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - python=2.7


The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/osx-64::ca-certificates-2024.2.2-h8857fd0_0
  certifi            conda-forge/osx-64::certifi-2019.11.28-py27h8c360ce_1
  libcxx             conda-forge/osx-64::libcxx-16.0.6-hd57cbcb_0
  libffi             conda-forge/osx-64::libffi-3.2.1-hb1e8313_1007
  libsqlite          conda-forge/osx-64::libsqlite-3.45.1-h92b6c6a_0
  libzlib            conda-forge/osx-64::libzlib-1.2.13-h8a1eda9_5
  ncurses            conda-forge/osx-64::ncurses-6.4-h93d8f39_2
  openssl            conda-forge/osx-64::openssl-1.1.1w-h8a1eda9_0
  pip                conda-forge/noarch::pip-20.1.1-pyh9f0ad1d_0
  python             conda-forge/osx-64::python-2.7.15-h8e446fc_1011_cpython
  python_abi         conda-forge/osx-64::python_abi-2.7-1_cp27m
  readline           conda-forge/osx-64::readline-8.2-h9e318b2_1
  setuptools         conda-forge/osx-64::setuptools-44.0.0-py27_0
  sqlite             conda-forge/osx-64::sqlite-3.45.1-h7461747_0
  tk                 conda-forge/osx-64::tk-8.6.13-h1abcd95_1
  wheel              conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
  zlib               conda-forge/osx-64::zlib-1.2.13-h8a1eda9_5


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 24.1.2

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /Users/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - python=2.7


The following packages will be UPDATED:

  certifi            conda-forge/osx-64::certifi-2019.11.2~ --> pkgs/main/noarch::certifi-2020.6.20-pyhd3eb1b0_3
  openssl            conda-forge::openssl-1.1.1w-h8a1eda9_0 --> pkgs/main::openssl-3.0.13-hca72f7f_0
  python             conda-forge::python-2.7.15-h8e446fc_1~ --> pkgs/main::python-2.7.18-hc817775_0

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

  ca-certificates    conda-forge::ca-certificates-2024.2.2~ --> pkgs/main::ca-certificates-2023.12.12-hecd8cb5_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: 24.1.2

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /Users/biocbuild/bbs-3.19-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - python[version='2.7.*,2.7.*']


The following packages will be UPDATED:

  ca-certificates    pkgs/main::ca-certificates-2023.12.12~ --> conda-forge::ca-certificates-2024.2.2-h8857fd0_0

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

  certifi            pkgs/main/noarch::certifi-2020.6.20-p~ --> conda-forge/osx-64::certifi-2016.9.26-py27_0
  openssl              pkgs/main::openssl-3.0.13-hca72f7f_0 --> conda-forge::openssl-1.1.1w-h8a1eda9_0
  python                pkgs/main::python-2.7.18-hc817775_0 --> conda-forge::python-2.7.15-h8e446fc_1011_cpython


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
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...

Example timings

basilisk.Rcheck/basilisk-Ex.timings

nameusersystemelapsed
BasiliskEnvironment-class0.0240.0020.031
PyPiLink0.0010.0010.001
basiliskOptions0.0010.0000.002
basiliskStart702.963 83.424993.601
configureBasiliskEnv0.0000.0000.001
createLocalBasiliskEnv216.143 35.619324.947
listPackages0.9490.3751.878
obtainEnvironmentPath0.0060.0020.009
setupBasiliskEnv0.0050.0020.007
useBasiliskEnv1.5830.5752.974