Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 134/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
basilisk 1.17.0  (landing page)
Aaron Lun
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/basilisk
git_branch: devel
git_last_commit: 1539ded
git_last_commit_date: 2024-04-30 11:20:50 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    TIMEOUT    OK  
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

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: 1.17.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:basilisk.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings basilisk_1.17.0.tar.gz
StartedAt: 2024-06-10 00:05:06 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 00:45:08 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 2401.1 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_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/basilisk.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘basilisk/DESCRIPTION’ ... OK
* this is package ‘basilisk’ version ‘1.17.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  inst/example/.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘basilisk’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/basilisk.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
basiliskStart          644.296 79.197 898.513
createLocalBasiliskEnv 226.982 35.442 377.816
* 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 version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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

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

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

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

## Package Plan ##

  environment location: /Users/biocbuild/bbs-3.20-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - python=3.9.12


The following NEW packages will be INSTALLED:

  bzip2              conda-forge/osx-64::bzip2-1.0.8-h10d778d_5
  ca-certificates    conda-forge/osx-64::ca-certificates-2024.6.2-h8857fd0_0
  libffi             conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
  libsqlite          conda-forge/osx-64::libsqlite-3.45.3-h92b6c6a_0
  libzlib            conda-forge/osx-64::libzlib-1.3.1-h87427d6_1
  ncurses            conda-forge/osx-64::ncurses-6.5-h5846eda_0
  openssl            conda-forge/osx-64::openssl-3.3.1-h87427d6_0
  pip                conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
  python             conda-forge/osx-64::python-3.9.12-h1cc4136_1_cpython
  readline           conda-forge/osx-64::readline-8.2-h9e318b2_1
  setuptools         conda-forge/noarch::setuptools-70.0.0-pyhd8ed1ab_0
  sqlite             conda-forge/osx-64::sqlite-3.45.3-h7461747_0
  tk                 conda-forge/osx-64::tk-8.6.13-h1abcd95_1
  tzdata             conda-forge/noarch::tzdata-2024a-h0c530f3_0
  wheel              conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
  xz                 conda-forge/osx-64::xz-5.2.6-h775f41a_0


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 24.5.0

Please update conda by running

    $ conda update -n base -c defaults conda



# All requested packages already installed.

Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 24.5.0

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /Users/biocbuild/bbs-3.20-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

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


The following NEW packages will be INSTALLED:

  libblas            conda-forge/osx-64::libblas-3.9.0-22_osx64_openblas
  libcblas           conda-forge/osx-64::libcblas-3.9.0-22_osx64_openblas
  libcxx             conda-forge/osx-64::libcxx-17.0.6-h88467a6_0
  libgfortran        conda-forge/osx-64::libgfortran-5.0.0-13_2_0_h97931a8_3
  libgfortran5       conda-forge/osx-64::libgfortran5-13.2.0-h2873a65_3
  liblapack          conda-forge/osx-64::liblapack-3.9.0-22_osx64_openblas
  libopenblas        conda-forge/osx-64::libopenblas-0.3.27-openmp_hfef2a42_0
  llvm-openmp        conda-forge/osx-64::llvm-openmp-18.1.7-h15ab845_0
  numpy              conda-forge/osx-64::numpy-1.26.4-py39h28c39a1_0
  pandas             conda-forge/osx-64::pandas-1.4.3-py39hf72b562_0
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
  python_abi         conda-forge/osx-64::python_abi-3.9-4_cp39
  pytz               conda-forge/noarch::pytz-2022.2.1-pyhd8ed1ab_0
  six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0


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

## Package Plan ##

  environment location: /Users/biocbuild/bbs-3.20-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - python=3.9.12


The following NEW packages will be INSTALLED:

  bzip2              conda-forge/osx-64::bzip2-1.0.8-h10d778d_5
  ca-certificates    conda-forge/osx-64::ca-certificates-2024.6.2-h8857fd0_0
  libffi             conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
  libsqlite          conda-forge/osx-64::libsqlite-3.45.3-h92b6c6a_0
  libzlib            conda-forge/osx-64::libzlib-1.3.1-h87427d6_1
  ncurses            conda-forge/osx-64::ncurses-6.5-h5846eda_0
  openssl            conda-forge/osx-64::openssl-3.3.1-h87427d6_0
  pip                conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
  python             conda-forge/osx-64::python-3.9.12-h1cc4136_1_cpython
  readline           conda-forge/osx-64::readline-8.2-h9e318b2_1
  setuptools         conda-forge/noarch::setuptools-70.0.0-pyhd8ed1ab_0
  sqlite             conda-forge/osx-64::sqlite-3.45.3-h7461747_0
  tk                 conda-forge/osx-64::tk-8.6.13-h1abcd95_1
  tzdata             conda-forge/noarch::tzdata-2024a-h0c530f3_0
  wheel              conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
  xz                 conda-forge/osx-64::xz-5.2.6-h775f41a_0


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 24.5.0

Please update conda by running

    $ conda update -n base -c defaults conda



# All requested packages already installed.

Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 24.5.0

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /Users/biocbuild/bbs-3.20-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

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


The following NEW packages will be INSTALLED:

  libblas            conda-forge/osx-64::libblas-3.9.0-22_osx64_openblas
  libcblas           conda-forge/osx-64::libcblas-3.9.0-22_osx64_openblas
  libcxx             conda-forge/osx-64::libcxx-17.0.6-h88467a6_0
  libgfortran        conda-forge/osx-64::libgfortran-5.0.0-13_2_0_h97931a8_3
  libgfortran5       conda-forge/osx-64::libgfortran5-13.2.0-h2873a65_3
  liblapack          conda-forge/osx-64::liblapack-3.9.0-22_osx64_openblas
  libopenblas        conda-forge/osx-64::libopenblas-0.3.27-openmp_hfef2a42_0
  llvm-openmp        conda-forge/osx-64::llvm-openmp-18.1.7-h15ab845_0
  numpy              conda-forge/osx-64::numpy-1.26.4-py39h28c39a1_0
  pandas             conda-forge/osx-64::pandas-1.4.2-py39hf72b562_2
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.1-py_0
  python_abi         conda-forge/osx-64::python_abi-3.9-4_cp39
  pytz               conda-forge/noarch::pytz-2022.1-pyhd8ed1ab_0
  six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0


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

Example timings

basilisk.Rcheck/basilisk-Ex.timings

nameusersystemelapsed
BasiliskEnvironment-class0.0060.0020.008
PyPiLink0.0010.0010.003
basiliskOptions0.0010.0010.002
basiliskStart644.296 79.197898.513
configureBasiliskEnv0.0000.0010.001
createLocalBasiliskEnv226.982 35.442377.816
listPackages0.9370.3421.726
obtainEnvironmentPath0.0070.0020.008
setupBasiliskEnv0.0050.0020.007
useBasiliskEnv1.5740.5592.769