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CHECK report for basilisk on tokay1

This page was generated on 2021-05-06 12:29:58 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the basilisk package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 121/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
basilisk 1.2.1  (landing page)
Aaron Lun
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/basilisk
Branch: RELEASE_3_12
Last Commit: 27516b7
Last Changed Date: 2020-12-16 13:41:00 -0400 (Wed, 16 Dec 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: basilisk
Version: 1.2.1
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:basilisk.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings basilisk_1.2.1.tar.gz
StartedAt: 2021-05-06 00:38:05 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 01:01:16 -0400 (Thu, 06 May 2021)
EllapsedTime: 1390.3 seconds
RetCode: 1
Status:   ERROR   
CheckDir: basilisk.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:basilisk.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings basilisk_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/basilisk.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'basilisk/DESCRIPTION' ... OK
* this is package 'basilisk' version '1.2.1'
* 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 whether package 'basilisk' can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See 'C:/Users/biocbuild/bbs-3.12-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 ... NOTE
basiliskRun: no visible binding for global variable '.basilisk.fun'
basiliskRun: no visible binding for global variable '.basilisk.args'
Undefined global functions or variables:
  .basilisk.args .basilisk.fun
* 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    0.86   0.38  209.52
setupBasiliskEnv 0.05   0.00   60.53
listPackages     0.00   0.00    9.42
* 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:
   6.     \-throw(new_callr_error(output, killmsg))
  -- Error (test-start.R:156:5): basilisk uses sockets as a fallback -------------
  Error: callr subprocess failed: could not start R, exited with non-zero status, has crashed or was killed
  Backtrace:
      x
   1. +-testthat::expect_true(...) test-start.R:156:4
   2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
   3. |   \-rlang::eval_bare(expr, quo_get_env(quo))
   4. \-callr::r(...)
   5.   \-callr:::get_result(output = out, options)
   6.     \-throw(new_callr_error(output, killmsg))
  
  [ FAIL 3 | WARN 7 | SKIP 2 | PASS 25 ]
  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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/basilisk.Rcheck/00check.log'
for details.


Installation output

basilisk.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch basilisk
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/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
  converting help for package 'basilisk'
    finding HTML links ... done
    BasiliskEnvironment-class               html  
    PyPiLink                                html  
    basiliskOptions                         html  
    basiliskStart                           html  
    finding level-2 HTML links ... done

    configureBasiliskEnv                    html  
    findPersistentEnv                       html  
    listPackages                            html  
    setupBasiliskEnv                        html  
    useBasiliskEnv                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (basilisk)
Making 'packages.html' ... done

Tests output

basilisk.Rcheck/tests/testthat.Rout.fail


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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... 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: C:\Users\biocbuild\bbs-3.12-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo

  added / updated specs:
    - python=3.7.7


The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/win-64::ca-certificates-2020.12.5-h5b45459_0
  certifi            conda-forge/win-64::certifi-2020.12.5-py37h03978a9_1
  openssl            conda-forge/win-64::openssl-1.1.1k-h8ffe710_0
  pip                conda-forge/noarch::pip-21.1.1-pyhd8ed1ab_0
  python             pkgs/main/win-64::python-3.7.7-h81c818b_4
  python_abi         conda-forge/win-64::python_abi-3.7-1_cp37m
  setuptools         conda-forge/win-64::setuptools-49.6.0-py37h03978a9_3
  sqlite             conda-forge/win-64::sqlite-3.35.5-h8ffe710_0
  vc                 conda-forge/win-64::vc-14.2-hb210afc_4
  vs2015_runtime     conda-forge/win-64::vs2015_runtime-14.28.29325-h5e1d092_4
  wheel              conda-forge/noarch::wheel-0.36.2-pyhd3deb0d_0
  wincertstore       conda-forge/win-64::wincertstore-0.2-py37h03978a9_1006


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.3
  latest version: 4.10.1

Please update conda by running

    $ conda update -n base -c defaults conda


#
# To activate this environment, use
#
#     $ conda activate C:\Users\biocbuild\bbs-3.12-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo
#
# To deactivate an active environment, use
#
#     $ conda deactivate

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

## Package Plan ##

  environment location: C:\Users\biocbuild\bbs-3.12-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo

  added / updated specs:
    - python=3.7.7


The following packages will be UPDATED:

  ca-certificates    conda-forge::ca-certificates-2020.12.~ --> pkgs/main::ca-certificates-2021.4.13-haa95532_1

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

  certifi            conda-forge::certifi-2020.12.5-py37h0~ --> pkgs/main::certifi-2020.12.5-py37haa95532_0
  openssl            conda-forge::openssl-1.1.1k-h8ffe710_0 --> pkgs/main::openssl-1.1.1k-h2bbff1b_0


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.3
  latest version: 4.10.1

Please update conda by running

    $ conda update -n base -c defaults conda


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

## Package Plan ##

  environment location: C:\Users\biocbuild\bbs-3.12-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo

  added / updated specs:
    - pandas=0.25.1
    - python-dateutil=2.8.0
    - python=3.7.7
    - pytz=2019.3


The following NEW packages will be INSTALLED:

  intel-openmp       conda-forge/win-64::intel-openmp-2021.2.0-h57928b3_616
  libblas            conda-forge/win-64::libblas-3.9.0-9_mkl
  libcblas           conda-forge/win-64::libcblas-3.9.0-9_mkl
  liblapack          conda-forge/win-64::liblapack-3.9.0-9_mkl
  mkl                conda-forge/win-64::mkl-2021.2.0-hb70f87d_389
  numpy              conda-forge/win-64::numpy-1.20.2-py37hcbcd69c_0
  pandas             conda-forge/win-64::pandas-0.25.1-py37he350917_0
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.0-py_0
  pytz               conda-forge/noarch::pytz-2019.3-py_0
  six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
  tbb                conda-forge/win-64::tbb-2021.2.0-h2d74725_0

The following packages will be UPDATED:

  certifi            pkgs/main::certifi-2020.12.5-py37haa9~ --> conda-forge::certifi-2020.12.5-py37h03978a9_1

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

  ca-certificates    pkgs/main::ca-certificates-2021.4.13-~ --> conda-forge::ca-certificates-2020.12.5-h5b45459_0
  openssl              pkgs/main::openssl-1.1.1k-h2bbff1b_0 --> conda-forge::openssl-1.1.1k-h8ffe710_0


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.3
  latest version: 4.10.1

Please update conda by running

    $ conda update -n base -c defaults conda


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: C:\Users\biocbuild\bbs-3.12-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo

  added / updated specs:
    - python=3.7.7


The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/win-64::ca-certificates-2020.12.5-h5b45459_0
  certifi            conda-forge/win-64::certifi-2020.12.5-py37h03978a9_1
  openssl            conda-forge/win-64::openssl-1.1.1k-h8ffe710_0
  pip                conda-forge/noarch::pip-21.1.1-pyhd8ed1ab_0
  python             pkgs/main/win-64::python-3.7.7-h81c818b_4
  python_abi         conda-forge/win-64::python_abi-3.7-1_cp37m
  setuptools         conda-forge/win-64::setuptools-49.6.0-py37h03978a9_3
  sqlite             conda-forge/win-64::sqlite-3.35.5-h8ffe710_0
  vc                 conda-forge/win-64::vc-14.2-hb210afc_4
  vs2015_runtime     conda-forge/win-64::vs2015_runtime-14.28.29325-h5e1d092_4
  wheel              conda-forge/noarch::wheel-0.36.2-pyhd3deb0d_0
  wincertstore       conda-forge/win-64::wincertstore-0.2-py37h03978a9_1006


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.3
  latest version: 4.10.1

Please update conda by running

    $ conda update -n base -c defaults conda


#
# To activate this environment, use
#
#     $ conda activate C:\Users\biocbuild\bbs-3.12-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo
#
# To deactivate an active environment, use
#
#     $ conda deactivate

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

## Package Plan ##

  environment location: C:\Users\biocbuild\bbs-3.12-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo

  added / updated specs:
    - python=3.7.7


The following packages will be UPDATED:

  ca-certificates    conda-forge::ca-certificates-2020.12.~ --> pkgs/main::ca-certificates-2021.4.13-haa95532_1

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

  certifi            conda-forge::certifi-2020.12.5-py37h0~ --> pkgs/main::certifi-2020.12.5-py37haa95532_0
  openssl            conda-forge::openssl-1.1.1k-h8ffe710_0 --> pkgs/main::openssl-1.1.1k-h2bbff1b_0


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.3
  latest version: 4.10.1

Please update conda by running

    $ conda update -n base -c defaults conda


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

## Package Plan ##

  environment location: C:\Users\biocbuild\bbs-3.12-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo

  added / updated specs:
    - pandas=0.24.1
    - python-dateutil=2.7.1
    - python=3.7.7
    - pytz=2018.7


The following NEW packages will be INSTALLED:

  intel-openmp       conda-forge/win-64::intel-openmp-2021.2.0-h57928b3_616
  libblas            conda-forge/win-64::libblas-3.9.0-9_mkl
  libcblas           conda-forge/win-64::libcblas-3.9.0-9_mkl
  liblapack          conda-forge/win-64::liblapack-3.9.0-9_mkl
  mkl                conda-forge/win-64::mkl-2021.2.0-hb70f87d_389
  numpy              conda-forge/win-64::numpy-1.20.2-py37hcbcd69c_0
  pandas             conda-forge/win-64::pandas-0.24.1-py37h6538335_0
  python-dateutil    conda-forge/noarch::python-dateutil-2.7.1-py_0
  pytz               conda-forge/noarch::pytz-2018.7-py_0
  six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
  tbb                conda-forge/win-64::tbb-2021.2.0-h2d74725_0

The following packages will be UPDATED:

  certifi            pkgs/main::certifi-2020.12.5-py37haa9~ --> conda-forge::certifi-2020.12.5-py37h03978a9_1

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

  ca-certificates    pkgs/main::ca-certificates-2021.4.13-~ --> conda-forge::ca-certificates-2020.12.5-h5b45459_0
  openssl              pkgs/main::openssl-1.1.1k-h2bbff1b_0 --> conda-forge::openssl-1.1.1k-h8ffe710_0


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.3
  latest version: 4.10.1

Please update conda by running

    $ conda update -n base -c defaults conda


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: C:\Users\biocbuild\bbs-3.12-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo

  added / updated specs:
    - python=2.7


The following NEW packages will be INSTALLED:

  certifi            conda-forge/win-64::certifi-2019.11.28-py27h8c360ce_1
  pip                conda-forge/noarch::pip-20.1.1-pyh9f0ad1d_0
  python             conda-forge/win-64::python-2.7.15-h2880e7c_1011_cpython
  python_abi         conda-forge/win-64::python_abi-2.7-1_cp27m
  setuptools         conda-forge/win-64::setuptools-44.0.0-py27_0
  vc                 pkgs/main/win-64::vc-9-h7299396_1
  vs2008_runtime     conda-forge/win-64::vs2008_runtime-9.0.30729.6161-0
  wheel              conda-forge/noarch::wheel-0.36.2-pyhd3deb0d_0
  wincertstore       conda-forge/win-64::wincertstore-0.2-py27_1003


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.3
  latest version: 4.10.1

Please update conda by running

    $ conda update -n base -c defaults conda


#
# To activate this environment, use
#
#     $ conda activate C:\Users\biocbuild\bbs-3.12-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo
#
# To deactivate an active environment, use
#
#     $ conda deactivate

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

## Package Plan ##

  environment location: C:\Users\biocbuild\bbs-3.12-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/win-64::certifi-2019.11.2~ --> pkgs/main/noarch::certifi-2020.6.20-pyhd3eb1b0_3


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.3
  latest version: 4.10.1

Please update conda by running

    $ conda update -n base -c defaults conda


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.3
  latest version: 4.10.1

Please update conda by running

    $ conda update -n base -c defaults conda



# All requested packages already installed.

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

## Package Plan ##

  environment location: C:\Users\biocbuild\bbs-3.12-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo

  added / updated specs:
    - python=3.7.7


The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/win-64::ca-certificates-2020.12.5-h5b45459_0
  certifi            conda-forge/win-64::certifi-2020.12.5-py37h03978a9_1
  openssl            conda-forge/win-64::openssl-1.1.1k-h8ffe710_0
  pip                conda-forge/noarch::pip-21.1.1-pyhd8ed1ab_0
  python             pkgs/main/win-64::python-3.7.7-h81c818b_4
  python_abi         conda-forge/win-64::python_abi-3.7-1_cp37m
  setuptools         conda-forge/win-64::setuptools-49.6.0-py37h03978a9_3
  sqlite             conda-forge/win-64::sqlite-3.35.5-h8ffe710_0
  vc                 conda-forge/win-64::vc-14.2-hb210afc_4
  vs2015_runtime     conda-forge/win-64::vs2015_runtime-14.28.29325-h5e1d092_4
  wheel              conda-forge/noarch::wheel-0.36.2-pyhd3deb0d_0
  wincertstore       conda-forge/win-64::wincertstore-0.2-py37h03978a9_1006


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.3
  latest version: 4.10.1

Please update conda by running

    $ conda update -n base -c defaults conda


#
# To activate this environment, use
#
#     $ conda activate C:\Users\biocbuild\bbs-3.12-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo
#
# To deactivate an active environment, use
#
#     $ conda deactivate

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

## Package Plan ##

  environment location: C:\Users\biocbuild\bbs-3.12-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo

  added / updated specs:
    - python=3.7.7


The following packages will be UPDATED:

  ca-certificates    conda-forge::ca-certificates-2020.12.~ --> pkgs/main::ca-certificates-2021.4.13-haa95532_1

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

  certifi            conda-forge::certifi-2020.12.5-py37h0~ --> pkgs/main::certifi-2020.12.5-py37haa95532_0
  openssl            conda-forge::openssl-1.1.1k-h8ffe710_0 --> pkgs/main::openssl-1.1.1k-h2bbff1b_0


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.3
  latest version: 4.10.1

Please update conda by running

    $ conda update -n base -c defaults conda


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

## Package Plan ##

  environment location: C:\Users\biocbuild\bbs-3.12-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo

  added / updated specs:
    - python-dateutil=2.7.1
    - python=3.7.7
    - pytz=2018.7


The following NEW packages will be INSTALLED:

  python-dateutil    conda-forge/noarch::python-dateutil-2.7.1-py_0
  pytz               conda-forge/noarch::pytz-2018.7-py_0
  six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0

The following packages will be UPDATED:

  certifi            pkgs/main::certifi-2020.12.5-py37haa9~ --> conda-forge::certifi-2020.12.5-py37h03978a9_1

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

  ca-certificates    pkgs/main::ca-certificates-2021.4.13-~ --> conda-forge::ca-certificates-2020.12.5-h5b45459_0
  openssl              pkgs/main::openssl-1.1.1k-h2bbff1b_0 --> conda-forge::openssl-1.1.1k-h8ffe710_0


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.3
  latest version: 4.10.1

Please update conda by running

    $ conda update -n base -c defaults conda


Collecting pandas==0.24.1
  Using cached pandas-0.24.1-cp37-cp37m-win_amd64.whl (9.0 MB)
Requirement already satisfied: pytz>=2011k in c:\users\biocbu~1\bbs-3~1.12-\meat\basili~1.rch\tests\testthat\instal~1\thingo\lib\site-packages (from pandas==0.24.1) (2018.7)
Collecting numpy>=1.12.0
  Using cached numpy-1.20.2-cp37-cp37m-win_amd64.whl (13.6 MB)
Requirement already satisfied: python-dateutil>=2.5.0 in c:\users\biocbu~1\bbs-3~1.12-\meat\basili~1.rch\tests\testthat\instal~1\thingo\lib\site-packages (from pandas==0.24.1) (2.7.1)
Requirement already satisfied: six>=1.5 in c:\users\biocbu~1\bbs-3~1.12-\meat\basili~1.rch\tests\testthat\instal~1\thingo\lib\site-packages (from python-dateutil>=2.5.0->pandas==0.24.1) (1.16.0)
Installing collected packages: numpy, pandas
  WARNING: The script f2py.exe is installed in 'C:\Users\BIOCBU~1\BBS-3~1.12-\meat\BASILI~1.RCH\tests\testthat\INSTAL~1\thingo\Scripts' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Successfully installed numpy-1.20.2 pandas-0.24.1
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: C:\Users\biocbuild\bbs-3.12-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo

  added / updated specs:
    - python=3.7.7


The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/win-64::ca-certificates-2020.12.5-h5b45459_0
  certifi            conda-forge/win-64::certifi-2020.12.5-py37h03978a9_1
  openssl            conda-forge/win-64::openssl-1.1.1k-h8ffe710_0
  pip                conda-forge/noarch::pip-21.1.1-pyhd8ed1ab_0
  python             pkgs/main/win-64::python-3.7.7-h81c818b_4
  python_abi         conda-forge/win-64::python_abi-3.7-1_cp37m
  setuptools         conda-forge/win-64::setuptools-49.6.0-py37h03978a9_3
  sqlite             conda-forge/win-64::sqlite-3.35.5-h8ffe710_0
  vc                 conda-forge/win-64::vc-14.2-hb210afc_4
  vs2015_runtime     conda-forge/win-64::vs2015_runtime-14.28.29325-h5e1d092_4
  wheel              conda-forge/noarch::wheel-0.36.2-pyhd3deb0d_0
  wincertstore       conda-forge/win-64::wincertstore-0.2-py37h03978a9_1006


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.3
  latest version: 4.10.1

Please update conda by running

    $ conda update -n base -c defaults conda


#
# To activate this environment, use
#
#     $ conda activate C:\Users\biocbuild\bbs-3.12-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo
#
# To deactivate an active environment, use
#
#     $ conda deactivate

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

## Package Plan ##

  environment location: C:\Users\biocbuild\bbs-3.12-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo

  added / updated specs:
    - python=3.7.7


The following packages will be UPDATED:

  ca-certificates    conda-forge::ca-certificates-2020.12.~ --> pkgs/main::ca-certificates-2021.4.13-haa95532_1

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

  certifi            conda-forge::certifi-2020.12.5-py37h0~ --> pkgs/main::certifi-2020.12.5-py37haa95532_0
  openssl            conda-forge::openssl-1.1.1k-h8ffe710_0 --> pkgs/main::openssl-1.1.1k-h2bbff1b_0


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.3
  latest version: 4.10.1

Please update conda by running

    $ conda update -n base -c defaults conda


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/win-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://repo.anaconda.com/pkgs/main/win-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/win-64
  - https://repo.anaconda.com/pkgs/r/noarch
  - https://repo.anaconda.com/pkgs/msys2/win-64
  - https://repo.anaconda.com/pkgs/msys2/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.


* installing *source* package 'son.of.basilisk' ...
** using non-staged installation via StagedInstall field
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'son.of.basilisk'
    finding HTML links ... done
    test                                    html  
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* DONE (son.of.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: C:\Users\biocbuild\bbs-3.12-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\my_package_A

  added / updated specs:
    - python=3.7.7


The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/win-64::ca-certificates-2020.12.5-h5b45459_0
  certifi            conda-forge/win-64::certifi-2020.12.5-py37h03978a9_1
  openssl            conda-forge/win-64::openssl-1.1.1k-h8ffe710_0
  pip                conda-forge/noarch::pip-21.1.1-pyhd8ed1ab_0
  python             pkgs/main/win-64::python-3.7.7-h81c818b_4
  python_abi         conda-forge/win-64::python_abi-3.7-1_cp37m
  setuptools         conda-forge/win-64::setuptools-49.6.0-py37h03978a9_3
  sqlite             conda-forge/win-64::sqlite-3.35.5-h8ffe710_0
  vc                 conda-forge/win-64::vc-14.2-hb210afc_4
  vs2015_runtime     conda-forge/win-64::vs2015_runtime-14.28.29325-h5e1d092_4
  wheel              conda-forge/noarch::wheel-0.36.2-pyhd3deb0d_0
  wincertstore       conda-forge/win-64::wincertstore-0.2-py37h03978a9_1006


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.3
  latest version: 4.10.1

Please update conda by running

    $ conda update -n base -c defaults conda


#
# To activate this environment, use
#
#     $ conda activate C:\Users\biocbuild\bbs-3.12-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\my_package_A
#
# To deactivate an active environment, use
#
#     $ conda deactivate

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

## Package Plan ##

  environment location: C:\Users\biocbuild\bbs-3.12-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\my_package_A

  added / updated specs:
    - python=3.7.7


The following packages will be UPDATED:

  ca-certificates    conda-forge::ca-certificates-2020.12.~ --> pkgs/main::ca-certificates-2021.4.13-haa95532_1

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

  certifi            conda-forge::certifi-2020.12.5-py37h0~ --> pkgs/main::certifi-2020.12.5-py37haa95532_0
  openssl            conda-forge::openssl-1.1.1k-h8ffe710_0 --> pkgs/main::openssl-1.1.1k-h2bbff1b_0


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.3
  latest version: 4.10.1

Please update conda by running

    $ conda update -n base -c defaults conda


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

## Package Plan ##

  environment location: C:\Users\biocbuild\bbs-3.12-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\my_package_A

  added / updated specs:
    - pandas=0.25.1
    - python-dateutil=2.8.0
    - python=3.7.7
    - pytz=2019.3


The following NEW packages will be INSTALLED:

  intel-openmp       conda-forge/win-64::intel-openmp-2021.2.0-h57928b3_616
  libblas            conda-forge/win-64::libblas-3.9.0-9_mkl
  libcblas           conda-forge/win-64::libcblas-3.9.0-9_mkl
  liblapack          conda-forge/win-64::liblapack-3.9.0-9_mkl
  mkl                conda-forge/win-64::mkl-2021.2.0-hb70f87d_389
  numpy              conda-forge/win-64::numpy-1.20.2-py37hcbcd69c_0
  pandas             conda-forge/win-64::pandas-0.25.1-py37he350917_0
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.0-py_0
  pytz               conda-forge/noarch::pytz-2019.3-py_0
  six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
  tbb                conda-forge/win-64::tbb-2021.2.0-h2d74725_0

The following packages will be UPDATED:

  certifi            pkgs/main::certifi-2020.12.5-py37haa9~ --> conda-forge::certifi-2020.12.5-py37h03978a9_1

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

  ca-certificates    pkgs/main::ca-certificates-2021.4.13-~ --> conda-forge::ca-certificates-2020.12.5-h5b45459_0
  openssl              pkgs/main::openssl-1.1.1k-h2bbff1b_0 --> conda-forge::openssl-1.1.1k-h8ffe710_0


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.3
  latest version: 4.10.1

Please update conda by running

    $ conda update -n base -c defaults conda


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: C:\Users\biocbuild\bbs-3.12-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\my_package_B

  added / updated specs:
    - python=3.7.7


The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/win-64::ca-certificates-2020.12.5-h5b45459_0
  certifi            conda-forge/win-64::certifi-2020.12.5-py37h03978a9_1
  openssl            conda-forge/win-64::openssl-1.1.1k-h8ffe710_0
  pip                conda-forge/noarch::pip-21.1.1-pyhd8ed1ab_0
  python             pkgs/main/win-64::python-3.7.7-h81c818b_4
  python_abi         conda-forge/win-64::python_abi-3.7-1_cp37m
  setuptools         conda-forge/win-64::setuptools-49.6.0-py37h03978a9_3
  sqlite             conda-forge/win-64::sqlite-3.35.5-h8ffe710_0
  vc                 conda-forge/win-64::vc-14.2-hb210afc_4
  vs2015_runtime     conda-forge/win-64::vs2015_runtime-14.28.29325-h5e1d092_4
  wheel              conda-forge/noarch::wheel-0.36.2-pyhd3deb0d_0
  wincertstore       conda-forge/win-64::wincertstore-0.2-py37h03978a9_1006


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.3
  latest version: 4.10.1

Please update conda by running

    $ conda update -n base -c defaults conda


#
# To activate this environment, use
#
#     $ conda activate C:\Users\biocbuild\bbs-3.12-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\my_package_B
#
# To deactivate an active environment, use
#
#     $ conda deactivate

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

## Package Plan ##

  environment location: C:\Users\biocbuild\bbs-3.12-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\my_package_B

  added / updated specs:
    - python=3.7.7


The following packages will be UPDATED:

  ca-certificates    conda-forge::ca-certificates-2020.12.~ --> pkgs/main::ca-certificates-2021.4.13-haa95532_1

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

  certifi            conda-forge::certifi-2020.12.5-py37h0~ --> pkgs/main::certifi-2020.12.5-py37haa95532_0
  openssl            conda-forge::openssl-1.1.1k-h8ffe710_0 --> pkgs/main::openssl-1.1.1k-h2bbff1b_0


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.3
  latest version: 4.10.1

Please update conda by running

    $ conda update -n base -c defaults conda


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

## Package Plan ##

  environment location: C:\Users\biocbuild\bbs-3.12-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\my_package_B

  added / updated specs:
    - pandas=0.24.1
    - python-dateutil=2.7.1
    - python=3.7.7
    - pytz=2018.7


The following NEW packages will be INSTALLED:

  intel-openmp       conda-forge/win-64::intel-openmp-2021.2.0-h57928b3_616
  libblas            conda-forge/win-64::libblas-3.9.0-9_mkl
  libcblas           conda-forge/win-64::libcblas-3.9.0-9_mkl
  liblapack          conda-forge/win-64::liblapack-3.9.0-9_mkl
  mkl                conda-forge/win-64::mkl-2021.2.0-hb70f87d_389
  numpy              conda-forge/win-64::numpy-1.20.2-py37hcbcd69c_0
  pandas             conda-forge/win-64::pandas-0.24.1-py37h6538335_0
  python-dateutil    conda-forge/noarch::python-dateutil-2.7.1-py_0
  pytz               conda-forge/noarch::pytz-2018.7-py_0
  six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
  tbb                conda-forge/win-64::tbb-2021.2.0-h2d74725_0

The following packages will be UPDATED:

  certifi            pkgs/main::certifi-2020.12.5-py37haa9~ --> conda-forge::certifi-2020.12.5-py37h03978a9_1

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

  ca-certificates    pkgs/main::ca-certificates-2021.4.13-~ --> conda-forge::ca-certificates-2020.12.5-h5b45459_0
  openssl              pkgs/main::openssl-1.1.1k-h2bbff1b_0 --> conda-forge::openssl-1.1.1k-h8ffe710_0


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.3
  latest version: 4.10.1

Please update conda by running

    $ conda update -n base -c defaults conda


== Skipped tests ===============================================================
* On Windows (2)

== Failed tests ================================================================
-- Error (test-start.R:130:5): basilisk directly loads Python when possible ----
Error: callr subprocess failed: could not start R, exited with non-zero status, has crashed or was killed
Backtrace:
    x
 1. +-testthat::expect_true(...) test-start.R:130:4
 2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
 3. |   \-rlang::eval_bare(expr, quo_get_env(quo))
 4. \-callr::r(FUN, args = list(version = new.version, envir = tA))
 5.   \-callr:::get_result(output = out, options)
 6.     \-throw(new_callr_error(output, killmsg))
-- Error (test-start.R:141:5): basilisk forks when possible --------------------
Error: callr subprocess failed: could not start R, exited with non-zero status, has crashed or was killed
Backtrace:
    x
 1. +-testthat::expect_true(...) test-start.R:141:4
 2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
 3. |   \-rlang::eval_bare(expr, quo_get_env(quo))
 4. \-callr::r(process_check, args = list(version = new.version, envir = tA))
 5.   \-callr:::get_result(output = out, options)
 6.     \-throw(new_callr_error(output, killmsg))
-- Error (test-start.R:156:5): basilisk uses sockets as a fallback -------------
Error: callr subprocess failed: could not start R, exited with non-zero status, has crashed or was killed
Backtrace:
    x
 1. +-testthat::expect_true(...) test-start.R:156:4
 2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
 3. |   \-rlang::eval_bare(expr, quo_get_env(quo))
 4. \-callr::r(...)
 5.   \-callr:::get_result(output = out, options)
 6.     \-throw(new_callr_error(output, killmsg))

[ FAIL 3 | WARN 7 | SKIP 2 | PASS 25 ]
Error: Test failures
Execution halted

Example timings

basilisk.Rcheck/basilisk-Ex.timings

nameusersystemelapsed
BasiliskEnvironment-class000
PyPiLink000
basiliskOptions000
basiliskStart 0.86 0.38209.52
configureBasiliskEnv0.010.000.02
findPersistentEnv0.040.002.97
listPackages0.000.009.42
setupBasiliskEnv 0.05 0.0060.53
useBasiliskEnv0.080.001.08