Multiple platform build/check report for BioC 3.12 - CHECK report for basilisk on tokay1

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

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###
### 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.

##############################################################################
##############################################################################
###
### 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


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

name	user	system	elapsed
BasiliskEnvironment-class	0	0	0
PyPiLink	0	0	0
basiliskOptions	0	0	0
basiliskStart	0.86	0.38	209.52
configureBasiliskEnv	0.01	0.00	0.02
findPersistentEnv	0.04	0.00	2.97
listPackages	0.00	0.00	9.42
setupBasiliskEnv	0.05	0.00	60.53
useBasiliskEnv	0.08	0.00	1.08

CHECK report for basilisk on tokay1

Summary

Command output

Installation output

Tests output

Example timings