Back to Multiple platform build/check report for BioC 3.14
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-10-27 13:52:53 -0400 (Wed, 27 Oct 2021).

CHECK results for basilisk on riesling1

To the developers/maintainers of the basilisk package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 120/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
basilisk 1.6.0  (landing page)
Aaron Lun
Snapshot Date: 2021-10-26 14:50:08 -0400 (Tue, 26 Oct 2021)
git_url: https://git.bioconductor.org/packages/basilisk
git_branch: RELEASE_3_14
git_last_commit: 8910ee2
git_last_commit_date: 2021-10-26 12:57:18 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  YES
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  YES
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  YES
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: basilisk
Version: 1.6.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:basilisk.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings basilisk_1.6.0.tar.gz
StartedAt: 2021-10-27 00:55:13 -0400 (Wed, 27 Oct 2021)
EndedAt: 2021-10-27 01:15:23 -0400 (Wed, 27 Oct 2021)
EllapsedTime: 1209.9 seconds
RetCode: 0
Status:   OK  
CheckDir: basilisk.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:basilisk.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings basilisk_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/basilisk.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.6.0'
* 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 'D:/biocbuild/bbs-3.14-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    0.52   0.25  202.62
setupBasiliskEnv 0.00   0.00   64.69
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* 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: 3 NOTEs
See
  'D:/biocbuild/bbs-3.14-bioc/meat/basilisk.Rcheck/00check.log'
for details.



Installation output

basilisk.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch basilisk
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.14-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


R version 4.1.1 (2021-08-10) -- "Kick Things"
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: D:\biocbuild\bbs-3.14-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-2021.10.8-h5b45459_0
  openssl            conda-forge/win-64::openssl-1.1.1l-h8ffe710_0
  pip                conda-forge/noarch::pip-21.3.1-pyhd8ed1ab_0
  python             pkgs/main/win-64::python-3.7.7-h81c818b_4
  python_abi         conda-forge/win-64::python_abi-3.7-2_cp37m
  setuptools         conda-forge/win-64::setuptools-58.2.0-py37h03978a9_0
  sqlite             conda-forge/win-64::sqlite-3.36.0-h8ffe710_2
  ucrt               conda-forge/win-64::ucrt-10.0.20348.0-h57928b3_0
  vc                 conda-forge/win-64::vc-14.2-hb210afc_5
  vs2015_runtime     conda-forge/win-64::vs2015_runtime-14.29.30037-h902a5da_5
  wheel              conda-forge/noarch::wheel-0.37.0-pyhd8ed1ab_1


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: 4.10.3

Please update conda by running

    $ conda update -n base -c defaults conda


#
# To activate this environment, use
#
#     $ conda activate D:\biocbuild\bbs-3.14-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: D:\biocbuild\bbs-3.14-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo

  added / updated specs:
    - python=3.7.7


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

  ca-certificates    conda-forge::ca-certificates-2021.10.~ --> pkgs/main::ca-certificates-2021.9.30-haa95532_1
  openssl            conda-forge::openssl-1.1.1l-h8ffe710_0 --> pkgs/main::openssl-1.1.1l-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: 4.10.3

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: D:\biocbuild\bbs-3.14-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-2021.4.0-h57928b3_3556
  libblas            conda-forge/win-64::libblas-3.9.0-12_win64_mkl
  libcblas           conda-forge/win-64::libcblas-3.9.0-12_win64_mkl
  liblapack          conda-forge/win-64::liblapack-3.9.0-12_win64_mkl
  mkl                conda-forge/win-64::mkl-2021.4.0-h0e2418a_729
  numpy              conda-forge/win-64::numpy-1.21.3-py37h940b05c_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-2021.4.0-h2d74725_0

The following packages will be UPDATED:

  ca-certificates    pkgs/main::ca-certificates-2021.9.30-~ --> conda-forge::ca-certificates-2021.10.8-h5b45459_0

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

  openssl              pkgs/main::openssl-1.1.1l-h2bbff1b_0 --> conda-forge::openssl-1.1.1l-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: 4.10.3

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: D:\biocbuild\bbs-3.14-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-2021.10.8-h5b45459_0
  openssl            conda-forge/win-64::openssl-1.1.1l-h8ffe710_0
  pip                conda-forge/noarch::pip-21.3.1-pyhd8ed1ab_0
  python             pkgs/main/win-64::python-3.7.7-h81c818b_4
  python_abi         conda-forge/win-64::python_abi-3.7-2_cp37m
  setuptools         conda-forge/win-64::setuptools-58.2.0-py37h03978a9_0
  sqlite             conda-forge/win-64::sqlite-3.36.0-h8ffe710_2
  ucrt               conda-forge/win-64::ucrt-10.0.20348.0-h57928b3_0
  vc                 conda-forge/win-64::vc-14.2-hb210afc_5
  vs2015_runtime     conda-forge/win-64::vs2015_runtime-14.29.30037-h902a5da_5
  wheel              conda-forge/noarch::wheel-0.37.0-pyhd8ed1ab_1


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: 4.10.3

Please update conda by running

    $ conda update -n base -c defaults conda


#
# To activate this environment, use
#
#     $ conda activate D:\biocbuild\bbs-3.14-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: D:\biocbuild\bbs-3.14-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo

  added / updated specs:
    - python=3.7.7


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

  ca-certificates    conda-forge::ca-certificates-2021.10.~ --> pkgs/main::ca-certificates-2021.9.30-haa95532_1
  openssl            conda-forge::openssl-1.1.1l-h8ffe710_0 --> pkgs/main::openssl-1.1.1l-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: 4.10.3

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: D:\biocbuild\bbs-3.14-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-2021.4.0-h57928b3_3556
  libblas            conda-forge/win-64::libblas-3.9.0-12_win64_mkl
  libcblas           conda-forge/win-64::libcblas-3.9.0-12_win64_mkl
  liblapack          conda-forge/win-64::liblapack-3.9.0-12_win64_mkl
  mkl                conda-forge/win-64::mkl-2021.4.0-h0e2418a_729
  numpy              conda-forge/win-64::numpy-1.21.3-py37h940b05c_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-2021.4.0-h2d74725_0

The following packages will be UPDATED:

  ca-certificates    pkgs/main::ca-certificates-2021.9.30-~ --> conda-forge::ca-certificates-2021.10.8-h5b45459_0

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

  openssl              pkgs/main::openssl-1.1.1l-h2bbff1b_0 --> conda-forge::openssl-1.1.1l-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: 4.10.3

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: D:\biocbuild\bbs-3.14-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo

  added / updated specs:
    - python=2.7


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    certifi-2019.11.28         |   py27h8c360ce_1         149 KB  conda-forge
    pip-20.1.1                 |     pyh9f0ad1d_0         1.1 MB  conda-forge
    python-2.7.15              |h2880e7c_1011_cpython        20.3 MB  conda-forge
    python_abi-2.7             |          1_cp27m           4 KB  conda-forge
    setuptools-44.0.0          |           py27_0         665 KB  conda-forge
    vc-9                       |       h7299396_1           3 KB
    vs2008_runtime-9.0.30729.6161|                0         1.0 MB  conda-forge
    wincertstore-0.2           |        py27_1003          13 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        23.2 MB

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-0.37.0-pyhd8ed1ab_1
  wincertstore       conda-forge/win-64::wincertstore-0.2-py27_1003



Downloading and Extracting Packages

setuptools-44.0.0    | 665 KB    |            |   0% 
setuptools-44.0.0    | 665 KB    | 2          |   2% 
setuptools-44.0.0    | 665 KB    | ####3      |  43% 
setuptools-44.0.0    | 665 KB    | ########## | 100% 

pip-20.1.1           | 1.1 MB    |            |   0% 
pip-20.1.1           | 1.1 MB    | ##6        |  27% 
pip-20.1.1           | 1.1 MB    | ########## | 100% 

python-2.7.15        | 20.3 MB   |            |   0% 
python-2.7.15        | 20.3 MB   | 1          |   2% 
python-2.7.15        | 20.3 MB   | ##4        |  25% 
python-2.7.15        | 20.3 MB   | ####3      |  44% 
python-2.7.15        | 20.3 MB   | #####6     |  57% 
python-2.7.15        | 20.3 MB   | ######6    |  66% 
python-2.7.15        | 20.3 MB   | #######4   |  74% 
python-2.7.15        | 20.3 MB   | ########1  |  82% 
python-2.7.15        | 20.3 MB   | ########## | 100% 

python_abi-2.7       | 4 KB      |            |   0% 
python_abi-2.7       | 4 KB      | ########## | 100% 

certifi-2019.11.28   | 149 KB    |            |   0% 
certifi-2019.11.28   | 149 KB    | ########## | 100% 

vs2008_runtime-9.0.3 | 1.0 MB    |            |   0% 
vs2008_runtime-9.0.3 | 1.0 MB    | ##3        |  24% 
vs2008_runtime-9.0.3 | 1.0 MB    | ########## | 100% 

wincertstore-0.2     | 13 KB     |            |   0% 
wincertstore-0.2     | 13 KB     | ########## | 100% 

vc-9                 | 3 KB      |            |   0% 
vc-9                 | 3 KB      | ########## | 100% 
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: 4.10.3

Please update conda by running

    $ conda update -n base -c defaults conda


#
# To activate this environment, use
#
#     $ conda activate D:\biocbuild\bbs-3.14-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: D:\biocbuild\bbs-3.14-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo

  added / updated specs:
    - python=2.7


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    certifi-2020.6.20          |     pyhd3eb1b0_3         155 KB
    ------------------------------------------------------------
                                           Total:         155 KB

The following packages will be UPDATED:

  certifi            conda-forge/win-64::certifi-2019.11.2~ --> pkgs/main/noarch::certifi-2020.6.20-pyhd3eb1b0_3



Downloading and Extracting Packages

certifi-2020.6.20    | 155 KB    |            |   0% 
certifi-2020.6.20    | 155 KB    | #          |  10% 
certifi-2020.6.20    | 155 KB    | ########## | 100% 
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: 4.10.3

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: 4.10.3

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: D:\biocbuild\bbs-3.14-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-2021.10.8-h5b45459_0
  openssl            conda-forge/win-64::openssl-1.1.1l-h8ffe710_0
  pip                conda-forge/noarch::pip-21.3.1-pyhd8ed1ab_0
  python             pkgs/main/win-64::python-3.7.7-h81c818b_4
  python_abi         conda-forge/win-64::python_abi-3.7-2_cp37m
  setuptools         conda-forge/win-64::setuptools-58.2.0-py37h03978a9_0
  sqlite             conda-forge/win-64::sqlite-3.36.0-h8ffe710_2
  ucrt               conda-forge/win-64::ucrt-10.0.20348.0-h57928b3_0
  vc                 conda-forge/win-64::vc-14.2-hb210afc_5
  vs2015_runtime     conda-forge/win-64::vs2015_runtime-14.29.30037-h902a5da_5
  wheel              conda-forge/noarch::wheel-0.37.0-pyhd8ed1ab_1


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: 4.10.3

Please update conda by running

    $ conda update -n base -c defaults conda


#
# To activate this environment, use
#
#     $ conda activate D:\biocbuild\bbs-3.14-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: D:\biocbuild\bbs-3.14-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo

  added / updated specs:
    - python=3.7.7


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

  ca-certificates    conda-forge::ca-certificates-2021.10.~ --> pkgs/main::ca-certificates-2021.9.30-haa95532_1
  openssl            conda-forge::openssl-1.1.1l-h8ffe710_0 --> pkgs/main::openssl-1.1.1l-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: 4.10.3

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: D:\biocbuild\bbs-3.14-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:

  ca-certificates    pkgs/main::ca-certificates-2021.9.30-~ --> conda-forge::ca-certificates-2021.10.8-h5b45459_0

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

  openssl              pkgs/main::openssl-1.1.1l-h2bbff1b_0 --> conda-forge::openssl-1.1.1l-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: 4.10.3

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 d:\biocbuild\bbs-3.14-bioc\meat\basilisk.rcheck\tests\testthat\install-test-client\thingo\lib\site-packages (from pandas==0.24.1) (2018.7)
Collecting numpy>=1.12.0
  Using cached numpy-1.21.3-cp37-cp37m-win_amd64.whl (14.0 MB)
Requirement already satisfied: python-dateutil>=2.5.0 in d:\biocbuild\bbs-3.14-bioc\meat\basilisk.rcheck\tests\testthat\install-test-client\thingo\lib\site-packages (from pandas==0.24.1) (2.7.1)
Requirement already satisfied: six>=1.5 in d:\biocbuild\bbs-3.14-bioc\meat\basilisk.rcheck\tests\testthat\install-test-client\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 'D:\biocbuild\bbs-3.14-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\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-1.21.3 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: D:\biocbuild\bbs-3.14-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-2021.10.8-h5b45459_0
  openssl            conda-forge/win-64::openssl-1.1.1l-h8ffe710_0
  pip                conda-forge/noarch::pip-21.3.1-pyhd8ed1ab_0
  python             pkgs/main/win-64::python-3.7.7-h81c818b_4
  python_abi         conda-forge/win-64::python_abi-3.7-2_cp37m
  setuptools         conda-forge/win-64::setuptools-58.2.0-py37h03978a9_0
  sqlite             conda-forge/win-64::sqlite-3.36.0-h8ffe710_2
  ucrt               conda-forge/win-64::ucrt-10.0.20348.0-h57928b3_0
  vc                 conda-forge/win-64::vc-14.2-hb210afc_5
  vs2015_runtime     conda-forge/win-64::vs2015_runtime-14.29.30037-h902a5da_5
  wheel              conda-forge/noarch::wheel-0.37.0-pyhd8ed1ab_1


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: 4.10.3

Please update conda by running

    $ conda update -n base -c defaults conda


#
# To activate this environment, use
#
#     $ conda activate D:\biocbuild\bbs-3.14-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: D:\biocbuild\bbs-3.14-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo

  added / updated specs:
    - python=3.7.7


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

  ca-certificates    conda-forge::ca-certificates-2021.10.~ --> pkgs/main::ca-certificates-2021.9.30-haa95532_1
  openssl            conda-forge::openssl-1.1.1l-h8ffe710_0 --> pkgs/main::openssl-1.1.1l-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: 4.10.3

Please update conda by running

    $ conda update -n base -c defaults conda


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

## Package Plan ##

  environment location: D:\biocbuild\bbs-3.14-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    pkgs/main::ca-certificates-2021.9.30-~ --> conda-forge::ca-certificates-2021.10.8-h5b45459_0

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

  openssl              pkgs/main::openssl-1.1.1l-h2bbff1b_0 --> conda-forge::openssl-1.1.1l-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: 4.10.3

Please update conda by running

    $ conda update -n base -c defaults conda


Processing d:\biocbuild\bbs-3.14-bioc\r\library\basilisk\example\inst\test_dummy
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Building wheels for collected packages: test-dummy
  Building wheel for test-dummy (setup.py): started
  Building wheel for test-dummy (setup.py): finished with status 'done'
  Created wheel for test-dummy: filename=test_dummy-0.1-py3-none-any.whl size=1295 sha256=a974cf33df4cfe8744891ffba05c7f222835e70ae6fb78874efb707ccf0ecc77
  Stored in directory: D:\biocbuild\bbs-3.14-bioc\tmpdir\pip-ephem-wheel-cache-2fbc91mu\wheels\75\01\ee\ae1244f79cbdd4d9c47f400e46b2b4992f600231eb3bcc3a47
Successfully built test-dummy
Installing collected packages: test-dummy
Successfully installed test-dummy-0.1
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... 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: D:\biocbuild\bbs-3.14-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-2021.10.8-h5b45459_0
  openssl            conda-forge/win-64::openssl-1.1.1l-h8ffe710_0
  pip                conda-forge/noarch::pip-21.3.1-pyhd8ed1ab_0
  python             pkgs/main/win-64::python-3.7.7-h81c818b_4
  python_abi         conda-forge/win-64::python_abi-3.7-2_cp37m
  setuptools         conda-forge/win-64::setuptools-58.2.0-py37h03978a9_0
  sqlite             conda-forge/win-64::sqlite-3.36.0-h8ffe710_2
  ucrt               conda-forge/win-64::ucrt-10.0.20348.0-h57928b3_0
  vc                 conda-forge/win-64::vc-14.2-hb210afc_5
  vs2015_runtime     conda-forge/win-64::vs2015_runtime-14.29.30037-h902a5da_5
  wheel              conda-forge/noarch::wheel-0.37.0-pyhd8ed1ab_1


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: 4.10.3

Please update conda by running

    $ conda update -n base -c defaults conda


#
# To activate this environment, use
#
#     $ conda activate D:\biocbuild\bbs-3.14-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: D:\biocbuild\bbs-3.14-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo

  added / updated specs:
    - python=3.7.7


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

  ca-certificates    conda-forge::ca-certificates-2021.10.~ --> pkgs/main::ca-certificates-2021.9.30-haa95532_1
  openssl            conda-forge::openssl-1.1.1l-h8ffe710_0 --> pkgs/main::openssl-1.1.1l-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: 4.10.3

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
** inst
** 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\AppData\Local\R\cache\R\basilisk\1.6.0\son.of.basilisk\0.99.0\env1

  added / updated specs:
    - python=3.7.7


The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/win-64::ca-certificates-2021.10.8-h5b45459_0
  openssl            conda-forge/win-64::openssl-1.1.1l-h8ffe710_0
  pip                conda-forge/noarch::pip-21.3.1-pyhd8ed1ab_0
  python             pkgs/main/win-64::python-3.7.7-h81c818b_4
  python_abi         conda-forge/win-64::python_abi-3.7-2_cp37m
  setuptools         conda-forge/win-64::setuptools-58.2.0-py37h03978a9_0
  sqlite             conda-forge/win-64::sqlite-3.36.0-h8ffe710_2
  ucrt               conda-forge/win-64::ucrt-10.0.20348.0-h57928b3_0
  vc                 conda-forge/win-64::vc-14.2-hb210afc_5
  vs2015_runtime     conda-forge/win-64::vs2015_runtime-14.29.30037-h902a5da_5
  wheel              conda-forge/noarch::wheel-0.37.0-pyhd8ed1ab_1


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: 4.10.3

Please update conda by running

    $ conda update -n base -c defaults conda


#
# To activate this environment, use
#
#     $ conda activate C:\Users\biocbuild\AppData\Local\R\cache\R\basilisk\1.6.0\son.of.basilisk\0.99.0\env1
#
# 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\AppData\Local\R\cache\R\basilisk\1.6.0\son.of.basilisk\0.99.0\env1

  added / updated specs:
    - python=3.7.7


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

  ca-certificates    conda-forge::ca-certificates-2021.10.~ --> pkgs/main::ca-certificates-2021.9.30-haa95532_1
  openssl            conda-forge::openssl-1.1.1l-h8ffe710_0 --> pkgs/main::openssl-1.1.1l-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: 4.10.3

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\AppData\Local\R\cache\R\basilisk\1.6.0\son.of.basilisk\0.99.0\env1

  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-2021.4.0-h57928b3_3556
  libblas            conda-forge/win-64::libblas-3.9.0-12_win64_mkl
  libcblas           conda-forge/win-64::libcblas-3.9.0-12_win64_mkl
  liblapack          conda-forge/win-64::liblapack-3.9.0-12_win64_mkl
  mkl                conda-forge/win-64::mkl-2021.4.0-h0e2418a_729
  numpy              conda-forge/win-64::numpy-1.21.3-py37h940b05c_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-2021.4.0-h2d74725_0

The following packages will be UPDATED:

  ca-certificates    pkgs/main::ca-certificates-2021.9.30-~ --> conda-forge::ca-certificates-2021.10.8-h5b45459_0

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

  openssl              pkgs/main::openssl-1.1.1l-h2bbff1b_0 --> conda-forge::openssl-1.1.1l-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: 4.10.3

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\AppData\Local\R\cache\R\basilisk\1.6.0\son.of.basilisk\0.99.0\env2

  added / updated specs:
    - python=3.7.7


The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/win-64::ca-certificates-2021.10.8-h5b45459_0
  openssl            conda-forge/win-64::openssl-1.1.1l-h8ffe710_0
  pip                conda-forge/noarch::pip-21.3.1-pyhd8ed1ab_0
  python             pkgs/main/win-64::python-3.7.7-h81c818b_4
  python_abi         conda-forge/win-64::python_abi-3.7-2_cp37m
  setuptools         conda-forge/win-64::setuptools-58.2.0-py37h03978a9_0
  sqlite             conda-forge/win-64::sqlite-3.36.0-h8ffe710_2
  ucrt               conda-forge/win-64::ucrt-10.0.20348.0-h57928b3_0
  vc                 conda-forge/win-64::vc-14.2-hb210afc_5
  vs2015_runtime     conda-forge/win-64::vs2015_runtime-14.29.30037-h902a5da_5
  wheel              conda-forge/noarch::wheel-0.37.0-pyhd8ed1ab_1


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: 4.10.3

Please update conda by running

    $ conda update -n base -c defaults conda


#
# To activate this environment, use
#
#     $ conda activate C:\Users\biocbuild\AppData\Local\R\cache\R\basilisk\1.6.0\son.of.basilisk\0.99.0\env2
#
# 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\AppData\Local\R\cache\R\basilisk\1.6.0\son.of.basilisk\0.99.0\env2

  added / updated specs:
    - python=3.7.7


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

  ca-certificates    conda-forge::ca-certificates-2021.10.~ --> pkgs/main::ca-certificates-2021.9.30-haa95532_1
  openssl            conda-forge::openssl-1.1.1l-h8ffe710_0 --> pkgs/main::openssl-1.1.1l-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: 4.10.3

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\AppData\Local\R\cache\R\basilisk\1.6.0\son.of.basilisk\0.99.0\env2

  added / updated specs:
    - joblib=0.13.1
    - python=3.7.7
    - scikit-learn=0.21.1


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    joblib-0.13.1              |             py_0         180 KB  conda-forge
    scikit-learn-0.21.1        |   py37h0ff8352_0         5.7 MB  conda-forge
    ------------------------------------------------------------
                                           Total:         5.9 MB

The following NEW packages will be INSTALLED:

  intel-openmp       conda-forge/win-64::intel-openmp-2021.4.0-h57928b3_3556
  joblib             conda-forge/noarch::joblib-0.13.1-py_0
  libblas            conda-forge/win-64::libblas-3.9.0-12_win64_mkl
  libcblas           conda-forge/win-64::libcblas-3.9.0-12_win64_mkl
  liblapack          conda-forge/win-64::liblapack-3.9.0-12_win64_mkl
  m2w64-gcc-libgfor~ conda-forge/win-64::m2w64-gcc-libgfortran-5.3.0-6
  m2w64-gcc-libs     conda-forge/win-64::m2w64-gcc-libs-5.3.0-7
  m2w64-gcc-libs-co~ conda-forge/win-64::m2w64-gcc-libs-core-5.3.0-7
  m2w64-gmp          conda-forge/win-64::m2w64-gmp-6.1.0-2
  m2w64-libwinpthre~ conda-forge/win-64::m2w64-libwinpthread-git-5.0.0.4634.697f757-2
  mkl                conda-forge/win-64::mkl-2021.4.0-h0e2418a_729
  msys2-conda-epoch  conda-forge/win-64::msys2-conda-epoch-20160418-1
  numpy              conda-forge/win-64::numpy-1.21.3-py37h940b05c_0
  scikit-learn       conda-forge/win-64::scikit-learn-0.21.1-py37h0ff8352_0
  scipy              conda-forge/win-64::scipy-1.7.1-py37hb6553fb_0
  tbb                conda-forge/win-64::tbb-2021.4.0-h2d74725_0

The following packages will be UPDATED:

  ca-certificates    pkgs/main::ca-certificates-2021.9.30-~ --> conda-forge::ca-certificates-2021.10.8-h5b45459_0

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

  openssl              pkgs/main::openssl-1.1.1l-h2bbff1b_0 --> conda-forge::openssl-1.1.1l-h8ffe710_0



Downloading and Extracting Packages

joblib-0.13.1        | 180 KB    |            |   0% 
joblib-0.13.1        | 180 KB    | 8          |   9% 
joblib-0.13.1        | 180 KB    | ########## | 100% 

scikit-learn-0.21.1  | 5.7 MB    |            |   0% 
scikit-learn-0.21.1  | 5.7 MB    |            |   0% 
scikit-learn-0.21.1  | 5.7 MB    | #3         |  13% 
scikit-learn-0.21.1  | 5.7 MB    | #########8 |  99% 
scikit-learn-0.21.1  | 5.7 MB    | ########## | 100% 
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: 4.10.3

Please update conda by running

    $ conda update -n base -c defaults conda


C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\1611D8~1.0\SONOF~1.BAS\099~1.0\env2\lib\site-packages\sklearn\linear_model\least_angle.py:30: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
  method='lar', copy_X=True, eps=np.finfo(np.float).eps,
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\1611D8~1.0\SONOF~1.BAS\099~1.0\env2\lib\site-packages\sklearn\linear_model\least_angle.py:167: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
  method='lar', copy_X=True, eps=np.finfo(np.float).eps,
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\1611D8~1.0\SONOF~1.BAS\099~1.0\env2\lib\site-packages\sklearn\linear_model\least_angle.py:284: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
  eps=np.finfo(np.float).eps, copy_Gram=True, verbose=0,
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\1611D8~1.0\SONOF~1.BAS\099~1.0\env2\lib\site-packages\sklearn\linear_model\least_angle.py:862: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
  eps=np.finfo(np.float).eps, copy_X=True, fit_path=True,
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\1611D8~1.0\SONOF~1.BAS\099~1.0\env2\lib\site-packages\sklearn\linear_model\least_angle.py:1101: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
  eps=np.finfo(np.float).eps, copy_X=True, fit_path=True,
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\1611D8~1.0\SONOF~1.BAS\099~1.0\env2\lib\site-packages\sklearn\linear_model\least_angle.py:1127: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
  eps=np.finfo(np.float).eps, positive=False):
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\1611D8~1.0\SONOF~1.BAS\099~1.0\env2\lib\site-packages\sklearn\linear_model\least_angle.py:1362: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
  max_n_alphas=1000, n_jobs=None, eps=np.finfo(np.float).eps,
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\1611D8~1.0\SONOF~1.BAS\099~1.0\env2\lib\site-packages\sklearn\linear_model\least_angle.py:1602: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
  max_n_alphas=1000, n_jobs=None, eps=np.finfo(np.float).eps,
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\1611D8~1.0\SONOF~1.BAS\099~1.0\env2\lib\site-packages\sklearn\linear_model\least_angle.py:1738: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
  eps=np.finfo(np.float).eps, copy_X=True, positive=False):
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\1611D8~1.0\SONOF~1.BAS\099~1.0\env2\lib\site-packages\sklearn\decomposition\online_lda.py:29: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
  EPS = np.finfo(np.float).eps
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\AppData\Local\R\cache\R\basilisk\1.6.0\son.of.basilisk\0.99.0\env3

  added / updated specs:
    - python=3.7.7


The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/win-64::ca-certificates-2021.10.8-h5b45459_0
  openssl            conda-forge/win-64::openssl-1.1.1l-h8ffe710_0
  pip                conda-forge/noarch::pip-21.3.1-pyhd8ed1ab_0
  python             pkgs/main/win-64::python-3.7.7-h81c818b_4
  python_abi         conda-forge/win-64::python_abi-3.7-2_cp37m
  setuptools         conda-forge/win-64::setuptools-58.2.0-py37h03978a9_0
  sqlite             conda-forge/win-64::sqlite-3.36.0-h8ffe710_2
  ucrt               conda-forge/win-64::ucrt-10.0.20348.0-h57928b3_0
  vc                 conda-forge/win-64::vc-14.2-hb210afc_5
  vs2015_runtime     conda-forge/win-64::vs2015_runtime-14.29.30037-h902a5da_5
  wheel              conda-forge/noarch::wheel-0.37.0-pyhd8ed1ab_1


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: 4.10.3

Please update conda by running

    $ conda update -n base -c defaults conda


#
# To activate this environment, use
#
#     $ conda activate C:\Users\biocbuild\AppData\Local\R\cache\R\basilisk\1.6.0\son.of.basilisk\0.99.0\env3
#
# 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\AppData\Local\R\cache\R\basilisk\1.6.0\son.of.basilisk\0.99.0\env3

  added / updated specs:
    - python=3.7.7


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

  ca-certificates    conda-forge::ca-certificates-2021.10.~ --> pkgs/main::ca-certificates-2021.9.30-haa95532_1
  openssl            conda-forge::openssl-1.1.1l-h8ffe710_0 --> pkgs/main::openssl-1.1.1l-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: 4.10.3

Please update conda by running

    $ conda update -n base -c defaults conda


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

## Package Plan ##

  environment location: C:\Users\biocbuild\AppData\Local\R\cache\R\basilisk\1.6.0\son.of.basilisk\0.99.0\env3

  added / updated specs:
    - python=3.7.7


The following packages will be UPDATED:

  ca-certificates    pkgs/main::ca-certificates-2021.9.30-~ --> conda-forge::ca-certificates-2021.10.8-h5b45459_0

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

  openssl              pkgs/main::openssl-1.1.1l-h2bbff1b_0 --> conda-forge::openssl-1.1.1l-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: 4.10.3

Please update conda by running

    $ conda update -n base -c defaults conda


Processing d:\biocbuild\bbs-3.14-bioc\tmpdir\rtmpchuxkb\rlib.3fe076643137\son.of.basilisk\test_dummy
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Building wheels for collected packages: test-dummy
  Building wheel for test-dummy (setup.py): started
  Building wheel for test-dummy (setup.py): finished with status 'done'
  Created wheel for test-dummy: filename=test_dummy-0.1-py3-none-any.whl size=1295 sha256=d848c01364c9a3b794f28398ced74e4b61c43a59ec6e46240327a58ab36cd20d
  Stored in directory: D:\biocbuild\bbs-3.14-bioc\tmpdir\pip-ephem-wheel-cache-k9p73nqv\wheels\a4\14\a9\07e8bb844bc24be256df81e56010897b5d77f1e12dc437fa5c
Successfully built test-dummy
Installing collected packages: test-dummy
Successfully installed test-dummy-0.1
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... 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: D:\biocbuild\bbs-3.14-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-2021.10.8-h5b45459_0
  openssl            conda-forge/win-64::openssl-1.1.1l-h8ffe710_0
  pip                conda-forge/noarch::pip-21.3.1-pyhd8ed1ab_0
  python             pkgs/main/win-64::python-3.7.7-h81c818b_4
  python_abi         conda-forge/win-64::python_abi-3.7-2_cp37m
  setuptools         conda-forge/win-64::setuptools-58.2.0-py37h03978a9_0
  sqlite             conda-forge/win-64::sqlite-3.36.0-h8ffe710_2
  ucrt               conda-forge/win-64::ucrt-10.0.20348.0-h57928b3_0
  vc                 conda-forge/win-64::vc-14.2-hb210afc_5
  vs2015_runtime     conda-forge/win-64::vs2015_runtime-14.29.30037-h902a5da_5
  wheel              conda-forge/noarch::wheel-0.37.0-pyhd8ed1ab_1


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: 4.10.3

Please update conda by running

    $ conda update -n base -c defaults conda


#
# To activate this environment, use
#
#     $ conda activate D:\biocbuild\bbs-3.14-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: D:\biocbuild\bbs-3.14-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\my_package_A

  added / updated specs:
    - python=3.7.7


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

  ca-certificates    conda-forge::ca-certificates-2021.10.~ --> pkgs/main::ca-certificates-2021.9.30-haa95532_1
  openssl            conda-forge::openssl-1.1.1l-h8ffe710_0 --> pkgs/main::openssl-1.1.1l-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: 4.10.3

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: D:\biocbuild\bbs-3.14-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-2021.4.0-h57928b3_3556
  libblas            conda-forge/win-64::libblas-3.9.0-12_win64_mkl
  libcblas           conda-forge/win-64::libcblas-3.9.0-12_win64_mkl
  liblapack          conda-forge/win-64::liblapack-3.9.0-12_win64_mkl
  mkl                conda-forge/win-64::mkl-2021.4.0-h0e2418a_729
  numpy              conda-forge/win-64::numpy-1.21.3-py37h940b05c_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-2021.4.0-h2d74725_0

The following packages will be UPDATED:

  ca-certificates    pkgs/main::ca-certificates-2021.9.30-~ --> conda-forge::ca-certificates-2021.10.8-h5b45459_0

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

  openssl              pkgs/main::openssl-1.1.1l-h2bbff1b_0 --> conda-forge::openssl-1.1.1l-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: 4.10.3

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: D:\biocbuild\bbs-3.14-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-2021.10.8-h5b45459_0
  openssl            conda-forge/win-64::openssl-1.1.1l-h8ffe710_0
  pip                conda-forge/noarch::pip-21.3.1-pyhd8ed1ab_0
  python             pkgs/main/win-64::python-3.7.7-h81c818b_4
  python_abi         conda-forge/win-64::python_abi-3.7-2_cp37m
  setuptools         conda-forge/win-64::setuptools-58.2.0-py37h03978a9_0
  sqlite             conda-forge/win-64::sqlite-3.36.0-h8ffe710_2
  ucrt               conda-forge/win-64::ucrt-10.0.20348.0-h57928b3_0
  vc                 conda-forge/win-64::vc-14.2-hb210afc_5
  vs2015_runtime     conda-forge/win-64::vs2015_runtime-14.29.30037-h902a5da_5
  wheel              conda-forge/noarch::wheel-0.37.0-pyhd8ed1ab_1


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: 4.10.3

Please update conda by running

    $ conda update -n base -c defaults conda


#
# To activate this environment, use
#
#     $ conda activate D:\biocbuild\bbs-3.14-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: D:\biocbuild\bbs-3.14-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\my_package_B

  added / updated specs:
    - python=3.7.7


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

  ca-certificates    conda-forge::ca-certificates-2021.10.~ --> pkgs/main::ca-certificates-2021.9.30-haa95532_1
  openssl            conda-forge::openssl-1.1.1l-h8ffe710_0 --> pkgs/main::openssl-1.1.1l-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: 4.10.3

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: D:\biocbuild\bbs-3.14-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-2021.4.0-h57928b3_3556
  libblas            conda-forge/win-64::libblas-3.9.0-12_win64_mkl
  libcblas           conda-forge/win-64::libcblas-3.9.0-12_win64_mkl
  liblapack          conda-forge/win-64::liblapack-3.9.0-12_win64_mkl
  mkl                conda-forge/win-64::mkl-2021.4.0-h0e2418a_729
  numpy              conda-forge/win-64::numpy-1.21.3-py37h940b05c_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-2021.4.0-h2d74725_0

The following packages will be UPDATED:

  ca-certificates    pkgs/main::ca-certificates-2021.9.30-~ --> conda-forge::ca-certificates-2021.10.8-h5b45459_0

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

  openssl              pkgs/main::openssl-1.1.1l-h2bbff1b_0 --> conda-forge::openssl-1.1.1l-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: 4.10.3

Please update conda by running

    $ conda update -n base -c defaults conda


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

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 37 ]
> 
> proc.time()
   user  system elapsed 
   2.54    6.79  736.54 

Example timings

basilisk.Rcheck/basilisk-Ex.timings

nameusersystemelapsed
BasiliskEnvironment-class000
PyPiLink000
basiliskOptions000
basiliskStart 0.52 0.25202.62
configureBasiliskEnv000
findPersistentEnv0.010.001.88
listPackages0.000.001.11
setupBasiliskEnv 0.00 0.0064.69
useBasiliskEnv0.010.000.79