Back to Multiple platform build/check report for BioC 3.11
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for basilisk on machv2

This page was generated on 2020-10-17 11:58:05 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE basilisk PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 117/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
basilisk 1.0.2
Aaron Lun
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/basilisk
Branch: RELEASE_3_11
Last Commit: 15b9066
Last Changed Date: 2020-05-11 12:16:45 -0400 (Mon, 11 May 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: basilisk
Version: 1.0.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:basilisk.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings basilisk_1.0.2.tar.gz
StartedAt: 2020-10-16 22:52:51 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 23:04:40 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 709.5 seconds
RetCode: 0
Status:  OK 
CheckDir: basilisk.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:basilisk.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings basilisk_1.0.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/basilisk.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘basilisk/DESCRIPTION’ ... OK
* this is package ‘basilisk’ version ‘1.0.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  inst/example/.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘basilisk’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Users/biocbuild/bbs-3.11-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    121.108 19.933 145.904
setupBasiliskEnv  27.129  8.336  36.004
* 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
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/basilisk.Rcheck/00check.log’
for details.

Installation output

basilisk.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘basilisk’ ...
** using non-staged installation via StagedInstall field
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (basilisk)

Tests output

basilisk.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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: /Users/biocbuild/bbs-3.11-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - python=3.7.6


The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/osx-64::ca-certificates-2020.6.20-hecda079_0
  certifi            conda-forge/osx-64::certifi-2020.6.20-py37h2987424_2
  libcxx             conda-forge/osx-64::libcxx-11.0.0-h439d374_0
  libffi             conda-forge/osx-64::libffi-3.2.1-hb1e8313_1007
  ncurses            conda-forge/osx-64::ncurses-6.2-hb1e8313_2
  openssl            conda-forge/osx-64::openssl-1.1.1h-haf1e3a3_0
  pip                conda-forge/noarch::pip-20.2.3-py_0
  python             conda-forge/osx-64::python-3.7.6-cpython_h1fd5dd1_6
  python_abi         conda-forge/osx-64::python_abi-3.7-1_cp37m
  readline           conda-forge/osx-64::readline-8.0-h0678c8f_2
  setuptools         conda-forge/osx-64::setuptools-49.6.0-py37h2987424_2
  sqlite             conda-forge/osx-64::sqlite-3.33.0-h960bd1c_1
  tk                 conda-forge/osx-64::tk-8.6.10-hb0a8c7a_1
  wheel              conda-forge/noarch::wheel-0.35.1-pyh9f0ad1d_0
  xz                 conda-forge/osx-64::xz-5.2.5-haf1e3a3_1
  zlib               conda-forge/osx-64::zlib-1.2.11-h7795811_1010


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: 4.8.5

Please update conda by running

    $ conda update -n base -c defaults conda


#
# To activate this environment, use
#
#     $ conda activate /Users/biocbuild/bbs-3.11-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: /Users/biocbuild/bbs-3.11-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - pandas=0.25.1
    - python-dateutil=2.8.0
    - python=3.7.6
    - pytz=2019.3


The following NEW packages will be INSTALLED:

  libblas            conda-forge/osx-64::libblas-3.8.0-17_openblas
  libcblas           conda-forge/osx-64::libcblas-3.8.0-17_openblas
  libgfortran        conda-forge/osx-64::libgfortran-5.0.0-h7cc5361_12
  libgfortran5       conda-forge/osx-64::libgfortran5-9.3.0-h7cc5361_12
  liblapack          conda-forge/osx-64::liblapack-3.8.0-17_openblas
  libopenblas        conda-forge/osx-64::libopenblas-0.3.10-openmp_h54245bb_5
  llvm-openmp        conda-forge/osx-64::llvm-openmp-11.0.0-h73239a0_1
  numpy              conda-forge/osx-64::numpy-1.19.2-py37h1efc2f6_1
  pandas             conda-forge/osx-64::pandas-0.25.1-py37h86efe34_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-1.15.0-pyh9f0ad1d_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: 4.8.5

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: /Users/biocbuild/bbs-3.11-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - python=3.7.6


The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/osx-64::ca-certificates-2020.6.20-hecda079_0
  certifi            conda-forge/osx-64::certifi-2020.6.20-py37h2987424_2
  libcxx             conda-forge/osx-64::libcxx-11.0.0-h439d374_0
  libffi             conda-forge/osx-64::libffi-3.2.1-hb1e8313_1007
  ncurses            conda-forge/osx-64::ncurses-6.2-hb1e8313_2
  openssl            conda-forge/osx-64::openssl-1.1.1h-haf1e3a3_0
  pip                conda-forge/noarch::pip-20.2.3-py_0
  python             conda-forge/osx-64::python-3.7.6-cpython_h1fd5dd1_6
  python_abi         conda-forge/osx-64::python_abi-3.7-1_cp37m
  readline           conda-forge/osx-64::readline-8.0-h0678c8f_2
  setuptools         conda-forge/osx-64::setuptools-49.6.0-py37h2987424_2
  sqlite             conda-forge/osx-64::sqlite-3.33.0-h960bd1c_1
  tk                 conda-forge/osx-64::tk-8.6.10-hb0a8c7a_1
  wheel              conda-forge/noarch::wheel-0.35.1-pyh9f0ad1d_0
  xz                 conda-forge/osx-64::xz-5.2.5-haf1e3a3_1
  zlib               conda-forge/osx-64::zlib-1.2.11-h7795811_1010


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: 4.8.5

Please update conda by running

    $ conda update -n base -c defaults conda


#
# To activate this environment, use
#
#     $ conda activate /Users/biocbuild/bbs-3.11-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... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /Users/biocbuild/bbs-3.11-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - pandas=0.24.1
    - python-dateutil=2.7.1
    - python=3.7.6
    - pytz=2018.7


The following NEW packages will be INSTALLED:

  libblas            conda-forge/osx-64::libblas-3.8.0-17_openblas
  libcblas           conda-forge/osx-64::libcblas-3.8.0-17_openblas
  libgfortran        conda-forge/osx-64::libgfortran-5.0.0-h7cc5361_12
  libgfortran5       conda-forge/osx-64::libgfortran5-9.3.0-h7cc5361_12
  liblapack          conda-forge/osx-64::liblapack-3.8.0-17_openblas
  libopenblas        conda-forge/osx-64::libopenblas-0.3.10-openmp_h54245bb_5
  llvm-openmp        conda-forge/osx-64::llvm-openmp-11.0.0-h73239a0_1
  numpy              conda-forge/osx-64::numpy-1.19.2-py37h1efc2f6_1
  pandas             conda-forge/osx-64::pandas-0.24.1-py37h0a44026_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-1.15.0-pyh9f0ad1d_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: 4.8.5

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: /Users/biocbuild/bbs-3.11-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - python=2.7


The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/osx-64::ca-certificates-2020.6.20-hecda079_0
  certifi            conda-forge/osx-64::certifi-2019.11.28-py27h8c360ce_1
  libcxx             conda-forge/osx-64::libcxx-11.0.0-h439d374_0
  libffi             conda-forge/osx-64::libffi-3.2.1-hb1e8313_1007
  ncurses            conda-forge/osx-64::ncurses-6.2-hb1e8313_2
  openssl            conda-forge/osx-64::openssl-1.1.1h-haf1e3a3_0
  pip                conda-forge/noarch::pip-20.1.1-pyh9f0ad1d_0
  python             conda-forge/osx-64::python-2.7.15-h8e446fc_1011_cpython
  python_abi         conda-forge/osx-64::python_abi-2.7-1_cp27m
  readline           conda-forge/osx-64::readline-8.0-h0678c8f_2
  setuptools         conda-forge/osx-64::setuptools-44.0.0-py27_0
  sqlite             conda-forge/osx-64::sqlite-3.33.0-h960bd1c_1
  tk                 conda-forge/osx-64::tk-8.6.10-hb0a8c7a_1
  wheel              conda-forge/noarch::wheel-0.35.1-pyh9f0ad1d_0
  zlib               conda-forge/osx-64::zlib-1.2.11-h7795811_1010


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: 4.8.5

Please update conda by running

    $ conda update -n base -c defaults conda


#
# To activate this environment, use
#
#     $ conda activate /Users/biocbuild/bbs-3.11-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


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.3
  latest version: 4.8.5

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: /Users/biocbuild/bbs-3.11-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - python=3.7.6


The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/osx-64::ca-certificates-2020.6.20-hecda079_0
  certifi            conda-forge/osx-64::certifi-2020.6.20-py37h2987424_2
  libcxx             conda-forge/osx-64::libcxx-11.0.0-h439d374_0
  libffi             conda-forge/osx-64::libffi-3.2.1-hb1e8313_1007
  ncurses            conda-forge/osx-64::ncurses-6.2-hb1e8313_2
  openssl            conda-forge/osx-64::openssl-1.1.1h-haf1e3a3_0
  pip                conda-forge/noarch::pip-20.2.3-py_0
  python             conda-forge/osx-64::python-3.7.6-cpython_h1fd5dd1_6
  python_abi         conda-forge/osx-64::python_abi-3.7-1_cp37m
  readline           conda-forge/osx-64::readline-8.0-h0678c8f_2
  setuptools         conda-forge/osx-64::setuptools-49.6.0-py37h2987424_2
  sqlite             conda-forge/osx-64::sqlite-3.33.0-h960bd1c_1
  tk                 conda-forge/osx-64::tk-8.6.10-hb0a8c7a_1
  wheel              conda-forge/noarch::wheel-0.35.1-pyh9f0ad1d_0
  xz                 conda-forge/osx-64::xz-5.2.5-haf1e3a3_1
  zlib               conda-forge/osx-64::zlib-1.2.11-h7795811_1010


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: 4.8.5

Please update conda by running

    $ conda update -n base -c defaults conda


#
# To activate this environment, use
#
#     $ conda activate /Users/biocbuild/bbs-3.11-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... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /Users/biocbuild/bbs-3.11-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - python-dateutil=2.7.1
    - python=3.7.6
    - 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-1.15.0-pyh9f0ad1d_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: 4.8.5

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-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (15.9 MB)
Requirement already satisfied: python-dateutil>=2.5.0 in ./install-test-client/thingo/lib/python3.7/site-packages (from pandas==0.24.1) (2.7.1)
Collecting numpy>=1.12.0
  Using cached numpy-1.19.2-cp37-cp37m-macosx_10_9_x86_64.whl (15.3 MB)
Requirement already satisfied: pytz>=2011k in ./install-test-client/thingo/lib/python3.7/site-packages (from pandas==0.24.1) (2018.7)
Requirement already satisfied: six>=1.5 in ./install-test-client/thingo/lib/python3.7/site-packages (from python-dateutil>=2.5.0->pandas==0.24.1) (1.15.0)
Installing collected packages: numpy, pandas
Successfully installed numpy-1.19.2 pandas-0.24.1
PREFIX=/tmp/RtmpTbe6UI/file3eec75260828/1.0.2/0
Unpacking payload ...

  0%|          | 0/35 [00:00<?, ?it/s]
Extracting : urllib3-1.25.8-py37_0.conda:   0%|          | 0/35 [00:00<?, ?it/s]
Extracting : urllib3-1.25.8-py37_0.conda:   3%|▎         | 1/35 [00:00<00:23,  1.48it/s]
Extracting : tqdm-4.42.1-py_0.conda:   3%|▎         | 1/35 [00:00<00:23,  1.48it/s]     
Extracting : libffi-3.2.1-h475c297_4.conda:   6%|▌         | 2/35 [00:00<00:22,  1.48it/s]
Extracting : certifi-2019.11.28-py37_0.conda:   9%|▊         | 3/35 [00:00<00:21,  1.48it/s]
Extracting : python-3.7.6-h359304d_2.conda:  11%|█▏        | 4/35 [00:03<00:20,  1.48it/s]  
Extracting : python-3.7.6-h359304d_2.conda:  14%|█▍        | 5/35 [00:03<00:20,  1.48it/s]
Extracting : sqlite-3.31.1-ha441bb4_0.conda:  14%|█▍        | 5/35 [00:03<00:20,  1.48it/s]
Extracting : requests-2.22.0-py37_1.conda:  17%|█▋        | 6/35 [00:03<00:19,  1.48it/s]  
Extracting : six-1.14.0-py37_0.conda:  20%|██        | 7/35 [00:03<00:18,  1.48it/s]     
Extracting : libcxxabi-4.0.1-hcfea43d_1.conda:  23%|██▎       | 8/35 [00:03<00:18,  1.48it/s]
Extracting : conda-package-handling-1.6.0-py37h1de35cc_0.conda:  26%|██▌       | 9/35 [00:03<00:17,  1.48it/s]
Extracting : pycosat-0.6.3-py37h1de35cc_0.conda:  29%|██▊       | 10/35 [00:03<00:16,  1.48it/s]              
Extracting : readline-7.0-h1de35cc_5.conda:  31%|███▏      | 11/35 [00:03<00:16,  1.48it/s]     
Extracting : openssl-1.1.1d-h1de35cc_4.conda:  34%|███▍      | 12/35 [00:03<00:15,  1.48it/s]
Extracting : cffi-1.14.0-py37hb5b8e2f_0.conda:  37%|███▋      | 13/35 [00:03<00:14,  1.48it/s]
Extracting : idna-2.8-py37_0.conda:  40%|████      | 14/35 [00:03<00:14,  1.48it/s]           
Extracting : chardet-3.0.4-py37_1003.conda:  43%|████▎     | 15/35 [00:03<00:13,  1.48it/s]
Extracting : zlib-1.2.11-h1de35cc_3.conda:  46%|████▌     | 16/35 [00:03<00:12,  1.48it/s] 
Extracting : ca-certificates-2020.1.1-0.conda:  49%|████▊     | 17/35 [00:03<00:12,  1.48it/s]
Extracting : python.app-2-py37_10.conda:  51%|█████▏    | 18/35 [00:03<00:11,  1.48it/s]      
Extracting : asn1crypto-1.3.0-py37_0.conda:  54%|█████▍    | 19/35 [00:03<00:10,  1.48it/s]
Extracting : xz-5.2.4-h1de35cc_4.conda:  57%|█████▋    | 20/35 [00:03<00:10,  1.48it/s]    
Extracting : ruamel_yaml-0.15.87-py37h1de35cc_0.conda:  60%|██████    | 21/35 [00:03<00:09,  1.48it/s]
Extracting : libedit-3.1.20181209-hb402a30_0.conda:  63%|██████▎   | 22/35 [00:03<00:08,  1.48it/s]   
Extracting : cryptography-2.8-py37ha12b0ac_0.conda:  66%|██████▌   | 23/35 [00:03<00:08,  1.48it/s]
Extracting : pycparser-2.19-py37_0.conda:  69%|██████▊   | 24/35 [00:03<00:07,  1.48it/s]          
Extracting : libcxx-4.0.1-hcfea43d_1.conda:  71%|███████▏  | 25/35 [00:03<00:06,  1.48it/s]
Extracting : pyopenssl-19.1.0-py37_0.conda:  74%|███████▍  | 26/35 [00:03<00:06,  1.48it/s]
Extracting : setuptools-45.2.0-py37_0.conda:  77%|███████▋  | 27/35 [00:03<00:05,  1.48it/s]
Extracting : yaml-0.1.7-hc338f04_2.conda:  80%|████████  | 28/35 [00:03<00:04,  1.48it/s]   
Extracting : pysocks-1.7.1-py37_0.conda:  83%|████████▎ | 29/35 [00:03<00:04,  1.48it/s] 
Extracting : pip-20.0.2-py37_1.conda:  86%|████████▌ | 30/35 [00:03<00:03,  1.48it/s]   
Extracting : tk-8.6.8-ha441bb4_0.conda:  89%|████████▊ | 31/35 [00:03<00:02,  1.48it/s]
Extracting : wheel-0.34.2-py37_0.conda:  91%|█████████▏| 32/35 [00:03<00:02,  1.48it/s]
Extracting : ncurses-6.2-h0a44026_0.tar.bz2:  94%|█████████▍| 33/35 [00:03<00:01,  1.48it/s]
Extracting : conda-4.8.2-py37_0.tar.bz2:  97%|█████████▋| 34/35 [00:03<00:00,  1.48it/s]    
                                                                                        
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /tmp/RtmpTbe6UI/file3eec75260828/1.0.2/0

  added / updated specs:
    - asn1crypto==1.3.0=py37_0
    - ca-certificates==2020.1.1=0
    - certifi==2019.11.28=py37_0
    - cffi==1.14.0=py37hb5b8e2f_0
    - chardet==3.0.4=py37_1003
    - conda-package-handling==1.6.0=py37h1de35cc_0
    - conda==4.8.2=py37_0
    - cryptography==2.8=py37ha12b0ac_0
    - idna==2.8=py37_0
    - libcxx==4.0.1=hcfea43d_1
    - libcxxabi==4.0.1=hcfea43d_1
    - libedit==3.1.20181209=hb402a30_0
    - libffi==3.2.1=h475c297_4
    - ncurses==6.2=h0a44026_0
    - openssl==1.1.1d=h1de35cc_4
    - pip==20.0.2=py37_1
    - pycosat==0.6.3=py37h1de35cc_0
    - pycparser==2.19=py37_0
    - pyopenssl==19.1.0=py37_0
    - pysocks==1.7.1=py37_0
    - python.app==2=py37_10
    - python==3.7.6=h359304d_2
    - readline==7.0=h1de35cc_5
    - requests==2.22.0=py37_1
    - ruamel_yaml==0.15.87=py37h1de35cc_0
    - setuptools==45.2.0=py37_0
    - six==1.14.0=py37_0
    - sqlite==3.31.1=ha441bb4_0
    - tk==8.6.8=ha441bb4_0
    - tqdm==4.42.1=py_0
    - urllib3==1.25.8=py37_0
    - wheel==0.34.2=py37_0
    - xz==5.2.4=h1de35cc_4
    - yaml==0.1.7=hc338f04_2
    - zlib==1.2.11=h1de35cc_3


The following NEW packages will be INSTALLED:

  asn1crypto         pkgs/main/osx-64::asn1crypto-1.3.0-py37_0
  ca-certificates    pkgs/main/osx-64::ca-certificates-2020.1.1-0
  certifi            pkgs/main/osx-64::certifi-2019.11.28-py37_0
  cffi               pkgs/main/osx-64::cffi-1.14.0-py37hb5b8e2f_0
  chardet            pkgs/main/osx-64::chardet-3.0.4-py37_1003
  conda              pkgs/main/osx-64::conda-4.8.2-py37_0
  conda-package-han~ pkgs/main/osx-64::conda-package-handling-1.6.0-py37h1de35cc_0
  cryptography       pkgs/main/osx-64::cryptography-2.8-py37ha12b0ac_0
  idna               pkgs/main/osx-64::idna-2.8-py37_0
  libcxx             pkgs/main/osx-64::libcxx-4.0.1-hcfea43d_1
  libcxxabi          pkgs/main/osx-64::libcxxabi-4.0.1-hcfea43d_1
  libedit            pkgs/main/osx-64::libedit-3.1.20181209-hb402a30_0
  libffi             pkgs/main/osx-64::libffi-3.2.1-h475c297_4
  ncurses            pkgs/main/osx-64::ncurses-6.2-h0a44026_0
  openssl            pkgs/main/osx-64::openssl-1.1.1d-h1de35cc_4
  pip                pkgs/main/osx-64::pip-20.0.2-py37_1
  pycosat            pkgs/main/osx-64::pycosat-0.6.3-py37h1de35cc_0
  pycparser          pkgs/main/osx-64::pycparser-2.19-py37_0
  pyopenssl          pkgs/main/osx-64::pyopenssl-19.1.0-py37_0
  pysocks            pkgs/main/osx-64::pysocks-1.7.1-py37_0
  python             pkgs/main/osx-64::python-3.7.6-h359304d_2
  python.app         pkgs/main/osx-64::python.app-2-py37_10
  readline           pkgs/main/osx-64::readline-7.0-h1de35cc_5
  requests           pkgs/main/osx-64::requests-2.22.0-py37_1
  ruamel_yaml        pkgs/main/osx-64::ruamel_yaml-0.15.87-py37h1de35cc_0
  setuptools         pkgs/main/osx-64::setuptools-45.2.0-py37_0
  six                pkgs/main/osx-64::six-1.14.0-py37_0
  sqlite             pkgs/main/osx-64::sqlite-3.31.1-ha441bb4_0
  tk                 pkgs/main/osx-64::tk-8.6.8-ha441bb4_0
  tqdm               pkgs/main/noarch::tqdm-4.42.1-py_0
  urllib3            pkgs/main/osx-64::urllib3-1.25.8-py37_0
  wheel              pkgs/main/osx-64::wheel-0.34.2-py37_0
  xz                 pkgs/main/osx-64::xz-5.2.4-h1de35cc_4
  yaml               pkgs/main/osx-64::yaml-0.1.7-hc338f04_2
  zlib               pkgs/main/osx-64::zlib-1.2.11-h1de35cc_3


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

## Package Plan ##

  environment location: /tmp/RtmpTbe6UI/file3eec75260828/1.0.2/0

  added / updated specs:
    - nomkl


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    blas-1.0                   |         openblas          45 KB
    ca-certificates-2020.10.14 |                0         121 KB
    certifi-2020.6.20          |           py37_0         156 KB
    conda-4.8.5                |           py37_0         2.9 MB
    nomkl-3.0                  |                0          45 KB
    openssl-1.1.1h             |       haf1e3a3_0         2.2 MB
    ------------------------------------------------------------
                                           Total:         5.4 MB

The following NEW packages will be INSTALLED:

  blas               pkgs/main/osx-64::blas-1.0-openblas
  nomkl              pkgs/main/osx-64::nomkl-3.0-0

The following packages will be UPDATED:

  ca-certificates                                2020.1.1-0 --> 2020.10.14-0
  certifi                                 2019.11.28-py37_0 --> 2020.6.20-py37_0
  conda                                        4.8.2-py37_0 --> 4.8.5-py37_0
  openssl                                 1.1.1d-h1de35cc_4 --> 1.1.1h-haf1e3a3_0



Downloading and Extracting Packages

certifi-2020.6.20    | 156 KB    |            |   0% 
certifi-2020.6.20    | 156 KB    | #          |  10% 
certifi-2020.6.20    | 156 KB    | ########## | 100% 

nomkl-3.0            | 45 KB     |            |   0% 
nomkl-3.0            | 45 KB     | ########## | 100% 

ca-certificates-2020 | 121 KB    |            |   0% 
ca-certificates-2020 | 121 KB    | ########## | 100% 

conda-4.8.5          | 2.9 MB    |            |   0% 
conda-4.8.5          | 2.9 MB    | ###        |  31% 
conda-4.8.5          | 2.9 MB    | #########  |  91% 
conda-4.8.5          | 2.9 MB    | ########## | 100% 

blas-1.0             | 45 KB     |            |   0% 
blas-1.0             | 45 KB     | ########## | 100% 

openssl-1.1.1h       | 2.2 MB    |            |   0% 
openssl-1.1.1h       | 2.2 MB    | ##4        |  25% 
openssl-1.1.1h       | 2.2 MB    | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
* 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
** building package indices
** testing if installed package can be loaded
* 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: /Users/biocbuild/bbs-3.11-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/my_package_A

  added / updated specs:
    - python=3.7.6


The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/osx-64::ca-certificates-2020.6.20-hecda079_0
  certifi            conda-forge/osx-64::certifi-2020.6.20-py37h2987424_2
  libcxx             conda-forge/osx-64::libcxx-11.0.0-h439d374_0
  libffi             conda-forge/osx-64::libffi-3.2.1-hb1e8313_1007
  ncurses            conda-forge/osx-64::ncurses-6.2-hb1e8313_2
  openssl            conda-forge/osx-64::openssl-1.1.1h-haf1e3a3_0
  pip                conda-forge/noarch::pip-20.2.3-py_0
  python             conda-forge/osx-64::python-3.7.6-cpython_h1fd5dd1_6
  python_abi         conda-forge/osx-64::python_abi-3.7-1_cp37m
  readline           conda-forge/osx-64::readline-8.0-h0678c8f_2
  setuptools         conda-forge/osx-64::setuptools-49.6.0-py37h2987424_2
  sqlite             conda-forge/osx-64::sqlite-3.33.0-h960bd1c_1
  tk                 conda-forge/osx-64::tk-8.6.10-hb0a8c7a_1
  wheel              conda-forge/noarch::wheel-0.35.1-pyh9f0ad1d_0
  xz                 conda-forge/osx-64::xz-5.2.5-haf1e3a3_1
  zlib               conda-forge/osx-64::zlib-1.2.11-h7795811_1010


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: 4.8.5

Please update conda by running

    $ conda update -n base -c defaults conda


#
# To activate this environment, use
#
#     $ conda activate /Users/biocbuild/bbs-3.11-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: /Users/biocbuild/bbs-3.11-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=3.7.6
    - pytz=2019.3


The following NEW packages will be INSTALLED:

  libblas            conda-forge/osx-64::libblas-3.8.0-17_openblas
  libcblas           conda-forge/osx-64::libcblas-3.8.0-17_openblas
  libgfortran        conda-forge/osx-64::libgfortran-5.0.0-h7cc5361_12
  libgfortran5       conda-forge/osx-64::libgfortran5-9.3.0-h7cc5361_12
  liblapack          conda-forge/osx-64::liblapack-3.8.0-17_openblas
  libopenblas        conda-forge/osx-64::libopenblas-0.3.10-openmp_h54245bb_5
  llvm-openmp        conda-forge/osx-64::llvm-openmp-11.0.0-h73239a0_1
  numpy              conda-forge/osx-64::numpy-1.19.2-py37h1efc2f6_1
  pandas             conda-forge/osx-64::pandas-0.25.1-py37h86efe34_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-1.15.0-pyh9f0ad1d_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: 4.8.5

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: /Users/biocbuild/bbs-3.11-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/my_package_B

  added / updated specs:
    - python=3.7.6


The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/osx-64::ca-certificates-2020.6.20-hecda079_0
  certifi            conda-forge/osx-64::certifi-2020.6.20-py37h2987424_2
  libcxx             conda-forge/osx-64::libcxx-11.0.0-h439d374_0
  libffi             conda-forge/osx-64::libffi-3.2.1-hb1e8313_1007
  ncurses            conda-forge/osx-64::ncurses-6.2-hb1e8313_2
  openssl            conda-forge/osx-64::openssl-1.1.1h-haf1e3a3_0
  pip                conda-forge/noarch::pip-20.2.3-py_0
  python             conda-forge/osx-64::python-3.7.6-cpython_h1fd5dd1_6
  python_abi         conda-forge/osx-64::python_abi-3.7-1_cp37m
  readline           conda-forge/osx-64::readline-8.0-h0678c8f_2
  setuptools         conda-forge/osx-64::setuptools-49.6.0-py37h2987424_2
  sqlite             conda-forge/osx-64::sqlite-3.33.0-h960bd1c_1
  tk                 conda-forge/osx-64::tk-8.6.10-hb0a8c7a_1
  wheel              conda-forge/noarch::wheel-0.35.1-pyh9f0ad1d_0
  xz                 conda-forge/osx-64::xz-5.2.5-haf1e3a3_1
  zlib               conda-forge/osx-64::zlib-1.2.11-h7795811_1010


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: 4.8.5

Please update conda by running

    $ conda update -n base -c defaults conda


#
# To activate this environment, use
#
#     $ conda activate /Users/biocbuild/bbs-3.11-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... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /Users/biocbuild/bbs-3.11-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=3.7.6
    - pytz=2018.7


The following NEW packages will be INSTALLED:

  libblas            conda-forge/osx-64::libblas-3.8.0-17_openblas
  libcblas           conda-forge/osx-64::libcblas-3.8.0-17_openblas
  libgfortran        conda-forge/osx-64::libgfortran-5.0.0-h7cc5361_12
  libgfortran5       conda-forge/osx-64::libgfortran5-9.3.0-h7cc5361_12
  liblapack          conda-forge/osx-64::liblapack-3.8.0-17_openblas
  libopenblas        conda-forge/osx-64::libopenblas-0.3.10-openmp_h54245bb_5
  llvm-openmp        conda-forge/osx-64::llvm-openmp-11.0.0-h73239a0_1
  numpy              conda-forge/osx-64::numpy-1.19.2-py37h1efc2f6_1
  pandas             conda-forge/osx-64::pandas-0.24.1-py37h0a44026_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-1.15.0-pyh9f0ad1d_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: 4.8.5

Please update conda by running

    $ conda update -n base -c defaults conda


══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 54 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
311.509  87.352 450.099

Example timings

basilisk.Rcheck/basilisk-Ex.timings

nameusersystemelapsed
BasiliskEnvironment-class0.0050.0010.006
PyPiLink0.0010.0010.001
basiliskOptions0.0010.0000.002
basiliskStart121.108 19.933145.904
configureBasiliskEnv0.0070.0000.008
findPersistentEnv0.0440.0063.020
listCorePackages0.6030.1830.845
setupBasiliskEnv27.129 8.33636.004
useBasiliskEnv0.0340.0020.036