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CHECK report for basilisk on malbec1

This page was generated on 2020-08-10 11:50:40 -0400 (Mon, 10 Aug 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 114/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
basilisk 1.1.9
Aaron Lun
Snapshot Date: 2020-08-09 14:51:29 -0400 (Sun, 09 Aug 2020)
URL: https://git.bioconductor.org/packages/basilisk
Branch: master
Last Commit: 6818dce
Last Changed Date: 2020-07-17 16:35:06 -0400 (Fri, 17 Jul 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: basilisk
Version: 1.1.9
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:basilisk.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings basilisk_1.1.9.tar.gz
StartedAt: 2020-08-10 05:40:33 -0400 (Mon, 10 Aug 2020)
EndedAt: 2020-08-10 05:49:09 -0400 (Mon, 10 Aug 2020)
EllapsedTime: 515.5 seconds
RetCode: 0
Status:  OK 
CheckDir: basilisk.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:basilisk.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings basilisk_1.1.9.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/basilisk.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘basilisk/DESCRIPTION’ ... OK
* this is package ‘basilisk’ version ‘1.1.9’
* 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 ‘/home/biocbuild/bbs-3.12-bioc/meat/basilisk.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
* 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    92.376  8.768 138.969
setupBasiliskEnv 24.056  2.756  33.159
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/basilisk.Rcheck/00check.log’
for details.



Installation output

basilisk.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL basilisk
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘basilisk’ ...
** using non-staged installation via StagedInstall field
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (basilisk)

Tests output

basilisk.Rcheck/tests/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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: /home/biocbuild/bbs-3.12-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - python=3.7.6


The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
  ca-certificates    conda-forge/linux-64::ca-certificates-2020.6.20-hecda079_0
  certifi            conda-forge/linux-64::certifi-2020.6.20-py37hc8dfbb8_0
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.34-hc38a660_9
  libffi             conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007
  libgcc-ng          conda-forge/linux-64::libgcc-ng-9.3.0-h24d8f2e_14
  libgomp            conda-forge/linux-64::libgomp-9.3.0-h24d8f2e_14
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-9.3.0-hdf63c60_14
  ncurses            conda-forge/linux-64::ncurses-6.2-he1b5a44_1
  openssl            conda-forge/linux-64::openssl-1.1.1g-h516909a_1
  pip                conda-forge/noarch::pip-20.2.1-py_0
  python             conda-forge/linux-64::python-3.7.6-cpython_h8356626_6
  python_abi         conda-forge/linux-64::python_abi-3.7-1_cp37m
  readline           conda-forge/linux-64::readline-8.0-he28a2e2_2
  setuptools         conda-forge/linux-64::setuptools-49.3.0-py37hc8dfbb8_0
  sqlite             conda-forge/linux-64::sqlite-3.32.3-hcee41ef_1
  tk                 conda-forge/linux-64::tk-8.6.10-hed695b0_0
  wheel              conda-forge/noarch::wheel-0.34.2-py_1
  xz                 conda-forge/linux-64::xz-5.2.5-h516909a_1
  zlib               conda-forge/linux-64::zlib-1.2.11-h516909a_1007


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.2
  latest version: 4.8.3

Please update conda by running

    $ conda update -n base -c defaults conda


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

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

## Package Plan ##

  environment location: /home/biocbuild/bbs-3.12-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

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


The following NEW packages will be INSTALLED:

  libblas            conda-forge/linux-64::libblas-3.8.0-17_openblas
  libcblas           conda-forge/linux-64::libcblas-3.8.0-17_openblas
  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-7.5.0-hdf63c60_14
  liblapack          conda-forge/linux-64::liblapack-3.8.0-17_openblas
  libopenblas        conda-forge/linux-64::libopenblas-0.3.10-pthreads_hb3c22a3_4
  numpy              conda-forge/linux-64::numpy-1.19.1-py37h8960a57_0
  pandas             conda-forge/linux-64::pandas-0.25.1-py37hb3f55d8_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: 4.8.2
  latest version: 4.8.3

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: /home/biocbuild/bbs-3.12-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - python=3.7.6


The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
  ca-certificates    conda-forge/linux-64::ca-certificates-2020.6.20-hecda079_0
  certifi            conda-forge/linux-64::certifi-2020.6.20-py37hc8dfbb8_0
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.34-hc38a660_9
  libffi             conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007
  libgcc-ng          conda-forge/linux-64::libgcc-ng-9.3.0-h24d8f2e_14
  libgomp            conda-forge/linux-64::libgomp-9.3.0-h24d8f2e_14
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-9.3.0-hdf63c60_14
  ncurses            conda-forge/linux-64::ncurses-6.2-he1b5a44_1
  openssl            conda-forge/linux-64::openssl-1.1.1g-h516909a_1
  pip                conda-forge/noarch::pip-20.2.1-py_0
  python             conda-forge/linux-64::python-3.7.6-cpython_h8356626_6
  python_abi         conda-forge/linux-64::python_abi-3.7-1_cp37m
  readline           conda-forge/linux-64::readline-8.0-he28a2e2_2
  setuptools         conda-forge/linux-64::setuptools-49.3.0-py37hc8dfbb8_0
  sqlite             conda-forge/linux-64::sqlite-3.32.3-hcee41ef_1
  tk                 conda-forge/linux-64::tk-8.6.10-hed695b0_0
  wheel              conda-forge/noarch::wheel-0.34.2-py_1
  xz                 conda-forge/linux-64::xz-5.2.5-h516909a_1
  zlib               conda-forge/linux-64::zlib-1.2.11-h516909a_1007


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.2
  latest version: 4.8.3

Please update conda by running

    $ conda update -n base -c defaults conda


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

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

## Package Plan ##

  environment location: /home/biocbuild/bbs-3.12-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

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


The following NEW packages will be INSTALLED:

  libblas            conda-forge/linux-64::libblas-3.8.0-17_openblas
  libcblas           conda-forge/linux-64::libcblas-3.8.0-17_openblas
  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-7.5.0-hdf63c60_14
  liblapack          conda-forge/linux-64::liblapack-3.8.0-17_openblas
  libopenblas        conda-forge/linux-64::libopenblas-0.3.10-pthreads_hb3c22a3_4
  numpy              conda-forge/linux-64::numpy-1.19.1-py37h8960a57_0
  pandas             conda-forge/linux-64::pandas-0.24.1-py37hf484d3e_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: 4.8.2
  latest version: 4.8.3

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: /home/biocbuild/bbs-3.12-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - python=2.7


The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
  ca-certificates    conda-forge/linux-64::ca-certificates-2020.6.20-hecda079_0
  certifi            conda-forge/linux-64::certifi-2019.11.28-py27h8c360ce_1
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.34-hc38a660_9
  libffi             conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007
  libgcc-ng          conda-forge/linux-64::libgcc-ng-9.3.0-h24d8f2e_14
  libgomp            conda-forge/linux-64::libgomp-9.3.0-h24d8f2e_14
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-9.3.0-hdf63c60_14
  ncurses            conda-forge/linux-64::ncurses-6.2-he1b5a44_1
  openssl            conda-forge/linux-64::openssl-1.1.1g-h516909a_1
  pip                conda-forge/noarch::pip-20.1.1-pyh9f0ad1d_0
  python             conda-forge/linux-64::python-2.7.15-h5a48372_1011_cpython
  python_abi         conda-forge/linux-64::python_abi-2.7-1_cp27mu
  readline           conda-forge/linux-64::readline-8.0-he28a2e2_2
  setuptools         conda-forge/linux-64::setuptools-44.0.0-py27_0
  sqlite             conda-forge/linux-64::sqlite-3.32.3-hcee41ef_1
  tk                 conda-forge/linux-64::tk-8.6.10-hed695b0_0
  wheel              conda-forge/noarch::wheel-0.34.2-py_1
  zlib               conda-forge/linux-64::zlib-1.2.11-h516909a_1007


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.2
  latest version: 4.8.3

Please update conda by running

    $ conda update -n base -c defaults conda


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

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


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.2
  latest version: 4.8.3

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: /home/biocbuild/bbs-3.12-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - python=3.7.6


The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
  ca-certificates    conda-forge/linux-64::ca-certificates-2020.6.20-hecda079_0
  certifi            conda-forge/linux-64::certifi-2020.6.20-py37hc8dfbb8_0
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.34-hc38a660_9
  libffi             conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007
  libgcc-ng          conda-forge/linux-64::libgcc-ng-9.3.0-h24d8f2e_14
  libgomp            conda-forge/linux-64::libgomp-9.3.0-h24d8f2e_14
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-9.3.0-hdf63c60_14
  ncurses            conda-forge/linux-64::ncurses-6.2-he1b5a44_1
  openssl            conda-forge/linux-64::openssl-1.1.1g-h516909a_1
  pip                conda-forge/noarch::pip-20.2.1-py_0
  python             conda-forge/linux-64::python-3.7.6-cpython_h8356626_6
  python_abi         conda-forge/linux-64::python_abi-3.7-1_cp37m
  readline           conda-forge/linux-64::readline-8.0-he28a2e2_2
  setuptools         conda-forge/linux-64::setuptools-49.3.0-py37hc8dfbb8_0
  sqlite             conda-forge/linux-64::sqlite-3.32.3-hcee41ef_1
  tk                 conda-forge/linux-64::tk-8.6.10-hed695b0_0
  wheel              conda-forge/noarch::wheel-0.34.2-py_1
  xz                 conda-forge/linux-64::xz-5.2.5-h516909a_1
  zlib               conda-forge/linux-64::zlib-1.2.11-h516909a_1007


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.2
  latest version: 4.8.3

Please update conda by running

    $ conda update -n base -c defaults conda


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

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

## Package Plan ##

  environment location: /home/biocbuild/bbs-3.12-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo

  added / updated specs:
    - python-dateutil=2.7.1
    - python=3.7.6
    - 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: 4.8.2
  latest version: 4.8.3

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-manylinux1_x86_64.whl (10.1 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)
Requirement already satisfied: pytz>=2011k in ./install-test-client/thingo/lib/python3.7/site-packages (from pandas==0.24.1) (2018.7)
Collecting numpy>=1.12.0
  Using cached numpy-1.19.1-cp37-cp37m-manylinux2010_x86_64.whl (14.5 MB)
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-1.19.1 pandas-0.24.1
PREFIX=/tmp/Rtmp4CQ0ck/file1ac06b266663/1.1.9/0
Unpacking payload ...

  0%|          | 0/36 [00:00<?, ?it/s]
Extracting : wheel-0.34.2-py37_0.conda:   0%|          | 0/36 [00:00<?, ?it/s]
Extracting : wheel-0.34.2-py37_0.conda:   3%|▎         | 1/36 [00:00<00:06,  5.03it/s]
Extracting : urllib3-1.25.8-py37_0.conda:   3%|▎         | 1/36 [00:00<00:06,  5.03it/s]
Extracting : libgcc-ng-9.1.0-hdf63c60_0.conda:   6%|▌         | 2/36 [00:00<00:06,  5.03it/s]
Extracting : libgcc-ng-9.1.0-hdf63c60_0.conda:   8%|▊         | 3/36 [00:00<00:06,  4.75it/s]
Extracting : _libgcc_mutex-0.1-main.conda:   8%|▊         | 3/36 [00:00<00:06,  4.75it/s]    
Extracting : libffi-3.2.1-hd88cf55_4.conda:  11%|█         | 4/36 [00:00<00:06,  4.75it/s]
Extracting : pycparser-2.19-py37_0.conda:  14%|█▍        | 5/36 [00:00<00:06,  4.75it/s]  
Extracting : certifi-2019.11.28-py37_0.conda:  17%|█▋        | 6/36 [00:00<00:06,  4.75it/s]
Extracting : cffi-1.14.0-py37h2e261b9_0.conda:  19%|█▉        | 7/36 [00:00<00:06,  4.75it/s]
Extracting : pip-20.0.2-py37_1.conda:  22%|██▏       | 8/36 [00:00<00:05,  4.75it/s]         
Extracting : yaml-0.1.7-had09818_2.conda:  25%|██▌       | 9/36 [00:00<00:05,  4.75it/s]
Extracting : ruamel_yaml-0.15.87-py37h7b6447c_0.conda:  28%|██▊       | 10/36 [00:00<00:05,  4.75it/s]
Extracting : chardet-3.0.4-py37_1003.conda:  31%|███       | 11/36 [00:00<00:05,  4.75it/s]           
Extracting : six-1.14.0-py37_0.conda:  33%|███▎      | 12/36 [00:00<00:05,  4.75it/s]      
Extracting : libstdcxx-ng-9.1.0-hdf63c60_0.conda:  36%|███▌      | 13/36 [00:00<00:04,  4.75it/s]
Extracting : idna-2.8-py37_0.conda:  39%|███▉      | 14/36 [00:00<00:04,  4.75it/s]              
Extracting : ld_impl_linux-64-2.33.1-h53a641e_7.conda:  42%|████▏     | 15/36 [00:00<00:04,  4.75it/s]
Extracting : libedit-3.1.20181209-hc058e9b_0.conda:  44%|████▍     | 16/36 [00:00<00:04,  4.75it/s]   
Extracting : requests-2.22.0-py37_1.conda:  47%|████▋     | 17/36 [00:00<00:03,  4.75it/s]         
Extracting : tk-8.6.8-hbc83047_0.conda:  50%|█████     | 18/36 [00:00<00:03,  4.75it/s]   
Extracting : pyopenssl-19.1.0-py37_0.conda:  53%|█████▎    | 19/36 [00:00<00:03,  4.75it/s]
Extracting : pycosat-0.6.3-py37h7b6447c_0.conda:  56%|█████▌    | 20/36 [00:00<00:03,  4.75it/s]
Extracting : cryptography-2.8-py37h1ba5d50_0.conda:  58%|█████▊    | 21/36 [00:00<00:03,  4.75it/s]
Extracting : ca-certificates-2020.1.1-0.conda:  61%|██████    | 22/36 [00:00<00:02,  4.75it/s]     
Extracting : readline-7.0-h7b6447c_5.conda:  64%|██████▍   | 23/36 [00:00<00:02,  4.75it/s]   
Extracting : zlib-1.2.11-h7b6447c_3.conda:  67%|██████▋   | 24/36 [00:00<00:02,  4.75it/s] 
Extracting : setuptools-45.2.0-py37_0.conda:  69%|██████▉   | 25/36 [00:00<00:02,  4.75it/s]
Extracting : tqdm-4.42.1-py_0.conda:  72%|███████▏  | 26/36 [00:00<00:02,  4.75it/s]        
Extracting : pysocks-1.7.1-py37_0.conda:  75%|███████▌  | 27/36 [00:00<00:01,  4.75it/s]
Extracting : python-3.7.6-h0371630_2.conda:  78%|███████▊  | 28/36 [00:01<00:01,  4.75it/s]
Extracting : python-3.7.6-h0371630_2.conda:  81%|████████  | 29/36 [00:01<00:01,  6.51it/s]
Extracting : conda-package-handling-1.6.0-py37h7b6447c_0.conda:  81%|████████  | 29/36 [00:01<00:01,  6.51it/s]
Extracting : sqlite-3.31.1-h7b6447c_0.conda:  83%|████████▎ | 30/36 [00:01<00:00,  6.51it/s]                   
Extracting : openssl-1.1.1d-h7b6447c_4.conda:  86%|████████▌ | 31/36 [00:01<00:00,  6.51it/s]
Extracting : asn1crypto-1.3.0-py37_0.conda:  89%|████████▉ | 32/36 [00:01<00:00,  6.51it/s]  
Extracting : xz-5.2.4-h14c3975_4.conda:  92%|█████████▏| 33/36 [00:01<00:00,  6.51it/s]    
Extracting : ncurses-6.2-he6710b0_0.tar.bz2:  94%|█████████▍| 34/36 [00:01<00:00,  6.51it/s]
Extracting : conda-4.8.2-py37_0.tar.bz2:  97%|█████████▋| 35/36 [00:01<00:00,  6.51it/s]    
Extracting : conda-4.8.2-py37_0.tar.bz2: 100%|██████████| 36/36 [00:01<00:00,  8.78it/s]
                                                                                        
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /tmp/Rtmp4CQ0ck/file1ac06b266663/1.1.9/0

  added / updated specs:
    - _libgcc_mutex==0.1=main
    - asn1crypto==1.3.0=py37_0
    - ca-certificates==2020.1.1=0
    - certifi==2019.11.28=py37_0
    - cffi==1.14.0=py37h2e261b9_0
    - chardet==3.0.4=py37_1003
    - conda-package-handling==1.6.0=py37h7b6447c_0
    - conda==4.8.2=py37_0
    - cryptography==2.8=py37h1ba5d50_0
    - idna==2.8=py37_0
    - ld_impl_linux-64==2.33.1=h53a641e_7
    - libedit==3.1.20181209=hc058e9b_0
    - libffi==3.2.1=hd88cf55_4
    - libgcc-ng==9.1.0=hdf63c60_0
    - libstdcxx-ng==9.1.0=hdf63c60_0
    - ncurses==6.2=he6710b0_0
    - openssl==1.1.1d=h7b6447c_4
    - pip==20.0.2=py37_1
    - pycosat==0.6.3=py37h7b6447c_0
    - pycparser==2.19=py37_0
    - pyopenssl==19.1.0=py37_0
    - pysocks==1.7.1=py37_0
    - python==3.7.6=h0371630_2
    - readline==7.0=h7b6447c_5
    - requests==2.22.0=py37_1
    - ruamel_yaml==0.15.87=py37h7b6447c_0
    - setuptools==45.2.0=py37_0
    - six==1.14.0=py37_0
    - sqlite==3.31.1=h7b6447c_0
    - tk==8.6.8=hbc83047_0
    - tqdm==4.42.1=py_0
    - urllib3==1.25.8=py37_0
    - wheel==0.34.2=py37_0
    - xz==5.2.4=h14c3975_4
    - yaml==0.1.7=had09818_2
    - zlib==1.2.11=h7b6447c_3


The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  asn1crypto         pkgs/main/linux-64::asn1crypto-1.3.0-py37_0
  ca-certificates    pkgs/main/linux-64::ca-certificates-2020.1.1-0
  certifi            pkgs/main/linux-64::certifi-2019.11.28-py37_0
  cffi               pkgs/main/linux-64::cffi-1.14.0-py37h2e261b9_0
  chardet            pkgs/main/linux-64::chardet-3.0.4-py37_1003
  conda              pkgs/main/linux-64::conda-4.8.2-py37_0
  conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.6.0-py37h7b6447c_0
  cryptography       pkgs/main/linux-64::cryptography-2.8-py37h1ba5d50_0
  idna               pkgs/main/linux-64::idna-2.8-py37_0
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7
  libedit            pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0
  libffi             pkgs/main/linux-64::libffi-3.2.1-hd88cf55_4
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
  ncurses            pkgs/main/linux-64::ncurses-6.2-he6710b0_0
  openssl            pkgs/main/linux-64::openssl-1.1.1d-h7b6447c_4
  pip                pkgs/main/linux-64::pip-20.0.2-py37_1
  pycosat            pkgs/main/linux-64::pycosat-0.6.3-py37h7b6447c_0
  pycparser          pkgs/main/linux-64::pycparser-2.19-py37_0
  pyopenssl          pkgs/main/linux-64::pyopenssl-19.1.0-py37_0
  pysocks            pkgs/main/linux-64::pysocks-1.7.1-py37_0
  python             pkgs/main/linux-64::python-3.7.6-h0371630_2
  readline           pkgs/main/linux-64::readline-7.0-h7b6447c_5
  requests           pkgs/main/linux-64::requests-2.22.0-py37_1
  ruamel_yaml        pkgs/main/linux-64::ruamel_yaml-0.15.87-py37h7b6447c_0
  setuptools         pkgs/main/linux-64::setuptools-45.2.0-py37_0
  six                pkgs/main/linux-64::six-1.14.0-py37_0
  sqlite             pkgs/main/linux-64::sqlite-3.31.1-h7b6447c_0
  tk                 pkgs/main/linux-64::tk-8.6.8-hbc83047_0
  tqdm               pkgs/main/noarch::tqdm-4.42.1-py_0
  urllib3            pkgs/main/linux-64::urllib3-1.25.8-py37_0
  wheel              pkgs/main/linux-64::wheel-0.34.2-py37_0
  xz                 pkgs/main/linux-64::xz-5.2.4-h14c3975_4
  yaml               pkgs/main/linux-64::yaml-0.1.7-had09818_2
  zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3


Preparing transaction: ...working... done
Executing transaction: ...working... done
installation finished.
* 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: /home/biocbuild/bbs-3.12-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:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
  ca-certificates    conda-forge/linux-64::ca-certificates-2020.6.20-hecda079_0
  certifi            conda-forge/linux-64::certifi-2020.6.20-py37hc8dfbb8_0
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.34-hc38a660_9
  libffi             conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007
  libgcc-ng          conda-forge/linux-64::libgcc-ng-9.3.0-h24d8f2e_14
  libgomp            conda-forge/linux-64::libgomp-9.3.0-h24d8f2e_14
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-9.3.0-hdf63c60_14
  ncurses            conda-forge/linux-64::ncurses-6.2-he1b5a44_1
  openssl            conda-forge/linux-64::openssl-1.1.1g-h516909a_1
  pip                conda-forge/noarch::pip-20.2.1-py_0
  python             conda-forge/linux-64::python-3.7.6-cpython_h8356626_6
  python_abi         conda-forge/linux-64::python_abi-3.7-1_cp37m
  readline           conda-forge/linux-64::readline-8.0-he28a2e2_2
  setuptools         conda-forge/linux-64::setuptools-49.3.0-py37hc8dfbb8_0
  sqlite             conda-forge/linux-64::sqlite-3.32.3-hcee41ef_1
  tk                 conda-forge/linux-64::tk-8.6.10-hed695b0_0
  wheel              conda-forge/noarch::wheel-0.34.2-py_1
  xz                 conda-forge/linux-64::xz-5.2.5-h516909a_1
  zlib               conda-forge/linux-64::zlib-1.2.11-h516909a_1007


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.2
  latest version: 4.8.3

Please update conda by running

    $ conda update -n base -c defaults conda


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

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

## Package Plan ##

  environment location: /home/biocbuild/bbs-3.12-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/my_package_A

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


The following NEW packages will be INSTALLED:

  libblas            conda-forge/linux-64::libblas-3.8.0-17_openblas
  libcblas           conda-forge/linux-64::libcblas-3.8.0-17_openblas
  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-7.5.0-hdf63c60_14
  liblapack          conda-forge/linux-64::liblapack-3.8.0-17_openblas
  libopenblas        conda-forge/linux-64::libopenblas-0.3.10-pthreads_hb3c22a3_4
  numpy              conda-forge/linux-64::numpy-1.19.1-py37h8960a57_0
  pandas             conda-forge/linux-64::pandas-0.25.1-py37hb3f55d8_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: 4.8.2
  latest version: 4.8.3

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: /home/biocbuild/bbs-3.12-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:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
  ca-certificates    conda-forge/linux-64::ca-certificates-2020.6.20-hecda079_0
  certifi            conda-forge/linux-64::certifi-2020.6.20-py37hc8dfbb8_0
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.34-hc38a660_9
  libffi             conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007
  libgcc-ng          conda-forge/linux-64::libgcc-ng-9.3.0-h24d8f2e_14
  libgomp            conda-forge/linux-64::libgomp-9.3.0-h24d8f2e_14
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-9.3.0-hdf63c60_14
  ncurses            conda-forge/linux-64::ncurses-6.2-he1b5a44_1
  openssl            conda-forge/linux-64::openssl-1.1.1g-h516909a_1
  pip                conda-forge/noarch::pip-20.2.1-py_0
  python             conda-forge/linux-64::python-3.7.6-cpython_h8356626_6
  python_abi         conda-forge/linux-64::python_abi-3.7-1_cp37m
  readline           conda-forge/linux-64::readline-8.0-he28a2e2_2
  setuptools         conda-forge/linux-64::setuptools-49.3.0-py37hc8dfbb8_0
  sqlite             conda-forge/linux-64::sqlite-3.32.3-hcee41ef_1
  tk                 conda-forge/linux-64::tk-8.6.10-hed695b0_0
  wheel              conda-forge/noarch::wheel-0.34.2-py_1
  xz                 conda-forge/linux-64::xz-5.2.5-h516909a_1
  zlib               conda-forge/linux-64::zlib-1.2.11-h516909a_1007


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.2
  latest version: 4.8.3

Please update conda by running

    $ conda update -n base -c defaults conda


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

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

## Package Plan ##

  environment location: /home/biocbuild/bbs-3.12-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/my_package_B

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


The following NEW packages will be INSTALLED:

  libblas            conda-forge/linux-64::libblas-3.8.0-17_openblas
  libcblas           conda-forge/linux-64::libcblas-3.8.0-17_openblas
  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-7.5.0-hdf63c60_14
  liblapack          conda-forge/linux-64::liblapack-3.8.0-17_openblas
  libopenblas        conda-forge/linux-64::libopenblas-0.3.10-pthreads_hb3c22a3_4
  numpy              conda-forge/linux-64::numpy-1.19.1-py37h8960a57_0
  pandas             conda-forge/linux-64::pandas-0.24.1-py37hf484d3e_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: 4.8.2
  latest version: 4.8.3

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 
230.076  32.080 290.086 

Example timings

basilisk.Rcheck/basilisk-Ex.timings

nameusersystemelapsed
BasiliskEnvironment-class0.0040.0000.005
PyPiLink0.0000.0000.001
basiliskOptions0.0000.0000.001
basiliskStart 92.376 8.768138.969
configureBasiliskEnv0.0080.0000.007
findPersistentEnv0.0440.0162.627
listPackages0.6560.1161.677
setupBasiliskEnv24.056 2.75633.159
useBasiliskEnv0.4240.0920.555