Back to "Blame Jeroen" build/check report for BioC 3.11

CHECK report for basilisk on tokay2

This page was generated on 2020-04-15 03:20:15 -0400 (Wed, 15 Apr 2020).

These builds are using Rtools40 and R-testing by Jeroen Ooms (available at https://cran.r-project.org/bin/windows/testing/rtools40.html)
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 10/89HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
basilisk 0.99.61
Aaron Lun
Snapshot Date: 2020-04-14 17:00:05 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/basilisk
Branch: master
Last Commit: 3a35b0b
Last Changed Date: 2020-04-14 02:50:12 -0400 (Tue, 14 Apr 2020)
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 

Summary

Package: basilisk
Version: 0.99.61
Command: C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:basilisk.install-out.txt --library=C:\Users\bioctesting\bbs-3.11-bioc-testing\R\library --no-vignettes --timings basilisk_0.99.61.tar.gz
StartedAt: 2020-04-14 22:56:23 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 23:29:43 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 2000.0 seconds
RetCode: 1
Status:  ERROR  
CheckDir: basilisk.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:basilisk.install-out.txt --library=C:\Users\bioctesting\bbs-3.11-bioc-testing\R\library --no-vignettes --timings basilisk_0.99.61.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/basilisk.Rcheck'
* using R version 4.0.0 alpha (Rtools40) (2020-03-31 r78116)
* 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 '0.99.61'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  inst/example/.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'basilisk' can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See 'C:/Users/bioctesting/bbs-3.11-bioc-testing/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 ... ERROR
Running examples in 'basilisk-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: basiliskStart
> ### Title: Start and stop 'basilisk'-related processes
> ### Aliases: basiliskStart basiliskStop basiliskRun
> 
> ### ** Examples
> 
> # Loading the base environment:
> cl <- basiliskStart(NULL)
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
    six                conda-forge/noarch::six-1.14.0-py_1
  
  The following packages will be UPDATED:
  
    ca-certificates     pkgs/main::ca-certificates-2020.1.1-0 --> conda-forge::ca-certificates-2020.4.5.1-hecc5488_0
  
  The following packages will be SUPERSEDED by a higher-priority channel:
  
    certifi              pkgs/main::certifi-2020.4.5.1-py37_0 --> conda-forge::certifi-2020.4.5.1-py37hc8dfbb8_0
    openssl              pkgs/main::openssl-1.1.1f-he774522_0 --> conda-forge::openssl-1.1.1f-hfa6e2cd_0
  
  
  Preparing transaction: ...working... done
  Verifying transaction: ...working... done
  Executing transaction: ...working... done
* 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: 2 ERRORs, 3 NOTEs
See
  'C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/basilisk.Rcheck/00check.log'
for details.

Installation output

basilisk.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch basilisk
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/bioctesting/bbs-3.11-bioc-testing/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  
    configureBasiliskEnv                    html  
    findPersistentEnv                       html  
    listCorePackages                        html  
    setupBasiliskEnv                        html  
    useBasiliskEnv                          html  
    finding level-2 HTML links ... done

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

Tests output

basilisk.Rcheck/tests/testthat.Rout.fail


R version 4.0.0 alpha (Rtools40) (2020-03-31 r78116) -- "Blame Jeroen"
Copyright (C) 2020 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")
-- 1. Failure: clearing out only obsolete versions works as expected (@test-clea
file.exists(placeholder) isn't true.

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


==> WARNING: A newer version of conda exists. <==
  current version: 4.7.12
  latest version: 4.8.3

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: C:\Users\bioctesting\bbs-3.11-bioc-testing\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo

  added / updated specs:
    - python=3.7.4


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2020.1.1   |                0         125 KB
    certifi-2020.4.5.1         |           py37_0         156 KB
    openssl-1.1.1f             |       he774522_0         4.8 MB
    pip-20.0.2                 |           py37_1         1.7 MB
    setuptools-46.1.3          |           py37_0         528 KB
    sqlite-3.31.1              |       he774522_0         637 KB
    vs2015_runtime-14.16.27012 |       hf0eaf9b_1         1.1 MB
    wheel-0.34.2               |           py37_0          66 KB
    ------------------------------------------------------------
                                           Total:         9.1 MB

The following NEW packages will be INSTALLED:

  ca-certificates    pkgs/main/win-64::ca-certificates-2020.1.1-0
  certifi            pkgs/main/win-64::certifi-2020.4.5.1-py37_0
  openssl            pkgs/main/win-64::openssl-1.1.1f-he774522_0
  pip                pkgs/main/win-64::pip-20.0.2-py37_1
  python             pkgs/main/win-64::python-3.7.4-h5263a28_0
  setuptools         pkgs/main/win-64::setuptools-46.1.3-py37_0
  sqlite             pkgs/main/win-64::sqlite-3.31.1-he774522_0
  vc                 pkgs/main/win-64::vc-14.1-h0510ff6_4
  vs2015_runtime     pkgs/main/win-64::vs2015_runtime-14.16.27012-hf0eaf9b_1
  wheel              pkgs/main/win-64::wheel-0.34.2-py37_0
  wincertstore       pkgs/main/win-64::wincertstore-0.2-py37_0



Downloading and Extracting Packages

wheel-0.34.2         | 66 KB     |            |   0% 
wheel-0.34.2         | 66 KB     | ##4        |  24% 
wheel-0.34.2         | 66 KB     | ########## | 100% 

openssl-1.1.1f       | 4.8 MB    |            |   0% 
openssl-1.1.1f       | 4.8 MB    | ######2    |  63% 
openssl-1.1.1f       | 4.8 MB    | ########## | 100% 

pip-20.0.2           | 1.7 MB    |            |   0% 
pip-20.0.2           | 1.7 MB    | ########## | 100% 

vs2015_runtime-14.16 | 1.1 MB    |            |   0% 
vs2015_runtime-14.16 | 1.1 MB    | ########## | 100% 

ca-certificates-2020 | 125 KB    |            |   0% 
ca-certificates-2020 | 125 KB    | ########## | 100% 

sqlite-3.31.1        | 637 KB    |            |   0% 
sqlite-3.31.1        | 637 KB    | ########## | 100% 

setuptools-46.1.3    | 528 KB    |            |   0% 
setuptools-46.1.3    | 528 KB    | ########## | 100% 

certifi-2020.4.5.1   | 156 KB    |            |   0% 
certifi-2020.4.5.1   | 156 KB    | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
#
# To activate this environment, use
#
#     $ conda activate C:\Users\bioctesting\bbs-3.11-bioc-testing\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


==> WARNING: A newer version of conda exists. <==
  current version: 4.7.12
  latest version: 4.8.3

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: C:\Users\bioctesting\bbs-3.11-bioc-testing\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo

  added / updated specs:
    - pandas=0.24.1
    - python-dateutil=2.7.1
    - python=3.7.4
    - pytz=2018.7


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2020.4.5.1 |       hecc5488_0         184 KB  conda-forge
    certifi-2020.4.5.1         |   py37hc8dfbb8_0         150 KB  conda-forge
    intel-openmp-2020.0        |              166         1.5 MB
    libblas-3.8.0              |           15_mkl         3.5 MB  conda-forge
    libcblas-3.8.0             |           15_mkl         3.5 MB  conda-forge
    liblapack-3.8.0            |           15_mkl         3.5 MB  conda-forge
    mkl-2020.0                 |              166        98.9 MB
    numpy-1.18.1               |   py37h90d3380_1         4.7 MB  conda-forge
    openssl-1.1.1f             |       hfa6e2cd_0         4.7 MB  conda-forge
    pandas-0.24.1              |   py37h6538335_0         9.4 MB  conda-forge
    python-dateutil-2.7.1      |             py_0         203 KB  conda-forge
    python_abi-3.7             |          1_cp37m           4 KB  conda-forge
    pytz-2018.7                |             py_0         226 KB  conda-forge
    six-1.14.0                 |             py_1          13 KB  conda-forge
    ------------------------------------------------------------
                                           Total:       130.7 MB

The following NEW packages will be INSTALLED:

  intel-openmp       pkgs/main/win-64::intel-openmp-2020.0-166
  libblas            conda-forge/win-64::libblas-3.8.0-15_mkl
  libcblas           conda-forge/win-64::libcblas-3.8.0-15_mkl
  liblapack          conda-forge/win-64::liblapack-3.8.0-15_mkl
  mkl                pkgs/main/win-64::mkl-2020.0-166
  numpy              conda-forge/win-64::numpy-1.18.1-py37h90d3380_1
  pandas             conda-forge/win-64::pandas-0.24.1-py37h6538335_0
  python-dateutil    conda-forge/noarch::python-dateutil-2.7.1-py_0
  python_abi         conda-forge/win-64::python_abi-3.7-1_cp37m
  pytz               conda-forge/noarch::pytz-2018.7-py_0
  six                conda-forge/noarch::six-1.14.0-py_1

The following packages will be UPDATED:

  ca-certificates     pkgs/main::ca-certificates-2020.1.1-0 --> conda-forge::ca-certificates-2020.4.5.1-hecc5488_0

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

  certifi              pkgs/main::certifi-2020.4.5.1-py37_0 --> conda-forge::certifi-2020.4.5.1-py37hc8dfbb8_0
  openssl              pkgs/main::openssl-1.1.1f-he774522_0 --> conda-forge::openssl-1.1.1f-hfa6e2cd_0



Downloading and Extracting Packages

six-1.14.0           | 13 KB     |            |   0% 
six-1.14.0           | 13 KB     | ########## | 100% 

python_abi-3.7       | 4 KB      |            |   0% 
python_abi-3.7       | 4 KB      | ########## | 100% 

pandas-0.24.1        | 9.4 MB    |            |   0% 
pandas-0.24.1        | 9.4 MB    |            |   0% 
pandas-0.24.1        | 9.4 MB    | 3          |   3% 
pandas-0.24.1        | 9.4 MB    | ###        |  30% 
pandas-0.24.1        | 9.4 MB    | ######2    |  63% 
pandas-0.24.1        | 9.4 MB    | ########## | 100% 

python-dateutil-2.7. | 203 KB    |            |   0% 
python-dateutil-2.7. | 203 KB    | ########## | 100% 

libcblas-3.8.0       | 3.5 MB    |            |   0% 
libcblas-3.8.0       | 3.5 MB    | ####2      |  43% 
libcblas-3.8.0       | 3.5 MB    | ########## | 100% 

liblapack-3.8.0      | 3.5 MB    |            |   0% 
liblapack-3.8.0      | 3.5 MB    | ######7    |  68% 
liblapack-3.8.0      | 3.5 MB    | ########## | 100% 

pytz-2018.7          | 226 KB    |            |   0% 
pytz-2018.7          | 226 KB    | ########## | 100% 

certifi-2020.4.5.1   | 150 KB    |            |   0% 
certifi-2020.4.5.1   | 150 KB    | ########## | 100% 

ca-certificates-2020 | 184 KB    |            |   0% 
ca-certificates-2020 | 184 KB    | ########## | 100% 

intel-openmp-2020.0  | 1.5 MB    |            |   0% 
intel-openmp-2020.0  | 1.5 MB    | 1          |   1% 
intel-openmp-2020.0  | 1.5 MB    | ########## | 100% 

openssl-1.1.1f       | 4.7 MB    |            |   0% 
openssl-1.1.1f       | 4.7 MB    | ##7        |  28% 
openssl-1.1.1f       | 4.7 MB    | ########## | 100% 

numpy-1.18.1         | 4.7 MB    |            |   0% 
numpy-1.18.1         | 4.7 MB    | ###6       |  37% 
numpy-1.18.1         | 4.7 MB    | ########## | 100% 

mkl-2020.0           | 98.9 MB   |            |   0% 
mkl-2020.0           | 98.9 MB   | 3          |   3% 
mkl-2020.0           | 98.9 MB   | #1         |  12% 
mkl-2020.0           | 98.9 MB   | ##1        |  22% 
mkl-2020.0           | 98.9 MB   | ###1       |  31% 
mkl-2020.0           | 98.9 MB   | ####       |  41% 
mkl-2020.0           | 98.9 MB   | #####2     |  52% 
mkl-2020.0           | 98.9 MB   | ######3    |  64% 
mkl-2020.0           | 98.9 MB   | #######3   |  74% 
mkl-2020.0           | 98.9 MB   | ########3  |  84% 
mkl-2020.0           | 98.9 MB   | #########3 |  94% 
mkl-2020.0           | 98.9 MB   | ########## | 100% 

libblas-3.8.0        | 3.5 MB    |            |   0% 
libblas-3.8.0        | 3.5 MB    | #########8 |  98% 
libblas-3.8.0        | 3.5 MB    | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
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


==> WARNING: A newer version of conda exists. <==
  current version: 4.7.12
  latest version: 4.8.3

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: C:\Users\bioctesting\bbs-3.11-bioc-testing\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         |           py27_0         153 KB
    pip-19.3.1                 |           py27_0         1.7 MB
    python-2.7.17              |       h930f6bb_0        15.9 MB
    setuptools-44.0.0          |           py27_0         528 KB
    sqlite-3.30.1              |       h0c8e037_0         588 KB
    vc-9                       |       h7299396_1           3 KB
    vs2008_runtime-9.00.30729.1|       hfaea7d5_1         500 KB
    wheel-0.33.6               |           py27_0          58 KB
    wincertstore-0.2           |   py27hf04cefb_0          14 KB
    ------------------------------------------------------------
                                           Total:        19.4 MB

The following NEW packages will be INSTALLED:

  ca-certificates    pkgs/main/win-64::ca-certificates-2020.1.1-0
  certifi            pkgs/main/win-64::certifi-2019.11.28-py27_0
  pip                pkgs/main/win-64::pip-19.3.1-py27_0
  python             pkgs/main/win-64::python-2.7.17-h930f6bb_0
  setuptools         pkgs/main/win-64::setuptools-44.0.0-py27_0
  sqlite             pkgs/main/win-64::sqlite-3.30.1-h0c8e037_0
  vc                 pkgs/main/win-64::vc-9-h7299396_1
  vs2008_runtime     pkgs/main/win-64::vs2008_runtime-9.00.30729.1-hfaea7d5_1
  wheel              pkgs/main/win-64::wheel-0.33.6-py27_0
  wincertstore       pkgs/main/win-64::wincertstore-0.2-py27hf04cefb_0



Downloading and Extracting Packages

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

vs2008_runtime-9.00. | 500 KB    |            |   0% 
vs2008_runtime-9.00. | 500 KB    | ########## | 100% 

python-2.7.17        | 15.9 MB   |            |   0% 
python-2.7.17        | 15.9 MB   | #6         |  17% 
python-2.7.17        | 15.9 MB   | #####8     |  59% 
python-2.7.17        | 15.9 MB   | ########## | 100% 

setuptools-44.0.0    | 528 KB    |            |   0% 
setuptools-44.0.0    | 528 KB    | ########## | 100% 

sqlite-3.30.1        | 588 KB    |            |   0% 
sqlite-3.30.1        | 588 KB    | ########## | 100% 

certifi-2019.11.28   | 153 KB    |            |   0% 
certifi-2019.11.28   | 153 KB    | ########## | 100% 

wincertstore-0.2     | 14 KB     |            |   0% 
wincertstore-0.2     | 14 KB     | ########## | 100% 

pip-19.3.1           | 1.7 MB    |            |   0% 
pip-19.3.1           | 1.7 MB    | ########## | 100% 

wheel-0.33.6         | 58 KB     |            |   0% 
wheel-0.33.6         | 58 KB     | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
#
# To activate this environment, use
#
#     $ conda activate C:\Users\bioctesting\bbs-3.11-bioc-testing\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: 4.7.12
  latest version: 4.8.3

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: C:\Users\bioctesting\bbs-3.11-bioc-testing\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo

  added / updated specs:
    - python[version='2.7.*,2.7.*']


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    python-2.7.15              |h2880e7c_1011_cpython        20.3 MB  conda-forge
    python_abi-2.7             |          1_cp27m           4 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        20.3 MB

The following NEW packages will be INSTALLED:

  python_abi         conda-forge/win-64::python_abi-2.7-1_cp27m

The following packages will be UPDATED:

  ca-certificates     pkgs/main::ca-certificates-2020.1.1-0 --> conda-forge::ca-certificates-2020.4.5.1-hecc5488_0

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

  python                pkgs/main::python-2.7.17-h930f6bb_0 --> conda-forge::python-2.7.15-h2880e7c_1011_cpython



Downloading and Extracting Packages

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

python-2.7.15        | 20.3 MB   |            |   0% 
python-2.7.15        | 20.3 MB   | 6          |   6% 
python-2.7.15        | 20.3 MB   | ##8        |  28% 
python-2.7.15        | 20.3 MB   | #####9     |  59% 
python-2.7.15        | 20.3 MB   | #########6 |  97% 
python-2.7.15        | 20.3 MB   | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
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


==> WARNING: A newer version of conda exists. <==
  current version: 4.7.12
  latest version: 4.8.3

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: C:\Users\bioctesting\bbs-3.11-bioc-testing\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo

  added / updated specs:
    - python=3.7.4


The following NEW packages will be INSTALLED:

  ca-certificates    pkgs/main/win-64::ca-certificates-2020.1.1-0
  certifi            pkgs/main/win-64::certifi-2020.4.5.1-py37_0
  openssl            pkgs/main/win-64::openssl-1.1.1f-he774522_0
  pip                pkgs/main/win-64::pip-20.0.2-py37_1
  python             pkgs/main/win-64::python-3.7.4-h5263a28_0
  setuptools         pkgs/main/win-64::setuptools-46.1.3-py37_0
  sqlite             pkgs/main/win-64::sqlite-3.31.1-he774522_0
  vc                 pkgs/main/win-64::vc-14.1-h0510ff6_4
  vs2015_runtime     pkgs/main/win-64::vs2015_runtime-14.16.27012-hf0eaf9b_1
  wheel              pkgs/main/win-64::wheel-0.34.2-py37_0
  wincertstore       pkgs/main/win-64::wincertstore-0.2-py37_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
#
# To activate this environment, use
#
#     $ conda activate C:\Users\bioctesting\bbs-3.11-bioc-testing\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


==> WARNING: A newer version of conda exists. <==
  current version: 4.7.12
  latest version: 4.8.3

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: C:\Users\bioctesting\bbs-3.11-bioc-testing\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo

  added / updated specs:
    - python-dateutil=2.7.1
    - python=3.7.4
    - pytz=2018.7


The following NEW packages will be INSTALLED:

  python-dateutil    conda-forge/noarch::python-dateutil-2.7.1-py_0
  python_abi         conda-forge/win-64::python_abi-3.7-1_cp37m
  pytz               conda-forge/noarch::pytz-2018.7-py_0
  six                conda-forge/noarch::six-1.14.0-py_1

The following packages will be UPDATED:

  ca-certificates     pkgs/main::ca-certificates-2020.1.1-0 --> conda-forge::ca-certificates-2020.4.5.1-hecc5488_0

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

  certifi              pkgs/main::certifi-2020.4.5.1-py37_0 --> conda-forge::certifi-2020.4.5.1-py37hc8dfbb8_0
  openssl              pkgs/main::openssl-1.1.1f-he774522_0 --> conda-forge::openssl-1.1.1f-hfa6e2cd_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting pandas==0.24.1
  Using cached pandas-0.24.1-cp37-cp37m-win_amd64.whl (9.0 MB)
Requirement already satisfied: python-dateutil>=2.5.0 in c:\users\biocte~1\bbs-3~1.11-\meat\basili~2.rch\tests\testthat\instal~1\thingo\lib\site-packages (from pandas==0.24.1) (2.7.1)
Requirement already satisfied: pytz>=2011k in c:\users\biocte~1\bbs-3~1.11-\meat\basili~2.rch\tests\testthat\instal~1\thingo\lib\site-packages (from pandas==0.24.1) (2018.7)
Collecting numpy>=1.12.0
  Using cached numpy-1.18.2-cp37-cp37m-win_amd64.whl (12.8 MB)
Requirement already satisfied: six>=1.5 in c:\users\biocte~1\bbs-3~1.11-\meat\basili~2.rch\tests\testthat\instal~1\thingo\lib\site-packages (from python-dateutil>=2.5.0->pandas==0.24.1) (1.14.0)
Installing collected packages: numpy, pandas
  WARNING: The script f2py.exe is installed in 'C:\Users\BIOCTE~1\BBS-3~1.11-\meat\BASILI~2.RCH\tests\testthat\INSTAL~1\thingo\Scripts' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Successfully installed numpy-1.18.2 pandas-0.24.1
* installing *source* package 'son.of.basilisk' ...
** using non-staged installation via StagedInstall field
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'son.of.basilisk'
    finding HTML links ... done
    test                                    html  
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* DONE (son.of.basilisk)
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.7.12
  latest version: 4.8.3

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: C:\Users\bioctesting\AppData\Local\basilisk\0.99.61\son.of.basilisk-0.99.0\env1

  added / updated specs:
    - python=3.7.4


The following NEW packages will be INSTALLED:

  ca-certificates    pkgs/main/win-64::ca-certificates-2020.1.1-0
  certifi            pkgs/main/win-64::certifi-2020.4.5.1-py37_0
  openssl            pkgs/main/win-64::openssl-1.1.1f-he774522_0
  pip                pkgs/main/win-64::pip-20.0.2-py37_1
  python             pkgs/main/win-64::python-3.7.4-h5263a28_0
  setuptools         pkgs/main/win-64::setuptools-46.1.3-py37_0
  sqlite             pkgs/main/win-64::sqlite-3.31.1-he774522_0
  vc                 pkgs/main/win-64::vc-14.1-h0510ff6_4
  vs2015_runtime     pkgs/main/win-64::vs2015_runtime-14.16.27012-hf0eaf9b_1
  wheel              pkgs/main/win-64::wheel-0.34.2-py37_0
  wincertstore       pkgs/main/win-64::wincertstore-0.2-py37_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
#
# To activate this environment, use
#
#     $ conda activate C:\Users\bioctesting\AppData\Local\basilisk\0.99.61\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... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.7.12
  latest version: 4.8.3

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: C:\Users\bioctesting\AppData\Local\basilisk\0.99.61\son.of.basilisk-0.99.0\env1

  added / updated specs:
    - pandas=0.24.1
    - python-dateutil=2.7.1
    - python=3.7.4
    - pytz=2018.7


The following NEW packages will be INSTALLED:

  intel-openmp       pkgs/main/win-64::intel-openmp-2020.0-166
  libblas            conda-forge/win-64::libblas-3.8.0-15_mkl
  libcblas           conda-forge/win-64::libcblas-3.8.0-15_mkl
  liblapack          conda-forge/win-64::liblapack-3.8.0-15_mkl
  mkl                pkgs/main/win-64::mkl-2020.0-166
  numpy              conda-forge/win-64::numpy-1.18.1-py37h90d3380_1
  pandas             conda-forge/win-64::pandas-0.24.1-py37h6538335_0
  python-dateutil    conda-forge/noarch::python-dateutil-2.7.1-py_0
  python_abi         conda-forge/win-64::python_abi-3.7-1_cp37m
  pytz               conda-forge/noarch::pytz-2018.7-py_0
  six                conda-forge/noarch::six-1.14.0-py_1

The following packages will be UPDATED:

  ca-certificates     pkgs/main::ca-certificates-2020.1.1-0 --> conda-forge::ca-certificates-2020.4.5.1-hecc5488_0

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

  certifi              pkgs/main::certifi-2020.4.5.1-py37_0 --> conda-forge::certifi-2020.4.5.1-py37hc8dfbb8_0
  openssl              pkgs/main::openssl-1.1.1f-he774522_0 --> conda-forge::openssl-1.1.1f-hfa6e2cd_0


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

Example timings

basilisk.Rcheck/basilisk-Ex.timings

nameusersystemelapsed
BasiliskEnvironment-class000
PyPiLink000
basiliskOptions000