Aaron Lun
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/basilisk |
| git_branch: master |
| git_last_commit: fdcfe4c |
| git_last_commit_date: 2021-12-16 15:47:03 -0400 (Thu, 16 Dec 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:06:59 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the basilisk package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/basilisk.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 117/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| basilisk 1.7.0 (landing page) Aaron Lun
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: basilisk |
| Version: 1.7.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:basilisk.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings basilisk_1.7.0.tar.gz |
| StartedAt: 2022-03-17 18:29:47 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:57:22 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 1654.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: basilisk.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:basilisk.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings basilisk_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/basilisk.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'basilisk/DESCRIPTION' ... OK
* this is package 'basilisk' version '1.7.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
inst/example/.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'basilisk' can be installed ... NOTE
Found the following notes/warnings:
Non-staged installation was used
See 'D:/biocbuild/bbs-3.15-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 1.08 0.44 390.00
setupBasiliskEnv 0.01 0.00 151.32
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/basilisk.Rcheck/00check.log'
for details.
basilisk.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL basilisk
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'basilisk' ...
** using non-staged installation via StagedInstall field
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'basilisk'
finding HTML links ... done
BasiliskEnvironment-class html
PyPiLink html
basiliskOptions html
basiliskStart html
finding level-2 HTML links ... done
configureBasiliskEnv html
findPersistentEnv html
listPackages html
setupBasiliskEnv html
useBasiliskEnv html
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (basilisk)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'OLINgui' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'ternarynet' is missing or broken
done
basilisk.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(basilisk)
> test_check("basilisk")
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: D:\biocbuild\bbs-3.15-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo
added / updated specs:
- python=3.7.7
The following NEW packages will be INSTALLED:
ca-certificates conda-forge/win-64::ca-certificates-2021.10.8-h5b45459_0
openssl conda-forge/win-64::openssl-1.1.1l-h8ffe710_0
pip conda-forge/noarch::pip-22.0.4-pyhd8ed1ab_0
python pkgs/main/win-64::python-3.7.7-h81c818b_4
python_abi conda-forge/win-64::python_abi-3.7-2_cp37m
setuptools conda-forge/win-64::setuptools-60.10.0-py37h03978a9_0
sqlite conda-forge/win-64::sqlite-3.37.1-h8ffe710_0
ucrt conda-forge/win-64::ucrt-10.0.20348.0-h57928b3_0
vc conda-forge/win-64::vc-14.2-hb210afc_6
vs2015_runtime conda-forge/win-64::vs2015_runtime-14.29.30037-h902a5da_6
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: D:\biocbuild\bbs-3.15-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo
added / updated specs:
- python=3.7.7
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2021.10.~ --> pkgs/main::ca-certificates-2022.2.1-haa95532_0
openssl conda-forge::openssl-1.1.1l-h8ffe710_0 --> pkgs/main::openssl-1.1.1m-h2bbff1b_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.8.3
latest version: 4.12.0
Please update conda by running
$ conda update -n base -c defaults conda
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: D:\biocbuild\bbs-3.15-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo
added / updated specs:
- pandas=0.25.1
- python-dateutil=2.8.0
- python=3.7.7
- pytz=2019.3
The following NEW packages will be INSTALLED:
intel-openmp conda-forge/win-64::intel-openmp-2022.0.0-h57928b3_3663
libblas conda-forge/win-64::libblas-3.9.0-13_win64_mkl
libcblas conda-forge/win-64::libcblas-3.9.0-13_win64_mkl
liblapack conda-forge/win-64::liblapack-3.9.0-13_win64_mkl
mkl conda-forge/win-64::mkl-2022.0.0-h0e2418a_796
numpy conda-forge/win-64::numpy-1.21.5-py37h5fa1a60_0
pandas pkgs/main/win-64::pandas-0.25.1-py37ha925a31_0
python-dateutil conda-forge/noarch::python-dateutil-2.8.0-py_0
pytz conda-forge/noarch::pytz-2019.3-py_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
tbb conda-forge/win-64::tbb-2021.5.0-h2d74725_0
The following packages will be SUPERSEDED by a higher-priority channel:
ca-certificates pkgs/main::ca-certificates-2022.2.1-h~ --> conda-forge::ca-certificates-2021.10.8-h5b45459_0
openssl pkgs/main::openssl-1.1.1m-h2bbff1b_0 --> conda-forge::openssl-1.1.1l-h8ffe710_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.8.3
latest version: 4.12.0
Please update conda by running
$ conda update -n base -c defaults conda
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: D:\biocbuild\bbs-3.15-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo
added / updated specs:
- python=3.7.7
The following NEW packages will be INSTALLED:
ca-certificates conda-forge/win-64::ca-certificates-2021.10.8-h5b45459_0
openssl conda-forge/win-64::openssl-1.1.1l-h8ffe710_0
pip conda-forge/noarch::pip-22.0.4-pyhd8ed1ab_0
python pkgs/main/win-64::python-3.7.7-h81c818b_4
python_abi conda-forge/win-64::python_abi-3.7-2_cp37m
setuptools conda-forge/win-64::setuptools-60.10.0-py37h03978a9_0
sqlite conda-forge/win-64::sqlite-3.37.1-h8ffe710_0
ucrt conda-forge/win-64::ucrt-10.0.20348.0-h57928b3_0
vc conda-forge/win-64::vc-14.2-hb210afc_6
vs2015_runtime conda-forge/win-64::vs2015_runtime-14.29.30037-h902a5da_6
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: D:\biocbuild\bbs-3.15-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo
added / updated specs:
- python=3.7.7
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2021.10.~ --> pkgs/main::ca-certificates-2022.2.1-haa95532_0
openssl conda-forge::openssl-1.1.1l-h8ffe710_0 --> pkgs/main::openssl-1.1.1m-h2bbff1b_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.8.3
latest version: 4.12.0
Please update conda by running
$ conda update -n base -c defaults conda
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: D:\biocbuild\bbs-3.15-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo
added / updated specs:
- pandas=0.24.1
- python-dateutil=2.7.1
- python=3.7.7
- pytz=2018.7
The following NEW packages will be INSTALLED:
intel-openmp conda-forge/win-64::intel-openmp-2022.0.0-h57928b3_3663
libblas conda-forge/win-64::libblas-3.9.0-13_win64_mkl
libcblas conda-forge/win-64::libcblas-3.9.0-13_win64_mkl
liblapack conda-forge/win-64::liblapack-3.9.0-13_win64_mkl
mkl conda-forge/win-64::mkl-2022.0.0-h0e2418a_796
numpy conda-forge/win-64::numpy-1.21.5-py37h5fa1a60_0
pandas pkgs/main/win-64::pandas-0.24.1-py37ha925a31_0
python-dateutil conda-forge/noarch::python-dateutil-2.7.1-py_0
pytz conda-forge/noarch::pytz-2018.7-py_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
tbb conda-forge/win-64::tbb-2021.5.0-h2d74725_0
The following packages will be SUPERSEDED by a higher-priority channel:
ca-certificates pkgs/main::ca-certificates-2022.2.1-h~ --> conda-forge::ca-certificates-2021.10.8-h5b45459_0
openssl pkgs/main::openssl-1.1.1m-h2bbff1b_0 --> conda-forge::openssl-1.1.1l-h8ffe710_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.8.3
latest version: 4.12.0
Please update conda by running
$ conda update -n base -c defaults conda
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: D:\biocbuild\bbs-3.15-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo
added / updated specs:
- python=2.7
The following NEW packages will be INSTALLED:
certifi conda-forge/win-64::certifi-2019.11.28-py27h8c360ce_1
pip conda-forge/noarch::pip-20.1.1-pyh9f0ad1d_0
python conda-forge/win-64::python-2.7.15-h2880e7c_1011_cpython
python_abi conda-forge/win-64::python_abi-2.7-1_cp27m
setuptools conda-forge/win-64::setuptools-44.0.0-py27_0
vc pkgs/main/win-64::vc-9-h2eaa2aa_6
vs2008_runtime conda-forge/win-64::vs2008_runtime-9.0.30729.6161-0
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
wincertstore conda-forge/win-64::wincertstore-0.2-py27_1003
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: D:\biocbuild\bbs-3.15-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo
added / updated specs:
- python=2.7
The following packages will be UPDATED:
certifi conda-forge/win-64::certifi-2019.11.2~ --> pkgs/main/noarch::certifi-2020.6.20-pyhd3eb1b0_3
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.8.3
latest version: 4.12.0
Please update conda by running
$ conda update -n base -c defaults conda
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.8.3
latest version: 4.12.0
Please update conda by running
$ conda update -n base -c defaults conda
# All requested packages already installed.
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: D:\biocbuild\bbs-3.15-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo
added / updated specs:
- python=3.7.7
The following NEW packages will be INSTALLED:
ca-certificates conda-forge/win-64::ca-certificates-2021.10.8-h5b45459_0
openssl conda-forge/win-64::openssl-1.1.1l-h8ffe710_0
pip conda-forge/noarch::pip-22.0.4-pyhd8ed1ab_0
python pkgs/main/win-64::python-3.7.7-h81c818b_4
python_abi conda-forge/win-64::python_abi-3.7-2_cp37m
setuptools conda-forge/win-64::setuptools-60.10.0-py37h03978a9_0
sqlite conda-forge/win-64::sqlite-3.37.1-h8ffe710_0
ucrt conda-forge/win-64::ucrt-10.0.20348.0-h57928b3_0
vc conda-forge/win-64::vc-14.2-hb210afc_6
vs2015_runtime conda-forge/win-64::vs2015_runtime-14.29.30037-h902a5da_6
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: D:\biocbuild\bbs-3.15-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo
added / updated specs:
- python=3.7.7
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2021.10.~ --> pkgs/main::ca-certificates-2022.2.1-haa95532_0
openssl conda-forge::openssl-1.1.1l-h8ffe710_0 --> pkgs/main::openssl-1.1.1m-h2bbff1b_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.8.3
latest version: 4.12.0
Please update conda by running
$ conda update -n base -c defaults conda
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: D:\biocbuild\bbs-3.15-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo
added / updated specs:
- python-dateutil=2.7.1
- python=3.7.7
- pytz=2018.7
The following NEW packages will be INSTALLED:
python-dateutil conda-forge/noarch::python-dateutil-2.7.1-py_0
pytz conda-forge/noarch::pytz-2018.7-py_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
The following packages will be SUPERSEDED by a higher-priority channel:
ca-certificates pkgs/main::ca-certificates-2022.2.1-h~ --> conda-forge::ca-certificates-2021.10.8-h5b45459_0
openssl pkgs/main::openssl-1.1.1m-h2bbff1b_0 --> conda-forge::openssl-1.1.1l-h8ffe710_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.8.3
latest version: 4.12.0
Please update conda by running
$ conda update -n base -c defaults conda
Collecting pandas==0.24.1
Using cached pandas-0.24.1-cp37-cp37m-win_amd64.whl (9.0 MB)
Requirement already satisfied: pytz>=2011k in d:\biocbuild\bbs-3.15-bioc\meat\basilisk.rcheck\tests\testthat\install-test-client\thingo\lib\site-packages (from pandas==0.24.1) (2018.7)
Collecting numpy>=1.12.0
Using cached numpy-1.21.5-cp37-cp37m-win_amd64.whl (14.0 MB)
Requirement already satisfied: python-dateutil>=2.5.0 in d:\biocbuild\bbs-3.15-bioc\meat\basilisk.rcheck\tests\testthat\install-test-client\thingo\lib\site-packages (from pandas==0.24.1) (2.7.1)
Requirement already satisfied: six>=1.5 in d:\biocbuild\bbs-3.15-bioc\meat\basilisk.rcheck\tests\testthat\install-test-client\thingo\lib\site-packages (from python-dateutil>=2.5.0->pandas==0.24.1) (1.16.0)
Installing collected packages: numpy, pandas
WARNING: The script f2py.exe is installed in 'D:\biocbuild\bbs-3.15-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo\Scripts' which is not on PATH.
Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Successfully installed numpy-1.21.5 pandas-0.24.1
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: D:\biocbuild\bbs-3.15-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo
added / updated specs:
- python=3.7.7
The following NEW packages will be INSTALLED:
ca-certificates conda-forge/win-64::ca-certificates-2021.10.8-h5b45459_0
openssl conda-forge/win-64::openssl-1.1.1l-h8ffe710_0
pip conda-forge/noarch::pip-22.0.4-pyhd8ed1ab_0
python pkgs/main/win-64::python-3.7.7-h81c818b_4
python_abi conda-forge/win-64::python_abi-3.7-2_cp37m
setuptools conda-forge/win-64::setuptools-60.10.0-py37h03978a9_0
sqlite conda-forge/win-64::sqlite-3.37.1-h8ffe710_0
ucrt conda-forge/win-64::ucrt-10.0.20348.0-h57928b3_0
vc conda-forge/win-64::vc-14.2-hb210afc_6
vs2015_runtime conda-forge/win-64::vs2015_runtime-14.29.30037-h902a5da_6
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: D:\biocbuild\bbs-3.15-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo
added / updated specs:
- python=3.7.7
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2021.10.~ --> pkgs/main::ca-certificates-2022.2.1-haa95532_0
openssl conda-forge::openssl-1.1.1l-h8ffe710_0 --> pkgs/main::openssl-1.1.1m-h2bbff1b_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.8.3
latest version: 4.12.0
Please update conda by running
$ conda update -n base -c defaults conda
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: D:\biocbuild\bbs-3.15-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo
added / updated specs:
- python=3.7.7
The following packages will be SUPERSEDED by a higher-priority channel:
ca-certificates pkgs/main::ca-certificates-2022.2.1-h~ --> conda-forge::ca-certificates-2021.10.8-h5b45459_0
openssl pkgs/main::openssl-1.1.1m-h2bbff1b_0 --> conda-forge::openssl-1.1.1l-h8ffe710_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.8.3
latest version: 4.12.0
Please update conda by running
$ conda update -n base -c defaults conda
Processing d:\biocbuild\bbs-3.15-bioc\r\library\basilisk\example\inst\test_dummy
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Building wheels for collected packages: test-dummy
Building wheel for test-dummy (setup.py): started
Building wheel for test-dummy (setup.py): finished with status 'done'
Created wheel for test-dummy: filename=test_dummy-0.1-py3-none-any.whl size=1295 sha256=da64167f9ecea0ad7265c6f7a48995c9ed096dba4d58f2844b48ec5112199d05
Stored in directory: D:\biocbuild\bbs-3.15-bioc\tmpdir\pip-ephem-wheel-cache-nhvyoqwn\wheels\cd\ad\ff\5f241962228cbd8b17d443fb7d400948208c9f0e8caad4a9d2
Successfully built test-dummy
Installing collected packages: test-dummy
Successfully installed test-dummy-0.1
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: D:\biocbuild\bbs-3.15-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo
added / updated specs:
- python=3.7.7
The following NEW packages will be INSTALLED:
ca-certificates conda-forge/win-64::ca-certificates-2021.10.8-h5b45459_0
openssl conda-forge/win-64::openssl-1.1.1l-h8ffe710_0
pip conda-forge/noarch::pip-22.0.4-pyhd8ed1ab_0
python pkgs/main/win-64::python-3.7.7-h81c818b_4
python_abi conda-forge/win-64::python_abi-3.7-2_cp37m
setuptools conda-forge/win-64::setuptools-60.10.0-py37h03978a9_0
sqlite conda-forge/win-64::sqlite-3.37.1-h8ffe710_0
ucrt conda-forge/win-64::ucrt-10.0.20348.0-h57928b3_0
vc conda-forge/win-64::vc-14.2-hb210afc_6
vs2015_runtime conda-forge/win-64::vs2015_runtime-14.29.30037-h902a5da_6
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: D:\biocbuild\bbs-3.15-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\thingo
added / updated specs:
- python=3.7.7
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2021.10.~ --> pkgs/main::ca-certificates-2022.2.1-haa95532_0
openssl conda-forge::openssl-1.1.1l-h8ffe710_0 --> pkgs/main::openssl-1.1.1m-h2bbff1b_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.8.3
latest version: 4.12.0
Please update conda by running
$ conda update -n base -c defaults conda
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
PackagesNotFoundError: The following packages are not available from current channels:
- whheeeeeeeeeeeeeeeeee=0.0.1
Current channels:
- https://conda.anaconda.org/conda-forge/win-64
- https://conda.anaconda.org/conda-forge/noarch
- https://repo.anaconda.com/pkgs/main/win-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/win-64
- https://repo.anaconda.com/pkgs/r/noarch
- https://repo.anaconda.com/pkgs/msys2/win-64
- https://repo.anaconda.com/pkgs/msys2/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
* installing *source* package 'son.of.basilisk' ...
** using non-staged installation via StagedInstall field
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'son.of.basilisk'
finding HTML links ... done
test html
** building package indices
** testing if installed package can be loaded
* DONE (son.of.basilisk)
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\1748C3~1.0\SONOF~1.BAS\099~1.0\env2\lib\site-packages\sklearn\linear_model\least_angle.py:30: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
method='lar', copy_X=True, eps=np.finfo(np.float).eps,
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\1748C3~1.0\SONOF~1.BAS\099~1.0\env2\lib\site-packages\sklearn\linear_model\least_angle.py:167: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
method='lar', copy_X=True, eps=np.finfo(np.float).eps,
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\1748C3~1.0\SONOF~1.BAS\099~1.0\env2\lib\site-packages\sklearn\linear_model\least_angle.py:284: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
eps=np.finfo(np.float).eps, copy_Gram=True, verbose=0,
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\1748C3~1.0\SONOF~1.BAS\099~1.0\env2\lib\site-packages\sklearn\linear_model\least_angle.py:862: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
eps=np.finfo(np.float).eps, copy_X=True, fit_path=True,
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\1748C3~1.0\SONOF~1.BAS\099~1.0\env2\lib\site-packages\sklearn\linear_model\least_angle.py:1101: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
eps=np.finfo(np.float).eps, copy_X=True, fit_path=True,
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\1748C3~1.0\SONOF~1.BAS\099~1.0\env2\lib\site-packages\sklearn\linear_model\least_angle.py:1127: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
eps=np.finfo(np.float).eps, positive=False):
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\1748C3~1.0\SONOF~1.BAS\099~1.0\env2\lib\site-packages\sklearn\linear_model\least_angle.py:1362: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
max_n_alphas=1000, n_jobs=None, eps=np.finfo(np.float).eps,
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\1748C3~1.0\SONOF~1.BAS\099~1.0\env2\lib\site-packages\sklearn\linear_model\least_angle.py:1602: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
max_n_alphas=1000, n_jobs=None, eps=np.finfo(np.float).eps,
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\1748C3~1.0\SONOF~1.BAS\099~1.0\env2\lib\site-packages\sklearn\linear_model\least_angle.py:1738: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
eps=np.finfo(np.float).eps, copy_X=True, positive=False):
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\1748C3~1.0\SONOF~1.BAS\099~1.0\env2\lib\site-packages\sklearn\decomposition\online_lda.py:29: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
EPS = np.finfo(np.float).eps
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: D:\biocbuild\bbs-3.15-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\my_package_A
added / updated specs:
- python=3.7.7
The following NEW packages will be INSTALLED:
ca-certificates conda-forge/win-64::ca-certificates-2021.10.8-h5b45459_0
openssl conda-forge/win-64::openssl-1.1.1l-h8ffe710_0
pip conda-forge/noarch::pip-22.0.4-pyhd8ed1ab_0
python pkgs/main/win-64::python-3.7.7-h81c818b_4
python_abi conda-forge/win-64::python_abi-3.7-2_cp37m
setuptools conda-forge/win-64::setuptools-60.10.0-py37h03978a9_0
sqlite conda-forge/win-64::sqlite-3.37.1-h8ffe710_0
ucrt conda-forge/win-64::ucrt-10.0.20348.0-h57928b3_0
vc conda-forge/win-64::vc-14.2-hb210afc_6
vs2015_runtime conda-forge/win-64::vs2015_runtime-14.29.30037-h902a5da_6
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: D:\biocbuild\bbs-3.15-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\my_package_A
added / updated specs:
- python=3.7.7
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2021.10.~ --> pkgs/main::ca-certificates-2022.2.1-haa95532_0
openssl conda-forge::openssl-1.1.1l-h8ffe710_0 --> pkgs/main::openssl-1.1.1m-h2bbff1b_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.8.3
latest version: 4.12.0
Please update conda by running
$ conda update -n base -c defaults conda
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: D:\biocbuild\bbs-3.15-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\my_package_A
added / updated specs:
- pandas=0.25.1
- python-dateutil=2.8.0
- python=3.7.7
- pytz=2019.3
The following NEW packages will be INSTALLED:
intel-openmp conda-forge/win-64::intel-openmp-2022.0.0-h57928b3_3663
libblas conda-forge/win-64::libblas-3.9.0-13_win64_mkl
libcblas conda-forge/win-64::libcblas-3.9.0-13_win64_mkl
liblapack conda-forge/win-64::liblapack-3.9.0-13_win64_mkl
mkl conda-forge/win-64::mkl-2022.0.0-h0e2418a_796
numpy conda-forge/win-64::numpy-1.21.5-py37h5fa1a60_0
pandas pkgs/main/win-64::pandas-0.25.1-py37ha925a31_0
python-dateutil conda-forge/noarch::python-dateutil-2.8.0-py_0
pytz conda-forge/noarch::pytz-2019.3-py_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
tbb conda-forge/win-64::tbb-2021.5.0-h2d74725_0
The following packages will be SUPERSEDED by a higher-priority channel:
ca-certificates pkgs/main::ca-certificates-2022.2.1-h~ --> conda-forge::ca-certificates-2021.10.8-h5b45459_0
openssl pkgs/main::openssl-1.1.1m-h2bbff1b_0 --> conda-forge::openssl-1.1.1l-h8ffe710_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.8.3
latest version: 4.12.0
Please update conda by running
$ conda update -n base -c defaults conda
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: D:\biocbuild\bbs-3.15-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\my_package_B
added / updated specs:
- python=3.7.7
The following NEW packages will be INSTALLED:
ca-certificates conda-forge/win-64::ca-certificates-2021.10.8-h5b45459_0
openssl conda-forge/win-64::openssl-1.1.1l-h8ffe710_0
pip conda-forge/noarch::pip-22.0.4-pyhd8ed1ab_0
python pkgs/main/win-64::python-3.7.7-h81c818b_4
python_abi conda-forge/win-64::python_abi-3.7-2_cp37m
setuptools conda-forge/win-64::setuptools-60.10.0-py37h03978a9_0
sqlite conda-forge/win-64::sqlite-3.37.1-h8ffe710_0
ucrt conda-forge/win-64::ucrt-10.0.20348.0-h57928b3_0
vc conda-forge/win-64::vc-14.2-hb210afc_6
vs2015_runtime conda-forge/win-64::vs2015_runtime-14.29.30037-h902a5da_6
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: D:\biocbuild\bbs-3.15-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\my_package_B
added / updated specs:
- python=3.7.7
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2021.10.~ --> pkgs/main::ca-certificates-2022.2.1-haa95532_0
openssl conda-forge::openssl-1.1.1l-h8ffe710_0 --> pkgs/main::openssl-1.1.1m-h2bbff1b_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.8.3
latest version: 4.12.0
Please update conda by running
$ conda update -n base -c defaults conda
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: D:\biocbuild\bbs-3.15-bioc\meat\basilisk.Rcheck\tests\testthat\install-test-client\my_package_B
added / updated specs:
- pandas=0.24.1
- python-dateutil=2.7.1
- python=3.7.7
- pytz=2018.7
The following NEW packages will be INSTALLED:
intel-openmp conda-forge/win-64::intel-openmp-2022.0.0-h57928b3_3663
libblas conda-forge/win-64::libblas-3.9.0-13_win64_mkl
libcblas conda-forge/win-64::libcblas-3.9.0-13_win64_mkl
liblapack conda-forge/win-64::liblapack-3.9.0-13_win64_mkl
mkl conda-forge/win-64::mkl-2022.0.0-h0e2418a_796
numpy conda-forge/win-64::numpy-1.21.5-py37h5fa1a60_0
pandas pkgs/main/win-64::pandas-0.24.1-py37ha925a31_0
python-dateutil conda-forge/noarch::python-dateutil-2.7.1-py_0
pytz conda-forge/noarch::pytz-2018.7-py_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
tbb conda-forge/win-64::tbb-2021.5.0-h2d74725_0
The following packages will be SUPERSEDED by a higher-priority channel:
ca-certificates pkgs/main::ca-certificates-2022.2.1-h~ --> conda-forge::ca-certificates-2021.10.8-h5b45459_0
openssl pkgs/main::openssl-1.1.1m-h2bbff1b_0 --> conda-forge::openssl-1.1.1l-h8ffe710_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.8.3
latest version: 4.12.0
Please update conda by running
$ conda update -n base -c defaults conda
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 37 ]
== Skipped tests ===============================================================
* On Windows (2)
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 37 ]
>
> proc.time()
user system elapsed
3.40 9.32 1051.65
basilisk.Rcheck/basilisk-Ex.timings
| name | user | system | elapsed | |
| BasiliskEnvironment-class | 0 | 0 | 0 | |
| PyPiLink | 0 | 0 | 0 | |
| basiliskOptions | 0 | 0 | 0 | |
| basiliskStart | 1.08 | 0.44 | 390.00 | |
| configureBasiliskEnv | 0 | 0 | 0 | |
| findPersistentEnv | 0.03 | 0.00 | 4.27 | |
| listPackages | 0.02 | 0.00 | 1.78 | |
| setupBasiliskEnv | 0.01 | 0.00 | 151.32 | |
| useBasiliskEnv | 0.02 | 0.03 | 1.77 | |