Aaron Lun
| Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022) |
| git_url: https://git.bioconductor.org/packages/basilisk |
| git_branch: RELEASE_3_15 |
| git_last_commit: 9cac618 |
| git_last_commit_date: 2022-08-25 02:14:08 -0400 (Thu, 25 Aug 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:21:08 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 120/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| basilisk 1.8.1 (landing page) Aaron Lun
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | 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: 1.8.1 |
| Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:basilisk.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings basilisk_1.8.1.tar.gz |
| StartedAt: 2022-10-18 22:09:40 -0400 (Tue, 18 Oct 2022) |
| EndedAt: 2022-10-18 22:38:04 -0400 (Tue, 18 Oct 2022) |
| EllapsedTime: 1704.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: basilisk.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:basilisk.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings basilisk_1.8.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/basilisk.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'basilisk/DESCRIPTION' ... OK
* this is package 'basilisk' version '1.8.1'
* 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 'F:/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 1.21 0.70 373.36
setupBasiliskEnv 0.03 0.03 94.58
findPersistentEnv 0.04 0.01 5.42
* 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
'F:/biocbuild/bbs-3.15-bioc/meat/basilisk.Rcheck/00check.log'
for details.
basilisk.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL basilisk ### ############################################################################## ############################################################################## * installing to library 'F:/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 ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (basilisk)
basilisk.Rcheck/tests/testthat.Rout
R version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 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: F:\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-2022.9.24-h5b45459_0
libsqlite conda-forge/win-64::libsqlite-3.39.4-hcfcfb64_0
openssl conda-forge/win-64::openssl-1.1.1q-h8ffe710_0
pip conda-forge/noarch::pip-22.3-pyhd8ed1ab_0
python pkgs/main/win-64::python-3.7.7-h81c818b_4
setuptools conda-forge/noarch::setuptools-65.5.0-pyhd8ed1ab_0
sqlite conda-forge/win-64::sqlite-3.39.4-hcfcfb64_0
ucrt conda-forge/win-64::ucrt-10.0.20348.0-h57928b3_0
vc conda-forge/win-64::vc-14.2-hac3ee0b_8
vs2015_runtime conda-forge/win-64::vs2015_runtime-14.29.30139-h890b9b1_8
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: F:\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 conda-forge::ca-certificates-2022.9.2~ --> pkgs/main::ca-certificates-2022.07.19-haa95532_0
openssl conda-forge::openssl-1.1.1q-h8ffe710_0 --> pkgs/main::openssl-1.1.1q-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: 22.9.0
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: F:\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-2022.1.0-h57928b3_3787
libblas conda-forge/win-64::libblas-3.9.0-16_win64_mkl
libcblas conda-forge/win-64::libcblas-3.9.0-16_win64_mkl
liblapack conda-forge/win-64::liblapack-3.9.0-16_win64_mkl
mkl conda-forge/win-64::mkl-2022.1.0-h6a75c08_874
numpy conda-forge/win-64::numpy-1.21.6-py37h2830a78_0
pandas pkgs/main/win-64::pandas-0.25.1-py37ha925a31_0
python-dateutil conda-forge/noarch::python-dateutil-2.8.0-py_0
python_abi conda-forge/win-64::python_abi-3.7-2_cp37m
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-2021.6.0-h91493d7_0
The following packages will be UPDATED:
ca-certificates pkgs/main::ca-certificates-2022.07.19~ --> conda-forge::ca-certificates-2022.9.24-h5b45459_0
The following packages will be SUPERSEDED by a higher-priority channel:
openssl pkgs/main::openssl-1.1.1q-h2bbff1b_0 --> conda-forge::openssl-1.1.1q-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: 22.9.0
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: F:\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-2022.9.24-h5b45459_0
libsqlite conda-forge/win-64::libsqlite-3.39.4-hcfcfb64_0
openssl conda-forge/win-64::openssl-1.1.1q-h8ffe710_0
pip conda-forge/noarch::pip-22.3-pyhd8ed1ab_0
python pkgs/main/win-64::python-3.7.7-h81c818b_4
setuptools conda-forge/noarch::setuptools-65.5.0-pyhd8ed1ab_0
sqlite conda-forge/win-64::sqlite-3.39.4-hcfcfb64_0
ucrt conda-forge/win-64::ucrt-10.0.20348.0-h57928b3_0
vc conda-forge/win-64::vc-14.2-hac3ee0b_8
vs2015_runtime conda-forge/win-64::vs2015_runtime-14.29.30139-h890b9b1_8
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: F:\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 conda-forge::ca-certificates-2022.9.2~ --> pkgs/main::ca-certificates-2022.07.19-haa95532_0
openssl conda-forge::openssl-1.1.1q-h8ffe710_0 --> pkgs/main::openssl-1.1.1q-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: 22.9.0
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: F:\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-2022.1.0-h57928b3_3787
libblas conda-forge/win-64::libblas-3.9.0-16_win64_mkl
libcblas conda-forge/win-64::libcblas-3.9.0-16_win64_mkl
liblapack conda-forge/win-64::liblapack-3.9.0-16_win64_mkl
mkl conda-forge/win-64::mkl-2022.1.0-h6a75c08_874
numpy conda-forge/win-64::numpy-1.21.6-py37h2830a78_0
pandas pkgs/main/win-64::pandas-0.24.1-py37ha925a31_0
python-dateutil conda-forge/noarch::python-dateutil-2.7.1-py_0
python_abi conda-forge/win-64::python_abi-3.7-2_cp37m
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-2021.6.0-h91493d7_0
The following packages will be UPDATED:
ca-certificates pkgs/main::ca-certificates-2022.07.19~ --> conda-forge::ca-certificates-2022.9.24-h5b45459_0
The following packages will be SUPERSEDED by a higher-priority channel:
openssl pkgs/main::openssl-1.1.1q-h2bbff1b_0 --> conda-forge::openssl-1.1.1q-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: 22.9.0
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: F:\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: F:\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: 22.9.0
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: 22.9.0
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: F:\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-2022.9.24-h5b45459_0
libsqlite conda-forge/win-64::libsqlite-3.39.4-hcfcfb64_0
openssl conda-forge/win-64::openssl-1.1.1q-h8ffe710_0
pip conda-forge/noarch::pip-22.3-pyhd8ed1ab_0
python pkgs/main/win-64::python-3.7.7-h81c818b_4
setuptools conda-forge/noarch::setuptools-65.5.0-pyhd8ed1ab_0
sqlite conda-forge/win-64::sqlite-3.39.4-hcfcfb64_0
ucrt conda-forge/win-64::ucrt-10.0.20348.0-h57928b3_0
vc conda-forge/win-64::vc-14.2-hac3ee0b_8
vs2015_runtime conda-forge/win-64::vs2015_runtime-14.29.30139-h890b9b1_8
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: F:\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 conda-forge::ca-certificates-2022.9.2~ --> pkgs/main::ca-certificates-2022.07.19-haa95532_0
openssl conda-forge::openssl-1.1.1q-h8ffe710_0 --> pkgs/main::openssl-1.1.1q-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: 22.9.0
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: F:\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 UPDATED:
ca-certificates pkgs/main::ca-certificates-2022.07.19~ --> conda-forge::ca-certificates-2022.9.24-h5b45459_0
The following packages will be SUPERSEDED by a higher-priority channel:
openssl pkgs/main::openssl-1.1.1q-h2bbff1b_0 --> conda-forge::openssl-1.1.1q-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: 22.9.0
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: python-dateutil>=2.5.0 in f:\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: pytz>=2011k in f:\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-1.21.6-cp37-cp37m-win_amd64.whl (14.0 MB)
Requirement already satisfied: six>=1.5 in f:\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 'F:\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-1.21.6 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: F:\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-2022.9.24-h5b45459_0
libsqlite conda-forge/win-64::libsqlite-3.39.4-hcfcfb64_0
openssl conda-forge/win-64::openssl-1.1.1q-h8ffe710_0
pip conda-forge/noarch::pip-22.3-pyhd8ed1ab_0
python pkgs/main/win-64::python-3.7.7-h81c818b_4
setuptools conda-forge/noarch::setuptools-65.5.0-pyhd8ed1ab_0
sqlite conda-forge/win-64::sqlite-3.39.4-hcfcfb64_0
ucrt conda-forge/win-64::ucrt-10.0.20348.0-h57928b3_0
vc conda-forge/win-64::vc-14.2-hac3ee0b_8
vs2015_runtime conda-forge/win-64::vs2015_runtime-14.29.30139-h890b9b1_8
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: F:\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 conda-forge::ca-certificates-2022.9.2~ --> pkgs/main::ca-certificates-2022.07.19-haa95532_0
openssl conda-forge::openssl-1.1.1q-h8ffe710_0 --> pkgs/main::openssl-1.1.1q-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: 22.9.0
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: F:\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 pkgs/main::ca-certificates-2022.07.19~ --> conda-forge::ca-certificates-2022.9.24-h5b45459_0
The following packages will be SUPERSEDED by a higher-priority channel:
openssl pkgs/main::openssl-1.1.1q-h2bbff1b_0 --> conda-forge::openssl-1.1.1q-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: 22.9.0
Please update conda by running
$ conda update -n base -c defaults conda
Processing f:\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=1280 sha256=a5e140e41faf3501ad5f3bae1a9686414ecb58dbb55f1165e5d8d0ceb44fd6f9
Stored in directory: F:\biocbuild\bbs-3.15-bioc\tmpdir\pip-ephem-wheel-cache-75zzphr0\wheels\70\5f\61\62f68eef46523769752e3616a9df4f98cfc54922c72f056047
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: F:\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-2022.9.24-h5b45459_0
libsqlite conda-forge/win-64::libsqlite-3.39.4-hcfcfb64_0
openssl conda-forge/win-64::openssl-1.1.1q-h8ffe710_0
pip conda-forge/noarch::pip-22.3-pyhd8ed1ab_0
python pkgs/main/win-64::python-3.7.7-h81c818b_4
setuptools conda-forge/noarch::setuptools-65.5.0-pyhd8ed1ab_0
sqlite conda-forge/win-64::sqlite-3.39.4-hcfcfb64_0
ucrt conda-forge/win-64::ucrt-10.0.20348.0-h57928b3_0
vc conda-forge/win-64::vc-14.2-hac3ee0b_8
vs2015_runtime conda-forge/win-64::vs2015_runtime-14.29.30139-h890b9b1_8
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: F:\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 conda-forge::ca-certificates-2022.9.2~ --> pkgs/main::ca-certificates-2022.07.19-haa95532_0
openssl conda-forge::openssl-1.1.1q-h8ffe710_0 --> pkgs/main::openssl-1.1.1q-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: 22.9.0
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
** building package indices
** testing if installed package can be loaded
* DONE (son.of.basilisk)
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\18E761~1.1\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\18E761~1.1\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\18E761~1.1\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\18E761~1.1\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\18E761~1.1\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\18E761~1.1\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\18E761~1.1\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\18E761~1.1\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\18E761~1.1\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\18E761~1.1\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: F:\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-2022.9.24-h5b45459_0
libsqlite conda-forge/win-64::libsqlite-3.39.4-hcfcfb64_0
openssl conda-forge/win-64::openssl-1.1.1q-h8ffe710_0
pip conda-forge/noarch::pip-22.3-pyhd8ed1ab_0
python pkgs/main/win-64::python-3.7.7-h81c818b_4
setuptools conda-forge/noarch::setuptools-65.5.0-pyhd8ed1ab_0
sqlite conda-forge/win-64::sqlite-3.39.4-hcfcfb64_0
ucrt conda-forge/win-64::ucrt-10.0.20348.0-h57928b3_0
vc conda-forge/win-64::vc-14.2-hac3ee0b_8
vs2015_runtime conda-forge/win-64::vs2015_runtime-14.29.30139-h890b9b1_8
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: F:\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 SUPERSEDED by a higher-priority channel:
ca-certificates conda-forge::ca-certificates-2022.9.2~ --> pkgs/main::ca-certificates-2022.07.19-haa95532_0
openssl conda-forge::openssl-1.1.1q-h8ffe710_0 --> pkgs/main::openssl-1.1.1q-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: 22.9.0
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: F:\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-2022.1.0-h57928b3_3787
libblas conda-forge/win-64::libblas-3.9.0-16_win64_mkl
libcblas conda-forge/win-64::libcblas-3.9.0-16_win64_mkl
liblapack conda-forge/win-64::liblapack-3.9.0-16_win64_mkl
mkl conda-forge/win-64::mkl-2022.1.0-h6a75c08_874
numpy conda-forge/win-64::numpy-1.21.6-py37h2830a78_0
pandas pkgs/main/win-64::pandas-0.25.1-py37ha925a31_0
python-dateutil conda-forge/noarch::python-dateutil-2.8.0-py_0
python_abi conda-forge/win-64::python_abi-3.7-2_cp37m
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-2021.6.0-h91493d7_0
The following packages will be UPDATED:
ca-certificates pkgs/main::ca-certificates-2022.07.19~ --> conda-forge::ca-certificates-2022.9.24-h5b45459_0
The following packages will be SUPERSEDED by a higher-priority channel:
openssl pkgs/main::openssl-1.1.1q-h2bbff1b_0 --> conda-forge::openssl-1.1.1q-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: 22.9.0
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: F:\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-2022.9.24-h5b45459_0
libsqlite conda-forge/win-64::libsqlite-3.39.4-hcfcfb64_0
openssl conda-forge/win-64::openssl-1.1.1q-h8ffe710_0
pip conda-forge/noarch::pip-22.3-pyhd8ed1ab_0
python pkgs/main/win-64::python-3.7.7-h81c818b_4
setuptools conda-forge/noarch::setuptools-65.5.0-pyhd8ed1ab_0
sqlite conda-forge/win-64::sqlite-3.39.4-hcfcfb64_0
ucrt conda-forge/win-64::ucrt-10.0.20348.0-h57928b3_0
vc conda-forge/win-64::vc-14.2-hac3ee0b_8
vs2015_runtime conda-forge/win-64::vs2015_runtime-14.29.30139-h890b9b1_8
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: F:\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 SUPERSEDED by a higher-priority channel:
ca-certificates conda-forge::ca-certificates-2022.9.2~ --> pkgs/main::ca-certificates-2022.07.19-haa95532_0
openssl conda-forge::openssl-1.1.1q-h8ffe710_0 --> pkgs/main::openssl-1.1.1q-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: 22.9.0
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: F:\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-2022.1.0-h57928b3_3787
libblas conda-forge/win-64::libblas-3.9.0-16_win64_mkl
libcblas conda-forge/win-64::libcblas-3.9.0-16_win64_mkl
liblapack conda-forge/win-64::liblapack-3.9.0-16_win64_mkl
mkl conda-forge/win-64::mkl-2022.1.0-h6a75c08_874
numpy conda-forge/win-64::numpy-1.21.6-py37h2830a78_0
pandas pkgs/main/win-64::pandas-0.24.1-py37ha925a31_0
python-dateutil conda-forge/noarch::python-dateutil-2.7.1-py_0
python_abi conda-forge/win-64::python_abi-3.7-2_cp37m
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-2021.6.0-h91493d7_0
The following packages will be UPDATED:
ca-certificates pkgs/main::ca-certificates-2022.07.19~ --> conda-forge::ca-certificates-2022.9.24-h5b45459_0
The following packages will be SUPERSEDED by a higher-priority channel:
openssl pkgs/main::openssl-1.1.1q-h2bbff1b_0 --> conda-forge::openssl-1.1.1q-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: 22.9.0
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
5.18 14.28 1157.70
basilisk.Rcheck/basilisk-Ex.timings
| name | user | system | elapsed | |
| BasiliskEnvironment-class | 0 | 0 | 0 | |
| PyPiLink | 0 | 0 | 0 | |
| basiliskOptions | 0 | 0 | 0 | |
| basiliskStart | 1.21 | 0.70 | 373.36 | |
| configureBasiliskEnv | 0.00 | 0.02 | 0.02 | |
| findPersistentEnv | 0.04 | 0.01 | 5.42 | |
| listPackages | 0.01 | 0.00 | 1.91 | |
| setupBasiliskEnv | 0.03 | 0.03 | 94.58 | |
| useBasiliskEnv | 0.05 | 0.03 | 2.66 | |