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 13:22:35 -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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:basilisk.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings basilisk_1.8.1.tar.gz |
| StartedAt: 2022-10-18 23:28:24 -0400 (Tue, 18 Oct 2022) |
| EndedAt: 2022-10-18 23:59:07 -0400 (Tue, 18 Oct 2022) |
| EllapsedTime: 1842.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: basilisk.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:basilisk.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings basilisk_1.8.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/basilisk.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘basilisk/DESCRIPTION’ ... OK
* this is package ‘basilisk’ version ‘1.8.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘basilisk’ can be installed ... NOTE
Found the following notes/warnings:
Non-staged installation was used
See ‘/Users/biocbuild/bbs-3.15-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 297.230 34.215 347.371
setupBasiliskEnv 59.609 13.338 79.124
findPersistentEnv 0.052 0.010 5.871
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.15-bioc/meat/basilisk.Rcheck/00check.log’
for details.
basilisk.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL basilisk ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘basilisk’ ... ** using non-staged installation via StagedInstall field ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (basilisk)
basilisk.Rcheck/tests/testthat.Rout
R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(basilisk)
> test_check("basilisk")
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /Users/biocbuild/bbs-3.15-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/osx-64::ca-certificates-2022.9.24-h033912b_0
libcxx conda-forge/osx-64::libcxx-14.0.6-hccf4f1f_0
libffi conda-forge/osx-64::libffi-3.3-h046ec9c_2
libsqlite conda-forge/osx-64::libsqlite-3.39.4-ha978bb4_0
libzlib conda-forge/osx-64::libzlib-1.2.13-hfd90126_4
ncurses conda-forge/osx-64::ncurses-6.3-h96cf925_1
openssl conda-forge/osx-64::openssl-1.1.1q-hfe4f2af_0
pip conda-forge/noarch::pip-22.3-pyhd8ed1ab_0
python pkgs/main/osx-64::python-3.7.7-hf48f09d_4
readline conda-forge/osx-64::readline-8.1.2-h3899abd_0
setuptools conda-forge/noarch::setuptools-65.5.0-pyhd8ed1ab_0
sqlite conda-forge/osx-64::sqlite-3.39.4-h9ae0607_0
tk conda-forge/osx-64::tk-8.6.12-h5dbffcc_0
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
xz conda-forge/osx-64::xz-5.2.6-h775f41a_0
zlib conda-forge/osx-64::zlib-1.2.13-hfd90126_4
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: /Users/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-hecd8cb5_0
openssl conda-forge::openssl-1.1.1q-hfe4f2af_0 --> pkgs/main::openssl-1.1.1q-hca72f7f_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: /Users/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:
libblas conda-forge/osx-64::libblas-3.9.0-16_osx64_openblas
libcblas conda-forge/osx-64::libcblas-3.9.0-16_osx64_openblas
libgfortran conda-forge/osx-64::libgfortran-5.0.0-10_4_0_h97931a8_25
libgfortran5 conda-forge/osx-64::libgfortran5-11.3.0-h082f757_25
liblapack conda-forge/osx-64::liblapack-3.9.0-16_osx64_openblas
libopenblas conda-forge/osx-64::libopenblas-0.3.21-openmp_h429af6e_3
llvm-openmp conda-forge/osx-64::llvm-openmp-14.0.4-ha654fa7_0
numpy conda-forge/osx-64::numpy-1.21.6-py37h345d48f_0
pandas conda-forge/osx-64::pandas-0.25.1-py37h86efe34_0
python-dateutil conda-forge/noarch::python-dateutil-2.8.0-py_0
python_abi conda-forge/osx-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
The following packages will be UPDATED:
ca-certificates pkgs/main::ca-certificates-2022.07.19~ --> conda-forge::ca-certificates-2022.9.24-h033912b_0
The following packages will be SUPERSEDED by a higher-priority channel:
openssl pkgs/main::openssl-1.1.1q-hca72f7f_0 --> conda-forge::openssl-1.1.1q-hfe4f2af_0
setuptools conda-forge/noarch::setuptools-65.5.0~ --> conda-forge/osx-64::setuptools-59.8.0-py37hf985489_1
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: /Users/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/osx-64::ca-certificates-2022.9.24-h033912b_0
libcxx conda-forge/osx-64::libcxx-14.0.6-hccf4f1f_0
libffi conda-forge/osx-64::libffi-3.3-h046ec9c_2
libsqlite conda-forge/osx-64::libsqlite-3.39.4-ha978bb4_0
libzlib conda-forge/osx-64::libzlib-1.2.13-hfd90126_4
ncurses conda-forge/osx-64::ncurses-6.3-h96cf925_1
openssl conda-forge/osx-64::openssl-1.1.1q-hfe4f2af_0
pip conda-forge/noarch::pip-22.3-pyhd8ed1ab_0
python pkgs/main/osx-64::python-3.7.7-hf48f09d_4
readline conda-forge/osx-64::readline-8.1.2-h3899abd_0
setuptools conda-forge/noarch::setuptools-65.5.0-pyhd8ed1ab_0
sqlite conda-forge/osx-64::sqlite-3.39.4-h9ae0607_0
tk conda-forge/osx-64::tk-8.6.12-h5dbffcc_0
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
xz conda-forge/osx-64::xz-5.2.6-h775f41a_0
zlib conda-forge/osx-64::zlib-1.2.13-hfd90126_4
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: /Users/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-hecd8cb5_0
openssl conda-forge::openssl-1.1.1q-hfe4f2af_0 --> pkgs/main::openssl-1.1.1q-hca72f7f_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: /Users/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:
libblas conda-forge/osx-64::libblas-3.9.0-16_osx64_openblas
libcblas conda-forge/osx-64::libcblas-3.9.0-16_osx64_openblas
libgfortran conda-forge/osx-64::libgfortran-5.0.0-10_4_0_h97931a8_25
libgfortran5 conda-forge/osx-64::libgfortran5-11.3.0-h082f757_25
liblapack conda-forge/osx-64::liblapack-3.9.0-16_osx64_openblas
libopenblas conda-forge/osx-64::libopenblas-0.3.21-openmp_h429af6e_3
llvm-openmp conda-forge/osx-64::llvm-openmp-14.0.4-ha654fa7_0
numpy conda-forge/osx-64::numpy-1.21.6-py37h345d48f_0
pandas pkgs/main/osx-64::pandas-0.24.1-py37h0a44026_0
python-dateutil conda-forge/noarch::python-dateutil-2.7.1-py_0
python_abi conda-forge/osx-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
The following packages will be UPDATED:
ca-certificates pkgs/main::ca-certificates-2022.07.19~ --> conda-forge::ca-certificates-2022.9.24-h033912b_0
The following packages will be SUPERSEDED by a higher-priority channel:
openssl pkgs/main::openssl-1.1.1q-hca72f7f_0 --> conda-forge::openssl-1.1.1q-hfe4f2af_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: /Users/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:
ca-certificates conda-forge/osx-64::ca-certificates-2022.9.24-h033912b_0
certifi conda-forge/osx-64::certifi-2019.11.28-py27h8c360ce_1
libcxx conda-forge/osx-64::libcxx-14.0.6-hccf4f1f_0
libffi conda-forge/osx-64::libffi-3.2.1-hb1e8313_1007
libsqlite conda-forge/osx-64::libsqlite-3.39.4-ha978bb4_0
libzlib conda-forge/osx-64::libzlib-1.2.13-hfd90126_4
ncurses conda-forge/osx-64::ncurses-6.3-h96cf925_1
openssl conda-forge/osx-64::openssl-1.1.1q-hfe4f2af_0
pip conda-forge/noarch::pip-20.1.1-pyh9f0ad1d_0
python conda-forge/osx-64::python-2.7.15-h8e446fc_1011_cpython
python_abi conda-forge/osx-64::python_abi-2.7-1_cp27m
readline conda-forge/osx-64::readline-8.1.2-h3899abd_0
setuptools conda-forge/osx-64::setuptools-44.0.0-py27_0
sqlite conda-forge/osx-64::sqlite-3.39.4-h9ae0607_0
tk conda-forge/osx-64::tk-8.6.12-h5dbffcc_0
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
zlib conda-forge/osx-64::zlib-1.2.13-hfd90126_4
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: /Users/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/osx-64::certifi-2019.11.2~ --> pkgs/main/noarch::certifi-2020.6.20-pyhd3eb1b0_3
python conda-forge::python-2.7.15-h8e446fc_1~ --> pkgs/main::python-2.7.18-hc817775_0
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-hecd8cb5_0
openssl conda-forge::openssl-1.1.1q-hfe4f2af_0 --> pkgs/main::openssl-1.1.1q-hca72f7f_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: /Users/biocbuild/bbs-3.15-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo
added / updated specs:
- python[version='2.7.*,2.7.*']
The following packages will be UPDATED:
ca-certificates pkgs/main::ca-certificates-2022.07.19~ --> conda-forge::ca-certificates-2022.9.24-h033912b_0
The following packages will be SUPERSEDED by a higher-priority channel:
certifi pkgs/main/noarch::certifi-2020.6.20-p~ --> conda-forge/osx-64::certifi-2016.9.26-py27_0
openssl pkgs/main::openssl-1.1.1q-hca72f7f_0 --> conda-forge::openssl-1.1.1q-hfe4f2af_0
python pkgs/main::python-2.7.18-hc817775_0 --> conda-forge::python-2.7.15-h8e446fc_1011_cpython
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: /Users/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/osx-64::ca-certificates-2022.9.24-h033912b_0
libcxx conda-forge/osx-64::libcxx-14.0.6-hccf4f1f_0
libffi conda-forge/osx-64::libffi-3.3-h046ec9c_2
libsqlite conda-forge/osx-64::libsqlite-3.39.4-ha978bb4_0
libzlib conda-forge/osx-64::libzlib-1.2.13-hfd90126_4
ncurses conda-forge/osx-64::ncurses-6.3-h96cf925_1
openssl conda-forge/osx-64::openssl-1.1.1q-hfe4f2af_0
pip conda-forge/noarch::pip-22.3-pyhd8ed1ab_0
python pkgs/main/osx-64::python-3.7.7-hf48f09d_4
readline conda-forge/osx-64::readline-8.1.2-h3899abd_0
setuptools conda-forge/noarch::setuptools-65.5.0-pyhd8ed1ab_0
sqlite conda-forge/osx-64::sqlite-3.39.4-h9ae0607_0
tk conda-forge/osx-64::tk-8.6.12-h5dbffcc_0
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
xz conda-forge/osx-64::xz-5.2.6-h775f41a_0
zlib conda-forge/osx-64::zlib-1.2.13-hfd90126_4
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: /Users/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-hecd8cb5_0
openssl conda-forge::openssl-1.1.1q-hfe4f2af_0 --> pkgs/main::openssl-1.1.1q-hca72f7f_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: /Users/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-h033912b_0
The following packages will be SUPERSEDED by a higher-priority channel:
openssl pkgs/main::openssl-1.1.1q-hca72f7f_0 --> conda-forge::openssl-1.1.1q-hfe4f2af_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-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (15.9 MB)
Requirement already satisfied: pytz>=2011k in ./install-test-client/thingo/lib/python3.7/site-packages (from pandas==0.24.1) (2018.7)
Collecting numpy>=1.12.0
Using cached numpy-1.21.6-cp37-cp37m-macosx_10_9_x86_64.whl (16.9 MB)
Requirement already satisfied: python-dateutil>=2.5.0 in ./install-test-client/thingo/lib/python3.7/site-packages (from pandas==0.24.1) (2.7.1)
Requirement already satisfied: six>=1.5 in ./install-test-client/thingo/lib/python3.7/site-packages (from python-dateutil>=2.5.0->pandas==0.24.1) (1.16.0)
Installing collected packages: numpy, pandas
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: /Users/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/osx-64::ca-certificates-2022.9.24-h033912b_0
libcxx conda-forge/osx-64::libcxx-14.0.6-hccf4f1f_0
libffi conda-forge/osx-64::libffi-3.3-h046ec9c_2
libsqlite conda-forge/osx-64::libsqlite-3.39.4-ha978bb4_0
libzlib conda-forge/osx-64::libzlib-1.2.13-hfd90126_4
ncurses conda-forge/osx-64::ncurses-6.3-h96cf925_1
openssl conda-forge/osx-64::openssl-1.1.1q-hfe4f2af_0
pip conda-forge/noarch::pip-22.3-pyhd8ed1ab_0
python pkgs/main/osx-64::python-3.7.7-hf48f09d_4
readline conda-forge/osx-64::readline-8.1.2-h3899abd_0
setuptools conda-forge/noarch::setuptools-65.5.0-pyhd8ed1ab_0
sqlite conda-forge/osx-64::sqlite-3.39.4-h9ae0607_0
tk conda-forge/osx-64::tk-8.6.12-h5dbffcc_0
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
xz conda-forge/osx-64::xz-5.2.6-h775f41a_0
zlib conda-forge/osx-64::zlib-1.2.13-hfd90126_4
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: /Users/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-hecd8cb5_0
openssl conda-forge::openssl-1.1.1q-hfe4f2af_0 --> pkgs/main::openssl-1.1.1q-hca72f7f_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: /Users/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-h033912b_0
The following packages will be SUPERSEDED by a higher-priority channel:
openssl pkgs/main::openssl-1.1.1q-hca72f7f_0 --> conda-forge::openssl-1.1.1q-hfe4f2af_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 /Library/Frameworks/R.framework/Versions/4.2/Resources/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=bbabe1c133c33987e6dafcd25189c6e0bddf8f9d4ca3aa75b9e81750803c4409
Stored in directory: /private/tmp/pip-ephem-wheel-cache-s51h48sr/wheels/66/43/5b/6f0493d50c03712ca5c7fc3f886f15e94743da28d846defbe0
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: /Users/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/osx-64::ca-certificates-2022.9.24-h033912b_0
libcxx conda-forge/osx-64::libcxx-14.0.6-hccf4f1f_0
libffi conda-forge/osx-64::libffi-3.3-h046ec9c_2
libsqlite conda-forge/osx-64::libsqlite-3.39.4-ha978bb4_0
libzlib conda-forge/osx-64::libzlib-1.2.13-hfd90126_4
ncurses conda-forge/osx-64::ncurses-6.3-h96cf925_1
openssl conda-forge/osx-64::openssl-1.1.1q-hfe4f2af_0
pip conda-forge/noarch::pip-22.3-pyhd8ed1ab_0
python pkgs/main/osx-64::python-3.7.7-hf48f09d_4
readline conda-forge/osx-64::readline-8.1.2-h3899abd_0
setuptools conda-forge/noarch::setuptools-65.5.0-pyhd8ed1ab_0
sqlite conda-forge/osx-64::sqlite-3.39.4-h9ae0607_0
tk conda-forge/osx-64::tk-8.6.12-h5dbffcc_0
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
xz conda-forge/osx-64::xz-5.2.6-h775f41a_0
zlib conda-forge/osx-64::zlib-1.2.13-hfd90126_4
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: /Users/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-hecd8cb5_0
openssl conda-forge::openssl-1.1.1q-hfe4f2af_0 --> pkgs/main::openssl-1.1.1q-hca72f7f_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/osx-64
- https://conda.anaconda.org/conda-forge/noarch
- https://repo.anaconda.com/pkgs/main/osx-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/osx-64
- https://repo.anaconda.com/pkgs/r/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.
trying URL 'https://repo.anaconda.com/miniconda/Miniconda3-py37_4.8.3-MacOSX-x86_64.sh'
Content type 'application/x-sh' length 54829425 bytes (52.3 MB)
==================================================
downloaded 52.3 MB
PREFIX=/tmp/RtmpnCgruP/file1112542af0ef5/1.8.1/0
Unpacking payload ...
0%| | 0/33 [00:00<?, ?it/s]
Extracting : ca-certificates-2020.1.1-0.conda: 0%| | 0/33 [00:01<?, ?it/s]
Extracting : ca-certificates-2020.1.1-0.conda: 3%|▎ | 1/33 [00:01<00:33, 1.03s/it]
Extracting : certifi-2020.4.5.1-py37_0.conda: 3%|▎ | 1/33 [00:01<00:33, 1.03s/it]
Extracting : cffi-1.14.0-py37hc512035_1.conda: 6%|▌ | 2/33 [00:01<00:32, 1.03s/it]
Extracting : cffi-1.14.0-py37hc512035_1.conda: 9%|▉ | 3/33 [00:01<00:22, 1.35it/s]
Extracting : chardet-3.0.4-py37_1003.conda: 9%|▉ | 3/33 [00:01<00:22, 1.35it/s]
Extracting : chardet-3.0.4-py37_1003.conda: 12%|█▏ | 4/33 [00:01<00:16, 1.72it/s]
Extracting : conda-package-handling-1.6.1-py37h1de35cc_0.conda: 12%|█▏ | 4/33 [00:01<00:16, 1.72it/s]
Extracting : cryptography-2.9.2-py37ha12b0ac_0.conda: 15%|█▌ | 5/33 [00:01<00:16, 1.72it/s]
Extracting : cryptography-2.9.2-py37ha12b0ac_0.conda: 18%|█▊ | 6/33 [00:01<00:11, 2.31it/s]
Extracting : idna-2.9-py_1.conda: 18%|█▊ | 6/33 [00:01<00:11, 2.31it/s]
Extracting : libcxx-10.0.0-1.conda: 21%|██ | 7/33 [00:01<00:11, 2.31it/s]
Extracting : libedit-3.1.20181209-hb402a30_0.conda: 24%|██▍ | 8/33 [00:01<00:10, 2.31it/s]
Extracting : libffi-3.3-h0a44026_1.conda: 27%|██▋ | 9/33 [00:01<00:10, 2.31it/s]
Extracting : ncurses-6.2-h0a44026_1.conda: 30%|███ | 10/33 [00:02<00:09, 2.31it/s]
Extracting : ncurses-6.2-h0a44026_1.conda: 33%|███▎ | 11/33 [00:02<00:08, 2.62it/s]
Extracting : openssl-1.1.1g-h1de35cc_0.conda: 33%|███▎ | 11/33 [00:02<00:08, 2.62it/s]
Extracting : pip-20.0.2-py37_3.conda: 36%|███▋ | 12/33 [00:02<00:08, 2.62it/s]
Extracting : pycosat-0.6.3-py37h1de35cc_0.conda: 39%|███▉ | 13/33 [00:02<00:07, 2.62it/s]
Extracting : pycparser-2.20-py_0.conda: 42%|████▏ | 14/33 [00:02<00:07, 2.62it/s]
Extracting : pyopenssl-19.1.0-py37_0.conda: 45%|████▌ | 15/33 [00:02<00:06, 2.62it/s]
Extracting : pysocks-1.7.1-py37_0.conda: 48%|████▊ | 16/33 [00:02<00:06, 2.62it/s]
Extracting : python-3.7.7-hf48f09d_4.conda: 52%|█████▏ | 17/33 [00:03<00:06, 2.62it/s]
Extracting : python-3.7.7-hf48f09d_4.conda: 55%|█████▍ | 18/33 [00:03<00:04, 3.52it/s]
Extracting : python.app-2-py37_10.conda: 55%|█████▍ | 18/33 [00:03<00:04, 3.52it/s]
Extracting : readline-8.0-h1de35cc_0.conda: 58%|█████▊ | 19/33 [00:03<00:03, 3.52it/s]
Extracting : requests-2.23.0-py37_0.conda: 61%|██████ | 20/33 [00:03<00:03, 3.52it/s]
Extracting : ruamel_yaml-0.15.87-py37h1de35cc_0.conda: 64%|██████▎ | 21/33 [00:03<00:03, 3.52it/s]
Extracting : setuptools-46.4.0-py37_0.conda: 67%|██████▋ | 22/33 [00:03<00:03, 3.52it/s]
Extracting : six-1.14.0-py37_0.conda: 70%|██████▉ | 23/33 [00:03<00:02, 3.52it/s]
Extracting : sqlite-3.31.1-h5c1f38d_1.conda: 73%|███████▎ | 24/33 [00:03<00:02, 3.52it/s]
Extracting : tk-8.6.8-ha441bb4_0.conda: 76%|███████▌ | 25/33 [00:03<00:02, 3.52it/s]
Extracting : tqdm-4.46.0-py_0.conda: 79%|███████▉ | 26/33 [00:03<00:01, 3.52it/s]
Extracting : urllib3-1.25.8-py37_0.conda: 82%|████████▏ | 27/33 [00:03<00:01, 3.52it/s]
Extracting : wheel-0.34.2-py37_0.conda: 85%|████████▍ | 28/33 [00:03<00:01, 3.52it/s]
Extracting : xz-5.2.5-h1de35cc_0.conda: 88%|████████▊ | 29/33 [00:03<00:01, 3.52it/s]
Extracting : yaml-0.1.7-hc338f04_2.conda: 91%|█████████ | 30/33 [00:03<00:00, 3.52it/s]
Extracting : zlib-1.2.11-h1de35cc_3.conda: 94%|█████████▍| 31/33 [00:03<00:00, 3.52it/s]
Extracting : conda-4.8.3-py37_0.tar.bz2: 97%|█████████▋| 32/33 [00:03<00:00, 3.52it/s]
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /tmp/RtmpnCgruP/file1112542af0ef5/1.8.1/0
added / updated specs:
- ca-certificates==2020.1.1=0
- certifi==2020.4.5.1=py37_0
- cffi==1.14.0=py37hc512035_1
- chardet==3.0.4=py37_1003
- conda-package-handling==1.6.1=py37h1de35cc_0
- conda==4.8.3=py37_0
- cryptography==2.9.2=py37ha12b0ac_0
- idna==2.9=py_1
- libcxx==10.0.0=1
- libedit==3.1.20181209=hb402a30_0
- libffi==3.3=h0a44026_1
- ncurses==6.2=h0a44026_1
- openssl==1.1.1g=h1de35cc_0
- pip==20.0.2=py37_3
- pycosat==0.6.3=py37h1de35cc_0
- pycparser==2.20=py_0
- pyopenssl==19.1.0=py37_0
- pysocks==1.7.1=py37_0
- python.app==2=py37_10
- python==3.7.7=hf48f09d_4
- readline==8.0=h1de35cc_0
- requests==2.23.0=py37_0
- ruamel_yaml==0.15.87=py37h1de35cc_0
- setuptools==46.4.0=py37_0
- six==1.14.0=py37_0
- sqlite==3.31.1=h5c1f38d_1
- tk==8.6.8=ha441bb4_0
- tqdm==4.46.0=py_0
- urllib3==1.25.8=py37_0
- wheel==0.34.2=py37_0
- xz==5.2.5=h1de35cc_0
- yaml==0.1.7=hc338f04_2
- zlib==1.2.11=h1de35cc_3
The following NEW packages will be INSTALLED:
ca-certificates pkgs/main/osx-64::ca-certificates-2020.1.1-0
certifi pkgs/main/osx-64::certifi-2020.4.5.1-py37_0
cffi pkgs/main/osx-64::cffi-1.14.0-py37hc512035_1
chardet pkgs/main/osx-64::chardet-3.0.4-py37_1003
conda pkgs/main/osx-64::conda-4.8.3-py37_0
conda-package-han~ pkgs/main/osx-64::conda-package-handling-1.6.1-py37h1de35cc_0
cryptography pkgs/main/osx-64::cryptography-2.9.2-py37ha12b0ac_0
idna pkgs/main/noarch::idna-2.9-py_1
libcxx pkgs/main/osx-64::libcxx-10.0.0-1
libedit pkgs/main/osx-64::libedit-3.1.20181209-hb402a30_0
libffi pkgs/main/osx-64::libffi-3.3-h0a44026_1
ncurses pkgs/main/osx-64::ncurses-6.2-h0a44026_1
openssl pkgs/main/osx-64::openssl-1.1.1g-h1de35cc_0
pip pkgs/main/osx-64::pip-20.0.2-py37_3
pycosat pkgs/main/osx-64::pycosat-0.6.3-py37h1de35cc_0
pycparser pkgs/main/noarch::pycparser-2.20-py_0
pyopenssl pkgs/main/osx-64::pyopenssl-19.1.0-py37_0
pysocks pkgs/main/osx-64::pysocks-1.7.1-py37_0
python pkgs/main/osx-64::python-3.7.7-hf48f09d_4
python.app pkgs/main/osx-64::python.app-2-py37_10
readline pkgs/main/osx-64::readline-8.0-h1de35cc_0
requests pkgs/main/osx-64::requests-2.23.0-py37_0
ruamel_yaml pkgs/main/osx-64::ruamel_yaml-0.15.87-py37h1de35cc_0
setuptools pkgs/main/osx-64::setuptools-46.4.0-py37_0
six pkgs/main/osx-64::six-1.14.0-py37_0
sqlite pkgs/main/osx-64::sqlite-3.31.1-h5c1f38d_1
tk pkgs/main/osx-64::tk-8.6.8-ha441bb4_0
tqdm pkgs/main/noarch::tqdm-4.46.0-py_0
urllib3 pkgs/main/osx-64::urllib3-1.25.8-py37_0
wheel pkgs/main/osx-64::wheel-0.34.2-py37_0
xz pkgs/main/osx-64::xz-5.2.5-h1de35cc_0
yaml pkgs/main/osx-64::yaml-0.1.7-hc338f04_2
zlib pkgs/main/osx-64::zlib-1.2.11-h1de35cc_3
Preparing transaction: ...working... done
Executing transaction: ...working... done
installation finished.
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... 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: /private/tmp/RtmpnCgruP/file1112542af0ef5/1.8.1/basilisk.utils/1.8.0/test
added / updated specs:
- python=3.7.7
The following packages will be downloaded:
package | build
---------------------------|-----------------
ca-certificates-2022.9.24 | h033912b_0 150 KB conda-forge
libcxx-14.0.6 | hccf4f1f_0 1.3 MB conda-forge
libffi-3.3 | h046ec9c_2 45 KB conda-forge
libsqlite-3.39.4 | ha978bb4_0 870 KB conda-forge
libzlib-1.2.13 | hfd90126_4 64 KB conda-forge
ncurses-6.3 | h96cf925_1 915 KB conda-forge
openssl-1.1.1q | hfe4f2af_0 1.9 MB conda-forge
pip-22.3 | pyhd8ed1ab_0 1.5 MB conda-forge
readline-8.1.2 | h3899abd_0 266 KB conda-forge
setuptools-65.5.0 | pyhd8ed1ab_0 768 KB conda-forge
sqlite-3.39.4 | h9ae0607_0 876 KB conda-forge
tk-8.6.12 | h5dbffcc_0 3.4 MB conda-forge
wheel-0.37.1 | pyhd8ed1ab_0 31 KB conda-forge
xz-5.2.6 | h775f41a_0 233 KB conda-forge
zlib-1.2.13 | hfd90126_4 93 KB conda-forge
------------------------------------------------------------
Total: 12.3 MB
The following NEW packages will be INSTALLED:
ca-certificates conda-forge/osx-64::ca-certificates-2022.9.24-h033912b_0
libcxx conda-forge/osx-64::libcxx-14.0.6-hccf4f1f_0
libffi conda-forge/osx-64::libffi-3.3-h046ec9c_2
libsqlite conda-forge/osx-64::libsqlite-3.39.4-ha978bb4_0
libzlib conda-forge/osx-64::libzlib-1.2.13-hfd90126_4
ncurses conda-forge/osx-64::ncurses-6.3-h96cf925_1
openssl conda-forge/osx-64::openssl-1.1.1q-hfe4f2af_0
pip conda-forge/noarch::pip-22.3-pyhd8ed1ab_0
python pkgs/main/osx-64::python-3.7.7-hf48f09d_4
readline conda-forge/osx-64::readline-8.1.2-h3899abd_0
setuptools conda-forge/noarch::setuptools-65.5.0-pyhd8ed1ab_0
sqlite conda-forge/osx-64::sqlite-3.39.4-h9ae0607_0
tk conda-forge/osx-64::tk-8.6.12-h5dbffcc_0
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
xz conda-forge/osx-64::xz-5.2.6-h775f41a_0
zlib conda-forge/osx-64::zlib-1.2.13-hfd90126_4
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: /private/tmp/RtmpnCgruP/file1112542af0ef5/1.8.1/basilisk.utils/1.8.0/test
added / updated specs:
- python=3.7.7
The following packages will be downloaded:
package | build
---------------------------|-----------------
ca-certificates-2022.07.19 | hecd8cb5_0 124 KB
openssl-1.1.1q | hca72f7f_0 2.2 MB
------------------------------------------------------------
Total: 2.4 MB
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-hecd8cb5_0
openssl conda-forge::openssl-1.1.1q-hfe4f2af_0 --> pkgs/main::openssl-1.1.1q-hca72f7f_0
Downloading and Extracting Packages
openssl-1.1.1q | 2.2 MB | | 0%
openssl-1.1.1q | 2.2 MB | ########8 | 89%
openssl-1.1.1q | 2.2 MB | ########## | 100%
ca-certificates-2022 | 124 KB | | 0%
ca-certificates-2022 | 124 KB | ########## | 100%
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: /private/tmp/RtmpnCgruP/file1112542af0ef5/1.8.1/basilisk.utils/1.8.0/test
added / updated specs:
- pandas=0.25.1
- python=3.7.7
The following packages will be downloaded:
package | build
---------------------------|-----------------
libblas-3.9.0 |16_osx64_openblas 13 KB conda-forge
libcblas-3.9.0 |16_osx64_openblas 13 KB conda-forge
libgfortran-5.0.0 |10_4_0_h97931a8_25 146 KB conda-forge
libgfortran5-11.3.0 | h082f757_25 1.9 MB conda-forge
liblapack-3.9.0 |16_osx64_openblas 13 KB conda-forge
libopenblas-0.3.21 |openmp_h429af6e_3 9.6 MB conda-forge
llvm-openmp-14.0.4 | ha654fa7_0 329 KB conda-forge
numpy-1.21.6 | py37h345d48f_0 6.0 MB conda-forge
pandas-0.25.1 | py37h86efe34_0 10.2 MB conda-forge
python-dateutil-2.8.2 | pyhd8ed1ab_0 240 KB conda-forge
python_abi-3.7 | 2_cp37m 4 KB conda-forge
pytz-2022.4 | pyhd8ed1ab_0 232 KB conda-forge
setuptools-59.8.0 | py37hf985489_1 1.0 MB conda-forge
six-1.16.0 | pyh6c4a22f_0 14 KB conda-forge
------------------------------------------------------------
Total: 29.6 MB
The following NEW packages will be INSTALLED:
libblas conda-forge/osx-64::libblas-3.9.0-16_osx64_openblas
libcblas conda-forge/osx-64::libcblas-3.9.0-16_osx64_openblas
libgfortran conda-forge/osx-64::libgfortran-5.0.0-10_4_0_h97931a8_25
libgfortran5 conda-forge/osx-64::libgfortran5-11.3.0-h082f757_25
liblapack conda-forge/osx-64::liblapack-3.9.0-16_osx64_openblas
libopenblas conda-forge/osx-64::libopenblas-0.3.21-openmp_h429af6e_3
llvm-openmp conda-forge/osx-64::llvm-openmp-14.0.4-ha654fa7_0
numpy conda-forge/osx-64::numpy-1.21.6-py37h345d48f_0
pandas conda-forge/osx-64::pandas-0.25.1-py37h86efe34_0
python-dateutil conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
python_abi conda-forge/osx-64::python_abi-3.7-2_cp37m
pytz conda-forge/noarch::pytz-2022.4-pyhd8ed1ab_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-h033912b_0
The following packages will be SUPERSEDED by a higher-priority channel:
openssl pkgs/main::openssl-1.1.1q-hca72f7f_0 --> conda-forge::openssl-1.1.1q-hfe4f2af_0
setuptools conda-forge/noarch::setuptools-65.5.0~ --> conda-forge/osx-64::setuptools-59.8.0-py37hf985489_1
Downloading and Extracting Packages
pytz-2022.4 | 232 KB | | 0%
pytz-2022.4 | 232 KB | ########## | 100%
libgfortran-5.0.0 | 146 KB | | 0%
libgfortran-5.0.0 | 146 KB | ########## | 100%
libcblas-3.9.0 | 13 KB | | 0%
libcblas-3.9.0 | 13 KB | ########## | 100%
libblas-3.9.0 | 13 KB | | 0%
libblas-3.9.0 | 13 KB | ########## | 100%
pandas-0.25.1 | 10.2 MB | | 0%
pandas-0.25.1 | 10.2 MB | ##7 | 28%
pandas-0.25.1 | 10.2 MB | #######4 | 75%
pandas-0.25.1 | 10.2 MB | ########## | 100%
setuptools-59.8.0 | 1.0 MB | | 0%
setuptools-59.8.0 | 1.0 MB | ########## | 100%
python-dateutil-2.8. | 240 KB | | 0%
python-dateutil-2.8. | 240 KB | ########## | 100%
python_abi-3.7 | 4 KB | | 0%
python_abi-3.7 | 4 KB | ########## | 100%
libopenblas-0.3.21 | 9.6 MB | | 0%
libopenblas-0.3.21 | 9.6 MB | ###4 | 35%
libopenblas-0.3.21 | 9.6 MB | ########4 | 84%
libopenblas-0.3.21 | 9.6 MB | ########## | 100%
liblapack-3.9.0 | 13 KB | | 0%
liblapack-3.9.0 | 13 KB | ########## | 100%
numpy-1.21.6 | 6.0 MB | | 0%
numpy-1.21.6 | 6.0 MB | #####1 | 52%
numpy-1.21.6 | 6.0 MB | ########## | 100%
llvm-openmp-14.0.4 | 329 KB | | 0%
llvm-openmp-14.0.4 | 329 KB | ########## | 100%
six-1.16.0 | 14 KB | | 0%
six-1.16.0 | 14 KB | ########## | 100%
libgfortran5-11.3.0 | 1.9 MB | | 0%
libgfortran5-11.3.0 | 1.9 MB | ########## | 100%
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
* 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)
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.8.1/son.of.basilisk/0.99.0/env2/lib/python3.7/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,
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.8.1/son.of.basilisk/0.99.0/env2/lib/python3.7/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,
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.8.1/son.of.basilisk/0.99.0/env2/lib/python3.7/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,
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.8.1/son.of.basilisk/0.99.0/env2/lib/python3.7/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,
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.8.1/son.of.basilisk/0.99.0/env2/lib/python3.7/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,
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.8.1/son.of.basilisk/0.99.0/env2/lib/python3.7/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):
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.8.1/son.of.basilisk/0.99.0/env2/lib/python3.7/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,
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.8.1/son.of.basilisk/0.99.0/env2/lib/python3.7/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,
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.8.1/son.of.basilisk/0.99.0/env2/lib/python3.7/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):
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.8.1/son.of.basilisk/0.99.0/env2/lib/python3.7/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: /Users/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/osx-64::ca-certificates-2022.9.24-h033912b_0
libcxx conda-forge/osx-64::libcxx-14.0.6-hccf4f1f_0
libffi conda-forge/osx-64::libffi-3.3-h046ec9c_2
libsqlite conda-forge/osx-64::libsqlite-3.39.4-ha978bb4_0
libzlib conda-forge/osx-64::libzlib-1.2.13-hfd90126_4
ncurses conda-forge/osx-64::ncurses-6.3-h96cf925_1
openssl conda-forge/osx-64::openssl-1.1.1q-hfe4f2af_0
pip conda-forge/noarch::pip-22.3-pyhd8ed1ab_0
python pkgs/main/osx-64::python-3.7.7-hf48f09d_4
readline conda-forge/osx-64::readline-8.1.2-h3899abd_0
setuptools conda-forge/noarch::setuptools-65.5.0-pyhd8ed1ab_0
sqlite conda-forge/osx-64::sqlite-3.39.4-h9ae0607_0
tk conda-forge/osx-64::tk-8.6.12-h5dbffcc_0
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
xz conda-forge/osx-64::xz-5.2.6-h775f41a_0
zlib conda-forge/osx-64::zlib-1.2.13-hfd90126_4
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: /Users/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-hecd8cb5_0
openssl conda-forge::openssl-1.1.1q-hfe4f2af_0 --> pkgs/main::openssl-1.1.1q-hca72f7f_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: /Users/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:
libblas conda-forge/osx-64::libblas-3.9.0-16_osx64_openblas
libcblas conda-forge/osx-64::libcblas-3.9.0-16_osx64_openblas
libgfortran conda-forge/osx-64::libgfortran-5.0.0-10_4_0_h97931a8_25
libgfortran5 conda-forge/osx-64::libgfortran5-11.3.0-h082f757_25
liblapack conda-forge/osx-64::liblapack-3.9.0-16_osx64_openblas
libopenblas conda-forge/osx-64::libopenblas-0.3.21-openmp_h429af6e_3
llvm-openmp conda-forge/osx-64::llvm-openmp-14.0.4-ha654fa7_0
numpy conda-forge/osx-64::numpy-1.21.6-py37h345d48f_0
pandas conda-forge/osx-64::pandas-0.25.1-py37h86efe34_0
python-dateutil conda-forge/noarch::python-dateutil-2.8.0-py_0
python_abi conda-forge/osx-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
The following packages will be UPDATED:
ca-certificates pkgs/main::ca-certificates-2022.07.19~ --> conda-forge::ca-certificates-2022.9.24-h033912b_0
The following packages will be SUPERSEDED by a higher-priority channel:
openssl pkgs/main::openssl-1.1.1q-hca72f7f_0 --> conda-forge::openssl-1.1.1q-hfe4f2af_0
setuptools conda-forge/noarch::setuptools-65.5.0~ --> conda-forge/osx-64::setuptools-59.8.0-py37hf985489_1
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: /Users/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/osx-64::ca-certificates-2022.9.24-h033912b_0
libcxx conda-forge/osx-64::libcxx-14.0.6-hccf4f1f_0
libffi conda-forge/osx-64::libffi-3.3-h046ec9c_2
libsqlite conda-forge/osx-64::libsqlite-3.39.4-ha978bb4_0
libzlib conda-forge/osx-64::libzlib-1.2.13-hfd90126_4
ncurses conda-forge/osx-64::ncurses-6.3-h96cf925_1
openssl conda-forge/osx-64::openssl-1.1.1q-hfe4f2af_0
pip conda-forge/noarch::pip-22.3-pyhd8ed1ab_0
python pkgs/main/osx-64::python-3.7.7-hf48f09d_4
readline conda-forge/osx-64::readline-8.1.2-h3899abd_0
setuptools conda-forge/noarch::setuptools-65.5.0-pyhd8ed1ab_0
sqlite conda-forge/osx-64::sqlite-3.39.4-h9ae0607_0
tk conda-forge/osx-64::tk-8.6.12-h5dbffcc_0
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
xz conda-forge/osx-64::xz-5.2.6-h775f41a_0
zlib conda-forge/osx-64::zlib-1.2.13-hfd90126_4
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: /Users/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-hecd8cb5_0
openssl conda-forge::openssl-1.1.1q-hfe4f2af_0 --> pkgs/main::openssl-1.1.1q-hca72f7f_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: /Users/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:
libblas conda-forge/osx-64::libblas-3.9.0-16_osx64_openblas
libcblas conda-forge/osx-64::libcblas-3.9.0-16_osx64_openblas
libgfortran conda-forge/osx-64::libgfortran-5.0.0-10_4_0_h97931a8_25
libgfortran5 conda-forge/osx-64::libgfortran5-11.3.0-h082f757_25
liblapack conda-forge/osx-64::liblapack-3.9.0-16_osx64_openblas
libopenblas conda-forge/osx-64::libopenblas-0.3.21-openmp_h429af6e_3
llvm-openmp conda-forge/osx-64::llvm-openmp-14.0.4-ha654fa7_0
numpy conda-forge/osx-64::numpy-1.21.6-py37h345d48f_0
pandas pkgs/main/osx-64::pandas-0.24.1-py37h0a44026_0
python-dateutil conda-forge/noarch::python-dateutil-2.7.1-py_0
python_abi conda-forge/osx-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
The following packages will be UPDATED:
ca-certificates pkgs/main::ca-certificates-2022.07.19~ --> conda-forge::ca-certificates-2022.9.24-h033912b_0
The following packages will be SUPERSEDED by a higher-priority channel:
openssl pkgs/main::openssl-1.1.1q-hca72f7f_0 --> conda-forge::openssl-1.1.1q-hfe4f2af_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 0 | PASS 47 ]
>
> proc.time()
user system elapsed
1036.130 183.583 1317.464
basilisk.Rcheck/basilisk-Ex.timings
| name | user | system | elapsed | |
| BasiliskEnvironment-class | 0.005 | 0.001 | 0.006 | |
| PyPiLink | 0.001 | 0.000 | 0.000 | |
| basiliskOptions | 0.001 | 0.000 | 0.001 | |
| basiliskStart | 297.230 | 34.215 | 347.371 | |
| configureBasiliskEnv | 0.008 | 0.001 | 0.010 | |
| findPersistentEnv | 0.052 | 0.010 | 5.871 | |
| listPackages | 1.102 | 0.341 | 1.548 | |
| setupBasiliskEnv | 59.609 | 13.338 | 79.124 | |
| useBasiliskEnv | 1.394 | 0.456 | 1.889 | |