| Back to Long Tests report for BioC 3.20 |
This page was generated on 2024-05-18 23:55:02 -0400 (Sat, 18 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4666 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4401 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4428 |
| 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 | ||||
| Package 3/32 | Hostname | OS / Arch | CHECK | |||||||
| basilisk 1.17.0 (landing page) Aaron Lun
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | |||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | ERROR | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | ||||||||
|
To the developers/maintainers of the basilisk package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: basilisk |
| Version: 1.17.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no basilisk_1.17.0.tar.gz |
| StartedAt: 2024-05-18 16:00:26 -0400 (Sat, 18 May 2024) |
| EndedAt: 2024-05-18 16:07:34 -0400 (Sat, 18 May 2024) |
| EllapsedTime: 428.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: basilisk.Rcheck |
| Warnings: 0 |
basilisk.Rcheck/tests/testthat.Rout
R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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)
Loading required package: reticulate
> test_check("basilisk")
* 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)
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: /var/cache/basilisk/1.17.0/son.of.basilisk/0.99.0/env1
added / updated specs:
- python=3.9.12
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-64::bzip2-1.0.8-hd590300_5
ca-certificates conda-forge/linux-64::ca-certificates-2024.2.2-hbcca054_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.40-h55db66e_0
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc-ng conda-forge/linux-64::libgcc-ng-13.2.0-h77fa898_7
libgomp conda-forge/linux-64::libgomp-13.2.0-h77fa898_7
libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0
libsqlite conda-forge/linux-64::libsqlite-3.45.3-h2797004_0
libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0
libzlib conda-forge/linux-64::libzlib-1.2.13-hd590300_5
ncurses conda-forge/linux-64::ncurses-6.5-h59595ed_0
openssl conda-forge/linux-64::openssl-3.3.0-hd590300_0
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/linux-64::python-3.9.12-h2660328_1_cpython
readline conda-forge/linux-64::readline-8.2-h8228510_1
setuptools conda-forge/noarch::setuptools-69.5.1-pyhd8ed1ab_0
sqlite conda-forge/linux-64::sqlite-3.45.3-h2c6b66d_0
tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101
tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0
wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
xz conda-forge/linux-64::xz-5.2.6-h166bdaf_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
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 24.5.0
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 initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 24.5.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /var/cache/basilisk/1.17.0/son.of.basilisk/0.99.0/env1
added / updated specs:
- pandas=1.4.3
- python-dateutil=2.8.2
- python=3.9.12
- pytz=2022.2.1
The following NEW packages will be INSTALLED:
libblas conda-forge/linux-64::libblas-3.9.0-22_linux64_openblas
libcblas conda-forge/linux-64::libcblas-3.9.0-22_linux64_openblas
libgfortran-ng conda-forge/linux-64::libgfortran-ng-13.2.0-h69a702a_7
libgfortran5 conda-forge/linux-64::libgfortran5-13.2.0-hca663fb_7
liblapack conda-forge/linux-64::liblapack-3.9.0-22_linux64_openblas
libopenblas conda-forge/linux-64::libopenblas-0.3.27-pthreads_h413a1c8_0
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-13.2.0-hc0a3c3a_7
numpy conda-forge/linux-64::numpy-1.26.4-py39h474f0d3_0
pandas conda-forge/linux-64::pandas-1.4.3-py39h1832856_0
python-dateutil conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
python_abi conda-forge/linux-64::python_abi-3.9-4_cp39
pytz conda-forge/noarch::pytz-2022.2.1-pyhd8ed1ab_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
sys:1: FutureWarning: pandas.Float64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead.
sys:1: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead.
sys:1: FutureWarning: pandas.UInt64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead.
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: /var/cache/basilisk/1.17.0/son.of.basilisk/0.99.0/env2
added / updated specs:
- python=3.9.12
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-64::bzip2-1.0.8-hd590300_5
ca-certificates conda-forge/linux-64::ca-certificates-2024.2.2-hbcca054_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.40-h55db66e_0
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc-ng conda-forge/linux-64::libgcc-ng-13.2.0-h77fa898_7
libgomp conda-forge/linux-64::libgomp-13.2.0-h77fa898_7
libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0
libsqlite conda-forge/linux-64::libsqlite-3.45.3-h2797004_0
libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0
libzlib conda-forge/linux-64::libzlib-1.2.13-hd590300_5
ncurses conda-forge/linux-64::ncurses-6.5-h59595ed_0
openssl conda-forge/linux-64::openssl-3.3.0-hd590300_0
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/linux-64::python-3.9.12-h2660328_1_cpython
readline conda-forge/linux-64::readline-8.2-h8228510_1
setuptools conda-forge/noarch::setuptools-69.5.1-pyhd8ed1ab_0
sqlite conda-forge/linux-64::sqlite-3.45.3-h2c6b66d_0
tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101
tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0
wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
xz conda-forge/linux-64::xz-5.2.6-h166bdaf_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
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 24.5.0
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 initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 24.5.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /var/cache/basilisk/1.17.0/son.of.basilisk/0.99.0/env2
added / updated specs:
- python-dateutil=2.8.1
- python=3.9.12
- pytz=2022.1
- scikit-learn=1.1.1
The following NEW packages will be INSTALLED:
joblib conda-forge/noarch::joblib-1.4.2-pyhd8ed1ab_0
libblas conda-forge/linux-64::libblas-3.9.0-22_linux64_openblas
libcblas conda-forge/linux-64::libcblas-3.9.0-22_linux64_openblas
libgfortran-ng conda-forge/linux-64::libgfortran-ng-13.2.0-h69a702a_7
libgfortran5 conda-forge/linux-64::libgfortran5-13.2.0-hca663fb_7
liblapack conda-forge/linux-64::liblapack-3.9.0-22_linux64_openblas
libopenblas conda-forge/linux-64::libopenblas-0.3.27-pthreads_h413a1c8_0
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-13.2.0-hc0a3c3a_7
numpy conda-forge/linux-64::numpy-1.26.4-py39h474f0d3_0
python-dateutil conda-forge/noarch::python-dateutil-2.8.1-py_0
python_abi conda-forge/linux-64::python_abi-3.9-4_cp39
pytz conda-forge/noarch::pytz-2022.1-pyhd8ed1ab_0
scikit-learn conda-forge/linux-64::scikit-learn-1.1.1-py39h4037b75_0
scipy conda-forge/linux-64::scipy-1.13.0-py39haf93ffa_1
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
threadpoolctl conda-forge/noarch::threadpoolctl-3.5.0-pyhc1e730c_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /var/cache/basilisk/1.17.0/son.of.basilisk/0.99.0/env3
added / updated specs:
- python=3.9.12
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-64::bzip2-1.0.8-hd590300_5
ca-certificates conda-forge/linux-64::ca-certificates-2024.2.2-hbcca054_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.40-h55db66e_0
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc-ng conda-forge/linux-64::libgcc-ng-13.2.0-h77fa898_7
libgomp conda-forge/linux-64::libgomp-13.2.0-h77fa898_7
libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0
libsqlite conda-forge/linux-64::libsqlite-3.45.3-h2797004_0
libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0
libzlib conda-forge/linux-64::libzlib-1.2.13-hd590300_5
ncurses conda-forge/linux-64::ncurses-6.5-h59595ed_0
openssl conda-forge/linux-64::openssl-3.3.0-hd590300_0
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/linux-64::python-3.9.12-h2660328_1_cpython
readline conda-forge/linux-64::readline-8.2-h8228510_1
setuptools conda-forge/noarch::setuptools-69.5.1-pyhd8ed1ab_0
sqlite conda-forge/linux-64::sqlite-3.45.3-h2c6b66d_0
tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101
tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0
wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
xz conda-forge/linux-64::xz-5.2.6-h166bdaf_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
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 24.5.0
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... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 24.5.0
Please update conda by running
$ conda update -n base -c defaults conda
# All requested packages already installed.
Processing /tmp/Rtmp9nkblS/Rlib.57db5a04eac8/son.of.basilisk/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=1281 sha256=bb212608fa56db39074d8565a430148897c1ddb42f4d01fca9d9bb9aa09e1f5d
Stored in directory: /tmp/pip-ephem-wheel-cache-a2rairzc/wheels/52/e8/19/346343ab6d4ad5f57ffdc7001d415c601a05e9d1459bf89da5
Successfully built test_dummy
Installing collected packages: test_dummy
Successfully installed test_dummy-0.1
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 4 ]
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
361.706 26.720 395.768
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no basilisk_1.17.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc-longtests/meat/basilisk.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘basilisk/DESCRIPTION’ ... OK
* this is package ‘basilisk’ version ‘1.17.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
inst/example/.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘basilisk’ can be installed ... NOTE
Found the following notes/warnings:
Non-staged installation was used
See ‘/home/biocbuild/bbs-3.20-bioc-longtests/meat/basilisk.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package 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 code 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 loading without being on the library search path ... 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* 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’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
Running ‘testthat.R’
OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.20-bioc-longtests/meat/basilisk.Rcheck/00check.log’
for details.
basilisk.Rcheck/00install.out
* 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)