Back to Long Tests report for BioC 3.20 |
This page was generated on 2024-06-29 23:55 -0400 (Sat, 29 Jun 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" | 4693 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4408 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4407 |
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 | |||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | ||||||||
lconway | macOS 12.7.1 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: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --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: 2024-06-29 16:01:46 -0400 (Sat, 29 Jun 2024) |
EndedAt: 2024-06-29 16:11:39 -0400 (Sat, 29 Jun 2024) |
EllapsedTime: 593.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: basilisk.Rcheck |
Warnings: 0 |
basilisk.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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: C:\Users\biocbuild\AppData\Local\R\cache\R\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: bzip2 conda-forge/win-64::bzip2-1.0.8-hcfcfb64_5 ca-certificates conda-forge/win-64::ca-certificates-2024.6.2-h56e8100_0 libffi conda-forge/win-64::libffi-3.4.2-h8ffe710_5 libsqlite conda-forge/win-64::libsqlite-3.46.0-h2466b09_0 libzlib conda-forge/win-64::libzlib-1.3.1-h2466b09_1 openssl conda-forge/win-64::openssl-3.3.1-h2466b09_1 pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 python conda-forge/win-64::python-3.9.12-hcf16a7b_1_cpython setuptools conda-forge/noarch::setuptools-70.1.1-pyhd8ed1ab_0 sqlite conda-forge/win-64::sqlite-3.46.0-h2466b09_0 tk conda-forge/win-64::tk-8.6.13-h5226925_1 tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0 ucrt conda-forge/win-64::ucrt-10.0.22621.0-h57928b3_0 vc conda-forge/win-64::vc-14.3-h8a93ad2_20 vc14_runtime conda-forge/win-64::vc14_runtime-14.40.33810-ha82c5b3_20 vs2015_runtime conda-forge/win-64::vs2015_runtime-14.40.33810-h3bf8584_20 wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1 xz conda-forge/win-64::xz-5.2.6-h8d14728_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: C:\Users\biocbuild\AppData\Local\R\cache\R\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 packages will be downloaded: package | build ---------------------------|----------------- numpy-1.26.4 | py39hddb5d58_0 5.6 MB conda-forge pandas-1.4.3 | py39h2e25243_0 11.0 MB conda-forge pytz-2022.2.1 | pyhd8ed1ab_0 224 KB conda-forge ------------------------------------------------------------ Total: 16.9 MB The following NEW packages will be INSTALLED: intel-openmp conda-forge/win-64::intel-openmp-2024.1.0-h57928b3_966 libblas conda-forge/win-64::libblas-3.9.0-22_win64_mkl libcblas conda-forge/win-64::libcblas-3.9.0-22_win64_mkl libhwloc conda-forge/win-64::libhwloc-2.10.0-default_h8125262_1001 libiconv conda-forge/win-64::libiconv-1.17-hcfcfb64_2 liblapack conda-forge/win-64::liblapack-3.9.0-22_win64_mkl libxml2 conda-forge/win-64::libxml2-2.12.7-h283a6d9_1 mkl conda-forge/win-64::mkl-2024.1.0-h66d3029_692 numpy conda-forge/win-64::numpy-1.26.4-py39hddb5d58_0 pandas conda-forge/win-64::pandas-1.4.3-py39h2e25243_0 pthreads-win32 conda-forge/win-64::pthreads-win32-2.9.1-hfa6e2cd_3 python-dateutil conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0 python_abi conda-forge/win-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 tbb conda-forge/win-64::tbb-2021.12.0-hc790b64_1 Downloading and Extracting Packages pytz-2022.2.1 | 224 KB | | 0% pytz-2022.2.1 | 224 KB | 7 | 7% pytz-2022.2.1 | 224 KB | ########## | 100% pytz-2022.2.1 | 224 KB | ########## | 100% pandas-1.4.3 | 11.0 MB | | 0% pandas-1.4.3 | 11.0 MB | #4 | 14% pandas-1.4.3 | 11.0 MB | ########## | 100% pandas-1.4.3 | 11.0 MB | ########## | 100% numpy-1.26.4 | 5.6 MB | | 0% numpy-1.26.4 | 5.6 MB | ########## | 100% numpy-1.26.4 | 5.6 MB | ########## | 100% 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: C:\Users\biocbuild\AppData\Local\R\cache\R\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: bzip2 conda-forge/win-64::bzip2-1.0.8-hcfcfb64_5 ca-certificates conda-forge/win-64::ca-certificates-2024.6.2-h56e8100_0 libffi conda-forge/win-64::libffi-3.4.2-h8ffe710_5 libsqlite conda-forge/win-64::libsqlite-3.46.0-h2466b09_0 libzlib conda-forge/win-64::libzlib-1.3.1-h2466b09_1 openssl conda-forge/win-64::openssl-3.3.1-h2466b09_1 pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 python conda-forge/win-64::python-3.9.12-hcf16a7b_1_cpython setuptools conda-forge/noarch::setuptools-70.1.1-pyhd8ed1ab_0 sqlite conda-forge/win-64::sqlite-3.46.0-h2466b09_0 tk conda-forge/win-64::tk-8.6.13-h5226925_1 tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0 ucrt conda-forge/win-64::ucrt-10.0.22621.0-h57928b3_0 vc conda-forge/win-64::vc-14.3-h8a93ad2_20 vc14_runtime conda-forge/win-64::vc14_runtime-14.40.33810-ha82c5b3_20 vs2015_runtime conda-forge/win-64::vs2015_runtime-14.40.33810-h3bf8584_20 wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1 xz conda-forge/win-64::xz-5.2.6-h8d14728_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: C:\Users\biocbuild\AppData\Local\R\cache\R\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 packages will be downloaded: package | build ---------------------------|----------------- python-dateutil-2.8.1 | py_0 220 KB conda-forge pytz-2022.1 | pyhd8ed1ab_0 242 KB conda-forge scikit-learn-1.1.1 | py39he931e04_0 7.5 MB conda-forge ------------------------------------------------------------ Total: 8.0 MB The following NEW packages will be INSTALLED: intel-openmp conda-forge/win-64::intel-openmp-2024.1.0-h57928b3_966 joblib conda-forge/noarch::joblib-1.4.2-pyhd8ed1ab_0 libblas conda-forge/win-64::libblas-3.9.0-22_win64_mkl libcblas conda-forge/win-64::libcblas-3.9.0-22_win64_mkl libhwloc conda-forge/win-64::libhwloc-2.10.0-default_h8125262_1001 libiconv conda-forge/win-64::libiconv-1.17-hcfcfb64_2 liblapack conda-forge/win-64::liblapack-3.9.0-22_win64_mkl libxml2 conda-forge/win-64::libxml2-2.12.7-h283a6d9_1 mkl conda-forge/win-64::mkl-2024.1.0-h66d3029_692 numpy conda-forge/win-64::numpy-1.26.4-py39hddb5d58_0 pthreads-win32 conda-forge/win-64::pthreads-win32-2.9.1-hfa6e2cd_3 python-dateutil conda-forge/noarch::python-dateutil-2.8.1-py_0 python_abi conda-forge/win-64::python_abi-3.9-4_cp39 pytz conda-forge/noarch::pytz-2022.1-pyhd8ed1ab_0 scikit-learn conda-forge/win-64::scikit-learn-1.1.1-py39he931e04_0 scipy conda-forge/win-64::scipy-1.13.1-py39h1a10956_0 six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0 tbb conda-forge/win-64::tbb-2021.12.0-hc790b64_1 threadpoolctl conda-forge/noarch::threadpoolctl-3.5.0-pyhc1e730c_0 Downloading and Extracting Packages python-dateutil-2.8. | 220 KB | | 0% python-dateutil-2.8. | 220 KB | ########## | 100% python-dateutil-2.8. | 220 KB | ########## | 100% scikit-learn-1.1.1 | 7.5 MB | | 0% scikit-learn-1.1.1 | 7.5 MB | | 0% scikit-learn-1.1.1 | 7.5 MB | ########## | 100% scikit-learn-1.1.1 | 7.5 MB | ########## | 100% pytz-2022.1 | 242 KB | | 0% pytz-2022.1 | 242 KB | ########## | 100% pytz-2022.1 | 242 KB | ########## | 100% Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Collecting package metadata (current_repodata.json): ...working... done Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: C:\Users\biocbuild\AppData\Local\R\cache\R\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: bzip2 conda-forge/win-64::bzip2-1.0.8-hcfcfb64_5 ca-certificates conda-forge/win-64::ca-certificates-2024.6.2-h56e8100_0 libffi conda-forge/win-64::libffi-3.4.2-h8ffe710_5 libsqlite conda-forge/win-64::libsqlite-3.46.0-h2466b09_0 libzlib conda-forge/win-64::libzlib-1.3.1-h2466b09_1 openssl conda-forge/win-64::openssl-3.3.1-h2466b09_1 pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 python conda-forge/win-64::python-3.9.12-hcf16a7b_1_cpython setuptools conda-forge/noarch::setuptools-70.1.1-pyhd8ed1ab_0 sqlite conda-forge/win-64::sqlite-3.46.0-h2466b09_0 tk conda-forge/win-64::tk-8.6.13-h5226925_1 tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0 ucrt conda-forge/win-64::ucrt-10.0.22621.0-h57928b3_0 vc conda-forge/win-64::vc-14.3-h8a93ad2_20 vc14_runtime conda-forge/win-64::vc14_runtime-14.40.33810-ha82c5b3_20 vs2015_runtime conda-forge/win-64::vs2015_runtime-14.40.33810-h3bf8584_20 wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1 xz conda-forge/win-64::xz-5.2.6-h8d14728_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 c:\users\biocbuild\bbs-3.20-bioc-longtests\tmpdir\rtmpcgk6tt\rlib.33fcc671628be\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=1286 sha256=7507514aff293695ca8808f5d7acd37d0c4794c4e67c9357a7833ec1ffb84f25 Stored in directory: C:\Users\biocbuild\bbs-3.20-bioc-longtests\tmpdir\pip-ephem-wheel-cache-e9rfc7rd\wheels\6a\87\7e\18967c0fcbf4343e6844ef08165879d5d431cdfa197bb61715 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 2.09 0.76 551.98
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --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 'C:/Users/biocbuild/bbs-3.20-bioc-longtests/meat/basilisk.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * 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 whether package 'basilisk' can be installed ... NOTE Found the following notes/warnings: Non-staged installation was used See 'C:/Users/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 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 'C:/Users/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)