Back to Long Tests report for BioC 3.19 |
This page was generated on 2024-05-04 23:55:02 -0400 (Sat, 04 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
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 3/33 | Hostname | OS / Arch | CHECK | |||||||
basilisk 1.16.0 (landing page) Aaron Lun
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | |||||||
palomino3 | Windows Server 2022 Datacenter / x64 | ERROR | ||||||||
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: 1.16.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no basilisk_1.16.0.tar.gz |
StartedAt: 2024-05-04 16:00:52 -0400 (Sat, 04 May 2024) |
EndedAt: 2024-05-04 16:08:04 -0400 (Sat, 04 May 2024) |
EllapsedTime: 432.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: basilisk.Rcheck |
Warnings: 0 |
basilisk.Rcheck/tests/testthat.Rout
R version 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/son.of.basilisk/0.99.0/env1 added / updated specs: - python=3.9.12 The following NEW packages will be INSTALLED: bzip2 conda-forge/osx-64::bzip2-1.0.8-h10d778d_5 ca-certificates conda-forge/osx-64::ca-certificates-2024.2.2-h8857fd0_0 libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5 libsqlite conda-forge/osx-64::libsqlite-3.45.3-h92b6c6a_0 libzlib conda-forge/osx-64::libzlib-1.2.13-h8a1eda9_5 ncurses conda-forge/osx-64::ncurses-6.4.20240210-h73e2aa4_0 openssl conda-forge/osx-64::openssl-3.3.0-hd75f5a5_0 pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 python conda-forge/osx-64::python-3.9.12-h1cc4136_1_cpython readline conda-forge/osx-64::readline-8.2-h9e318b2_1 setuptools conda-forge/noarch::setuptools-69.5.1-pyhd8ed1ab_0 sqlite conda-forge/osx-64::sqlite-3.45.3-h7461747_0 tk conda-forge/osx-64::tk-8.6.13-h1abcd95_1 tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0 wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1 xz conda-forge/osx-64::xz-5.2.6-h775f41a_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: 24.4.0 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: 24.4.0 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/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/osx-64::libblas-3.9.0-22_osx64_openblas libcblas conda-forge/osx-64::libcblas-3.9.0-22_osx64_openblas libcxx conda-forge/osx-64::libcxx-16.0.6-hd57cbcb_0 libgfortran conda-forge/osx-64::libgfortran-5.0.0-13_2_0_h97931a8_3 libgfortran5 conda-forge/osx-64::libgfortran5-13.2.0-h2873a65_3 liblapack conda-forge/osx-64::liblapack-3.9.0-22_osx64_openblas libopenblas conda-forge/osx-64::libopenblas-0.3.27-openmp_hfef2a42_0 llvm-openmp conda-forge/osx-64::llvm-openmp-18.1.4-h2c61cee_0 numpy conda-forge/osx-64::numpy-1.26.4-py39h28c39a1_0 pandas conda-forge/osx-64::pandas-1.4.3-py39hf72b562_0 python-dateutil conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0 python_abi conda-forge/osx-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: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/son.of.basilisk/0.99.0/env2 added / updated specs: - python=3.9.12 The following NEW packages will be INSTALLED: bzip2 conda-forge/osx-64::bzip2-1.0.8-h10d778d_5 ca-certificates conda-forge/osx-64::ca-certificates-2024.2.2-h8857fd0_0 libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5 libsqlite conda-forge/osx-64::libsqlite-3.45.3-h92b6c6a_0 libzlib conda-forge/osx-64::libzlib-1.2.13-h8a1eda9_5 ncurses conda-forge/osx-64::ncurses-6.4.20240210-h73e2aa4_0 openssl conda-forge/osx-64::openssl-3.3.0-hd75f5a5_0 pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 python conda-forge/osx-64::python-3.9.12-h1cc4136_1_cpython readline conda-forge/osx-64::readline-8.2-h9e318b2_1 setuptools conda-forge/noarch::setuptools-69.5.1-pyhd8ed1ab_0 sqlite conda-forge/osx-64::sqlite-3.45.3-h7461747_0 tk conda-forge/osx-64::tk-8.6.13-h1abcd95_1 tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0 wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1 xz conda-forge/osx-64::xz-5.2.6-h775f41a_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: 24.4.0 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: 24.4.0 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/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 ---------------------------|----------------- scipy-1.13.0 | py39h72a3afc_1 14.8 MB conda-forge ------------------------------------------------------------ Total: 14.8 MB The following NEW packages will be INSTALLED: joblib conda-forge/noarch::joblib-1.4.2-pyhd8ed1ab_0 libblas conda-forge/osx-64::libblas-3.9.0-22_osx64_openblas libcblas conda-forge/osx-64::libcblas-3.9.0-22_osx64_openblas libcxx conda-forge/osx-64::libcxx-16.0.6-hd57cbcb_0 libgfortran conda-forge/osx-64::libgfortran-5.0.0-13_2_0_h97931a8_3 libgfortran5 conda-forge/osx-64::libgfortran5-13.2.0-h2873a65_3 liblapack conda-forge/osx-64::liblapack-3.9.0-22_osx64_openblas libopenblas conda-forge/osx-64::libopenblas-0.3.27-openmp_hfef2a42_0 llvm-openmp conda-forge/osx-64::llvm-openmp-18.1.4-h2c61cee_0 numpy conda-forge/osx-64::numpy-1.26.4-py39h28c39a1_0 python-dateutil conda-forge/noarch::python-dateutil-2.8.1-py_0 python_abi conda-forge/osx-64::python_abi-3.9-4_cp39 pytz conda-forge/noarch::pytz-2022.1-pyhd8ed1ab_0 scikit-learn conda-forge/osx-64::scikit-learn-1.1.1-py39hafe9688_0 scipy conda-forge/osx-64::scipy-1.13.0-py39h72a3afc_1 six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0 threadpoolctl conda-forge/noarch::threadpoolctl-3.5.0-pyhc1e730c_0 Downloading and Extracting Packages scipy-1.13.0 | 14.8 MB | | 0% scipy-1.13.0 | 14.8 MB | | 0% scipy-1.13.0 | 14.8 MB | 2 | 3% scipy-1.13.0 | 14.8 MB | 9 | 10% scipy-1.13.0 | 14.8 MB | ##1 | 21% scipy-1.13.0 | 14.8 MB | ###2 | 33% scipy-1.13.0 | 14.8 MB | ####5 | 46% scipy-1.13.0 | 14.8 MB | #####7 | 57% scipy-1.13.0 | 14.8 MB | ######7 | 68% scipy-1.13.0 | 14.8 MB | #######9 | 80% scipy-1.13.0 | 14.8 MB | #########1 | 92% scipy-1.13.0 | 14.8 MB | ########## | 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: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/son.of.basilisk/0.99.0/env3 added / updated specs: - python=3.9.12 The following NEW packages will be INSTALLED: bzip2 conda-forge/osx-64::bzip2-1.0.8-h10d778d_5 ca-certificates conda-forge/osx-64::ca-certificates-2024.2.2-h8857fd0_0 libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5 libsqlite conda-forge/osx-64::libsqlite-3.45.3-h92b6c6a_0 libzlib conda-forge/osx-64::libzlib-1.2.13-h8a1eda9_5 ncurses conda-forge/osx-64::ncurses-6.4.20240210-h73e2aa4_0 openssl conda-forge/osx-64::openssl-3.3.0-hd75f5a5_0 pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 python conda-forge/osx-64::python-3.9.12-h1cc4136_1_cpython readline conda-forge/osx-64::readline-8.2-h9e318b2_1 setuptools conda-forge/noarch::setuptools-69.5.1-pyhd8ed1ab_0 sqlite conda-forge/osx-64::sqlite-3.45.3-h7461747_0 tk conda-forge/osx-64::tk-8.6.13-h1abcd95_1 tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0 wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1 xz conda-forge/osx-64::xz-5.2.6-h775f41a_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: 24.4.0 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: 24.4.0 Please update conda by running $ conda update -n base -c defaults conda # All requested packages already installed. Processing /private/tmp/RtmpBxdChs/Rlib.15405200ff113/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=4b8222a3762a3515fafd55aeb517e887d07c9c31662b9b71d221b35c3741f243 Stored in directory: /private/tmp/pip-ephem-wheel-cache-sm5qzvb5/wheels/1c/fc/61/ca0dde9f584d24a16f4d14d285646e3cf7928ea8bec545e67f 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 290.234 44.350 397.022
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no basilisk_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc-longtests/meat/basilisk.Rcheck’ * using R version 4.4.0 beta (2024-04-14 r86421) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * 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 ‘1.16.0’ * 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 ‘/Users/biocbuild/bbs-3.19-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 ‘/Users/biocbuild/bbs-3.19-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)