Back to Long Tests report for BioC 3.19 |
This page was generated on 2024-05-11 23:55:01 -0400 (Sat, 11 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4751 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4485 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4515 |
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: F:\biocbuild\bbs-3.19-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_1.16.0.tar.gz |
StartedAt: 2024-05-11 16:04:45 -0400 (Sat, 11 May 2024) |
EndedAt: 2024-05-11 16:11:41 -0400 (Sat, 11 May 2024) |
EllapsedTime: 415.1 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: basilisk.Rcheck |
Warnings: NA |
basilisk.Rcheck/tests/testthat.Rout.fail
R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 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\1.16.0\son.of.basilisk\0.99.0\env1 added / updated specs: - python=3.9.12 The following NEW packages will be INSTALLED: bzip2 conda-forge/win-64::bzip2-1.0.8-hcfcfb64_5 ca-certificates conda-forge/win-64::ca-certificates-2024.2.2-h56e8100_0 libffi conda-forge/win-64::libffi-3.4.2-h8ffe710_5 libsqlite conda-forge/win-64::libsqlite-3.45.3-hcfcfb64_0 libzlib conda-forge/win-64::libzlib-1.2.13-hcfcfb64_5 openssl conda-forge/win-64::openssl-3.3.0-hcfcfb64_0 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-69.5.1-pyhd8ed1ab_0 sqlite conda-forge/win-64::sqlite-3.45.3-hcfcfb64_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-hcf57466_18 vc14_runtime conda-forge/win-64::vc14_runtime-14.38.33130-h82b7239_18 vs2015_runtime conda-forge/win-64::vs2015_runtime-14.38.33130-hcb4865c_18 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: 24.4.0 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: C:\Users\biocbuild\AppData\Local\R\cache\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 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_965 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_h2fffb23_1000 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::libxml2-2.12.6-hc3477c8_2 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-h91493d7_0 Downloading and Extracting Packages numpy-1.26.4 | 5.6 MB | | 0% numpy-1.26.4 | 5.6 MB | #2 | 12% numpy-1.26.4 | 5.6 MB | ########## | 100% numpy-1.26.4 | 5.6 MB | ########## | 100% pytz-2022.2.1 | 224 KB | | 0% 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 | #######1 | 71% pandas-1.4.3 | 11.0 MB | ########## | 100% Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done ERROR conda.core.link:_execute(730): An error occurred while installing package 'conda-forge::numpy-1.26.4-py39hddb5d58_0'. Rolling back transaction: ...working... done [Errno 28] No space left on device: 'C:\\Users\\biocbuild\\AppData\\Local\\R\\cache\\R\\basilisk\\1.16.0\\son.of.basilisk\\0.99.0\\env1\\Lib\\site-packages\\numpy\\f2py\\__pycache__\\_src_pyf.cpython-39.pyc' () [ FAIL 2 | WARN 2 | SKIP 0 | PASS 0 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-package.R:14:5'): internal test package installs correctly ───── Error: one or more Python packages failed to install [error code 1] Backtrace: ▆ 1. └─son.of.basilisk::test() at test-package.R:14:5 2. └─basilisk::basiliskStart(env1) 3. └─basilisk::obtainEnvironmentPath(env) 4. └─basilisk::setupBasiliskEnv(...) 5. └─reticulate::conda_install(...) 6. └─reticulate:::stopf(fmt, result) ── Error ('test-package.R:14:5'): internal test package installs correctly ───── Error in `unlink2(envpath)`: failed to remove 'C:\Users\biocbuild\AppData\Local/R/cache/R/basilisk/1.16.0/son.of.basilisk/0.99.0/env1' Backtrace: ▆ 1. └─son.of.basilisk::test() at test-package.R:14:5 2. └─basilisk::basiliskStart(env1) 3. └─basilisk::obtainEnvironmentPath(env) 4. └─basilisk::setupBasiliskEnv(...) 5. └─basilisk.utils::unlink2(envpath) [ FAIL 2 | WARN 2 | SKIP 0 | PASS 0 ] Error: Test failures Execution halted
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-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_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.19-bioc-longtests/meat/basilisk.Rcheck' * using R version 4.4.0 (2024-04-24 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 '1.16.0' * 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 whether package 'basilisk' can be installed ... NOTE Found the following notes/warnings: Non-staged installation was used See 'F:/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' ERROR Running the tests in 'longtests/testthat.R' failed. Last 13 lines of output: 5. └─reticulate::conda_install(...) 6. └─reticulate:::stopf(fmt, result) ── Error ('test-package.R:14:5'): internal test package installs correctly ───── Error in `unlink2(envpath)`: failed to remove 'C:\Users\biocbuild\AppData\Local/R/cache/R/basilisk/1.16.0/son.of.basilisk/0.99.0/env1' Backtrace: ▆ 1. └─son.of.basilisk::test() at test-package.R:14:5 2. └─basilisk::basiliskStart(env1) 3. └─basilisk::obtainEnvironmentPath(env) 4. └─basilisk::setupBasiliskEnv(...) 5. └─basilisk.utils::unlink2(envpath) [ FAIL 2 | WARN 2 | SKIP 0 | PASS 0 ] Error: Test failures Execution halted * DONE Status: 1 ERROR, 2 NOTEs See 'F:/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)