| 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)