Back to Long Tests report for BioC 3.21

This page was generated on 2025-04-19 23:55 -0400 (Sat, 19 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4831
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
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 3/30HostnameOS / ArchCHECK
basilisk 1.20.0  (landing page)
Aaron Lun
Snapshot Date: 2025-04-19 09:55 -0400 (Sat, 19 Apr 2025)
git_url: https://git.bioconductor.org/packages/basilisk
git_branch: RELEASE_3_21
git_last_commit: 072c38e
git_last_commit_date: 2025-04-15 11:54:33 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK  
palomino7Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  OK  


CHECK results for basilisk on palomino7

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.

raw results


Summary

Package: basilisk
Version: 1.20.0
Command: E:\biocbuild\bbs-3.21-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_1.20.0.tar.gz
StartedAt: 2025-04-19 16:03:46 -0400 (Sat, 19 Apr 2025)
EndedAt: 2025-04-19 16:04:53 -0400 (Sat, 19 Apr 2025)
EllapsedTime: 66.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: basilisk.Rcheck
Warnings: NA

Tests output

basilisk.Rcheck/tests/testthat.Rout.fail


R version 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six"
Copyright (C) 2025 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' ...
** this is package 'son.of.basilisk' version '0.99.0'
** 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)
Channels:
 - conda-forge
Platform: win-64
Collecting package metadata (repodata.json): ...working... failed

NoSpaceLeftError: No space left on devices.

[ FAIL 1 | WARN 2 | SKIP 0 | PASS 0 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-package.R:14:5'): internal test package installs correctly ─────
Error: Error creating conda environment 'C:/Users/biocbuild/.basilisk/1.20.0/son.of.basilisk/0.99.0/env1' [exit 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::conda_create(...)
 7.             └─reticulate:::stopf(fmt, envname, result, call. = FALSE)

[ FAIL 1 | WARN 2 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-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_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc-longtests/meat/basilisk.Rcheck'
* using R version 4.5.0 RC (2025-04-04 r88126 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* 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 '1.20.0'
* 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 'E:/biocbuild/bbs-3.21-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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  basiliskStart.Rd: activateEnvironment, getExternalDir
  listPackages.Rd: installConda
  useBasiliskEnv.Rd: activateEnvironment
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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:
  ── Error ('test-package.R:14:5'): internal test package installs correctly ─────
  Error: Error creating conda environment 'C:/Users/biocbuild/.basilisk/1.20.0/son.of.basilisk/0.99.0/env1' [exit 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::conda_create(...)
   7.             └─reticulate:::stopf(fmt, envname, result, call. = FALSE)
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 3 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc-longtests/meat/basilisk.Rcheck/00check.log'
for details.


Installation output

basilisk.Rcheck/00install.out

* installing *source* package 'basilisk' ...
** this is package 'basilisk' version '1.20.0'
** 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)