atena.check failure

[martin-g]

biocbuild@kunpeng1 ~/git> R CMD build --keep-empty-dirs --no-resave-data atena
* checking for file ‘atena/DESCRIPTION’ ... OK
* preparing ‘atena’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘atena_1.5.10.tar.gz’

biocbuild@kunpeng1 ~/git> R CMD check atena_1.5.10.tar.gz 
* using log directory ‘/home/biocbuild/git/atena.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘atena/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘atena’ version ‘1.5.10’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘atena’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 R 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 startup messages can be suppressed ... 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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘atena-Ex.R’ failed
The error most likely occurred in:

> ### Name: annotaTEs
> ### Title: Get RepeatMasker UCSC annotations
> ### Aliases: annotaTEs
> 
> ### ** Examples
> 
> rmsk_gr <- annotaTEs(genome = "hg19", parsefun = rmskidentity)
snapshotDate(): 2023-03-21
loading from cache
Error: failed to load resource
  name: AH99002
  title: UCSC RepeatMasker annotations (Mar2020) for Human (hg19)
  reason: error reading from connection
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  1 Test Suite : 
  atena RUnit Tests - 13 test functions, 0 errors, 1 failure
  FAILURE in test_TEtranscripts: Error in checkEqualsNumeric(head(sort(assay(ttSE), decreasing = TRUE)),  : 
    Mean relative difference: 0.007352941

  Test files with failing tests

     test_TEtranscripts.R 
       test_TEtranscripts 

  Error in BiocGenerics:::testPackage("atena") : 
    unit tests failed for package atena
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘atena.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/home/biocbuild/git/atena.Rcheck/00check.log’
for details.

[martin-g]

Reported upstream - https://github.com/functionalgenomics/atena/issues/6

[martin-g]

The issue has been fixed upstream!

[martin-g]

https://bioconductor.org/checkResults/3.18/bioc-LATEST/atena/kunpeng2-checksrc.html is fully green!