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### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:GenomeInfoDb.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings GenomeInfoDb_1.37.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/GenomeInfoDb.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘GenomeInfoDb/DESCRIPTION’ ... OK
* this is package ‘GenomeInfoDb’ version ‘1.37.1’
* 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 ‘GenomeInfoDb’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
* 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    NEW FEATURES
  Cannot process chunk/lines:
    SIGNIFICANT USER-VISIBLE CHANGES
* 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 ... NOTE
Unexported object imported by a ':::' call: ‘utils:::.roman2numeric’
  See the note in ?`:::` about the use of this operator.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
GenomeDescription-class 10.673  0.171  10.867
loadTaxonomyDb          10.346  0.212  10.575
seqlevels-wrappers       5.734  0.201   5.948
seqlevelsStyle           4.415  1.328  23.284
seqinfo                  5.045  0.184   5.259
getChromInfoFromEnsembl  0.544  0.143 109.354
getChromInfoFromNCBI     0.276  0.023  10.177
NCBI-utils               0.071  0.016  11.586
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 ERROR
Running the tests in ‘tests/run_unitTests.R’ failed.
Last 13 lines of output:
  1 Test Suite : 
  GenomeInfoDb RUnit Tests - 21 test functions, 1 error, 0 failures
  ERROR in test_seqlevelsStyle_Seqinfo: Error in download.file(url, destfile, quiet = TRUE) : 
    download from 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/663/975/GCA_001663975.1_Xenopus_laevis_v2/GCA_001663975.1_Xenopus_laevis_v2_assembly_report.txt' failed
  
  Test files with failing tests
  
     test_seqlevelsStyle.R 
       test_seqlevelsStyle_Seqinfo 
  
  
  Error in BiocGenerics:::testPackage("GenomeInfoDb") : 
    unit tests failed for package GenomeInfoDb
  Calls: <Anonymous> -> <Anonymous>
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘Accept-organism-for-GenomeInfoDb.Rmd’ using ‘UTF-8’... OK
  ‘GenomeInfoDb.Rnw’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/GenomeInfoDb.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL GenomeInfoDb
###
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* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘GenomeInfoDb’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenomeInfoDb)

R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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.

> require("GenomeInfoDb") || stop("unable to load GenomeInfoDb package")
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
[1] TRUE
> GenomeInfoDb:::.test()
Timing stopped at: 173 4.268 966.9
Error in download.file(url, destfile, quiet = TRUE) : 
  download from 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/663/975/GCA_001663975.1_Xenopus_laevis_v2/GCA_001663975.1_Xenopus_laevis_v2_assembly_report.txt' failed
In addition: There were 31 warnings (use warnings() to see them)


RUNIT TEST PROTOCOL -- Mon Jun  5 23:16:09 2023 
*********************************************** 
Number of test functions: 21 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
GenomeInfoDb RUnit Tests - 21 test functions, 1 error, 0 failures
ERROR in test_seqlevelsStyle_Seqinfo: Error in download.file(url, destfile, quiet = TRUE) : 
  download from 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/663/975/GCA_001663975.1_Xenopus_laevis_v2/GCA_001663975.1_Xenopus_laevis_v2_assembly_report.txt' failed

Test files with failing tests

   test_seqlevelsStyle.R 
     test_seqlevelsStyle_Seqinfo 


Error in BiocGenerics:::testPackage("GenomeInfoDb") : 
  unit tests failed for package GenomeInfoDb
Calls: <Anonymous> -> <Anonymous>
Execution halted