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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:GenomeInfoDb.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GenomeInfoDb_1.45.7.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/GenomeInfoDb.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomeInfoDb/DESCRIPTION’ ... OK
* this is package ‘GenomeInfoDb’ version ‘1.45.7’
* 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 ... INFO
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   3.6Mb
* 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 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 loading without being on the library search path ... OK
* checking whether 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  seqlevels-wrappers.Rd: seqinfo
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 ... 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
getChromInfoFromUCSC    10.204  0.291  12.311
loadTaxonomyDb           9.363  0.147   9.534
seqlevels-wrappers       6.113  0.331   6.498
seqlevelsStyle           5.530  0.164  25.291
getChromInfoFromEnsembl  0.591  0.065 105.807
getChromInfoFromNCBI     0.267  0.011  10.103
NCBI-utils               0.069  0.008  15.304
* 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:
    'special_mappings' contains sequence names not found in the NCBI assembly
  ERROR in test_switching_Seqinfo_to_RefSeq_style: Error in .map_UCSC_seqlevels_to_NCBI_seqlevels(UCSC_seqlevels, NCBI_seqlevels,  : 
    'special_mappings' contains sequence names not found in the NCBI assembly
  
  Test files with failing tests
  
     test_seqlevelsStyle.R 
       test_switching_Seqinfo_between_UCSC_and_NCBI_styles 
       test_switching_Seqinfo_to_RefSeq_style 
  
  
  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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/GenomeInfoDb.Rcheck/00check.log’
for details.