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### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:GenomeInfoDb.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings GenomeInfoDb_1.47.2.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/GenomeInfoDb.Rcheck’
* using R Under development (unstable) (2025-10-28 r88973)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘GenomeInfoDb/DESCRIPTION’ ... OK
* this is package ‘GenomeInfoDb’ version ‘1.47.2’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Hervé Pagès <hpages.on.github@gmail.com>’

Unknown, possibly misspelled, fields in DESCRIPTION:
  ‘Video’ ‘git_url’ ‘git_branch’ ‘git_last_commit’ ‘git_last_commit_date’

The Title field should be in title case. Current version is:
  ‘Utilities for manipulating chromosome names, including modifying them to follow a particular naming style’
In title case that is:
  ‘Utilities for Manipulating Chromosome Names, Including Modifying Them to Follow a Particular Naming Style’
* 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 use of S3 registration ... 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 sizes of PDF files under ‘inst/doc’ ...* checking files in ‘vignettes’ ... OK
* checking examples ... NOTE
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
loadTaxonomyDb          7.272  0.241   7.517
getChromInfoFromUCSC    6.210  0.367   7.181
seqlevelsStyle          2.530  0.071   6.475
getChromInfoFromEnsembl 0.421  0.047  38.525
* 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:
  GenomeInfoDb RUnit Tests - 16 test functions, 1 error, 0 failures
  ERROR in test_switching_Seqinfo_between_UCSC_and_NCBI_styles: Error in download.file(url, destfile, quiet = TRUE) : 
    download from 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/231/765/GCA_000231765.1_GadMor_May2010/GCA_000231765.1_GadMor_May2010_assembly_report.txt' failed
  
  Test files with failing tests
  
     test_seqlevelsStyle.R 
       test_switching_Seqinfo_between_UCSC_and_NCBI_styles 
  
  
  Error in BiocGenerics:::testPackage("GenomeInfoDb") : 
    unit tests failed for package GenomeInfoDb
  Calls: <Anonymous> -> <Anonymous>
  In addition: There were 50 or more warnings (use warnings() to see the first 50)
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/GenomeInfoDb.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL GenomeInfoDb
###
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library’
* installing *source* package ‘GenomeInfoDb’ ...
** this is package ‘GenomeInfoDb’ version ‘1.47.2’
** 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 Under development (unstable) (2025-10-28 r88973) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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
Loading required package: Seqinfo
[1] TRUE
> GenomeInfoDb:::.test()
Timing stopped at: 28.19 0.831 88.11
Error in download.file(url, destfile, quiet = TRUE) : 
  download from 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/231/765/GCA_000231765.1_GadMor_May2010/GCA_000231765.1_GadMor_May2010_assembly_report.txt' failed
In addition: There were 11 warnings (use warnings() to see them)


RUNIT TEST PROTOCOL -- Thu Dec 11 13:07:33 2025 
*********************************************** 
Number of test functions: 16 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
GenomeInfoDb RUnit Tests - 16 test functions, 1 error, 0 failures
ERROR in test_switching_Seqinfo_between_UCSC_and_NCBI_styles: Error in download.file(url, destfile, quiet = TRUE) : 
  download from 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/231/765/GCA_000231765.1_GadMor_May2010/GCA_000231765.1_GadMor_May2010_assembly_report.txt' failed

Test files with failing tests

   test_seqlevelsStyle.R 
     test_switching_Seqinfo_between_UCSC_and_NCBI_styles 


Error in BiocGenerics:::testPackage("GenomeInfoDb") : 
  unit tests failed for package GenomeInfoDb
Calls: <Anonymous> -> <Anonymous>
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted