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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomeInfoDb.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomeInfoDb_1.45.10.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/GenomeInfoDb.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomeInfoDb/DESCRIPTION’ ... OK
* this is package ‘GenomeInfoDb’ version ‘1.45.10’
* 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 ‘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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘GenomeInfoDb-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getChromInfoFromEnsembl
> ### Title: Get chromosome information for an Ensembl species
> ### Aliases: getChromInfoFromEnsembl
> ### Keywords: manip
> 
> ### ** Examples
> 
> ## ---------------------------------------------------------------------
> ## A. BASIC EXAMPLES
> ## ---------------------------------------------------------------------
> 
> ## Internet access required!
> 
> ## === Worm ===
> ## https://uswest.ensembl.org/Caenorhabditis_elegans
> 
> celegans <- getChromInfoFromEnsembl("celegans")
> attr(celegans, "species_info")
$name
[1] "Caenorhabditis elegans (Nematode, N2)"

$species
[1] "caenorhabditis_elegans"

$division
[1] "EnsemblVertebrates"

$Ensembl_release
[1] 115

$taxonomy_id
[1] 6239

$assembly
[1] "WBcel235"

$assembly_accession
[1] "GCA_000002985.3"

$core_db
[1] "caenorhabditis_elegans_core_115_282"

> 
> getChromInfoFromEnsembl("celegans", as.Seqinfo=TRUE)
Seqinfo object with 7 sequences (1 circular) from WBcel235 genome:
  seqnames seqlengths isCircular   genome
  I          15072434         NA WBcel235
  II         15279421         NA WBcel235
  III        13783801         NA WBcel235
  IV         17493829         NA WBcel235
  V          20924180         NA WBcel235
  X          17718942         NA WBcel235
  MtDNA         13794       TRUE WBcel235
> 
> celegans <- getChromInfoFromEnsembl("celegans", map.NCBI=TRUE)
> 
> ## === Yeast ===
> ## https://uswest.ensembl.org/Saccharomyces_cerevisiae
> 
> scerevisiae <- getChromInfoFromEnsembl("scerevisiae")
> attr(scerevisiae, "species_info")
$name
[1] "Saccharomyces cerevisiae"

$species
[1] "saccharomyces_cerevisiae"

$division
[1] "EnsemblVertebrates"

$Ensembl_release
[1] 115

$taxonomy_id
[1] 559292

$assembly
[1] "R64-1-1"

$assembly_accession
[1] "GCA_000146045.2"

$core_db
[1] "saccharomyces_cerevisiae_core_115_4"

> 
> getChromInfoFromEnsembl("scerevisiae", as.Seqinfo=TRUE)
Seqinfo object with 17 sequences (1 circular) from R64-1-1 genome:
  seqnames seqlengths isCircular  genome
  XI           666816       <NA> R64-1-1
  IX           439888       <NA> R64-1-1
  IV          1531933       <NA> R64-1-1
  III          316620       <NA> R64-1-1
  X            745751       <NA> R64-1-1
  ...             ...        ...     ...
  XVI          948066       <NA> R64-1-1
  XV          1091291       <NA> R64-1-1
  I            230218       <NA> R64-1-1
  Mito          85779       TRUE R64-1-1
  VII         1090940       <NA> R64-1-1
> 
> scerevisiae <- getChromInfoFromEnsembl("scerevisiae", map.NCBI=TRUE)
> 
> ## Arabidopsis thaliana:
> athaliana <- getChromInfoFromEnsembl("athaliana", division="plants",
+                                      map.NCBI=TRUE)
Error in download.file(url, destfile, quiet = TRUE) : 
  cannot open URL 'ftp://ftp.ensemblgenomes.org/pub/plants/current/mysql/arabidopsis_thaliana_core_61_114_11/coord_system.txt.gz'
Calls: getChromInfoFromEnsembl ... fetch_table_dump_from_Ensembl_FTP -> fetch_table_from_url
Execution halted
* 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:
    is_primary_key(sequence_name) is not TRUE
  ERROR in test_switching_Seqinfo_to_RefSeq_style: Error in .format_NCBI_chrom_info(assembly_report, circ_seqs = circ_seqs) : 
    is_primary_key(sequence_name) is not TRUE
  
  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: 2 ERRORs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/GenomeInfoDb.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GenomeInfoDb
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘GenomeInfoDb’ ...
** this is package ‘GenomeInfoDb’ version ‘1.45.10’
** 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 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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: 140.6 10.81 198.3
Error in .format_NCBI_chrom_info(assembly_report, circ_seqs = circ_seqs) : 
  is_primary_key(sequence_name) is not TRUE
In addition: There were 31 warnings (use warnings() to see them)
Timing stopped at: 148.9 11.01 161.6
Error in .format_NCBI_chrom_info(assembly_report, circ_seqs = circ_seqs) : 
  is_primary_key(sequence_name) is not TRUE
In addition: There were 50 or more warnings (use warnings() to see the first 50)


RUNIT TEST PROTOCOL -- Wed Sep  3 21:09:18 2025 
*********************************************** 
Number of test functions: 21 
Number of errors: 2 
Number of failures: 0 

 
1 Test Suite : 
GenomeInfoDb RUnit Tests - 21 test functions, 2 errors, 0 failures
ERROR in test_switching_Seqinfo_between_UCSC_and_NCBI_styles: Error in .format_NCBI_chrom_info(assembly_report, circ_seqs = circ_seqs) : 
  is_primary_key(sequence_name) is not TRUE
ERROR in test_switching_Seqinfo_to_RefSeq_style: Error in .format_NCBI_chrom_info(assembly_report, circ_seqs = circ_seqs) : 
  is_primary_key(sequence_name) is not TRUE

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