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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:txdbmaker.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings txdbmaker_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/txdbmaker.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-29 10:05:52 UTC
* checking for file ‘txdbmaker/DESCRIPTION’ ... OK
* this is package ‘txdbmaker’ version ‘1.8.0’
* 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 ‘txdbmaker’ 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 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘AnnotationDbi:::dbEasyQuery’ ‘BiocGenerics:::testPackage’
  ‘GenomeInfoDb:::check_tax_id’
  ‘GenomeInfoDb:::lookup_organism_by_tax_id’
  ‘GenomeInfoDb:::lookup_tax_id_by_organism’
  ‘GenomeInfoDb:::make_circ_flags_from_circ_seqs’
  ‘S4Vectors:::anyMissingOrOutside’
  ‘S4Vectors:::extract_data_frame_rows’
  ‘S4Vectors:::load_package_gracefully’ ‘S4Vectors:::quick_togroup’
  ‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’
  ‘rtracklayer:::resourceDescription’
  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 ... ERROR
Running examples in ‘txdbmaker-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: makeFeatureDbFromUCSC
> ### Title: Making a FeatureDb object from annotations available at the UCSC
> ###   Genome Browser
> ### Aliases: supportedUCSCFeatureDbTracks supportedUCSCFeatureDbTables
> ###   UCSCFeatureDbTableSchema makeFeatureDbFromUCSC
> 
> ### ** Examples
> 
> ## Display the list of genomes available at UCSC:
> library(UCSC.utils)
> list_UCSC_genomes()[ , "genome"]
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [api.genome.ucsc.edu]:
SSL connection timeout
Calls: list_UCSC_genomes ... request_fetch.write_memory -> <Anonymous> -> raise_libcurl_error
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:
  SSL connection timeout
  
  Test files with failing tests
  
     test_makeTxDbFromBiomart.R 
       test_makeTxDbFromBiomart 
  
     test_makeTxDbFromUCSC.R 
       test_makeTxDbFromUCSC 
  
  
  Error in BiocGenerics:::testPackage("txdbmaker") : 
    unit tests failed for package txdbmaker
  Calls: <Anonymous> -> <Anonymous>
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘txdbmaker.Rmd’ using rmarkdown

Quitting from txdbmaker.Rmd:66-71 [supportedUCSCtables]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Timeout was reached [api.genome.ucsc.edu]:
SSL connection timeout
---
Backtrace:
     ▆
  1. ├─txdbmaker::supportedUCSCtables(genome = "mm9")
  2. │ └─UCSC.utils::list_UCSC_tracks(genome, group = "genes")
  3. │   └─UCSC.utils:::.get_UCSC_genome_tracks(...)
  4. │     └─UCSC.utils:::check_genome(genome)
  5. │       ├─genome %in% list_UCSC_genomes()[, "genome"]
  6. │       └─UCSC.utils::list_UCSC_genomes()
  7. │         └─UCSC.utils:::.list_UCSC_genomes(api.url = api.url, recache = recache)
  8. │           └─UCSC.utils:::API_list_genomes(api.url = api.url)
  9. │             └─UCSC.utils:::.query_API(endpoint, api.url = api.url, fallback_errmsg = fallback_errmsg)
 10. │               └─httr::GET(url, user_agent("Bioconductor UCSC.utils"), query = query)
 11. │                 └─httr:::request_perform(req, hu$handle$handle)
 12. │                   ├─httr:::request_fetch(req$output, req$url, handle)
 13. │                   └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 14. │                     └─curl::curl_fetch_memory(url, handle = handle)
 15. └─curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'txdbmaker.Rmd' failed with diagnostics:
Timeout was reached [api.genome.ucsc.edu]:
SSL connection timeout
--- failed re-building ‘txdbmaker.Rmd’

SUMMARY: processing the following file failed:
  ‘txdbmaker.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/txdbmaker.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL txdbmaker
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘txdbmaker’ ...
** this is package ‘txdbmaker’ version ‘1.8.0’
** 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 (txdbmaker)

R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 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("txdbmaker") || stop("unable to load txdbmaker package")
Loading required package: txdbmaker
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: Seqinfo
Loading required package: GenomicRanges
Loading required package: IRanges
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

[1] TRUE
> txdbmaker:::.test()
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... Timing stopped at: 5.651 0.344 270.8
Error in .prepareBiomartMetadata(mart, is_full_dataset, host, taxonomyId) : 
  the BioMart database "ENSEMBL_MART_ENSEMBL" has no (or more than one)
  "hsapiens_gene_ensembl" datasets
In addition: Warning message:
In .makeTxDb_normarg_chrominfo(chrominfo) :
  genome version information is not available for this TxDb object
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Timing stopped at: 0.202 0.002 10.16
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [api.genome.ucsc.edu]:
SSL connection timeout
In addition: There were 24 warnings (use warnings() to see them)


RUNIT TEST PROTOCOL -- Fri May 29 06:15:55 2026 
*********************************************** 
Number of test functions: 9 
Number of errors: 2 
Number of failures: 0 

 
1 Test Suite : 
txdbmaker RUnit Tests - 9 test functions, 2 errors, 0 failures
ERROR in test_makeTxDbFromBiomart: Error in .prepareBiomartMetadata(mart, is_full_dataset, host, taxonomyId) : 
  the BioMart database "ENSEMBL_MART_ENSEMBL" has no (or more than one)
  "hsapiens_gene_ensembl" datasets
ERROR in test_makeTxDbFromUCSC: Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [api.genome.ucsc.edu]:
SSL connection timeout

Test files with failing tests

   test_makeTxDbFromBiomart.R 
     test_makeTxDbFromBiomart 

   test_makeTxDbFromUCSC.R 
     test_makeTxDbFromUCSC 


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