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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BUSpaRse.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BUSpaRse_1.21.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BUSpaRse.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘BUSpaRse/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BUSpaRse’ version ‘1.21.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘BUSpaRse’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... 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:
  annot_circular.Rd: BSgenome, XStringSet, genomeStyles, seqlevels
  check_genome.Rd: BSgenome, XStringSet, genomeStyles
  dl_transcriptome.Rd: listEnsemblArchives
  dot-get_velocity_files.Rd: str_length, BSgenome, XStringSet,
    genomeStyles
  get_velocity_files.Rd: TxDb, EnsDb, str_length, BSgenome, XStringSet,
    genomeStyles
  match_style.Rd: BSgenome, XStringSet, genomeStyles, seqlevels
  subset_annot.Rd: BSgenome, XStringSet, genomeStyles
  tr2g_EnsDb.Rd: BSgenome, XStringSet, genomeStyles, columns
  tr2g_GRanges.Rd: GRanges, BSgenome, XStringSet, genomeStyles
  tr2g_TxDb.Rd: TxDb, BSgenome, XStringSet, genomeStyles
  tr2g_ensembl.Rd: listAttributes, listEnsemblArchives, useMart
  tr2g_gff3.Rd: BSgenome, XStringSet, genomeStyles
  tr2g_gtf.Rd: BSgenome, XStringSet, genomeStyles
  transcript2gene.Rd: useMart
  validate_velocity_input.Rd: str_length, BSgenome, XStringSet,
    genomeStyles
  write_velocity_output.Rd: BSgenome, XStringSet, genomeStyles
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘BUSpaRse-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_knee_df
> ### Title: Plot the transposed knee plot and inflection point
> ### Aliases: get_knee_df get_inflection knee_plot
> 
> ### ** Examples
> 
> # Download dataset already in BUS format
> library(TENxBUSData)
> TENxBUSData(".", dataset = "hgmm100")
see ?TENxBUSData and browseVignettes('TENxBUSData') for documentation
loading from cache
The downloaded files are in /home/biocbuild/bbs-3.21-bioc/meat/BUSpaRse.Rcheck/out_hgmm100 
[1] "/home/biocbuild/bbs-3.21-bioc/meat/BUSpaRse.Rcheck/out_hgmm100"
> tr2g <- transcript2gene(c("Homo sapiens", "Mus musculus"), 
+   type = "vertebrate",
+   ensembl_version = 99, kallisto_out_path = "./out_hgmm100")
Querying biomart for transcript and gene IDs of Homo sapiens
Error in `req_perform()`:
! HTTP 500 Internal Server Error.
Backtrace:
     ▆
  1. └─BUSpaRse::transcript2gene(...)
  2.   └─base::mapply(...)
  3.     └─BUSpaRse (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]], ensembl_version = 99)
  4.       └─BUSpaRse:::my_useMart(ensembl_version, mart_use, ds_name, host_use)
  5.         └─biomaRt::useMart(biomart = mart_use, dataset = ds_name, host = host_use)
  6.           └─biomaRt:::.useMart(...)
  7.             └─biomaRt:::.listMarts(...)
  8.               └─biomaRt:::bmRequest(...)
  9.                 └─httr2::req_perform(request)
 10.                   └─httr2:::handle_resp(req, resp, error_call = error_call)
 11.                     └─httr2:::resp_failure_cnd(req, resp, error_call = error_call)
 12.                       ├─rlang::catch_cnd(...)
 13.                       │ ├─rlang::eval_bare(...)
 14.                       │ ├─base::tryCatch(...)
 15.                       │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 16.                       │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 17.                       │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 18.                       │ └─base::force(expr)
 19.                       └─rlang::abort(...)
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
dl_transcriptome 8.861  0.512  15.006
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    7.             └─httr2::req_perform(request)
    8.               └─httr2:::handle_resp(req, resp, error_call = error_call)
    9.                 └─httr2:::resp_failure_cnd(req, resp, error_call = error_call)
   10.                   ├─rlang::catch_cnd(...)
   11.                   │ ├─rlang::eval_bare(...)
   12.                   │ ├─base::tryCatch(...)
   13.                   │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   14.                   │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   15.                   │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   16.                   │ └─base::force(expr)
   17.                   └─rlang::abort(...)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 95 ]
  Error: Test failures
  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 ‘sparse-matrix.Rmd’ using rmarkdown

Quitting from sparse-matrix.Rmd:42-46 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'sparse-matrix.Rmd' failed with diagnostics:
HTTP 500 Internal Server Error.
--- failed re-building ‘sparse-matrix.Rmd’

--- re-building ‘tr2g.Rmd’ using rmarkdown

Quitting from tr2g.Rmd:47-51 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'tr2g.Rmd' failed with diagnostics:
HTTP 500 Internal Server Error.
--- failed re-building ‘tr2g.Rmd’

SUMMARY: processing the following files failed:
  ‘sparse-matrix.Rmd’ ‘tr2g.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 3 ERRORs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/BUSpaRse.Rcheck/00check.log’
for details.