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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BUSpaRse.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BUSpaRse_1.21.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BUSpaRse.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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
tar: Error opening archive: Unrecognized archive format
Warning in untar(fileName(ds)[id], exdir = file_path) :
  '/usr/bin/tar -xf '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/5e817969dc82_3348' -C '/Users/biocbuild/bbs-3.21-bioc/meat/BUSpaRse.Rcheck'' returned error code 1
The downloaded files are in /Users/biocbuild/bbs-3.21-bioc/meat/BUSpaRse.Rcheck/out_hgmm100 
[1] "/Users/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")
Error in normalizePath(kallisto_out_path, mustWork = TRUE) : 
  path[1]="./out_hgmm100": No such file or directory
Calls: transcript2gene -> normalizePath
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
dl_transcriptome 4.119  0.238   9.406
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/BUSpaRse.Rcheck/00check.log’
for details.