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###
### Running command:
###
###   /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_1.23.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BUSpaRse.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 ‘BUSpaRse/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BUSpaRse’ version ‘1.23.1’
* 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 14.0.0 (clang-1400.0.29.202)’
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
tr2g_TxDb        45.543  9.987  60.797
knee_plot        25.038  2.861  35.776
dl_transcriptome 10.764  0.663  16.094
tr2g_EnsDb        4.194  1.327   5.668
transcript2gene   5.077  0.355   9.067
tr2g_ensembl      1.588  0.124   5.922
* 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:
  > 
  > test_check("BUSpaRse")
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 95 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_tr2g.R:34:3'): Sensible results from biomart query ─────────────
  Error in `my_useMart(ensembl_version, mart_use, ds_name, host_use)`: Version 98 is unavailable in the archive.
  Backtrace:
      ▆
   1. └─BUSpaRse::tr2g_ensembl(...) at test_tr2g.R:34:3
   2.   └─BUSpaRse:::my_useMart(ensembl_version, mart_use, ds_name, host_use)
  
  [ 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 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-3.22-bioc/meat/BUSpaRse.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BUSpaRse
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘BUSpaRse’ ...
** this is package ‘BUSpaRse’ version ‘1.23.1’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c fill_cell_gene.cpp -o fill_cell_gene.o
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o BUSpaRse.so RcppExports.o fill_cell_gene.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-BUSpaRse/00new/BUSpaRse/libs
** R
** data
*** moving datasets to lazyload DB
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BUSpaRse)

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.

> library(testthat)
> library(BUSpaRse)
> 
> test_check("BUSpaRse")
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 95 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_tr2g.R:34:3'): Sensible results from biomart query ─────────────
Error in `my_useMart(ensembl_version, mart_use, ds_name, host_use)`: Version 98 is unavailable in the archive.
Backtrace:
    ▆
 1. └─BUSpaRse::tr2g_ensembl(...) at test_tr2g.R:34:3
 2.   └─BUSpaRse:::my_useMart(ensembl_version, mart_use, ds_name, host_use)

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 95 ]
Error: Test failures
Execution halted