##############################################################################
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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BUSpaRse.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings BUSpaRse_1.22.0.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/BUSpaRse.Rcheck'
* using R version 4.5.0 RC (2025-04-04 r88126 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BUSpaRse/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BUSpaRse' version '1.22.0'
* 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 whether package 'BUSpaRse' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
* 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 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 for x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/BUSpaRse/libs/x64/BUSpaRse.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
tr2g_TxDb        57.30   8.88  285.18
knee_plot        35.97   4.54   87.98
dl_transcriptome 11.00   0.60   15.36
tr2g_EnsDb        6.25   2.00    8.63
transcript2gene   7.07   0.49    9.25
* 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: 4 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/BUSpaRse.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL BUSpaRse
###
##############################################################################
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'BUSpaRse' ...
** this is package 'BUSpaRse' version '1.22.0'
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
using C++11
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppProgress/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppProgress/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c fill_cell_gene.cpp -o fill_cell_gene.o
In file included from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/iterator/iterator_adaptor.hpp:14,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/token_iterator.hpp:22,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/tokenizer.hpp:20,
                 from fill_cell_gene.cpp:16:
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
      |     -
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
E:/biocbuild/bbs-3.21-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
      |     -
g++ -shared -s -static-libgcc -o BUSpaRse.dll tmp.def RcppExports.o fill_cell_gene.o -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lRlapack -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lRblas -lgfortran -lquadmath -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-BUSpaRse/00new/BUSpaRse/libs/x64
** 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
** 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 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 0 | WARN 1 | SKIP 0 | PASS 102 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 102 ]
> 
> proc.time()
   user  system elapsed 
  47.29    2.10   52.21