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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BASiCS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BASiCS_2.21.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BASiCS.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BASiCS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BASiCS’ version ‘2.21.1’
* 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 ‘BASiCS’ can be installed ... WARNING
Found the following significant warnings:
  ./utils.h:357:15: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  ./utils.h:357:45: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  ./utils.h:357:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ./utils.h:358:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ./updates.h:163:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ./updates.h:258:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ./updates.h:266:13: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ./updatesNoSpikes.h:76:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ./updatesNoSpikes.h:102:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ./updatesRegNoSpikes.h:107:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ./updatesRegNoSpikes.h:139:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ./MCMCReg.h:383:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ./MCMCRegNoSpikes.h:382:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/Users/biocbuild/bbs-3.22-bioc/meat/BASiCS.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.1.sdk’
* 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 whether startup messages can be suppressed ... 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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... 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
BASiCS_DivideAndConquer 1.236  0.022  10.884
* 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 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/BASiCS.Rcheck/00check.log’
for details.