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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BUScorrect.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BUScorrect_1.24.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/BUScorrect.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BUScorrect/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BUScorrect' version '1.24.0'
* 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 whether package 'BUScorrect' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* 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 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 ... NOTE
checkRd: (-1) NEWS.Rd:12: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) BUSgibbs.Rd:34: Lost braces; missing escapes or markup?
    34 |         \code{a_inv_gamma}: the shape of the gamma prior for 1/sigma^2_{bg};
       |                                                                        ^
checkRd: (-1) BUSgibbs.Rd:35: Lost braces; missing escapes or markup?
    35 |         \code{b_inv_gamma}: the rate of the gamma prior for 1/sigma^2_{bg};
       |                                                                       ^
checkRd: (-1) BUSgibbs.Rd:36: Lost braces; missing escapes or markup?
    36 |         \code{a_tau0}: the shape of the gamma prior for 1/tau^2_{mu 0};
       |                                                                 ^
checkRd: (-1) BUSgibbs.Rd:39: Lost braces; missing escapes or markup?
    39 |         \code{tau_{mu1}}: the standard deviation of the normal prior of mu_{gk} (k >= 2) when the gene expression level in subtype k is different from that in subtype one.
       |                                                                            ^
checkRd: (-1) BUSgibbs.Rd:52: Lost braces; missing escapes or markup?
    52 |    \item{tau_mu_zero}{The estimated tau_{mu 0}, which is the prior normal distribution's standard deviation of the subtype effects when there is no differential expression.}
       |                                         ^
checkRd: (-1) BUSgibbs.Rd:57: Lost braces; missing escapes or markup?
    57 |    \item{gamma}{The estimated location batch effects, a G by B matrix, where gamma_{gb} is the ``location'' batch effect on gene g in the batch b. Note that the first column is zero as the first batch is taken as the reference batch without batch effects.}
       |                                                                                    ^
* 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 compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.20-bioc/R/library/BUScorrect/libs/x64/BUScorrect.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
BUSgibbs           18.61   2.55   21.16
BUScorrect-package 18.21   1.61   20.03
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'runTests.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: 2 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/BUScorrect.Rcheck/00check.log'
for details.