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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MungeSumstats.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MungeSumstats_1.11.8.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/MungeSumstats.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MungeSumstats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MungeSumstats’ version ‘1.11.8’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MungeSumstats’ can be installed ... OK
* 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 ... NOTE
checkRd: (-1) check_no_chr_bp.Rd:56-57: Lost braces
    56 | \item \code{sumstats_dt}{
       |                         ^
checkRd: (-1) check_no_chr_bp.Rd:58-59: Lost braces
    58 | \item \code{rsids}{
       |                   ^
checkRd: (-1) check_no_chr_bp.Rd:60-61: Lost braces
    60 | \item \code{log_files}{
       |                       ^
checkRd: (-1) check_on_ref_genome.Rd:65-66: Lost braces
    65 | \item \code{sumstats_dt}{
       |                         ^
checkRd: (-1) check_on_ref_genome.Rd:67-68: Lost braces
    67 | \item \code{rsids}{
       |                   ^
checkRd: (-1) check_on_ref_genome.Rd:69-70: Lost braces
    69 | \item \code{log_files}{
       |                       ^
checkRd: (-1) compute_nsize.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_nsize.Rd:33-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_nsize.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_nsize.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_nsize.Rd:41-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_nsize.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_sample_size.Rd:21-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_sample_size.Rd:30-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_sample_size.Rd:36-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_sample_size.Rd:42-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_sample_size.Rd:48-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_sample_size_n.Rd:16-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_sample_size_n.Rd:25-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_sample_size_n.Rd:31-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_sample_size_n.Rd:37-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_sample_size_n.Rd:43-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_sample_size_neff.Rd:21-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_sample_size_neff.Rd:30-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_sample_size_neff.Rd:36-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_sample_size_neff.Rd:42-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_sample_size_neff.Rd:48-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_sumstats.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_sumstats.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_sumstats.Rd:31-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_vcf.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_vcf.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_vcf.Rd:66-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_vcf_parallel.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_vcf_parallel.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_vcf_parallel.Rd:42-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) select_vcf_fields.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) select_vcf_fields.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) select_vcf_fields.Rd:29-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sort_coords.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sort_coords.Rd:22-24: Lost braces in \itemize; meant \describe ?
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
get_genome_builds 81.445  5.326  87.896
format_sumstats   75.083  4.320  80.862
liftover           3.917  0.073   5.978
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/MungeSumstats.Rcheck/00check.log’
for details.