############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MungeSumstats.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MungeSumstats_1.14.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/MungeSumstats.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘MungeSumstats/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MungeSumstats’ version ‘1.14.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 loading without being on the library search path ... 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 60.885 9.268 70.387 format_sumstats 52.451 8.301 61.607 liftover 3.594 0.051 5.162 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/MungeSumstats.Rcheck/00check.log’ for details.