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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:made4.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings made4_1.80.0.tar.gz
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* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/made4.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 ‘made4/DESCRIPTION’ ... OK
* this is package ‘made4’ version ‘1.80.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘made4’ 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 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) NCI60.Rd:19: Escaped LaTeX specials: \$
checkRd: (-1) NCI60.Rd:19-20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NCI60.Rd:22: Escaped LaTeX specials: \$
checkRd: (-1) NCI60.Rd:22-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NCI60.Rd:25: Escaped LaTeX specials: \$
checkRd: (-1) NCI60.Rd:25-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NCI60.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) NCI60.Rd:30-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NCI60.Rd:31: Escaped LaTeX specials: \$ \$
checkRd: (-1) NCI60.Rd:32: Escaped LaTeX specials: \$ \$
checkRd: (-1) NCI60.Rd:33: Escaped LaTeX specials: \$ \$
checkRd: (-1) NCI60.Rd:50: Escaped LaTeX specials: \$
checkRd: (-1) NCI60.Rd:52: Escaped LaTeX specials: \$ \$
checkRd: (-1) NCI60.Rd:60: Escaped LaTeX specials: \$
checkRd: (-1) NCI60.Rd:64: Escaped LaTeX specials: \$ \$
prepare_Rd: asDataFrame.Rd:30: Dropping empty section \examples
checkRd: (-1) between.graph.Rd:17: Escaped LaTeX specials: \$ \$
checkRd: (-1) between.graph.Rd:25: Escaped LaTeX specials: \$
checkRd: (-1) between.graph.Rd:26: Escaped LaTeX specials: \$
checkRd: (-1) between.graph.Rd:32: Escaped LaTeX specials: \$ \$
checkRd: (-1) between.graph.Rd:34: Escaped LaTeX specials: \$
checkRd: (-1) bga.Rd:27: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) bga.Rd:70: Escaped LaTeX specials: \$ \$
checkRd: (-1) bga.Rd:76: Escaped LaTeX specials: \$
checkRd: (-1) bga.Rd:95: Escaped LaTeX specials: \$
checkRd: (-1) cia.Rd:69: Escaped LaTeX specials: \$ \$
checkRd: (-1) cia.Rd:77: Escaped LaTeX specials: \$
checkRd: (-1) cia.Rd:78: Escaped LaTeX specials: \$
checkRd: (-1) cia.Rd:85: Escaped LaTeX specials: \$ \$
checkRd: (-1) do3d.Rd:22: Escaped LaTeX specials: \$ \$
checkRd: (-1) do3d.Rd:24: Escaped LaTeX specials: \$ \$
checkRd: (-1) genes1d.Rd:9: Escaped LaTeX specials: \$ \$
checkRd: (-1) genes1d.Rd:16: Escaped LaTeX specials: \$ \$
checkRd: (-1) genes1d.Rd:22: Escaped LaTeX specials: \$ \$
checkRd: (-1) html3D.Rd:19: Escaped LaTeX specials: \$ \$
checkRd: (-1) html3D.Rd:20: Escaped LaTeX specials: \$ \$
checkRd: (-1) jmol3D.Rd:14: Escaped LaTeX specials: \$ \$
checkRd: (-1) jmol3D.Rd:15: Escaped LaTeX specials: \$ \$
checkRd: (-1) khan.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) khan.Rd:15-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) khan.Rd:17: Escaped LaTeX specials: \$
checkRd: (-1) khan.Rd:17-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) khan.Rd:19: Escaped LaTeX specials: \$
checkRd: (-1) khan.Rd:19-20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) khan.Rd:20: Escaped LaTeX specials: \$ \$
checkRd: (-1) khan.Rd:21: Escaped LaTeX specials: \$
checkRd: (-1) khan.Rd:21-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) khan.Rd:23: Escaped LaTeX specials: \$
checkRd: (-1) khan.Rd:24: Escaped LaTeX specials: \$
checkRd: (-1) khan.Rd:24-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) khan.Rd:26: Escaped LaTeX specials: \$
checkRd: (-1) khan.Rd:27: Escaped LaTeX specials: \$
checkRd: (-1) khan.Rd:27-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) khan.Rd:31: Escaped LaTeX specials: \$
checkRd: (-1) khan.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) khan.Rd:32: Escaped LaTeX specials: \$
checkRd: (-1) khan.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) khan.Rd:33: Escaped LaTeX specials: \$
checkRd: (-1) khan.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) khan.Rd:34: Escaped LaTeX specials: \$
checkRd: (-1) khan.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) khan.Rd:35: Escaped LaTeX specials: \$
checkRd: (-1) khan.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) khan.Rd:36: Escaped LaTeX specials: \$
checkRd: (-1) khan.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) khan.Rd:37: Escaped LaTeX specials: \$
checkRd: (-1) khan.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) khan.Rd:38: Escaped LaTeX specials: \$
checkRd: (-1) khan.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ord.Rd:27: Escaped LaTeX specials: \$ \$
checkRd: (-1) ord.Rd:53: Escaped LaTeX specials: \$
checkRd: (-1) ord.Rd:66: Escaped LaTeX specials: \$ \$
checkRd: (-1) ord.Rd:74: Escaped LaTeX specials: \$
checkRd: (-1) plotarrays.Rd:6: Escaped LaTeX specials: \$
checkRd: (-1) plotgenes.Rd:6: Escaped LaTeX specials: \$
checkRd: (-1) s.var.Rd:35: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) s.var.Rd:38: Escaped LaTeX specials: \$ \$
checkRd: (-1) sumstats.Rd:16: Escaped LaTeX specials: \$ \$
checkRd: (-1) sumstats.Rd:17: Escaped LaTeX specials: \$
checkRd: (-1) topgenes.Rd:16: Escaped LaTeX specials: \$ \$
checkRd: (-1) topgenes.Rd:17: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) topgenes.Rd:22: Escaped LaTeX specials: \$ \$
checkRd: (-1) topgenes.Rd:33: Escaped LaTeX specials: \$ \$
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'forrwcoa.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'genes1d.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... 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
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/made4.Rcheck/00check.log’
for details.