############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:RNAmodR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings RNAmodR_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/RNAmodR.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 ‘RNAmodR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RNAmodR’ version ‘1.20.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘RNAmodR’ 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 ... NOTE Unexported objects imported by ':::' calls: 'BiocGenerics:::replaceSlots' 'Biostrings:::XString' 'IRanges:::.valid.CompressedList' 'IRanges:::coerceToCompressedList' 'S4Vectors:::.valid.DataFrame' 'S4Vectors:::labeledLine' 'S4Vectors:::make_zero_col_DataFrame' 'S4Vectors:::prepare_objects_to_bind' See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: '.get_inosine_score' * 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) ModInosine-functions.Rd:64-66: Lost braces in \itemize; meant \describe ? checkRd: (-1) ModInosine-functions.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) ModInosine-functions.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) ModInosine-functions.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) ModInosine-functions.Rd:47-49: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) ModInosine-functions.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) ModInosine-functions.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) ModInosine.Rd:39-40: Lost braces in \itemize; meant \describe ? checkRd: (-1) ModInosine.Rd:41-42: Lost braces in \itemize; meant \describe ? checkRd: (-1) ModInosine.Rd:43-44: Lost braces in \itemize; meant \describe ? checkRd: (-1) Modifier-class.Rd:124-126: Lost braces in \itemize; meant \describe ? checkRd: (-1) Modifier-class.Rd:127-128: Lost braces in \itemize; meant \describe ? checkRd: (-1) Modifier-class.Rd:129-130: Lost braces in \itemize; meant \describe ? checkRd: (-1) Modifier-class.Rd:78-81: Lost braces in \itemize; meant \describe ? checkRd: (-1) Modifier-class.Rd:82: Lost braces in \itemize; meant \describe ? checkRd: (-1) Modifier-class.Rd:83-85: Lost braces in \itemize; meant \describe ? checkRd: (-1) Modifier-class.Rd:103-105: Lost braces in \itemize; meant \describe ? checkRd: (-1) Modifier-class.Rd:194-195: Lost braces in \itemize; meant \describe ? checkRd: (-1) Modifier-class.Rd:196-197: Lost braces in \itemize; meant \describe ? checkRd: (-1) Modifier-class.Rd:198-199: Lost braces in \itemize; meant \describe ? checkRd: (-1) Modifier-functions.Rd:138-139: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Modifier-functions.Rd:140-141: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Modifier-functions.Rd:142-143: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Modifier-functions.Rd:144: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Modifier-functions.Rd:145: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Modifier-functions.Rd:146-147: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Modifier-functions.Rd:148: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Modifier-functions.Rd:149: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Modifier-functions.Rd:150-151: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Modifier-functions.Rd:152: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Modifier-functions.Rd:153-154: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Modifier-functions.Rd:155-156: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) ModifierSet-class.Rd:49-51: Lost braces in \itemize; meant \describe ? checkRd: (-1) ModifierSet-class.Rd:52-53: Lost braces in \itemize; meant \describe ? checkRd: (-1) ModifierSet-class.Rd:54-57: Lost braces in \itemize; meant \describe ? checkRd: (-1) ModifierSet-class.Rd:74-80: Lost braces in \itemize; meant \describe ? checkRd: (-1) RNAmodR-datasets.Rd:20: Lost braces in \itemize; meant \describe ? checkRd: (-1) RNAmodR-datasets.Rd:21: Lost braces in \itemize; meant \describe ? checkRd: (-1) RNAmodR-datasets.Rd:22: Lost braces in \itemize; meant \describe ? checkRd: (-1) RNAmodR-datasets.Rd:23: Lost braces in \itemize; meant \describe ? checkRd: (-1) RNAmodR-datasets.Rd:24: Lost braces in \itemize; meant \describe ? checkRd: (-1) RNAmodR-datasets.Rd:25: Lost braces in \itemize; meant \describe ? checkRd: (-1) RNAmodR-datasets.Rd:26: Lost braces in \itemize; meant \describe ? checkRd: (-1) RNAmodR-datasets.Rd:27: Lost braces in \itemize; meant \describe ? checkRd: (-1) RNAmodR-datasets.Rd:28: Lost braces in \itemize; meant \describe ? checkRd: (-1) RNAmodR-datasets.Rd:29: Lost braces in \itemize; meant \describe ? checkRd: (-1) RNAmodR-datasets.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) RNAmodR-development.Rd:49-55: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) RNAmodR-development.Rd:56-57: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SequenceData-class.Rd:56-57: Lost braces in \itemize; meant \describe ? checkRd: (-1) SequenceData-class.Rd:58-59: Lost braces in \itemize; meant \describe ? checkRd: (-1) SequenceData-class.Rd:60-62: Lost braces in \itemize; meant \describe ? checkRd: (-1) SequenceData-class.Rd:63-64: Lost braces in \itemize; meant \describe ? checkRd: (-1) SequenceData-class.Rd:75: Lost braces in \itemize; meant \describe ? checkRd: (-1) SequenceData-class.Rd:76-78: Lost braces in \itemize; meant \describe ? checkRd: (-1) SequenceData-functions.Rd:159: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SequenceData-functions.Rd:160-161: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SequenceData-functions.Rd:162-163: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SequenceData-functions.Rd:164-165: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) aggregate.Rd:64-68: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) aggregate.Rd:69-72: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) aggregate.Rd:73-74: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) aggregate.Rd:79-80: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) aggregate.Rd:82-83: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) aggregate.Rd:85-86: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) compareByCoord.Rd:45-46: Lost braces in \itemize; meant \describe ? checkRd: (-1) compareByCoord.Rd:47: Lost braces in \itemize; meant \describe ? checkRd: (-1) compareByCoord.Rd:48-50: Lost braces in \itemize; meant \describe ? checkRd: (-1) compareByCoord.Rd:51-54: Lost braces in \itemize; meant \describe ? checkRd: (-1) compareByCoord.Rd:55-56: Lost braces in \itemize; meant \describe ? checkRd: (-1) compareByCoord.Rd:57: Lost braces in \itemize; meant \describe ? checkRd: (-1) modify.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) modify.Rd:42-43: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plotData.Rd:122-124: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotData.Rd:125-127: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotData.Rd:128-129: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotData.Rd:130-131: Lost braces in \itemize; meant \describe ? checkRd: (-1) subsetByCoord.Rd:99-105: Lost braces in \itemize; meant \describe ? checkRd: (-1) subsetByCoord.Rd:106-107: Lost braces in \itemize; meant \describe ? checkRd: (-1) subsetByCoord.Rd:108-110: Lost braces in \itemize; meant \describe ? checkRd: (-1) subsetByCoord.Rd:111-113: Lost braces in \itemize; meant \describe ? checkRd: (-1) subsetByCoord.Rd:124-125: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) subsetByCoord.Rd:128-129: Lost braces in \itemize; \value handles \item{}{} directly * 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 'RNAmodR-internals.Rd': ‘object’ ‘range’ ‘data’ ‘modType’ ‘scoreFun’ ‘source’ ‘type’ ‘j’ ‘value’ 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 data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed stats 42.496 4.718 40.113 CoverageSequenceData-class 8.904 0.925 10.476 ModInosine 8.028 1.152 9.535 EndSequenceData-class 6.506 0.924 7.786 PileupSequenceData-class 5.510 0.530 6.387 ProtectedEndSequenceData-class 5.422 0.565 6.347 * 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/RNAmodR.Rcheck/00check.log’ for details.