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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RNAmodR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RNAmodR_1.21.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/RNAmodR.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAmodR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RNAmodR’ version ‘1.21.0’
* 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 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                          35.379  4.282  31.626
CoverageSequenceData-class      9.411  1.386  11.419
ModInosine                      7.070  0.376   7.851
EndSequenceData-class           5.613  0.401   6.435
ProtectedEndSequenceData-class  4.995  0.350   5.733
PileupSequenceData-class        4.887  0.336   5.722
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/RNAmodR.Rcheck/00check.log’
for details.