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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RNAmodR.RiboMethSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RNAmodR.RiboMethSeq_1.21.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/RNAmodR.RiboMethSeq.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.RiboMethSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RNAmodR.RiboMethSeq’ 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.RiboMethSeq’ 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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.get_rms_scores'
* 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) ModRiboMethSeq-functions.Rd:96-98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ModRiboMethSeq-functions.Rd:75-76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ModRiboMethSeq-functions.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ModRiboMethSeq-functions.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ModRiboMethSeq-functions.Rd:79-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ModRiboMethSeq-functions.Rd:81-82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ModRiboMethSeq-functions.Rd:83-84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ModRiboMethSeq.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ModRiboMethSeq.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ModRiboMethSeq.Rd:41-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ModRiboMethSeq.Rd:44-45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ModRiboMethSeq.Rd:46-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ModRiboMethSeq.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ModRiboMethSeq.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ModRiboMethSeq.Rd:52-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ModRiboMethSeq.Rd:55-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ModRiboMethSeq.Rd:59-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ModRiboMethSeq.Rd:65-66: 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
ModRiboMethSeq 26.186  3.324  26.073
* 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-3.21-bioc/meat/RNAmodR.RiboMethSeq.Rcheck/00check.log’
for details.