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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:RNAmodR.RiboMethSeq.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings RNAmodR.RiboMethSeq_1.21.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/RNAmodR.RiboMethSeq.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* 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.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 ... 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 loading without being on the library search path ... 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 28.762   3.38  28.414
* 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-3.21-bioc/meat/RNAmodR.RiboMethSeq.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL RNAmodR.RiboMethSeq
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘RNAmodR.RiboMethSeq’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RNAmodR.RiboMethSeq)

R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(RNAmodR.RiboMethSeq)
Loading required package: RNAmodR
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Modstrings
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit


Attaching package: 'RNAmodR'

The following object is masked from 'package:testthat':

    compare

> 
> test_check("RNAmodR.RiboMethSeq")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 89 ]
> 
> proc.time()
   user  system elapsed 
 25.359   1.529  26.875