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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RNAmodR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings RNAmodR_1.9.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/RNAmodR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RNAmodR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RNAmodR' version '1.9.1'
* 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 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 R 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 ... OK
* 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
stats                          17.27   2.28   54.50
CoverageSequenceData-class      8.23   1.47   11.44
ModInosine                      5.20   0.31    6.42
ProtectedEndSequenceData-class  4.41   0.46    5.90
PileupSequenceData-class        3.98   0.45    5.27
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/RNAmodR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL RNAmodR
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'RNAmodR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RNAmodR'
    finding HTML links ... done
    CoverageSequenceData-class              html  
    EndSequenceData-class                   html  
    ModInosine-functions                    html  
    ModInosine-internals                    html  
    ModInosine                              html  
    Modifier-class                          html  
    Modifier-functions                      html  
    ModifierSet-class                       html  
    NormEndSequenceData-class               html  
    PileupSequenceData-class                html  
    ProtectedEndSequenceData-class          html  
    RNAmodR-datasets                        html  
    RNAmodR-development                     html  
    RNAmodR-internals                       html  
    RNAmodR                                 html  
    SequenceData-class                      html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-RNAmodR/00new/RNAmodR/help/SequenceData.html
    SequenceData-functions                  html  
    SequenceDataFrame-class                 html  
    SequenceDataList-class                  html  
    SequenceDataSet-class                   html  
    SequenceModDNAStringSetTrack-class      html  
    SequenceModRNAStringSetTrack-class      html  
    aggregate                               html  
    compareByCoord                          html  
    modify                                  html  
    plotData                                html  
    plotROC                                 html  
    settings                                html  
    stats                                   html  
    subsetByCoord                           html  
** 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)
Making 'packages.html' ... done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics

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, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

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")
[ FAIL 0 | WARN 1 | SKIP 9 | PASS 192 ]

== Skipped tests ===============================================================
* On Bioconductor (9)

[ FAIL 0 | WARN 1 | SKIP 9 | PASS 192 ]
> 
> proc.time()
   user  system elapsed 
  48.71    3.67   54.21