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This page was generated on 2025-09-26 12:04 -0400 (Fri, 26 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4831
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4619
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4563
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4563
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1798/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RNAmodR 1.23.2  (landing page)
Felix G.M. Ernst
Snapshot Date: 2025-09-25 13:45 -0400 (Thu, 25 Sep 2025)
git_url: https://git.bioconductor.org/packages/RNAmodR
git_branch: devel
git_last_commit: c241cdb
git_last_commit_date: 2025-09-23 16:09:50 -0400 (Tue, 23 Sep 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for RNAmodR on nebbiolo2

To the developers/maintainers of the RNAmodR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RNAmodR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: RNAmodR
Version: 1.23.2
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:RNAmodR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings RNAmodR_1.23.2.tar.gz
StartedAt: 2025-09-26 03:29:49 -0400 (Fri, 26 Sep 2025)
EndedAt: 2025-09-26 03:41:35 -0400 (Fri, 26 Sep 2025)
EllapsedTime: 706.8 seconds
RetCode: 0
Status:   OK  
CheckDir: RNAmodR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:RNAmodR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings RNAmodR_1.23.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/RNAmodR.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘RNAmodR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RNAmodR’ version ‘1.23.2’
* 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’ 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 ... 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 ... 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                          47.518  4.814  41.580
CoverageSequenceData-class      9.933  0.577  11.062
ModInosine                      7.405  0.158   7.944
ProtectedEndSequenceData-class  5.871  0.137   6.327
PileupSequenceData-class        5.789  0.118   6.220
EndSequenceData-class           5.371  0.151   5.829
* 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-3.22-bioc/meat/RNAmodR.Rcheck/00check.log’
for details.


Installation output

RNAmodR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL RNAmodR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘RNAmodR’ ...
** this is package ‘RNAmodR’ version ‘1.23.2’
** 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)

Tests output

RNAmodR.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 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)
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: Seqinfo
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")
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/15ea605481c509_2547'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/15ea605481c509_2547'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/15ea605481c509_2547'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/15ea605481c509_2547'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/15ea605481c509_2547'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/15ea605481c509_2547'
[ FAIL 0 | WARN 2 | SKIP 9 | PASS 192 ]

══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• On Bioconductor (9): 'test-0SequenceData.R:53:3',
  'test-0SequenceDataFrame.R:23:3', 'test-1SequenceDataSet.R:57:3',
  'test-2Modifier.R:85:3', 'test-3normalization.R:3:3', 'test-3subset.R:4:3',
  'test-3zcomparison.R:4:3', 'test-4roc.R:3:3', 'test-8visualization.R:158:3'

[ FAIL 0 | WARN 2 | SKIP 9 | PASS 192 ]
> 
> proc.time()
   user  system elapsed 
 46.165   1.970  48.720 

Example timings

RNAmodR.Rcheck/RNAmodR-Ex.timings

nameusersystemelapsed
CoverageSequenceData-class 9.933 0.57711.062
EndSequenceData-class5.3710.1515.829
ModInosine-functions0.5940.0060.600
ModInosine7.4050.1587.944
Modifier-functions0.2150.0050.221
NormEndSequenceData-class000
PileupSequenceData-class5.7890.1186.220
ProtectedEndSequenceData-class5.8710.1376.327
RNAmodR-development0.0610.0000.061
SequenceData-functions0.0540.0030.056
SequenceDataFrame-class0.0400.0020.042
SequenceDataList-class0.2000.0020.202
SequenceDataSet-class0.0680.0020.071
SequenceModDNAStringSetTrack-class1.5800.0021.582
SequenceModRNAStringSetTrack-class0.0240.0000.023
aggregate0.4500.0010.451
compareByCoord2.0600.0212.082
modify0.4800.0010.482
plotData2.0360.0402.076
plotROC1.3080.0601.368
settings0.0830.0040.087
stats47.518 4.81441.580
subsetByCoord0.5800.0210.600