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This page was generated on 2024-07-16 11:41 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
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 1740/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RNAmodR 1.19.0  (landing page)
Felix G.M. Ernst
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/RNAmodR
git_branch: devel
git_last_commit: ac36c21
git_last_commit_date: 2024-04-30 11:15:21 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


CHECK results for RNAmodR on palomino6

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: 1.19.0
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RNAmodR.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings RNAmodR_1.19.0.tar.gz
StartedAt: 2024-07-16 03:23:52 -0400 (Tue, 16 Jul 2024)
EndedAt: 2024-07-16 03:34:54 -0400 (Tue, 16 Jul 2024)
EllapsedTime: 662.1 seconds
RetCode: 0
Status:   OK  
CheckDir: RNAmodR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RNAmodR.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings RNAmodR_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/RNAmodR.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'RNAmodR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RNAmodR' version '1.19.0'
* 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 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                          27.77   5.68   75.61
CoverageSequenceData-class     11.07   2.53   15.29
EndSequenceData-class           8.82   0.79   11.18
ModInosine                      8.66   0.70   10.41
ProtectedEndSequenceData-class  4.99   1.72    7.31
PileupSequenceData-class        5.76   0.53    6.97
* 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
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/RNAmodR.Rcheck/00check.log'
for details.


Installation output

RNAmodR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL RNAmodR
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-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
** 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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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, aperm, 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, table, tapply,
    union, 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

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")
[E::idx_find_and_load] Could not retrieve index file for 'C:\Users\biocbuild\ExperimentHub_cache/12343cd1736d_2547'
[E::idx_find_and_load] Could not retrieve index file for 'C:\Users\biocbuild\ExperimentHub_cache/12343cd1736d_2547'
[E::idx_find_and_load] Could not retrieve index file for 'C:\Users\biocbuild\ExperimentHub_cache/12343cd1736d_2547'
[E::idx_find_and_load] Could not retrieve index file for 'C:\Users\biocbuild\ExperimentHub_cache/12343cd1736d_2547'
[E::idx_find_and_load] Could not retrieve index file for 'C:\Users\biocbuild\ExperimentHub_cache/12343cd1736d_2547'
[E::idx_find_and_load] Could not retrieve index file for 'C:\Users\biocbuild\ExperimentHub_cache/12343cd1736d_2547'
Error in x$.self$finalize() : attempt to apply non-function
[ FAIL 0 | WARN 1 | 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 1 | SKIP 9 | PASS 192 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
  49.40    6.39   60.03 

Example timings

RNAmodR.Rcheck/RNAmodR-Ex.timings

nameusersystemelapsed
CoverageSequenceData-class11.07 2.5315.29
EndSequenceData-class 8.82 0.7911.18
ModInosine-functions0.420.120.55
ModInosine 8.66 0.7010.41
Modifier-functions0.190.080.28
NormEndSequenceData-class000
PileupSequenceData-class5.760.536.97
ProtectedEndSequenceData-class4.991.727.31
RNAmodR-development0.060.000.06
SequenceData-functions0.060.060.13
SequenceDataFrame-class0.030.080.10
SequenceDataList-class0.080.140.22
SequenceDataSet-class0.070.130.20
SequenceModDNAStringSetTrack-class1.710.001.71
SequenceModRNAStringSetTrack-class0.090.010.10
aggregate1.780.721.94
compareByCoord1.600.101.69
modify0.430.090.55
plotData2.000.082.07
plotROC2.070.062.13
settings0.090.060.16
stats27.77 5.6875.61
subsetByCoord0.420.120.54