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This page was generated on 2024-03-04 11:37:47 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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 1773/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RNAmodR 1.16.0  (landing page)
Felix G.M. Ernst
Snapshot Date: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 2024)
git_url: https://git.bioconductor.org/packages/RNAmodR
git_branch: RELEASE_3_18
git_last_commit: 721aa3d
git_last_commit_date: 2023-10-24 11:14:34 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    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
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for RNAmodR on lconway


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: 1.16.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RNAmodR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RNAmodR_1.16.0.tar.gz
StartedAt: 2024-03-03 23:02:40 -0500 (Sun, 03 Mar 2024)
EndedAt: 2024-03-03 23:13:45 -0500 (Sun, 03 Mar 2024)
EllapsedTime: 665.6 seconds
RetCode: 0
Status:   OK  
CheckDir: RNAmodR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RNAmodR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RNAmodR_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/RNAmodR.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAmodR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RNAmodR’ version ‘1.16.0’
* 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’ 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                          54.081  5.576  47.148
CoverageSequenceData-class     14.571  1.951  17.342
ModInosine                     10.089  0.491  11.079
EndSequenceData-class           7.921  0.487   8.874
ProtectedEndSequenceData-class  6.657  0.431   7.597
PileupSequenceData-class        6.452  0.431   7.371
* 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
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/RNAmodR.Rcheck/00check.log’
for details.



Installation output

RNAmodR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RNAmodR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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, 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, sort, 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
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 '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/a15471c3cd2f_2547'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/a15471c3cd2f_2547'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/a15471c3cd2f_2547'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/a15471c3cd2f_2547'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/a15471c3cd2f_2547'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/a15471c3cd2f_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 
 58.729   3.504  66.619 

Example timings

RNAmodR.Rcheck/RNAmodR-Ex.timings

nameusersystemelapsed
CoverageSequenceData-class14.571 1.95117.342
EndSequenceData-class7.9210.4878.874
ModInosine-functions0.7890.0230.820
ModInosine10.089 0.49111.079
Modifier-functions0.3100.0170.337
NormEndSequenceData-class0.0000.0000.001
PileupSequenceData-class6.4520.4317.371
ProtectedEndSequenceData-class6.6570.4317.597
RNAmodR-development0.0830.0040.092
SequenceData-functions0.0820.0070.096
SequenceDataFrame-class0.0780.0040.085
SequenceDataList-class0.1560.0080.166
SequenceDataSet-class0.1050.0080.115
SequenceModDNAStringSetTrack-class1.5620.0351.617
SequenceModRNAStringSetTrack-class0.1550.0040.166
aggregate0.6750.0150.698
compareByCoord2.4530.0512.533
modify0.6600.0120.680
plotData2.1650.0272.210
plotROC1.7980.0351.851
settings0.1650.0060.173
stats54.081 5.57647.148
subsetByCoord0.7710.0170.796