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This page was generated on 2021-10-15 15:05:51 -0400 (Fri, 15 Oct 2021).

CHECK results for RNAmodR on nebbiolo1

To the developers/maintainers of the RNAmodR package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1603/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RNAmodR 1.6.0  (landing page)
Felix G.M. Ernst
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/RNAmodR
git_branch: RELEASE_3_13
git_last_commit: c7b25bf
git_last_commit_date: 2021-05-19 12:44:18 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: RNAmodR
Version: 1.6.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:RNAmodR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings RNAmodR_1.6.0.tar.gz
StartedAt: 2021-10-14 11:22:09 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 11:31:00 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 531.6 seconds
RetCode: 0
Status:   OK  
CheckDir: RNAmodR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:RNAmodR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings RNAmodR_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/RNAmodR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAmodR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RNAmodR’ version ‘1.6.0’
* 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                          56.410  4.219  48.166
CoverageSequenceData-class     14.884  0.791  16.710
ModInosine                     12.196  0.196  12.921
ProtectedEndSequenceData-class  9.302  0.175  10.058
PileupSequenceData-class        9.058  0.188   9.799
EndSequenceData-class           9.050  0.152   9.732
* 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
  ‘/home/biocbuild/bbs-3.13-bioc/meat/RNAmodR.Rcheck/00check.log’
for details.



Installation output

RNAmodR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL RNAmodR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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
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")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (9)

[ FAIL 0 | WARN 0 | SKIP 9 | PASS 192 ]
> 
> proc.time()
   user  system elapsed 
 52.857   2.979  56.801 

Example timings

RNAmodR.Rcheck/RNAmodR-Ex.timings

nameusersystemelapsed
CoverageSequenceData-class14.884 0.79116.710
EndSequenceData-class9.0500.1529.732
ModInosine-functions0.7510.0320.782
ModInosine12.196 0.19612.921
Modifier-functions0.2680.0160.284
NormEndSequenceData-class0.0010.0000.000
PileupSequenceData-class9.0580.1889.799
ProtectedEndSequenceData-class 9.302 0.17510.058
RNAmodR-development0.0580.0080.066
SequenceData-functions0.0740.0000.073
SequenceDataFrame-class0.0640.0000.064
SequenceDataList-class0.1210.0000.121
SequenceDataSet-class0.0790.0000.079
SequenceModDNAStringSetTrack-class1.6820.0321.713
SequenceModRNAStringSetTrack-class0.1220.0000.123
aggregate0.5280.0000.528
compareByCoord2.0710.0442.115
modify0.5820.0000.582
plotData2.3080.0242.332
plotROC1.4430.0161.460
settings0.0960.0040.100
stats56.410 4.21948.166
subsetByCoord0.6180.0040.622