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CHECK report for RNAmodR on malbec2

This page was generated on 2020-10-17 11:55:36 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE RNAmodR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1508/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RNAmodR 1.2.3
Felix G.M. Ernst
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/RNAmodR
Branch: RELEASE_3_11
Last Commit: c0299cf
Last Changed Date: 2020-08-30 07:11:07 -0400 (Sun, 30 Aug 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RNAmodR
Version: 1.2.3
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:RNAmodR.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings RNAmodR_1.2.3.tar.gz
StartedAt: 2020-10-17 04:51:58 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:03:49 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 710.8 seconds
RetCode: 0
Status:  OK 
CheckDir: RNAmodR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:RNAmodR.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings RNAmodR_1.2.3.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/RNAmodR.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.2.3’
* 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                          78.146  3.363  67.899
CoverageSequenceData-class     22.231  0.793  24.174
ModInosine                     16.243  0.096  17.251
ProtectedEndSequenceData-class 13.714  0.164  14.671
PileupSequenceData-class       13.700  0.128  14.769
EndSequenceData-class          13.455  0.168  14.526
* 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-3.11-bioc/meat/RNAmodR.Rcheck/00check.log’
for details.



Installation output

RNAmodR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL RNAmodR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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: IRanges
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, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

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")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 187 | SKIPPED: 9 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 64.467   1.938  70.122 

Example timings

RNAmodR.Rcheck/RNAmodR-Ex.timings

nameusersystemelapsed
CoverageSequenceData-class22.231 0.79324.174
EndSequenceData-class13.455 0.16814.526
ModInosine-functions1.1000.0441.149
ModInosine16.243 0.09617.251
Modifier-functions0.2950.0240.320
NormEndSequenceData-class000
PileupSequenceData-class13.700 0.12814.769
ProtectedEndSequenceData-class13.714 0.16414.671
RNAmodR-development0.0660.0000.066
SequenceData-functions0.0980.0320.130
SequenceDataFrame-class0.1270.0400.167
SequenceDataList-class0.2940.0800.374
SequenceDataSet-class0.1620.0360.198
SequenceModDNAStringSetTrack-class1.3370.0001.337
SequenceModRNAStringSetTrack-class0.1270.0000.127
aggregate0.8040.0760.881
compareByCoord2.5700.0282.610
modify0.8690.0480.944
plotData2.0410.0322.073
plotROC1.8750.0321.914
settings0.2090.0360.246
stats78.146 3.36367.899
subsetByCoord1.0840.0361.119