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CHECK report for EpiTxDb.Sc.sacCer3 on malbec1

This page was generated on 2020-08-05 15:30:06 -0400 (Wed, 05 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE EpiTxDb.Sc.sacCer3 PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 4/11HostnameOS / ArchINSTALLBUILDCHECK
EpiTxDb.Sc.sacCer3 0.99.3
Felix G.M. Ernst
Snapshot Date: 2020-08-05 08:00:01 -0400 (Wed, 05 Aug 2020)
URL: https://git.bioconductor.org/packages/EpiTxDb.Sc.sacCer3
Branch: master
Last Commit: b8c61c9
Last Changed Date: 2020-03-07 10:41:37 -0400 (Sat, 07 Mar 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: EpiTxDb.Sc.sacCer3
Version: 0.99.3
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:EpiTxDb.Sc.sacCer3.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings EpiTxDb.Sc.sacCer3_0.99.3.tar.gz
StartedAt: 2020-08-05 09:02:59 -0400 (Wed, 05 Aug 2020)
EndedAt: 2020-08-05 09:06:23 -0400 (Wed, 05 Aug 2020)
EllapsedTime: 204.0 seconds
RetCode: 0
Status:  OK 
CheckDir: EpiTxDb.Sc.sacCer3.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:EpiTxDb.Sc.sacCer3.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings EpiTxDb.Sc.sacCer3_0.99.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-data-annotation/meat/EpiTxDb.Sc.sacCer3.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EpiTxDb.Sc.sacCer3/DESCRIPTION’ ... OK
* this is package ‘EpiTxDb.Sc.sacCer3’ version ‘0.99.3’
* 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 ‘EpiTxDb.Sc.sacCer3’ 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: OK


Installation output

EpiTxDb.Sc.sacCer3.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL EpiTxDb.Sc.sacCer3
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘EpiTxDb.Sc.sacCer3’ ...
** using staged installation
** R
** 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 (EpiTxDb.Sc.sacCer3)

Tests output

EpiTxDb.Sc.sacCer3.Rcheck/tests/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
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(EpiTxDb.Sc.sacCer3)
Loading required package: AnnotationHub
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

Loading required package: BiocFileCache
Loading required package: dbplyr
Loading required package: EpiTxDb
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

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

    cache

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: Modstrings
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

> 
> test_check("EpiTxDb.Sc.sacCer3")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 13.208   0.440  14.191 

Example timings

EpiTxDb.Sc.sacCer3.Rcheck/EpiTxDb.Sc.sacCer3-Ex.timings

nameusersystemelapsed
EpiTxDb.Sc.sacCer33.0800.1243.706