Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-17 15:05:35 -0400 (Fri, 17 Sep 2021).

CHECK results for annotatr on nebbiolo1

To the developers/maintainers of the annotatr package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/annotatr.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 69/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annotatr 1.18.1  (landing page)
Raymond G. Cavalcante
Snapshot Date: 2021-09-16 04:50:11 -0400 (Thu, 16 Sep 2021)
git_url: https://git.bioconductor.org/packages/annotatr
git_branch: RELEASE_3_13
git_last_commit: 0066d80
git_last_commit_date: 2021-07-12 10:41:46 -0400 (Mon, 12 Jul 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: annotatr
Version: 1.18.1
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:annotatr.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings annotatr_1.18.1.tar.gz
StartedAt: 2021-09-16 08:50:44 -0400 (Thu, 16 Sep 2021)
EndedAt: 2021-09-16 08:56:01 -0400 (Thu, 16 Sep 2021)
EllapsedTime: 316.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: annotatr.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:annotatr.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings annotatr_1.18.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/annotatr.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 ‘annotatr/DESCRIPTION’ ... OK
* this is package ‘annotatr’ version ‘1.18.1’
* 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 ‘annotatr’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘AnnotationHub::hubUrl’ by ‘rtracklayer::hubUrl’ when loading ‘annotatr’
See ‘/home/biocbuild/bbs-3.13-bioc/meat/annotatr.Rcheck/00install.out’ for details.
* 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 ... NOTE
plot_coannotations: no visible binding for global variable ‘.’
plot_numerical_coannotations: no visible binding for global variable
  ‘.’
Undefined global functions or variables:
  .
* 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 LazyData ... 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
build_ah_annots 5.486  0.205   6.537
* 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 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/annotatr.Rcheck/00check.log’
for details.



Installation output

annotatr.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘annotatr’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘AnnotationHub::hubUrl’ by ‘rtracklayer::hubUrl’ when loading ‘annotatr’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘AnnotationHub::hubUrl’ by ‘rtracklayer::hubUrl’ when loading ‘annotatr’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘AnnotationHub::hubUrl’ by ‘rtracklayer::hubUrl’ when loading ‘annotatr’
** testing if installed package keeps a record of temporary installation path
* DONE (annotatr)

Tests output

annotatr.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(annotatr)
Warning message:
replacing previous import 'AnnotationHub::hubUrl' by 'rtracklayer::hubUrl' when loading 'annotatr' 
> 
> test_check("annotatr")
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 72 ]
> 
> proc.time()
   user  system elapsed 
 37.690   1.679  64.781 

Example timings

annotatr.Rcheck/annotatr-Ex.timings

nameusersystemelapsed
annotate_regions0.3790.0040.383
annotatr_cache1.4320.1671.600
build_ah_annots5.4860.2056.537
build_annotations4.2560.1404.397
builtin_annotations0.0060.0040.009
builtin_genomes0.0010.0000.000
plot_annotation2.4720.1242.596
plot_categorical2.6520.0042.659
plot_coannotations0.7540.0040.758
plot_numerical0.3730.0000.374
plot_numerical_coannotations0.6430.0000.644
randomize_regions2.5270.0202.548
read_annotations0.3970.0080.405
read_regions0.4190.0120.432
summarize_annotations2.6590.0122.671
summarize_categorical0.4490.0120.462
summarize_numerical0.6200.0240.645