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This page was generated on 2021-12-01 17:18:11 -0500 (Wed, 01 Dec 2021).

CHECK results for annotatr on machv2

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 66/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annotatr 1.20.0  (landing page)
Raymond G. Cavalcante
Snapshot Date: 2021-11-30 04:15:05 -0500 (Tue, 30 Nov 2021)
git_url: https://git.bioconductor.org/packages/annotatr
git_branch: RELEASE_3_14
git_last_commit: aa03096
git_last_commit_date: 2021-10-26 12:30:59 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 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: annotatr
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:annotatr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings annotatr_1.20.0.tar.gz
StartedAt: 2021-11-30 13:42:50 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 13:49:58 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 428.3 seconds
RetCode: 0
Status:   OK  
CheckDir: annotatr.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:annotatr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings annotatr_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/annotatr.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotatr/DESCRIPTION’ ... OK
* this is package ‘annotatr’ version ‘1.20.0’
* 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 ... 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 ... 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   7.346  0.500   9.496
build_annotations 6.763  0.168   7.055
* 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-3.14-bioc/meat/annotatr.Rcheck/00check.log’
for details.



Installation output

annotatr.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘annotatr’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (annotatr)

Tests output

annotatr.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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)
> 
> test_check("annotatr")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 72 ]
> 
> proc.time()
   user  system elapsed 
 51.029   2.177  54.973 

Example timings

annotatr.Rcheck/annotatr-Ex.timings

nameusersystemelapsed
annotate_regions1.4590.0231.484
annotatr_cache2.5690.6263.197
build_ah_annots7.3460.5009.496
build_annotations6.7630.1687.055
builtin_annotations0.0110.0060.017
builtin_genomes0.0000.0000.001
plot_annotation3.3420.0883.434
plot_categorical3.3480.0413.392
plot_coannotations1.3900.0131.407
plot_numerical0.6200.0100.632
plot_numerical_coannotations0.9000.0140.918
randomize_regions2.7720.0362.814
read_annotations0.7140.0170.732
read_regions0.5780.0180.622
summarize_annotations4.4500.0494.500
summarize_categorical0.6450.0150.660
summarize_numerical0.6990.0240.723