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CHECK report for annotatr on celaya2

This page was generated on 2020-01-16 13:46:30 -0500 (Thu, 16 Jan 2020).

Package 68/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annotatr 1.13.1
Raymond G. Cavalcante
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/annotatr
Branch: master
Last Commit: 611fc8d
Last Changed Date: 2019-11-12 09:57:11 -0500 (Tue, 12 Nov 2019)
malbec2 Linux (Ubuntu 18.04.3 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: annotatr
Version: 1.13.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:annotatr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings annotatr_1.13.1.tar.gz
StartedAt: 2020-01-16 01:43:31 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 01:52:25 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 534.4 seconds
RetCode: 0
Status:  OK 
CheckDir: annotatr.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:annotatr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings annotatr_1.13.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/annotatr.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotatr/DESCRIPTION’ ... OK
* this is package ‘annotatr’ version ‘1.13.1’
* 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 ... 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 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   6.507  0.797   9.850
build_annotations 6.749  0.423   7.176
plot_annotation   2.635  0.184   5.353
* 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-3.11-bioc/meat/annotatr.Rcheck/00check.log’
for details.



Installation output

annotatr.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL annotatr
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 72 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 55.620   4.102  96.165 

Example timings

annotatr.Rcheck/annotatr-Ex.timings

nameusersystemelapsed
annotate_regions1.8170.0421.874
annotatr_cache2.8670.5693.443
build_ah_annots6.5070.7979.850
build_annotations6.7490.4237.176
builtin_annotations0.0170.0070.023
builtin_genomes0.0010.0010.001
plot_annotation2.6350.1845.353
plot_categorical2.5240.1024.137
plot_coannotations1.2510.0801.331
plot_numerical0.7030.0480.752
plot_numerical_coannotations0.9360.0320.967
randomize_regions1.7460.0823.859
read_annotations0.8210.0920.913
read_regions0.7250.0510.791
summarize_annotations3.1580.1494.863
summarize_categorical0.6280.0480.676
summarize_numerical0.6700.0460.716