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CHECK report for Organism.dplyr on malbec1

This page was generated on 2021-05-06 12:28:28 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the Organism.dplyr package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1279/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Organism.dplyr 1.18.0  (landing page)
Martin Morgan
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/Organism.dplyr
Branch: RELEASE_3_12
Last Commit: f57cfd5
Last Changed Date: 2020-10-27 11:21:56 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: Organism.dplyr
Version: 1.18.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:Organism.dplyr.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings Organism.dplyr_1.18.0.tar.gz
StartedAt: 2021-05-06 04:14:08 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:23:01 -0400 (Thu, 06 May 2021)
EllapsedTime: 533.0 seconds
RetCode: 0
Status:   OK  
CheckDir: Organism.dplyr.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:Organism.dplyr.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings Organism.dplyr_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/Organism.dplyr.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Organism.dplyr/DESCRIPTION’ ... OK
* this is package ‘Organism.dplyr’ version ‘1.18.0’
* 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 ‘Organism.dplyr’ 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:
  ‘AnnotationDbi:::smartKeys’ ‘GenomicFeatures:::.exons_with_3utr’
  ‘GenomicFeatures:::.exons_with_5utr’
  ‘GenomicFeatures:::get_TxDb_seqinfo0’
  ‘S4Vectors:::extract_data_frame_rows’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.toGRanges: no visible binding for global variable ‘.’
intronsByTranscript,src_organism: 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
Genomic-Extractors 8.800  0.104  12.081
select             6.396  0.004   8.607
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/Organism.dplyr.Rcheck/00check.log’
for details.



Installation output

Organism.dplyr.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL Organism.dplyr
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘Organism.dplyr’ ...
** 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 (Organism.dplyr)

Tests output

Organism.dplyr.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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(Organism.dplyr)
Loading required package: dplyr

Attaching package: 'dplyr'

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

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: AnnotationFilter

Attaching package: 'AnnotationFilter'

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

    not

> 
> test_check("Organism.dplyr")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 50 | SKIP 1 | PASS 190 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
205.864   1.952 219.675 

Example timings

Organism.dplyr.Rcheck/Organism.dplyr-Ex.timings

nameusersystemelapsed
Genomic-Extractors 8.800 0.10412.081
filter0.5480.0000.558
select6.3960.0048.607
src0.6080.0001.062
utils0.0000.0000.002