Back to Build/check report for BioC 3.14 annotations
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This page was generated on 2022-01-19 06:00:08 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for GenomicState on nebbiolo2


To the developers/maintainers of the GenomicState package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 20/33HostnameOS / ArchINSTALLBUILDCHECK
GenomicState 0.99.15  (landing page)
Leonardo Collado-Torres
Snapshot Date: 2022-01-19 02:30:01 -0500 (Wed, 19 Jan 2022)
git_url: https://git.bioconductor.org/packages/GenomicState
git_branch: master
git_last_commit: 6135721
git_last_commit_date: 2021-08-09 22:16:51 -0500 (Mon, 09 Aug 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GenomicState
Version: 0.99.15
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:GenomicState.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings GenomicState_0.99.15.tar.gz
StartedAt: 2022-01-19 03:02:30 -0500 (Wed, 19 Jan 2022)
EndedAt: 2022-01-19 03:05:47 -0500 (Wed, 19 Jan 2022)
EllapsedTime: 197.7 seconds
RetCode: 0
Status:   OK  
CheckDir: GenomicState.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:GenomicState.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings GenomicState_0.99.15.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-data-annotation/meat/GenomicState.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicState/DESCRIPTION’ ... OK
* this is package ‘GenomicState’ version ‘0.99.15’
* 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 ‘GenomicState’ 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:
  ‘GenomicFeatures:::.prepareGFFMetadata’
  ‘GenomicFeatures:::.tidy_seqinfo’
  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 ... 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
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
gencode_annotated_genes 14.023  0.164  14.187
GenomicStateHub         11.938  0.324  12.876
gencode_genomic_state    6.692  0.064   6.756
* 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
  ‘/home/biocbuild/bbs-3.14-data-annotation/meat/GenomicState.Rcheck/00check.log’
for details.



Installation output

GenomicState.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL GenomicState
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘GenomicState’ ...
** 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 (GenomicState)

Tests output

GenomicState.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-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(GenomicState)
Loading required package: AnnotationHub
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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
> 
> test_check("GenomicState")
trying URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_31/GRCh37_mapping/gencode.v31lift37.annotation.gtf.gz'
Content type 'unknown' length 56214326 bytes (53.6 MB)
==================================================
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
 81.333   2.576  88.268 

Example timings

GenomicState.Rcheck/GenomicState-Ex.timings

nameusersystemelapsed
GenomicStateHub11.938 0.32412.876
gencode_annotated_genes14.023 0.16414.187
gencode_genomic_state6.6920.0646.756
gencode_txdb0.2040.0000.205
local_metadata0.0050.0000.005