Back to Build/check report for BioC 3.18 annotations
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This page was generated on 2024-04-17 08:30:07 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4677
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

Package 26/45HostnameOS / ArchINSTALLBUILDCHECK
gwascatData 0.99.6  (landing page)
Sara Stankiewicz
Snapshot Date: 2024-04-17 06:00:01 -0400 (Wed, 17 Apr 2024)
git_url: https://git.bioconductor.org/packages/gwascatData
git_branch: RELEASE_3_18
git_last_commit: cf9495a
git_last_commit_date: 2021-05-07 12:20:10 -0400 (Fri, 07 May 2021)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

CHECK results for gwascatData on nebbiolo2


To the developers/maintainers of the gwascatData package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: gwascatData
Version: 0.99.6
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:gwascatData.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings gwascatData_0.99.6.tar.gz
StartedAt: 2024-04-17 06:33:59 -0400 (Wed, 17 Apr 2024)
EndedAt: 2024-04-17 06:34:38 -0400 (Wed, 17 Apr 2024)
EllapsedTime: 38.7 seconds
RetCode: 0
Status:   OK  
CheckDir: gwascatData.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:gwascatData.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings gwascatData_0.99.6.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-data-annotation/meat/gwascatData.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘gwascatData/DESCRIPTION’ ... OK
* this is package ‘gwascatData’ version ‘0.99.6’
* 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 ‘gwascatData’ 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 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 loading without being on the library search path ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* 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 ...
  ‘gwascatData.Rmd’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
  ...
--- re-building ‘gwascatData.Rmd’ using rmarkdown
Error: processing vignette 'gwascatData.Rmd' failed with diagnostics:
there is no package called ‘BiocStyle’
--- failed re-building ‘gwascatData.Rmd’

SUMMARY: processing the following file failed:
  ‘gwascatData.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-data-annotation/meat/gwascatData.Rcheck/00check.log’
for details.



Installation output

gwascatData.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL gwascatData
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘gwascatData’ ...
** using staged installation
** inst
** help
No man pages found in package  ‘gwascatData’ 
*** 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 (gwascatData)

Tests output

gwascatData.Rcheck/tests/testthat.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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(gwascatData)
> library(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, aperm, 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
> library(testthat)
> test_check("gwascatData")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
 13.506   0.916  14.801 

Example timings