Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-07-31 12:05:31 -0400 (Sat, 31 Jul 2021).

CHECK results for biocViews on nebbiolo2

To the developers/maintainers of the biocViews package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biocViews.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 171/2015HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biocViews 1.61.1  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2021-07-30 14:50:06 -0400 (Fri, 30 Jul 2021)
URL: https://git.bioconductor.org/packages/biocViews
Branch: master
Last Commit: f059205
Last Changed Date: 2021-07-30 09:56:02 -0400 (Fri, 30 Jul 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  YES
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  YES
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  YES

Summary

Package: biocViews
Version: 1.61.1
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:biocViews.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings biocViews_1.61.1.tar.gz
StartedAt: 2021-07-30 18:54:34 -0400 (Fri, 30 Jul 2021)
EndedAt: 2021-07-30 18:55:17 -0400 (Fri, 30 Jul 2021)
EllapsedTime: 43.7 seconds
RetCode: 0
Status:   OK  
CheckDir: biocViews.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:biocViews.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings biocViews_1.61.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/biocViews.Rcheck’
* using R version 4.1.0 beta (2021-05-03 r80259)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biocViews/DESCRIPTION’ ... OK
* this is package ‘biocViews’ version ‘1.61.1’
* 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 ‘biocViews’ 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
':::' call which should be '::': ‘tools:::vignetteInfo’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘tools:::.build_news_db_from_package_NEWS_Rd’
  ‘tools:::.build_news_db_from_package_NEWS_md’
  ‘tools:::.build_repository_package_db’
  ‘tools:::.get_standard_repository_db_fields’
  ‘tools:::.news_reader_default’ ‘tools:::.split_dependencies’
  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
getPackageNEWS : getNews: no visible binding for global variable
  ‘Version’
getReverseDepends : <anonymous>: no visible binding for global variable
  ‘Package’
Undefined global functions or variables:
  Package Version
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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-3.14-bioc/meat/biocViews.Rcheck/00check.log’
for details.



Installation output

biocViews.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘biocViews’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘HOWTO-BCV.Rnw’ 
   ‘createReposHtml.Rnw’ 
** 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 (biocViews)

Tests output

biocViews.Rcheck/tests/runTests.Rout


R version 4.1.0 beta (2021-05-03 r80259) -- "Camp Pontanezen"
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.

> BiocGenerics:::testPackage("biocViews")
Generate citation for /tmp/RtmpUWAmlT/testing/testrepos/src/contrib/biocViews2_1.61.1.tar.gz ... (try to process CITATION file) OK
Generate citation for /tmp/RtmpUWAmlT/testing/testrepos/src/contrib/biocViews_1.61.1.tar.gz ... /usr/bin/tar: biocViews/inst/CITATION: Not found in archive
/usr/bin/tar: Exiting with failure status due to previous errors
(auto-generate from DESCRIPTION file) OK


RUNIT TEST PROTOCOL -- Fri Jul 30 18:55:14 2021 
*********************************************** 
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
biocViews RUnit Tests - 5 test functions, 0 errors, 0 failures
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 
Warning message:
In untar(tarball, tpaths, exdir = tmpdir) :
  '/usr/bin/tar -xf '/tmp/RtmpUWAmlT/testing/testrepos/src/contrib/biocViews_1.61.1.tar.gz' -C '/tmp/RtmpUWAmlT' 'biocViews/DESCRIPTION' 'biocViews/inst/CITATION'' returned error code 2
> 
> proc.time()
   user  system elapsed 
  2.987   0.084   4.131 

Example timings

biocViews.Rcheck/biocViews-Ex.timings

nameusersystemelapsed
PackageDetail-class0.0710.0000.071
biocViews-package0.0480.0000.048
biocViewsVocab0.0040.0000.004
getBiocSubViews0.8880.0120.900
getBiocViews0.6750.0080.683
getCurrentbiocViews0.0060.0000.006
getPackageTitles000
getSubTerms0.1140.0040.119
guessPackageType0.0120.0000.012
recommendPackages0.3600.0040.617
validation_tests0.0030.0000.002