Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:20:01 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 biocViews on nebbiolo1


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? 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 174/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biocViews 1.64.1  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/biocViews
git_branch: RELEASE_3_15
git_last_commit: 1075b4d
git_last_commit_date: 2022-07-18 15:58:17 -0400 (Mon, 18 Jul 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: biocViews
Version: 1.64.1
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:biocViews.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings biocViews_1.64.1.tar.gz
StartedAt: 2022-10-18 18:45:58 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 18:46:46 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 48.7 seconds
RetCode: 0
Status:   OK  
CheckDir: biocViews.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:biocViews.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings biocViews_1.64.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/biocViews.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘1.64.1’
* 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:::.expand_package_description_db_R_fields’
  ‘tools:::.get_standard_repository_db_fields’
  ‘tools:::.news_reader_default’ ‘tools:::.read_description’
  ‘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-3.15-bioc/meat/biocViews.Rcheck/00check.log’
for details.



Installation output

biocViews.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL biocViews
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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
** 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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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/RtmpWiSjZN/testing/testrepos/src/contrib/biocViews2_1.64.1.tar.gz ... (try to process CITATION file) OK
Generate citation for /tmp/RtmpWiSjZN/testing/testrepos/src/contrib/biocViews_1.64.1.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 -- Tue Oct 18 18:46:42 2022 
*********************************************** 
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/RtmpWiSjZN/testing/testrepos/src/contrib/biocViews_1.64.1.tar.gz' -C '/tmp/RtmpWiSjZN' 'biocViews/DESCRIPTION' 'biocViews/inst/CITATION'' returned error code 2
> 
> proc.time()
   user  system elapsed 
  3.330   0.131   6.078 

Example timings

biocViews.Rcheck/biocViews-Ex.timings

nameusersystemelapsed
PackageDetail-class0.1010.0000.101
biocViews-package0.1130.0040.118
biocViewsVocab0.0040.0000.004
getBiocSubViews0.730.020.75
getBiocViews0.6440.0090.654
getCurrentbiocViews0.0030.0020.006
getPackageTitles000
getSubTerms0.1090.0040.113
guessPackageType0.0110.0000.011
recommendPackages0.4080.0081.057
validation_tests0.0030.0000.003