Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 194/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biocViews 1.73.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/biocViews
git_branch: devel
git_last_commit: acbc4c9
git_last_commit_date: 2024-04-30 10:14:31 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for biocViews on palomino4

To the developers/maintainers of the biocViews package:
- 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 Troubleshooting Build Report for more information.
- 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: biocViews
Version: 1.73.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biocViews.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings biocViews_1.73.0.tar.gz
StartedAt: 2024-06-10 00:15:50 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 00:20:36 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 286.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: biocViews.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biocViews.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings biocViews_1.73.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/biocViews.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'biocViews/DESCRIPTION' ... OK
* this is package 'biocViews' version '1.73.0'
* 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 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 code 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 ... WARNING
Codoc mismatches from Rd file 'getPackageTitles.Rd':
getPackageTitles
  Code: function(prevBranch = "RELEASE_3_6", currBranch = "devel",
                 manifest = c("software.txt", "data-experiment.txt",
                 "workflows.txt", "data-annotation.txt", "books.txt"),
                 status = c("new", "removed"))
  Docs: function(prevBranch = "RELEASE_3_6", currBranch = "master",
                 manifest = c("software.txt", "data-experiment.txt",
                 "workflows.txt"), status = c("new", "removed"))
  Mismatches in argument default values:
    Name: 'currBranch' Code: "devel" Docs: "master"
    Name: 'manifest'
    Code: c("software.txt", "data-experiment.txt", "workflows.txt", "data-annotation.txt", 
          "books.txt")
    Docs: c("software.txt", "data-experiment.txt", "workflows.txt")

* 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/biocViews.Rcheck/00check.log'
for details.


Installation output

biocViews.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL biocViews
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-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 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpohTl3W/testing/testrepos/src/contrib/biocViews2_1.73.0.tar.gz ... (try to process CITATION file) OK
Generate citation for F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpohTl3W/testing/testrepos/src/contrib/biocViews_1.73.0.tar.gz ... tar.exe: biocViews/inst/CITATION: Not found in archive
tar.exe: Error exit delayed from previous errors.
(auto-generate from DESCRIPTION file) OK


RUNIT TEST PROTOCOL -- Mon Jun 10 00:19:55 2024 
*********************************************** 
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) :
  'tar.exe -xf "F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpohTl3W/testing/testrepos/src/contrib/biocViews_1.73.0.tar.gz" -C "F:/biocbuild/bbs-3.20-bioc/tmpdir/RtmpohTl3W" "biocViews/DESCRIPTION" "biocViews/inst/CITATION"' returned error code 1
> 
> proc.time()
   user  system elapsed 
   4.81    7.00   63.37 

Example timings

biocViews.Rcheck/biocViews-Ex.timings

nameusersystemelapsed
PackageDetail-class0.110.000.11
biocViews-package0.170.000.22
biocViewsVocab0.020.000.01
getBiocSubViews1.000.022.39
getBiocViews0.980.021.00
getCurrentbiocViews0.000.000.02
getPackageTitles000
getSubTerms0.170.000.19
guessPackageType0.020.000.03
recommendPackages0.560.010.92
validation_tests0.000.020.02