Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-06-24 11:06:08 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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 palomino4


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 173/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biocViews 1.65.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/biocViews
git_branch: master
git_last_commit: ea53cba
git_last_commit_date: 2022-04-26 10:57:30 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: biocViews
Version: 1.65.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biocViews.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings biocViews_1.65.0.tar.gz
StartedAt: 2022-06-23 23:36:08 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 23:37:16 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 67.4 seconds
RetCode: 0
Status:   OK  
CheckDir: biocViews.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biocViews.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings biocViews_1.65.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/biocViews.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'biocViews/DESCRIPTION' ... OK
* this is package 'biocViews' version '1.65.0'
* 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 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 sizes of PDF files under 'inst/doc' ... 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
  'F:/biocbuild/bbs-3.16-bioc/meat/biocViews.Rcheck/00check.log'
for details.



Installation output

biocViews.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/biocViews_1.65.0.tar.gz && rm -rf biocViews.buildbin-libdir && mkdir biocViews.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biocViews.buildbin-libdir biocViews_1.65.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL biocViews_1.65.0.zip && rm biocViews_1.65.0.tar.gz biocViews_1.65.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 75470  100 75470    0     0  1314k      0 --:--:-- --:--:-- --:--:-- 1340k
only one architecture so ignoring '--merge-multiarch'
* 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
* MD5 sums
packaged installation of 'biocViews' as biocViews_1.65.0.zip
* DONE (biocViews)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'biocViews' successfully unpacked and MD5 sums checked

Tests output

biocViews.Rcheck/tests/runTests.Rout


R version 4.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpsrzRli/testing/testrepos/src/contrib/biocViews2_1.65.0.tar.gz ... (try to process CITATION file) OK
Generate citation for F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpsrzRli/testing/testrepos/src/contrib/biocViews_1.65.0.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 -- Thu Jun 23 23:37:05 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 messages:
1: In untar(tarball, tpaths, exdir = tmpdir) :
  'tar.exe -xf "F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpsrzRli/testing/testrepos/src/contrib/biocViews_1.65.0.tar.gz" -C "F:/biocbuild/bbs-3.16-bioc/tmpdir/RtmpsrzRli" "biocViews/DESCRIPTION" "biocViews/inst/CITATION"' returned error code 1
2: In citation(pkgname, lib.loc = tmpdir, auto = description) :
  no date field in DESCRIPTION file of package 'biocViews'
3: In citation(pkgname, lib.loc = tmpdir, auto = description) :
  could not determine year for 'biocViews' from package DESCRIPTION file
> 
> proc.time()
   user  system elapsed 
   4.00    0.21    4.71 

Example timings

biocViews.Rcheck/biocViews-Ex.timings

nameusersystemelapsed
PackageDetail-class0.080.000.08
biocViews-package0.050.000.04
biocViewsVocab000
getBiocSubViews0.820.020.83
getBiocViews0.640.010.65
getCurrentbiocViews000
getPackageTitles000
getSubTerms0.140.000.14
guessPackageType0.020.000.02
recommendPackages0.590.000.68
validation_tests000