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CHECK report for biocViews on tokay1

This page was generated on 2020-08-10 12:10:50 -0400 (Mon, 10 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE biocViews PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 164/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biocViews 1.57.3
Bioconductor Package Maintainer
Snapshot Date: 2020-08-09 14:51:29 -0400 (Sun, 09 Aug 2020)
URL: https://git.bioconductor.org/packages/biocViews
Branch: master
Last Commit: d1f0be2
Last Changed Date: 2020-07-17 16:45:15 -0400 (Fri, 17 Jul 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: biocViews
Version: 1.57.3
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biocViews.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings biocViews_1.57.3.tar.gz
StartedAt: 2020-08-09 23:50:04 -0400 (Sun, 09 Aug 2020)
EndedAt: 2020-08-09 23:54:03 -0400 (Sun, 09 Aug 2020)
EllapsedTime: 239.5 seconds
RetCode: 0
Status:  OK  
CheckDir: biocViews.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biocViews.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings biocViews_1.57.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/biocViews.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'biocViews/DESCRIPTION' ... OK
* this is package 'biocViews' version '1.57.3'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
recommendPackages 10.3   2.42    12.8
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
recommendPackages 6.99   2.88    9.91
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/biocViews.Rcheck/00check.log'
for details.



Installation output

biocViews.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/biocViews_1.57.3.tar.gz && rm -rf biocViews.buildbin-libdir && mkdir biocViews.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biocViews.buildbin-libdir biocViews_1.57.3.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL biocViews_1.57.3.zip && rm biocViews_1.57.3.tar.gz biocViews_1.57.3.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 73507  100 73507    0     0  1379k      0 --:--:-- --:--:-- --:--:-- 1495k

install for i386

* installing *source* package 'biocViews' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'biocViews'
    finding HTML links ... done
    BiocView-class                          html  
    Htmlized-class                          html  
    PackageDetail-class                     html  
    RepositoryDetail-class                  html  
    biocViews-package                       html  
    biocViewsVocab                          html  
    extractManuals                          html  
    extractNEWS                             html  
    extractTopLevelFiles                    html  
    extractVignettes                        html  
    genReposControlFiles                    html  
    getBiocSubViews                         html  
    getBiocViews                            html  
    getCurrentbiocViews                     html  
    getPackageNEWS                          html  
    getPackageTitles                        html  
    getPacksAndViews                        html  
    getSubTerms                             html  
    guessPackageType                        html  
    htmlDoc                                 html  
    htmlFilename                            html  
    htmlValue                               html  
    recommendBiocViews                      html  
    recommendPackages                       html  
    validation_tests                        html  
    writeBiocViews                          html  
    writeHtmlDoc                            html  
    writePackageDetailHtml                  html  
    writeRFilesFromVignettes                html  
    writeRepositoryHtml                     html  
    writeTopLevelView                       html  
    write_REPOSITORY                        html  
    write_SYMBOLS                           html  
    write_VIEWS                             html  
** 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

install for x64

* installing *source* package 'biocViews' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'biocViews' as biocViews_1.57.3.zip
* DONE (biocViews)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'biocViews' successfully unpacked and MD5 sums checked

Tests output

biocViews.Rcheck/tests_i386/runTests.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpAX8BIW/testing/testrepos/src/contrib/biocViews2_1.57.3.tar.gz ... (try to process CITATION file) OK
Generate citation for C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpAX8BIW/testing/testrepos/src/contrib/biocViews_1.57.3.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 -- Sun Aug 09 23:52:42 2020 
*********************************************** 
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 "C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpAX8BIW/testing/testrepos/src/contrib/biocViews_1.57.3.tar.gz" -C "C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpAX8BIW" "biocViews/DESCRIPTION" "biocViews/inst/CITATION"' returned error code 2
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 
  59.00   13.65   73.01 

biocViews.Rcheck/tests_x64/runTests.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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 C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpSKIB5m/testing/testrepos/src/contrib/biocViews2_1.57.3.tar.gz ... (try to process CITATION file) OK
Generate citation for C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpSKIB5m/testing/testrepos/src/contrib/biocViews_1.57.3.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 -- Sun Aug 09 23:53:36 2020 
*********************************************** 
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 "C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpSKIB5m/testing/testrepos/src/contrib/biocViews_1.57.3.tar.gz" -C "C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSKIB5m" "biocViews/DESCRIPTION" "biocViews/inst/CITATION"' returned error code 2
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 
  38.93   14.87   54.20 

Example timings

biocViews.Rcheck/examples_i386/biocViews-Ex.timings

nameusersystemelapsed
PackageDetail-class0.070.000.08
biocViews-package0.040.020.05
biocViewsVocab000
getBiocSubViews0.890.000.89
getBiocViews0.780.000.78
getCurrentbiocViews000
getPackageTitles000
getSubTerms0.140.000.14
guessPackageType0.020.000.01
recommendPackages10.30 2.4212.80
validation_tests000

biocViews.Rcheck/examples_x64/biocViews-Ex.timings

nameusersystemelapsed
PackageDetail-class0.060.000.06
biocViews-package0.030.020.05
biocViewsVocab000
getBiocSubViews0.950.000.96
getBiocViews0.800.000.79
getCurrentbiocViews000
getPackageTitles000
getSubTerms0.140.000.14
guessPackageType0.010.000.01
recommendPackages6.992.889.91
validation_tests000