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CHECK report for biocViews on tokay1

This page was generated on 2019-04-13 11:19:46 -0400 (Sat, 13 Apr 2019).

Package 147/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biocViews 1.50.10
Bioconductor Package Maintainer
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/biocViews
Branch: RELEASE_3_8
Last Commit: 24d1431
Last Changed Date: 2018-12-18 07:38:48 -0400 (Tue, 18 Dec 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: biocViews
Version: 1.50.10
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biocViews.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings biocViews_1.50.10.tar.gz
StartedAt: 2019-04-13 00:48:05 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 00:52:14 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 248.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: biocViews.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biocViews.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings biocViews_1.50.10.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/biocViews.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.50.10'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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
Unexported objects imported by ':::' calls:
  'tools:::.build_news_db_from_package_NEWS_Rd'
  'tools:::.build_repository_package_db'
  'tools:::.get_standard_repository_db_fields'
  'tools:::.news_reader_default' 'tools:::.split_dependencies'
  'tools:::vignetteInfo'
  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 documentation object 'genReposControlFiles':
genReposControlFiles
  Code: function(reposRoot, contribPaths, manifestFile = NA, meatPath =
                 NA)
  Docs: function(reposRoot, contribPaths)
  Argument names in code not in docs:
    manifestFile meatPath

Codoc mismatches from documentation object 'write_VIEWS':
write_VIEWS
  Code: function(reposRootPath, fields = NULL, verbose = FALSE,
                 vignette.dir = "vignettes", manifestFile = NA,
                 meatPath = NA)
  Docs: function(reposRootPath, fields = NULL, type = c("source",
                 "win.binary", "mac.binary", "mac.binary.mavericks",
                 "mac.binary.el-capitan"), verbose = FALSE,
                 vignette.dir = "vignettes")
  Argument names in code not in docs:
    manifestFile meatPath
  Argument names in docs not in code:
    type
  Mismatches in argument names:
    Position: 3 Code: verbose Docs: type
    Position: 4 Code: vignette.dir Docs: verbose
    Position: 5 Code: manifestFile Docs: vignette.dir

* 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 or elapsed time > 5s
                  user system elapsed
recommendPackages 8.95   2.96   11.97
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
recommendPackages 6.01   2.05    8.13
* 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: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/biocViews.Rcheck/00check.log'
for details.



Installation output

biocViews.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/biocViews_1.50.10.tar.gz && rm -rf biocViews.buildbin-libdir && mkdir biocViews.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biocViews.buildbin-libdir biocViews_1.50.10.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL biocViews_1.50.10.zip && rm biocViews_1.50.10.tar.gz biocViews_1.50.10.zip
###
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  % 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 70026  100 70026    0     0  1804k      0 --:--:-- --:--:-- --:--:-- 2011k

install for i386

* installing *source* package 'biocViews' ...
** 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
In R CMD INSTALL

install for x64

* installing *source* package 'biocViews' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'biocViews' as biocViews_1.50.10.zip
* DONE (biocViews)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'biocViews' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

biocViews.Rcheck/tests_i386/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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")
/cygdrive/c/Rtools/bin/tar: Record size = 10 blocks
/cygdrive/c/Rtools/bin/tar: Record size = 6 blocks


RUNIT TEST PROTOCOL -- Sat Apr 13 00:51:19 2019 
*********************************************** 
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 
> 
> proc.time()
   user  system elapsed 
  47.54   14.06   63.15 

biocViews.Rcheck/tests_x64/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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")
/cygdrive/c/Rtools/bin/tar: Record size = 10 blocks
/cygdrive/c/Rtools/bin/tar: Record size = 6 blocks


RUNIT TEST PROTOCOL -- Sat Apr 13 00:52:09 2019 
*********************************************** 
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 
> 
> proc.time()
   user  system elapsed 
  33.18   15.87   49.93 

Example timings

biocViews.Rcheck/examples_i386/biocViews-Ex.timings

nameusersystemelapsed
PackageDetail-class0.180.000.18
biocViews-package0.030.000.03
biocViewsVocab000
getBiocSubViews0.920.021.00
getBiocViews0.720.000.72
getCurrentbiocViews000
getPackageTitles000
getSubTerms0.130.000.13
guessPackageType000
recommendPackages 8.95 2.9611.97
validation_tests000

biocViews.Rcheck/examples_x64/biocViews-Ex.timings

nameusersystemelapsed
PackageDetail-class0.220.000.22
biocViews-package0.030.000.03
biocViewsVocab000
getBiocSubViews0.810.010.83
getBiocViews0.730.000.73
getCurrentbiocViews000
getPackageTitles000
getSubTerms0.140.000.14
guessPackageType0.020.000.01
recommendPackages6.012.058.13
validation_tests0.000.010.01