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BioC 3.4: CHECK report for biocViews on tokay1

This page was generated on 2017-04-15 16:14:48 -0400 (Sat, 15 Apr 2017).

Package 118/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biocViews 1.42.0
Bioconductor Package Maintainer
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/biocViews
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 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
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: biocViews
Version: 1.42.0
Command: rm -rf biocViews.buildbin-libdir biocViews.Rcheck && mkdir biocViews.buildbin-libdir biocViews.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=biocViews.buildbin-libdir biocViews_1.42.0.tar.gz >biocViews.Rcheck\00install.out 2>&1 && cp biocViews.Rcheck\00install.out biocViews-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=biocViews.buildbin-libdir --install="check:biocViews-install.out" --force-multiarch --no-vignettes --timings biocViews_1.42.0.tar.gz
StartedAt: 2017-04-14 21:11:52 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 21:14:22 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 150.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: biocViews.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf biocViews.buildbin-libdir biocViews.Rcheck && mkdir biocViews.buildbin-libdir biocViews.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=biocViews.buildbin-libdir biocViews_1.42.0.tar.gz >biocViews.Rcheck\00install.out 2>&1 && cp biocViews.Rcheck\00install.out biocViews-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=biocViews.buildbin-libdir --install="check:biocViews-install.out" --force-multiarch --no-vignettes --timings biocViews_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/biocViews.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.42.0'
* 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 ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Found the following CITATION file in a non-standard place:
  inst/unitTests/CITATION
Most likely 'inst/CITATION' should be used instead.
* 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
.extract1Citation: no visible global function definition for 'untar'
.extract1Citation: no visible global function definition for
  'packageDescription'
.extract1Citation: no visible global function definition for
  'readCitationFile'
.extract1Citation: no visible global function definition for
  'capture.output'
.getChildren: no visible global function definition for 'data'
.getChildren: no visible binding for global variable 'biocViewsVocab'
extractHTMLDocuments : extractHTMLDocumentsFromTarball: no visible
  global function definition for 'untar'
getNEWSFromFile: no visible global function definition for 'file_test'
getNEWSFromFile: no visible global function definition for
  'capture.output'
getNewPackageTitles: no visible global function definition for
  'available.packages'
getNewPackageTitles: no visible global function definition for
  'contrib.url'
getPackageNEWS: no visible global function definition for
  'available.packages'
getPackageNEWS: no visible global function definition for 'contrib.url'
getPackageNEWS: no visible global function definition for 'setNames'
getPackageNEWS : getNews: no visible global function definition for
  'head'
getPackageNEWS : getNews: no visible binding for global variable
  'Version'
getReverseDepends : <anonymous>: no visible binding for global variable
  'Package'
printNEWS: no visible global function definition for 'capture.output'
recommendBiocViews: no visible global function definition for
  'complete.cases'
validate_bioc_views: no visible global function definition for
  'packageDescription'
validate_bioc_views: no visible global function definition for 'data'
validate_bioc_views: no visible binding for global variable
  'biocViewsVocab'
htmlDoc,BiocView: no visible binding for global variable 'stylesheet'
Undefined global functions or variables:
  Package Version available.packages biocViewsVocab capture.output
  complete.cases contrib.url data file_test head packageDescription
  readCitationFile setNames stylesheet untar
Consider adding
  importFrom("stats", "complete.cases", "setNames")
  importFrom("utils", "available.packages", "capture.output",
             "contrib.url", "data", "file_test", "head",
             "packageDescription", "readCitationFile", "untar")
to your NAMESPACE file.
* 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 'getPackageNEWS':
getPackageNEWS
  Code: function(prevRepos =
                 "https://bioconductor.org/packages/release/bioc",
                 currRepos =
                 "https://bioconductor.org/packages/devel/bioc",
                 srcDir)
  Docs: function(prevRepos =
                 "http://www.bioconductor.org/packages/2.10/bioc",
                 currRepos =
                 "http://www.bioconductor.org/packages/2.11/bioc",
                 srcDir)
  Mismatches in argument default values:
    Name: 'prevRepos' Code: "https://bioconductor.org/packages/release/bioc" Docs: "http://www.bioconductor.org/packages/2.10/bioc"
    Name: 'currRepos' Code: "https://bioconductor.org/packages/devel/bioc" Docs: "http://www.bioconductor.org/packages/2.11/bioc"

* 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 6.04   3.72    9.89
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
recommendPackages 3.93    1.9     5.9
* 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, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/biocViews.Rcheck/00check.log'
for details.


biocViews.Rcheck/00install.out:


install for i386

* installing *source* package 'biocViews' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'biocViews' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'biocViews' as biocViews_1.42.0.zip
* DONE (biocViews)

biocViews.Rcheck/examples_i386/biocViews-Ex.timings:

nameusersystemelapsed
PackageDetail-class0.080.000.07
biocViews-package0.030.000.04
biocViewsVocab000
getBiocSubViews1.230.001.23
getBiocViews1.100.001.09
getCurrentbiocViews000
getSubTerms0.110.010.13
recommendPackages6.043.729.89
validation_tests000

biocViews.Rcheck/examples_x64/biocViews-Ex.timings:

nameusersystemelapsed
PackageDetail-class0.080.000.08
biocViews-package0.030.020.04
biocViewsVocab000
getBiocSubViews1.610.001.61
getBiocViews1.390.021.41
getCurrentbiocViews0.020.000.01
getSubTerms0.130.000.13
recommendPackages3.931.905.90
validation_tests000