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 | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ WARNINGS ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings biocViews_1.42.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/biocViews.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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 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: 1 WARNING, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.4-bioc/meat/biocViews.Rcheck/00check.log’
for details.