biocViews 1.32.1
Bioconductor Package Maintainer
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/biocViews | | Last Changed Rev: 89407 / Revision: 95116 | | Last Changed Date: 2014-04-23 14:00:46 -0700 (Wed, 23 Apr 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ WARNINGS ] | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | 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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### rm -rf biocViews.buildbin-libdir && mkdir biocViews.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=biocViews.buildbin-libdir biocViews_1.32.1.tar.gz >biocViews-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=biocViews.buildbin-libdir --install="check:biocViews-install.out" --force-multiarch --no-vignettes --timings biocViews_1.32.1.tar.gz
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* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/biocViews.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'biocViews/DESCRIPTION' ... OK
* this is package 'biocViews' version '1.32.1'
* 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
Package listed in more than one of Depends, Imports, Suggests, Enhances:
'Biobase'
A package should be listed in only one of these fields.
* 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.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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'
validate_bioc_views: no visible binding for global variable
'biocViewsVocab'
htmlDoc,BiocView: no visible binding for global variable 'stylesheet'
* 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 'write_VIEWS':
write_VIEWS
Code: function(reposRootPath, fields = NULL, type = c("source",
"win.binary", "win64.binary", "mac.binary",
"mac.binary.leopard", "mac.binary.mavericks"), verbose
= FALSE, vignette.dir = "vignettes")
Docs: function(reposRootPath, fields = NULL, type = c("source",
"win.binary", "win64.binary", "mac.binary",
"mac.binary.leopard"), verbose = FALSE, vignette.dir =
"vignettes")
Mismatches in argument default values:
Name: 'type'
Code: c("source", "win.binary", "win64.binary", "mac.binary", "mac.binary.leopard",
"mac.binary.mavericks")
Docs: c("source", "win.binary", "win64.binary", "mac.binary", "mac.binary.leopard")
* 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' ... [6s] OK
** running examples for arch 'x64' ... [6s] 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
WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
'E:/biocbld/bbs-2.14-bioc/meat/biocViews.Rcheck/00check.log'
for details.
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_1.32.1.zip
* DONE (biocViews)