BioC experimental data: CHECK report for RnBeads.rn5 on petty

Package: RnBeads.rn5

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RnBeads.rn5_1.0.0.tar.gz

StartedAt: 2015-10-07 09:48:05 -0700 (Wed, 07 Oct 2015)

EndedAt: 2015-10-07 10:20:05 -0700 (Wed, 07 Oct 2015)

EllapsedTime: 1920.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: RnBeads.rn5.Rcheck

Warnings: 3

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RnBeads.rn5_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-data-experiment/meat/RnBeads.rn5.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RnBeads.rn5/DESCRIPTION’ ... OK
* this is package ‘RnBeads.rn5’ version ‘1.0.0’
* 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 ‘RnBeads.rn5’ can be installed ... [9s/10s] OK
* checking installed package size ... NOTE
  installed size is 85.8Mb
  sub-directories of 1Mb or more:
    data  85.7Mb
* checking package 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 ... OK
* 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
Package in Depends field not imported from: ‘GenomicRanges’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'rn5.Rd':
  ‘rnb.get.assemblies’ ‘rnb.get.chromosomes’ ‘rnb.get.annotation’
  ‘rnb.set.annotation’ ‘rnb.get.mapping’ ‘rnb.annotation.size’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... WARNING
Undocumented data sets:
  ‘sites’ ‘regions’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                    old_size new_size compress
  rn5.CpG.RData       80.9Mb   50.2Mb       xz
  rn5.regions.RData    4.8Mb    1.9Mb       xz
* checking examples ... NONE
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-data-experiment/meat/RnBeads.rn5.Rcheck/00check.log’
for details.

* installing *source* package ‘RnBeads.rn5’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (RnBeads.rn5)