BioC experimental data: CHECK report for SpikeIn on perceval

Package: SpikeIn

Version: 1.4.11

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SpikeIn_1.4.11.tar.gz

StartedAt: 2014-04-04 11:43:06 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-04 11:43:54 -0700 (Fri, 04 Apr 2014)

EllapsedTime: 48.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: SpikeIn.Rcheck

Warnings: 5

* using log directory ‘/Users/biocbuild/bbs-2.13-data-experiment/meat/SpikeIn.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpikeIn/DESCRIPTION’ ... OK
* this is package ‘SpikeIn’ version ‘1.4.11’
* 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 ‘SpikeIn’ can be installed ... [3s/4s] OK
* checking installed package size ... NOTE
  installed size is 63.1Mb
  sub-directories of 1Mb or more:
    data  63.0Mb
* checking package 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 ... WARNING
Found directory ‘R’ with no source files.
* 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
Error in tools:::.check_packages_used(package = "SpikeIn") : 
  directory ‘/Users/biocbuild/bbs-2.13-data-experiment/meat/SpikeIn.Rcheck/SpikeIn’ does not contain R code
Execution halted
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... WARNING
Error in tools::checkS3methods(package = "SpikeIn") : 
  directory ‘/Users/biocbuild/bbs-2.13-data-experiment/meat/SpikeIn.Rcheck/SpikeIn’ does not contain R code
Execution halted
See section ‘Generic functions and methods’ of the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Error in tools::checkReplaceFuns(package = "SpikeIn") : 
  directory ‘/Users/biocbuild/bbs-2.13-data-experiment/meat/SpikeIn.Rcheck/SpikeIn’ does not contain R code
Execution halted
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Error in tools::checkFF(package = "SpikeIn") : 
  directory ‘/Users/biocbuild/bbs-2.13-data-experiment/meat/SpikeIn.Rcheck/SpikeIn’ does not contain R code
Execution halted
See the chapter ‘System and foreign language interfaces’ of the
‘Writing R Extensions’ manual.
* checking R code for possible problems ... OK
* 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
Error in tools::codoc(package = "SpikeIn") : 
  directory '/Users/biocbuild/bbs-2.13-data-experiment/meat/SpikeIn.Rcheck/SpikeIn' does not contain R code
Execution halted
Error in tools::codocClasses(package = "SpikeIn") : 
  directory '/Users/biocbuild/bbs-2.13-data-experiment/meat/SpikeIn.Rcheck/SpikeIn' does not contain R code
Execution halted
* checking Rd \usage sections ... NOTE
Error in tools::checkDocStyle(package = "SpikeIn") : 
  directory '/Users/biocbuild/bbs-2.13-data-experiment/meat/SpikeIn.Rcheck/SpikeIn' does not contain R code
Execution halted
The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
  Warning: package needs dependence on R (>= 2.10)
* checking examples ... NONE
* checking PDF version of manual ... OK

WARNING: There were 5 warnings.
NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-2.13-data-experiment/meat/SpikeIn.Rcheck/00check.log’
for details.

* installing *source* package ‘SpikeIn’ ...
** data
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (SpikeIn)