Package: yeastCC

Version: 1.2.17

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch yeastCC_1.2.17.tar.gz

StartedAt: 2013-03-24 12:35:26 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 12:36:18 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 51.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: yeastCC.Rcheck

Warnings: 6

* using log directory '/Users/biocbuild/bbs-2.11-data-experiment/meat/yeastCC.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'yeastCC/DESCRIPTION' ... OK
* this is package 'yeastCC' version '1.2.17'
* 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 whether package 'yeastCC' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    2.6Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 for unstated dependencies in R code ... WARNING
Error in tools:::.check_packages_used(package = "yeastCC") : 
  directory '/Users/biocbuild/bbs-2.11-data-experiment/meat/yeastCC.Rcheck/yeastCC' 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 = "yeastCC") : 
  directory '/Users/biocbuild/bbs-2.11-data-experiment/meat/yeastCC.Rcheck/yeastCC' 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 = "yeastCC") : 
  directory '/Users/biocbuild/bbs-2.11-data-experiment/meat/yeastCC.Rcheck/yeastCC' 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 = "yeastCC") : 
  directory '/Users/biocbuild/bbs-2.11-data-experiment/meat/yeastCC.Rcheck/yeastCC' 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 = "yeastCC") : 
  directory '/Users/biocbuild/bbs-2.11-data-experiment/meat/yeastCC.Rcheck/yeastCC' does not contain R code
Execution halted
Error in tools::codocClasses(package = "yeastCC") : 
  directory '/Users/biocbuild/bbs-2.11-data-experiment/meat/yeastCC.Rcheck/yeastCC' does not contain R code
Execution halted
* checking Rd \usage sections ... NOTE
Error in tools::checkDocStyle(package = "yeastCC") : 
  directory '/Users/biocbuild/bbs-2.11-data-experiment/meat/yeastCC.Rcheck/yeastCC' 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: large data file(s) saved inefficiently:
                 size ASCII compress
  spYCCmeta.rda 430Kb FALSE     none
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                old_size new_size compress
  breeden.rda      1.9Mb    1.5Mb       xz
  spYCCES.rda      757Kb    484Kb       xz
  spYCCmeta.rda    430Kb     55Kb       xz
  yeastCC.rda      1.5Mb    485Kb       xz
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
* checking PDF version of manual ... OK

WARNING: There were 6 warnings.
NOTE: There were 3 notes.
See
  '/Users/biocbuild/bbs-2.11-data-experiment/meat/yeastCC.Rcheck/00check.log'
for details.

* installing *source* package 'yeastCC' ...
** data
**  moving datasets to lazyload DB
** inst
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

* DONE (yeastCC)

name	user	system	elapsed
breeden	0.266	0.040	0.318
orf800	0.001	0.000	0.003
spYCCmeta	0.014	0.004	0.020
yeastCC	0.407	0.048	0.525