Package: pumadata

Version: 1.0.6

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch pumadata_1.0.6.tar.gz

StartedAt: 2012-06-21 15:11:30 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 15:13:57 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 147.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: pumadata.Rcheck

Warnings: 2

* using log directory '/Users/biocbuild/bbs-2.11-data-experiment/meat/pumadata.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'pumadata/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pumadata' version '1.0.6'
* 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 'pumadata' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 15.5Mb
  sub-directories of 1Mb or more:
    data  15.3Mb
* 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 index information ... OK
* checking package subdirectories ... WARNING
Invalid citation information in 'inst/CITATION':
  arguments imply differing number of rows: 1, 0
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File 'pumadata/R/zzz.R':
  .onLoad calls:
    require(Biobase)

Package startup functions should not change the search path.
See section 'Good practice' in ?.onAttach.

* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* 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 ... NOTE
  No methods found in "Biobase" for requests: geneNames
* 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
  affybatch.estrogen.rda    8.3Mb    5.2Mb       xz
  eset_estrogen_comb.rda    860Kb    752Kb       xz
  eset_estrogen_rma.rda     810Kb    698Kb       xz
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 2 warnings.
NOTE: There were 3 notes.
See
  '/Users/biocbuild/bbs-2.11-data-experiment/meat/pumadata.Rcheck/00check.log'
for details.

* installing *source* package 'pumadata' ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "Biobase" for requests: geneNames
** help
*** installing help indices
** building package indices
** installing vignettes
   'pumadata.Rnw' 
** testing if installed package can be loaded
No methods found in "Biobase" for requests: geneNames

* DONE (pumadata)

name	user	system	elapsed
eset_estrogen_comb	0.089	0.009	0.098
eset_estrogen_mmgmos	0.383	0.023	0.420
eset_estrogen_rma	0.059	0.005	0.064
pumapca_estrogen	0.013	0.001	0.014