BioC experimental data: CHECK report for pumadata on zin1

Package: pumadata

Version: 1.99.7

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings pumadata_1.99.7.tar.gz

StartedAt: 2014-04-04 09:38:01 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-04 09:38:39 -0700 (Fri, 04 Apr 2014)

EllapsedTime: 37.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: pumadata.Rcheck

Warnings: 1

* using log directory ‘/home/biocbuild/bbs-2.13-data-experiment/meat/pumadata.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pumadata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pumadata’ version ‘1.99.7’
* 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 ‘pumadata’ can be installed ... [3s/3s] OK
* checking installed package size ... NOTE
  installed size is 47.8Mb
  sub-directories of 1Mb or more:
    data  47.6Mb
* checking package directory ... OK
* checking ‘build’ 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
Invalid citation information in ‘inst/CITATION’:
  Error in utils::readCitationFile(cfile, meta): attempt to set an attribute on NULL
* 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
‘library’ or ‘require’ call to ‘Biobase’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Biobase’ ‘affy’ ‘puma’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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
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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [2s/2s] 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
  ‘/home/biocbuild/bbs-2.13-data-experiment/meat/pumadata.Rcheck/00check.log’
for details.

* installing *source* package ‘pumadata’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (pumadata)

name	user	system	elapsed
eset_estrogen_comb	0.132	0.004	0.134
eset_estrogen_mmgmos	0.268	0.008	0.275
eset_estrogen_pmmmgmos	0.156	0.000	0.155
eset_estrogen_rma	0.092	0.000	0.094
pumapca_estrogen	0.008	0.004	0.011