BioC 2.14: CHECK report for PADOG on petty

Package: PADOG

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PADOG_1.6.0.tar.gz

StartedAt: 2014-10-07 23:20:16 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:27:34 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 438.9 seconds

RetCode: 0

Status:  OK

CheckDir: PADOG.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PADOG_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/PADOG.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PADOG/DESCRIPTION’ ... OK
* this is package ‘PADOG’ version ‘1.6.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘KEGGdzPathwaysGEO’ ‘limma’ ‘AnnotationDbi’ ‘Biobase’ ‘nlme’ ‘GSA’
  ‘KEGG.db’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘PADOG’ can be installed ... [18s/18s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘graphics’ ‘limma’ ‘KEGG.db’ ‘AnnotationDbi’ ‘Biobase’ ‘methods’ ‘nlme’
A package should be listed in only one of these fields.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  ‘GSA’ ‘KEGG.db’ ‘limma’ ‘nlme’
  Please remove these calls from your code.
Namespaces in Imports field not imported from:
  ‘Biobase’ ‘hgu133a.db’ ‘hgu133plus2.db’ ‘KEGG.db’ ‘limma’ ‘methods’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘Biobase’ ‘GSA’ ‘KEGG.db’ ‘KEGGdzPathwaysGEO’ ‘limma’ ‘methods’
  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 ... 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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [338s/250s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
compPADOG  210.972 22.322 162.875
padog       58.152 10.051  68.653
filteranot   8.097  0.676   8.833
* 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/PADOG.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
compPADOG	210.972	22.322	162.875
filteranot	8.097	0.676	8.833
padog	58.152	10.051	68.653