BioC 2.13: CHECK report for GeneExpressionSignature on zin1

Package: GeneExpressionSignature

Version: 1.8.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings GeneExpressionSignature_1.8.0.tar.gz

StartedAt: 2014-04-05 01:20:21 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:22:10 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 109.3 seconds

RetCode: 0

Status:  OK

CheckDir: GeneExpressionSignature.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/GeneExpressionSignature.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 ‘GeneExpressionSignature/DESCRIPTION’ ... OK
* this is package ‘GeneExpressionSignature’ version ‘1.8.0’
* 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 ‘GeneExpressionSignature’ can be installed ... [7s/7s] OK
* checking installed package size ... OK
* 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 ... 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘PGSEA’
  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 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘GeneExpressionSignature.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [40s/41s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
ScoreGSEA         11.153  0.028  11.198
SignatureDistance 10.937  0.016  10.983
ScorePGSEA         7.672  0.060   7.755
RankMerging        5.796  0.028   5.832
* 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 2 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/GeneExpressionSignature.Rcheck/00check.log’
for details.

* installing *source* package ‘GeneExpressionSignature’ ...
** 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 (GeneExpressionSignature)

name	user	system	elapsed
RankMerging	5.796	0.028	5.832
ScoreGSEA	11.153	0.028	11.198
ScorePGSEA	7.672	0.060	7.755
SignatureDistance	10.937	0.016	10.983
exampleSet	0.316	0.008	0.328
getRLs	0.700	0.012	0.712