Package: PCpheno

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PCpheno_1.16.0.tar.gz

StartedAt: 2012-03-24 03:08:39 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 03:13:26 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 286.6 seconds

RetCode: 0

Status:  OK

CheckDir: PCpheno.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/PCpheno.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'PCpheno/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PCpheno' version '1.16.0'
* 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 whether package 'PCpheno' can be installed ... OK
* checking installed package size ... OK
* 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 ... 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 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 ... 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                      old_size new_size compress
  DudleyGenelist.rda      35Kb      8Kb       xz
  DudleyPhenoFull.rda     10Kb      7Kb    bzip2
  DudleySign.rda          11Kb      9Kb       xz
  GiaeverGene.rda         16Kb      6Kb       xz
  GiaeverPheno.rda       1.0Mb    589Kb       xz
  OsterbergRaw.rda        44Kb     38Kb       xz
  SGDphenoL.rda          135Kb     95Kb       xz
* checking sizes of PDF files under '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

* installing *source* package 'PCpheno' ...
** R
** data
** inst
** preparing package for lazy loading
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "connection" in package 'graph' seems equivalent to one from package 'IRanges' and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "file" in package 'graph' seems equivalent to one from package 'IRanges' and is not turning on duplicate class definitions for this class

*** Deprecation warning ***:
The package 'ppiData' is deprecated and will not be supported after Bioconductor release 2.11


** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'PCpheno.Rnw' 
** testing if installed package can be loaded

*** Deprecation warning ***:
The package 'ppiData' is deprecated and will not be supported after Bioconductor release 2.11



* DONE (PCpheno)

name	user	system	elapsed
CoHyperGResult-class	1.247	0.063	1.366
Dudley	0.015	0.002	0.019
Giaever	0.165	0.007	0.173
HI	0.003	0.001	0.003
KEGG2SCISI	0.712	0.041	0.776
Kastenmayer	0.022	0.003	0.025
Lesage	0.010	0.002	0.012
Osterberg	0.029	0.003	0.032
SGDphenoL	0.046	0.004	0.050
YEASTOHNOLOG	0.011	0.001	0.012
buildFDMat	0.275	0.079	0.360
categoryToEntrezBuilder	0.595	0.057	0.679
complexStatus	1.736	0.084	1.849
deResult-class	0.320	0.022	0.349
densityEstimate	3.740	0.386	4.186
getDescr	1.239	0.197	1.510
getFDgene	0.168	0.007	0.175
graphTheory	13.148	0.757	14.084
gtResult-class	10.450	4.336	15.255
overlap	0.001	0.001	0.002
plot	3.518	0.421	3.963
ppiInteraction	8.912	1.762	10.885
reduceM	0.000	0.000	0.001
truncName	0.001	0.000	0.000