Package: PCpheno

Version: 1.16.0

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch PCpheno_1.16.0.tar.gz

StartedAt: 2012-01-09 04:40:56 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 04:44:08 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 192.9 seconds

RetCode: 0

Status:  OK

CheckDir: PCpheno.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/PCpheno.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 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    590Kb       xz
  OsterbergRaw.rda        44Kb     38Kb       xz
  SGDphenoL.rda          135Kb     95Kb       xz
* 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	1.15	0.00	1.25
Dudley	0.02	0.00	0.02
Giaever	0.12	0.00	0.12
HI	0	0	0
KEGG2SCISI	0.61	0.02	0.66
Kastenmayer	0.02	0.00	0.01
Lesage	0	0	0
Osterberg	0.01	0.00	0.01
SGDphenoL	0.02	0.00	0.02
YEASTOHNOLOG	0.01	0.00	0.02
buildFDMat	0.52	0.03	0.54
categoryToEntrezBuilder	0.25	0.01	0.33
complexStatus	1.22	0.02	1.30
deResult-class	0.25	0.00	0.25
densityEstimate	2.45	0.14	2.62
getDescr	0.84	0.01	0.96
getFDgene	0.10	0.02	0.11
graphTheory	12.83	0.27	13.26
gtResult-class	9.76	1.03	10.92
overlap	0	0	0
plot	2.31	0.12	2.44
ppiInteraction	4.86	0.00	5.11
reduceM	0	0	0
truncName	0.02	0.00	0.02