Package: PGSEA

Version: 1.27.0

Command: mkdir PGSEA.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PGSEA.buildbin-libdir PGSEA_1.27.0.tar.gz >PGSEA-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=PGSEA.buildbin-libdir --install="check:PGSEA-install.out" --force-multiarch --no-vignettes --timings PGSEA_1.27.0.tar.gz && mv PGSEA.buildbin-libdir/* PGSEA.Rcheck/ && rmdir PGSEA.buildbin-libdir

StartedAt: 2011-07-07 05:55:11 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 05:56:37 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 86.5 seconds

RetCode: 0

Status:  OK

CheckDir: PGSEA.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/PGSEA.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-20 r56188)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PGSEA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PGSEA' version '1.27.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'PGSEA' 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
* loading checks for arch 'i386'
** 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 name space can be loaded with stated dependencies ... OK
** checking whether the name space can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** 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 name space can be loaded with stated dependencies ... OK
** checking whether the name space 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 ... NOTE
'library' or 'require' calls not declared from:
  'GO' 'KEGG'
* 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 tools::resaveRdaFiles() or R CMD build --resave-data
               old_size new_size compress
  GOLUBmcs.rda     94Kb     57Kb    bzip2
  VAIgsc.rda       14Kb     10Kb    bzip2
  VAImcs.rda       13Kb     10Kb    bzip2
  nbEset.rda      943Kb    843Kb       xz
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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

install for i386

* installing *source* package 'PGSEA' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: AnnotationDbi
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

Loading required package: DBI


** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'PGSEA.Rnw' 
   'PGSEA2.Rnw' 
** testing if installed package can be loaded

add DLL for x64

* installing *source* package 'PGSEA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PGSEA' as PGSEA_1.27.0.zip

* DONE (PGSEA)

name	user	system	elapsed
GOLUBmcs	0.12	0.00	0.14
PGSEA	0.70	0.02	0.72
VAIgsc	1.38	0.01	1.39
VAImcs	0.28	0.02	0.29
aggregateExprs	0.37	0.03	0.41
convertSmc	0	0	0
editSmc	0.03	0.00	0.03
go2smc	0	0	0
kegg2smc	0	0	0
nbEset	0.06	0.00	0.06
readGmt	0.03	0.00	0.03
readSmc	0.05	0.00	0.05
scanSmc	0.01	0.00	0.01
smcPlot	0.74	0.00	0.74
writeGmt	0.03	0.02	0.04
writeSmc	0.03	0.00	0.03