Package: phenoTest

Version: 1.2.0

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch phenoTest_1.2.0.tar.gz

StartedAt: 2012-01-09 04:52:03 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 04:56:59 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 295.7 seconds

RetCode: 0

Status:  OK

CheckDir: phenoTest.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/phenoTest.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'phenoTest/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'phenoTest' version '1.2.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'multicore'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'phenoTest' 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 ... NOTE
S3 methods shown with full name in documentation object 'plot.gseaSignatures':
  'plot.gseaSignaturesSign' 'plot.gseaSignaturesVar'

S3 methods shown with full name in documentation object 'summary.gseaSignificance':
  'summary.gseaSignificanceSign' 'summary.gseaSignificanceVar'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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
  eset.RData    664Kb    382Kb       xz
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... 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 'phenoTest' ...
** libs
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -mtune=core2 -c getEs.c -o getEs.o
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o phenoTest.dll tmp.def getEs.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/phenoTest.Rcheck/phenoTest/libs/x64
** 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
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'phenoTest.Rnw' 
** testing if installed package can be loaded

* DONE (phenoTest)

name	user	system	elapsed
ClusterPhenoTest	0.10	0.00	0.09
ExpressionPhenoTest	5.95	0.01	5.99
epheno-class	0	0	0
epheno	0.01	0.00	0.01
epheno2html	0	0	0
eset	0.04	0.00	0.03
findCopyNumber	0	0	0
genesInArea	0.42	0.02	0.90
getEsPositions	0.19	0.00	0.18
getVars2test	0	0	0
gseaSignatures-class	0.02	0.00	0.01
gseaSignatures	0	0	0
gseaSignaturesSign-class	0.01	0.00	0.02
gseaSignaturesVar-class	0	0	0
gseaSignificance	0	0	0
gseaSignificanceSign-class	0	0	0
gseaSignificanceVar-class	0	0	0
heatmapPhenoTest	0.28	0.00	0.28
pAdjust	0.02	0.00	0.02
plot.gseaSignatures	0	0	0
plots4epheno	0.05	0.00	0.04
smoothCoxph	0.04	0.00	0.11
summary.gseaSignificance	0	0	0